Last login: Wed Feb 22 10:35:16 from 192.168.1.2 odd-2% pwd /Users/stevel odd-2% cd wp/lecture/2012_01_Intro_Programming odd-2% mkdir lec13 odd-2% cd lec13 odd-2% ls odd-2% ipython Python 2.7.1 (r271:86832, Jun 16 2011, 16:59:05) Type "copyright", "credits" or "license" for more information. IPython 0.10.2 -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %quickref -> Quick reference. help -> Python's own help system. object? -> Details about 'object'. ?object also works, ?? prints more. In [1]: import sqlite3 In [2]: conn=sqlite3.connect("my.db") In [3]: curs=conn.cursor() In [4]: !ls my.db In [5]: curs.execute("CREATE TABLE Person(Id INT, Name TEXT, Zip INT);") Out[5]: In [6]: curs.execute("INSERT INTO Person VALUES (1,'Steve',77884)") Out[6]: In [7]: curs.execute("INSERT INTO Person VALUES (2,'Sarah',77884)") Out[7]: In [8]: curs.execute("INSERT INTO Person VALUES (3,'Amanda',77584)") Out[8]: In [9]: curs.execute("INSERT INTO Person VALUES (4,'Joe',77030)") Out[9]: In [10]: curs.execute("SELECT * FROM Person") Out[10]: In [11]: results=curs.fetchall() In [12]: results Out[12]: [(1, u'Steve', 77884), (2, u'Sarah', 77884), (3, u'Amanda', 77584), (4, u'Joe', 77030)] In [13]: curs.execute("SELECT (Id,Zip) FROM Person") --------------------------------------------------------------------------- OperationalError Traceback (most recent call last) /Users/stevel/wp/lecture/2012_01_Intro_Programming/lec13/ in () OperationalError: near ",": syntax error In [14]: curs.execute("SELECT Id,Zip FROM Person") Out[14]: In [15]: results=curs.fetchall() In [16]: results Out[16]: [(1, 77884), (2, 77884), (3, 77584), (4, 77030)] In [17]: curs.execute("SELECT * FROM Person WHERE Zip=77884") Out[17]: In [18]: results=curs.fetchall() In [19]: results Out[19]: [(1, u'Steve', 77884), (2, u'Sarah', 77884)] In [20]: cur.execute("UPDATE Person SET Zip=77584 WHERE Zip is 77884") --------------------------------------------------------------------------- NameError Traceback (most recent call last) /Users/stevel/wp/lecture/2012_01_Intro_Programming/lec13/ in () NameError: name 'cur' is not defined In [21]: curs.execute("UPDATE Person SET Zip=77584 WHERE Zip is 77884") Out[21]: In [22]: curs.execute("SELECT * FROM Person") Out[22]: In [23]: curs.fetchall() Out[23]: [(1, u'Steve', 77584), (2, u'Sarah', 77584), (3, u'Amanda', 77584), (4, u'Joe', 77030)] In [24]: Do you really want to exit ([y]/n)? odd-2% ipython Python 2.7.1 (r271:86832, Jun 16 2011, 16:59:05) Type "copyright", "credits" or "license" for more information. IPython 0.10.2 -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %quickref -> Quick reference. help -> Python's own help system. object? -> Details about 'object'. ?object also works, ?? prints more. In [1]: from Bio import ExPASy In [2]: from Bio import SeqIO In [3]: handle = ExPASy.get_sprot_raw("A0LR17") --------------------------------------------------------------------------- IOError Traceback (most recent call last) /Users/stevel/wp/lecture/2012_01_Intro_Programming/lec13/ in () /Library/Python/2.7/site-packages/biopython-1.58-py2.7-macosx-10.7-intel.egg/Bio/ExPASy/__init__.pyc in get_sprot_raw(id) 67 (as per the http://www.expasy.ch/expasy_urls.html documentation). 68 """ ---> 69 return urllib.urlopen("http://www.uniprot.org/uniprot/%s.txt" % id) 70 71 def sprot_search_ful(text, make_wild=None, swissprot=1, trembl=None, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib.pyc in urlopen(url, data, proxies) 82 opener = _urlopener 83 if data is None: ---> 84 return opener.open(url) 85 else: 86 return opener.open(url, data) /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib.pyc in open(self, fullurl, data) 203 try: 204 if data is None: --> 205 return getattr(self, name)(url) 206 else: 207 return getattr(self, name)(url, data) /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib.pyc in open_http(self, url, data) 340 if realhost: h.putheader('Host', realhost) 341 for args in self.addheaders: h.putheader(*args) --> 342 h.endheaders(data) 343 errcode, errmsg, headers = h.getreply() 344 fp = h.getfile() /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.pyc in endheaders(self, message_body) 935 else: 936 raise CannotSendHeader() --> 937 self._send_output(message_body) 938 939 def request(self, method, url, body=None, headers={}): /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.pyc in _send_output(self, message_body) 795 msg += message_body 796 message_body = None --> 797 self.send(msg) 798 if message_body is not None: 799 #message_body was not a string (i.e. it is a file) and /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.pyc in send(self, data) 757 if self.sock is None: 758 if self.auto_open: --> 759 self.connect() 760 else: 761 raise NotConnected() /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.pyc in connect(self) 738 """Connect to the host and port specified in __init__.""" 739 self.sock = socket.create_connection((self.host,self.port), --> 740 self.timeout, self.source_address) 741 742 if self._tunnel_host: /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.pyc in create_connection(address, timeout, source_address) 551 host, port = address 552 err = None --> 553 for res in getaddrinfo(host, port, 0, SOCK_STREAM): 554 af, socktype, proto, canonname, sa = res 555 sock = None IOError: [Errno socket error] [Errno 8] nodename nor servname provided, or not known In [4]: seq_record = SeqIO.read(handle, "swiss") --------------------------------------------------------------------------- NameError Traceback (most recent call last) /Users/stevel/wp/lecture/2012_01_Intro_Programming/lec13/ in () NameError: name 'handle' is not defined In [5]: from Bio import ExPASy In [6]: from Bio import SeqIO In [7]: handle = ExPASy.get_sprot_raw("A0LR17") --------------------------------------------------------------------------- IOError Traceback (most recent call last) /Users/stevel/wp/lecture/2012_01_Intro_Programming/lec13/ in () /Library/Python/2.7/site-packages/biopython-1.58-py2.7-macosx-10.7-intel.egg/Bio/ExPASy/__init__.pyc in get_sprot_raw(id) 67 (as per the http://www.expasy.ch/expasy_urls.html documentation). 68 """ ---> 69 return urllib.urlopen("http://www.uniprot.org/uniprot/%s.txt" % id) 70 71 def sprot_search_ful(text, make_wild=None, swissprot=1, trembl=None, /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib.pyc in urlopen(url, data, proxies) 82 opener = _urlopener 83 if data is None: ---> 84 return opener.open(url) 85 else: 86 return opener.open(url, data) /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib.pyc in open(self, fullurl, data) 203 try: 204 if data is None: --> 205 return getattr(self, name)(url) 206 else: 207 return getattr(self, name)(url, data) /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib.pyc in open_http(self, url, data) 340 if realhost: h.putheader('Host', realhost) 341 for args in self.addheaders: h.putheader(*args) --> 342 h.endheaders(data) 343 errcode, errmsg, headers = h.getreply() 344 fp = h.getfile() /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.pyc in endheaders(self, message_body) 935 else: 936 raise CannotSendHeader() --> 937 self._send_output(message_body) 938 939 def request(self, method, url, body=None, headers={}): /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.pyc in _send_output(self, message_body) 795 msg += message_body 796 message_body = None --> 797 self.send(msg) 798 if message_body is not None: 799 #message_body was not a string (i.e. it is a file) and /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.pyc in send(self, data) 757 if self.sock is None: 758 if self.auto_open: --> 759 self.connect() 760 else: 761 raise NotConnected() /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.pyc in connect(self) 738 """Connect to the host and port specified in __init__.""" 739 self.sock = socket.create_connection((self.host,self.port), --> 740 self.timeout, self.source_address) 741 742 if self._tunnel_host: /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.pyc in create_connection(address, timeout, source_address) 551 host, port = address 552 err = None --> 553 for res in getaddrinfo(host, port, 0, SOCK_STREAM): 554 af, socktype, proto, canonname, sa = res 555 sock = None IOError: [Errno socket error] [Errno 8] nodename nor servname provided, or not known In [8]: Do you really want to exit ([y]/n)? odd-2% ipython Python 2.7.1 (r271:86832, Jun 16 2011, 16:59:05) Type "copyright", "credits" or "license" for more information. IPython 0.10.2 -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %quickref -> Quick reference. help -> Python's own help system. object? -> Details about 'object'. ?object also works, ?? prints more. In [1]: from Bio import ExPASy In [2]: from Bio import SeqIO In [3]: handle = ExPASy.get_sprot_raw("A0LR17") In [4]: seq_record = SeqIO.read(handle, "swiss") In [5]: handle.close() In [6]: handle Out[6]: In [7]: handle = ExPASy.get_sprot_raw("A0LR17") In [8]: handle.read() Out[8]: 'ID CH601_ACIC1 Reviewed; 539 AA.\nAC A0LR17;\nDT 29-APR-2008, integrated into UniProtKB/Swiss-Prot.\nDT 12-DEC-2006, sequence version 1.\nDT 22-FEB-2012, entry version 36.\nDE RecName: Full=60 kDa chaperonin 1;\nDE AltName: Full=GroEL protein 1;\nDE AltName: Full=Protein Cpn60 1;\nGN Name=groL1; Synonyms=groEL1; OrderedLocusNames=Acel_0101;\nOS Acidothermus cellulolyticus (strain ATCC 43068 / 11B).\nOC Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales;\nOC Frankineae; Acidothermaceae; Acidothermus.\nOX NCBI_TaxID=351607;\nRN [1]\nRP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].\nRC STRAIN=ATCC 43068 / 11B;\nRA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,\nRA Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H.,\nRA Pitluck S., Zharchuk I., Schmutz J., Larimer F., Land M., Hauser L.,\nRA Kyrpides N., Mikhailova N., Berry A.M., Adney W.S., Normand P.,\nRA Leu D., Pujic P., Richardson P.;\nRT "Complete sequence of Acidothermus cellulolyticus 11B.";\nRL Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.\nCC -!- FUNCTION: Prevents misfolding and promotes the refolding and\nCC proper assembly of unfolded polypeptides generated under stress\nCC conditions (By similarity).\nCC -!- SUBUNIT: Oligomer of 14 subunits composed of two stacked rings of\nCC 7 subunits (By similarity).\nCC -!- SUBCELLULAR LOCATION: Cytoplasm (By similarity).\nCC -!- SIMILARITY: Belongs to the chaperonin (HSP60) family.\nCC -----------------------------------------------------------------------\nCC Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms\nCC Distributed under the Creative Commons Attribution-NoDerivs License\nCC -----------------------------------------------------------------------\nDR EMBL; CP000481; ABK51877.1; -; Genomic_DNA.\nDR RefSeq; YP_871863.1; NC_008578.1.\nDR ProteinModelPortal; A0LR17; -.\nDR SMR; A0LR17; 2-525.\nDR STRING; A0LR17; -.\nDR GeneID; 4484544; -.\nDR GenomeReviews; CP000481_GR; Acel_0101.\nDR KEGG; ace:Acel_0101; -.\nDR PATRIC; 20670514; VBIAciCel132453_0110.\nDR eggNOG; COG0459; -.\nDR HOGENOM; HBG625289; -.\nDR KO; K04077; -.\nDR OMA; MQSNKPL; -.\nDR ProtClustDB; PRK00013; -.\nDR BioCyc; ACEL351607:ACEL_0101-MONOMER; -.\nDR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.\nDR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.\nDR GO; GO:0042026; P:protein refolding; IEA:InterPro.\nDR HAMAP; MF_00600; CH60; 1; -.\nDR InterPro; IPR018370; Chaperonin_Cpn60_CS.\nDR InterPro; IPR001844; Chaprnin_Cpn60.\nDR InterPro; IPR002423; Cpn60/TCP-1.\nDR PANTHER; PTHR11353; Cpn60/TCP-1; 1.\nDR Pfam; PF00118; Cpn60_TCP1; 1.\nDR PRINTS; PR00298; CHAPERONIN60.\nDR SUPFAM; SSF48592; GroEL-ATPase; 1.\nDR TIGRFAMs; TIGR02348; GroEL; 1.\nDR PROSITE; PS00296; CHAPERONINS_CPN60; 1.\nPE 3: Inferred from homology;\nKW ATP-binding; Chaperone; Complete proteome; Cytoplasm;\nKW Nucleotide-binding.\nFT CHAIN 1 539 60 kDa chaperonin 1.\nFT /FTId=PRO_0000331961.\nSQ SEQUENCE 539 AA; 57154 MW; 84ACA73AB7F72F08 CRC64;\n MAKMIAFDEA ARRALERGMN QLADAVKVTL GPKGRNVVLE KKWGAPTITN DGVSIAKEIE\n LEDPYEKIGA ELVKEVAKKT DDVAGDGTTT ATVLAQTLVR EGLRNVAAGA NPMALKRGIE\n AATERVCQAL LEIAKDVETR EQIASTASIS AGDTAVGEMI AEAMDKVGKE GVITVEESNT\n FGLELELTEG MRFDKGYISP YFVTDSERME AVLEDPYILI ANQKISAVKD LLPVLEKVMQ\n AGKPLAIIAE DVEGEALATL VVNKIRGTFR SVAVKAPGFG DRRKAMLGDI AVLTGGQVIS\n EEVGLKLENV GLDLLGRARK VVVTKDETTI VEGAGDPEQI AGRVNQIRAE IEKTDSDYDR\n EKLQERLAKL AGGVAVIKVG AATEVELKER KHRIEDAVRN AKAAVEEGIV AGGGVALLQA\n GKTAFEKLDL EGDEATGARI VELALEAPLK QIAINAGLEG GVVVEKVRSL EPGWGLNAQT\n GEYVDMIKAG IIDPAKVTRS ALQNAASIAG LFLTTEAVVA EKPEKEKTPA APGGGDMDF\n//\n' In [9]: In [10]: seq_record Out[10]: SeqRecord(seq=Seq('MAKMIAFDEAARRALERGMNQLADAVKVTLGPKGRNVVLEKKWGAPTITNDGVS...MDF', ProteinAlphabet()), id='A0LR17', name='CH601_ACIC1', description='RecName: Full=60 kDa chaperonin 1; AltName: Full=GroEL protein 1; AltName: Full=Protein Cpn60 1;', dbxrefs=['EMBL:CP000481', 'RefSeq:YP_871863.1', 'ProteinModelPortal:A0LR17', 'SMR:A0LR17', 'STRING:A0LR17', 'GeneID:4484544', 'GenomeReviews:CP000481_GR', 'KEGG:ace:Acel_0101', 'PATRIC:20670514', 'eggNOG:COG0459', 'HOGENOM:HBG625289', 'KO:K04077', 'OMA:MQSNKPL', 'ProtClustDB:PRK00013', 'BioCyc:ACEL351607:ACEL_0101-MONOMER', 'GO:GO:0005737', 'GO:GO:0005524', 'GO:GO:0042026', 'HAMAP:MF_00600', 'InterPro:IPR018370', 'InterPro:IPR001844', 'InterPro:IPR002423', 'PANTHER:PTHR11353', 'Pfam:PF00118', 'PRINTS:PR00298', 'SUPFAM:SSF48592', 'TIGRFAMs:TIGR02348', 'PROSITE:PS00296']) In [11]: seq_record.seq Out[11]: Seq('MAKMIAFDEAARRALERGMNQLADAVKVTLGPKGRNVVLEKKWGAPTITNDGVS...MDF', ProteinAlphabet()) In [12]: seq_record.seq[10:20] Out[12]: Seq('ARRALERGMN', ProteinAlphabet()) In [13]: seq_record.seq. seq_record.seq.__add__ seq_record.seq.__class__ seq_record.seq.__cmp__ seq_record.seq.__contains__ seq_record.seq.__delattr__ seq_record.seq.__dict__ seq_record.seq.__doc__ seq_record.seq.__format__ seq_record.seq.__getattribute__ seq_record.seq.__getitem__ seq_record.seq.__hash__ seq_record.seq.__init__ seq_record.seq.__len__ seq_record.seq.__module__ seq_record.seq.__new__ seq_record.seq.__radd__ seq_record.seq.__reduce__ seq_record.seq.__reduce_ex__ seq_record.seq.__repr__ seq_record.seq.__setattr__ seq_record.seq.__sizeof__ seq_record.seq.__str__ seq_record.seq.__subclasshook__ seq_record.seq.__weakref__ seq_record.seq._data seq_record.seq._get_seq_str_and_check_alphabet seq_record.seq.alphabet seq_record.seq.back_transcribe seq_record.seq.complement seq_record.seq.count seq_record.seq.data seq_record.seq.endswith seq_record.seq.find seq_record.seq.lower seq_record.seq.lstrip seq_record.seq.reverse_complement seq_record.seq.rfind seq_record.seq.rsplit seq_record.seq.rstrip seq_record.seq.split seq_record.seq.startswith seq_record.seq.strip seq_record.seq.tomutable seq_record.seq.tostring seq_record.seq.transcribe seq_record.seq.translate seq_record.seq.ungap seq_record.seq.upper In [13]: str(seq_record.seq) Out[13]: 'MAKMIAFDEAARRALERGMNQLADAVKVTLGPKGRNVVLEKKWGAPTITNDGVSIAKEIELEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQTLVREGLRNVAAGANPMALKRGIEAATERVCQALLEIAKDVETREQIASTASISAGDTAVGEMIAEAMDKVGKEGVITVEESNTFGLELELTEGMRFDKGYISPYFVTDSERMEAVLEDPYILIANQKISAVKDLLPVLEKVMQAGKPLAIIAEDVEGEALATLVVNKIRGTFRSVAVKAPGFGDRRKAMLGDIAVLTGGQVISEEVGLKLENVGLDLLGRARKVVVTKDETTIVEGAGDPEQIAGRVNQIRAEIEKTDSDYDREKLQERLAKLAGGVAVIKVGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALLQAGKTAFEKLDLEGDEATGARIVELALEAPLKQIAINAGLEGGVVVEKVRSLEPGWGLNAQTGEYVDMIKAGIIDPAKVTRSALQNAASIAGLFLTTEAVVAEKPEKEKTPAAPGGGDMDF' In [14]: len(seq_record.seq) Out[14]: 539 In [15]: In [16]: In [17]: In [18]: In [19]: from Bio.Blast import NCBIWWW In [20]: from Bio.Blast import NCBIXML In [21]: In [22]: result=NCBIWWW.qblast("blastp","swissprot","MAKMIAFDEAARRALERGMNQLADAVKVTLGPKGRNVVLEKKWGAPTITNDGVSIAKEIELEDPYEKIGAELVKEVAKK") In [23]: blast_record = NCBIXML.read(result) In [24]: result.close() In [25]: blast_record.alignments Out[25]: [, , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ] In [26]: blast_recordOut[26]: In [27]: blast_record. blast_record.__class__ blast_record.__delattr__ blast_record.__dict__ blast_record.__doc__ blast_record.__format__ blast_record.__getattribute__ blast_record.__hash__ blast_record.__init__ blast_record.__module__ blast_record.__new__ blast_record.__reduce__ blast_record.__reduce_ex__ blast_record.__repr__ blast_record.__setattr__ blast_record.__sizeof__ blast_record.__str__ blast_record.__subclasshook__ blast_record.__weakref__ blast_record.alignments blast_record.application blast_record.blast_cutoff blast_record.database blast_record.database_length blast_record.database_letters blast_record.database_name blast_record.database_sequences blast_record.date blast_record.descriptions blast_record.dropoff_1st_pass blast_record.effective_database_length blast_record.effective_hsp_length blast_record.effective_query_length blast_record.effective_search_space blast_record.effective_search_space_used blast_record.expect blast_record.filter blast_record.frameshift blast_record.gap_penalties blast_record.gap_trigger blast_record.gap_x_dropoff blast_record.gap_x_dropoff_final blast_record.gapped blast_record.hsps_gapped blast_record.hsps_no_gap blast_record.hsps_prelim_gapped blast_record.hsps_prelim_gapped_attemped blast_record.ka_params blast_record.ka_params_gap blast_record.matrix blast_record.multiple_alignment blast_record.num_good_extends blast_record.num_hits blast_record.num_letters_in_database blast_record.num_seqs_better_e blast_record.num_sequences blast_record.num_sequences_in_database blast_record.posted_date blast_record.query blast_record.query_id blast_record.query_length blast_record.query_letters blast_record.reference blast_record.sc_match blast_record.sc_mismatch blast_record.threshold blast_record.version blast_record.window_size In [27]: blast_record.alignments Out[27]: [, , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ] In [28]: ali=blast_record.alignments[0] In [29]: ali. ali.__class__ ali.__module__ ali.__subclasshook__ ali.__delattr__ ali.__new__ ali.__weakref__ ali.__dict__ ali.__reduce__ ali.accession ali.__doc__ ali.__reduce_ex__ ali.hit_def ali.__format__ ali.__repr__ ali.hit_id ali.__getattribute__ ali.__setattr__ ali.hsps ali.__hash__ ali.__sizeof__ ali.length ali.__init__ ali.__str__ ali.title In [29]: ali.accession Out[29]: u'A0LR17' In [30]: len(blast_record.alignments) Out[30]: 50 In [31]: from Bio import Entrez In [32]: from Bio import Medline In [33]: Entrez.email = "sludtke@bcm.edu" In [34]: In [35]: handle = Entrez.esearch(db="pubmed", term="Ludtke SJ", retmax=100) In [36]: record=Entrez.read(handle) In [37]: handle.close() In [38]: idlist=record["IdList"] In [39]: idlist Out[39]: ['22325770', '21827954', '21827945', '21220123', '21121065', '21038867', '20935055', '20888963', '20885381', '20835797', '20462491', '20194787', '20090755', '20080547', '19580754', '19446530', '19264960', '19191587', '18621707', '18536725', '18334219', '18158904', '17327167', '17098196', '16931051', '16928740', '16859925', '16491093', '16364911', '16271896', '16140524', '16084392', '16075070', '15811380', '15581887', '15272307', '15242589', '15193640', '15166242', '15065668', '14962379', '14750990', '14643210', '12714606', '12218169', '12149473', '11756679', '11718559', '11356062', '11352589', '10600563', '9199788', '8913604', '8901513', '8744303', '7495788', '7647240', '8110813', '7510532', '7679294'] In [40]: len(idlis) --------------------------------------------------------------------------- NameError Traceback (most recent call last) /Users/stevel/wp/lecture/2012_01_Intro_Programming/lec13/ in () NameError: name 'idlis' is not defined In [41]: len(idlist) Out[41]: 60 In [42]: handle=Entrez.efetch(db="pubmed", id=",".join(idlist), rettype="medline", retmode="text") In [43]: records=list(Medline.parse(handle)) In [44]: handle.close() In [45]: records Out[45]: [{'AB': 'This Meeting Review describes the proceedings and conclusions from the inaugural meeting of the Electron Microscopy Validation Task Force organized by the Unified Data Resource for 3DEM (http://www.emdatabank.org) and held at Rutgers University in New Brunswick, NJ on September 28 and 29, 2010. At the workshop, a group of scientists involved in collecting electron microscopy data, using the data to determine three-dimensional electron microscopy (3DEM) density maps, and building molecular models into the maps explored how to assess maps, models, and other data that are deposited into the Electron Microscopy Data Bank and Protein Data Bank public data archives. The specific recommendations resulting from the workshop aim to increase the impact of 3DEM in biology and medicine.', 'AD': 'MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.', 'AID': ['S0969-2126(12)00014-7 [pii]', '10.1016/j.str.2011.12.014 [doi]'], 'AU': ['Henderson R', 'Sali A', 'Baker ML', 'Carragher B', 'Devkota B', 'Downing KH', 'Egelman EH', 'Feng Z', 'Frank J', 'Grigorieff N', 'Jiang W', 'Ludtke SJ', 'Medalia O', 'Penczek PA', 'Rosenthal PB', 'Rossmann MG', 'Schmid MF', 'Schroder GF', 'Steven AC', 'Stokes DL', 'Westbrook JD', 'Wriggers W', 'Yang H', 'Young J', 'Berman HM', 'Chiu W', 'Kleywegt GJ', 'Lawson CL'], 'CI': ['Copyright (c) 2012 Elsevier Ltd. All rights reserved.'], 'CRDT': ['2012/02/14 06:00'], 'DA': '20120213', 'DP': '2012 Feb 8', 'EDAT': '2012/02/14 06:00', 'FAU': ['Henderson, Richard', 'Sali, Andrej', 'Baker, Matthew L', 'Carragher, Bridget', 'Devkota, Batsal', 'Downing, Kenneth H', 'Egelman, Edward H', 'Feng, Zukang', 'Frank, Joachim', 'Grigorieff, Nikolaus', 'Jiang, Wen', 'Ludtke, Steven J', 'Medalia, Ohad', 'Penczek, Pawel A', 'Rosenthal, Peter B', 'Rossmann, Michael G', 'Schmid, Michael F', 'Schroder, Gunnar F', 'Steven, Alasdair C', 'Stokes, David L', 'Westbrook, John D', 'Wriggers, Willy', 'Yang, Huanwang', 'Young, Jasmine', 'Berman, Helen M', 'Chiu, Wah', 'Kleywegt, Gerard J', 'Lawson, Catherine L'], 'IP': '2', 'IS': '1878-4186 (Electronic) 0969-2126 (Linking)', 'JID': '101087697', 'JT': 'Structure (London, England : 1993)', 'LA': ['eng'], 'MHDA': '2012/02/14 06:00', 'OWN': 'NLM', 'PG': '205-14', 'PHST': ['2011/11/07 [received]', '2011/12/29 [revised]', '2011/12/29 [accepted]'], 'PL': 'United States', 'PMID': '22325770', 'PST': 'ppublish', 'PT': ['Journal Article'], 'SB': 'IM', 'SO': 'Structure. 2012 Feb 8;20(2):205-14.', 'STAT': 'In-Data-Review', 'TA': 'Structure', 'TI': 'Outcome of the first electron microscopy validation task force meeting.', 'VI': '20'}, {'AB': 'Inositol 1,4,5-trisphosphate receptors (IP3Rs) play a fundamental role in generating Ca2+ signals that trigger many cellular processes in virtually all eukaryotic cells. Thus far, the three-dimensional (3D) structure of these channels has remained extremely controversial. Here, we report a subnanometer resolution electron cryomicroscopy (cryo-EM) structure of a fully functional type 1 IP3R from cerebellum in the closed state. The transmembrane region reveals a twisted bundle of four alpha helices, one from each subunit, that form a funnel shaped structure around the 4-fold symmetry axis, strikingly similar to the ion-conduction pore of K+ channels. The lumenal face of IP3R1 has prominent densities that surround the pore entrance and similar to the highly structured turrets of Kir channels. 3D statistical analysis of the cryo-EM density map identifies high variance in the cytoplasmic region. This structural variation could be attributed to genuine structural flexibility of IP3R1.', 'AD': 'National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.', 'AID': ['S0969-2126(11)00180-8 [pii]', '10.1016/j.str.2011.05.003 [doi]'], 'AU': ['Ludtke SJ', 'Tran TP', 'Ngo QT', 'Moiseenkova-Bell VY', 'Chiu W', 'Serysheva II'], 'CI': ['Copyright (c) 2011 Elsevier Ltd. All rights reserved.'], 'CRDT': ['2011/08/11 06:00'], 'DA': '20110810', 'DCOM': '20111130', 'DP': '2011 Aug 10', 'EDAT': '2011/08/11 06:00', 'FAU': ['Ludtke, Steven J', 'Tran, Thao P', 'Ngo, Que T', 'Moiseenkova-Bell, Vera Yu', 'Chiu, Wah', 'Serysheva, Irina I'], 'GR': ['P41RR002250/RR/NCRR NIH HHS/United States', 'R01 GM072804-01/GM/NIGMS NIH HHS/United States', 'R01 GM072804-02/GM/NIGMS NIH HHS/United States', 'R01 GM072804-03/GM/NIGMS NIH HHS/United States', 'R01 GM072804-04/GM/NIGMS NIH HHS/United States', 'R01 GM072804-05/GM/NIGMS NIH HHS/United States', 'R01 GM072804-05S1/GM/NIGMS NIH HHS/United States', 'R01GM072804/GM/NIGMS NIH HHS/United States', 'R01GM080139/GM/NIGMS NIH HHS/United States', 'RGM072804Z/PHS HHS/United States'], 'IP': '8', 'IS': '1878-4186 (Electronic) 0969-2126 (Linking)', 'JID': '101087697', 'JT': 'Structure (London, England : 1993)', 'LA': ['eng'], 'MH': ['Animals', 'Calcium/chemistry', 'Cerebellum/metabolism', '*Cryoelectron Microscopy', 'Inositol 1,4,5-Trisphosphate Receptors/*chemistry/isolation &', 'purification/metabolism', 'Inositol Phosphates/chemistry', 'Liposomes/chemistry', 'Protein Structure, Quaternary', 'Protein Structure, Secondary', 'Protein Structure, Tertiary', 'Rats', 'Surface Properties'], 'MHDA': '2011/12/13 00:00', 'MID': ['NIHMS300432'], 'OID': ['NLM: NIHMS300432 [Available on 08/10/12]', 'NLM: PMC3154621 [Available on 08/10/12]'], 'OWN': 'NLM', 'PG': '1192-9', 'PHST': ['2011/03/06 [received]', '2011/04/28 [revised]', '2011/05/02 [accepted]'], 'PL': 'United States', 'PMC': 'PMC3154621', 'PMCR': ['2012/08/10'], 'PMID': '21827954', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural', "Research Support, Non-U.S. Gov't"], 'RN': ['0 (Inositol 1,4,5-Trisphosphate Receptors)', '0 (Inositol Phosphates)', '0 (Liposomes)', '7440-70-2 (Calcium)'], 'SB': 'IM', 'SO': 'Structure. 2011 Aug 10;19(8):1192-9.', 'STAT': 'MEDLINE', 'TA': 'Structure', 'TI': 'Flexible architecture of IP3R1 by Cryo-EM.', 'VI': '19'}, {'AB': 'Activation of procaspase-9 on the apoptosome is a pivotal step in the intrinsic cell death pathway. We now provide further evidence that caspase recruitment domains of pc-9 and Apaf-1 form a CARD-CARD disk that is flexibly tethered to the apoptosome. In addition, a 3D reconstruction of the pc-9 apoptosome was calculated without symmetry restraints. In this structure, p20 and p10 catalytic domains of a single pc-9 interact with nucleotide binding domains of adjacent Apaf-1 subunits. Together, disk assembly and pc-9 binding create an asymmetric proteolysis machine. We also show that CARD-p20 and p20-p10 linkers play important roles in pc-9 activation. Based on the data, we propose a proximity-induced association model for pc-9 activation on the apoptosome. We also show that pc-9 and caspase-3 have overlapping binding sites on the central hub. These binding sites may play a role in pc-3 activation and could allow the formation of hybrid apoptosomes with pc-9 and caspase-3 proteolytic activities.', 'AD': 'Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118-2526, USA.', 'AID': ['S0969-2126(11)00233-4 [pii]', '10.1016/j.str.2011.07.001 [doi]'], 'AU': ['Yuan S', 'Yu X', 'Asara JM', 'Heuser JE', 'Ludtke SJ', 'Akey CW'], 'CI': ['Copyright (c) 2011 Elsevier Ltd. All rights reserved.'], 'CRDT': ['2011/08/11 06:00'], 'DA': '20110810', 'DCOM': '20111130', 'DP': '2011 Aug 10', 'EDAT': '2011/08/11 06:00', 'FAU': ['Yuan, Shujun', 'Yu, Xinchao', 'Asara, John M', 'Heuser, John E', 'Ludtke, Steven J', 'Akey, Christopher W'], 'GR': ['P41RR02250/RR/NCRR NIH HHS/United States', 'R01 GM063834-08/GM/NIGMS NIH HHS/United States', 'R01 GM63834/GM/NIGMS NIH HHS/United States', 'R01GM080139/GM/NIGMS NIH HHS/United States'], 'IP': '8', 'IS': '1878-4186 (Electronic) 0969-2126 (Linking)', 'JID': '101087697', 'JT': 'Structure (London, England : 1993)', 'LA': ['eng'], 'MH': ['Amino Acid Sequence', 'Apoptosis', 'Apoptosomes/*chemistry', 'Apoptotic Protease-Activating Factor 1/chemistry', 'CARD Signaling Adaptor Proteins/chemistry/genetics', 'Caspase 3/*chemistry', 'Caspase 9/*chemistry', 'Enzyme Activation', 'Humans', 'Models, Molecular', 'Molecular Sequence Data', 'Mutation, Missense', 'Protein Binding', 'Protein Interaction Domains and Motifs', 'Protein Structure, Quaternary', 'Thrombin/chemistry'], 'MHDA': '2011/12/13 00:00', 'MID': ['NIHMS310876'], 'OID': ['NLM: NIHMS310876 [Available on 08/10/12]', 'NLM: PMC3155825 [Available on 08/10/12]'], 'OWN': 'NLM', 'PG': '1084-96', 'PHST': ['2011/04/14 [received]', '2011/06/12 [revised]', '2011/06/23 [accepted]'], 'PL': 'United States', 'PMC': 'PMC3155825', 'PMCR': ['2012/08/10'], 'PMID': '21827945', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural'], 'RN': ['0 (APAF1 protein, human)', '0 (Apoptosomes)', '0 (Apoptotic Protease-Activating Factor 1)', '0 (CARD Signaling Adaptor Proteins)', 'EC 3.4.21.5 (Thrombin)', 'EC 3.4.22.- (Caspase 3)', 'EC 3.4.22.- (Caspase 9)'], 'SB': 'IM', 'SO': 'Structure. 2011 Aug 10;19(8):1084-96.', 'STAT': 'MEDLINE', 'TA': 'Structure', 'TI': 'The holo-apoptosome: activation of procaspase-9 and interactions with caspase-3.', 'VI': '19'}, {'AB': 'The Drosophila Apaf-1 related killer forms an apoptosome in the intrinsic cell death pathway. In this study we show that Dark forms a single ring when initiator procaspases are bound. This Dark-Dronc complex cleaves DrICE efficiently; hence, a single ring represents the Drosophila apoptosome. We then determined the 3D structure of a double ring at approximately 6.9 A resolution and created a model of the apoptosome. Subunit interactions in the Dark complex are similar to those in Apaf-1 and CED-4 apoptosomes, but there are significant differences. In particular, Dark has "lost" a loop in the nucleotide-binding pocket, which opens a path for possible dATP exchange in the apoptosome. In addition, caspase recruitment domains (CARDs) form a crown on the central hub of the Dark apoptosome. This CARD geometry suggests that conformational changes will be required to form active Dark-Dronc complexes. When taken together, these data provide insights into apoptosome structure, function, and evolution.', 'AD': 'Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA.', 'AID': ['S0969-2126(10)00399-0 [pii]', '10.1016/j.str.2010.10.009 [doi]'], 'AU': ['Yuan S', 'Yu X', 'Topf M', 'Dorstyn L', 'Kumar S', 'Ludtke SJ', 'Akey CW'], 'CI': ['Copyright A(c) 2011 Elsevier Ltd. All rights reserved.'], 'CIN': ['Structure. 2011 Jan 12;19(1):4-6. PMID: 21220110'], 'CRDT': ['2011/01/12 06:00'], 'DA': '20110111', 'DCOM': '20110418', 'DP': '2011 Jan 12', 'EDAT': '2011/01/12 06:00', 'FAU': ['Yuan, Shujun', 'Yu, Xinchao', 'Topf, Maya', 'Dorstyn, Loretta', 'Kumar, Sharad', 'Ludtke, Steven J', 'Akey, Christopher W'], 'GR': ['R01 GM063834-08/GM/NIGMS NIH HHS/United States', 'R01GM080139/GM/NIGMS NIH HHS/United States', 'R01GM63834/GM/NIGMS NIH HHS/United States'], 'IP': '1', 'IS': '1878-4186 (Electronic) 0969-2126 (Linking)', 'JID': '101087697', 'JT': 'Structure (London, England : 1993)', 'LA': ['eng'], 'LR': '20120113', 'MH': ['Animals', 'Apoptosomes/*chemistry', 'Caspases/*chemistry', 'Cryoelectron Microscopy', 'Drosophila Proteins/*chemistry', 'Drosophila melanogaster/*chemistry', 'Protein Binding', 'Protein Interaction Domains and Motifs', 'Protein Multimerization', 'Protein Structure, Quaternary', 'Protein Structure, Secondary', 'Protein Structure, Tertiary', 'Structural Homology, Protein'], 'MHDA': '2011/04/19 06:00', 'MID': ['NIHMS261977'], 'OID': ['NLM: NIHMS261977', 'NLM: PMC3053581'], 'OWN': 'NLM', 'PG': '128-40', 'PHST': ['2010/07/30 [received]', '2010/09/26 [revised]', '2010/10/01 [accepted]'], 'PL': 'United States', 'PMC': 'PMC3053581', 'PMID': '21220123', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural', "Research Support, Non-U.S. Gov't"], 'RN': ['0 (Apoptosomes)', '0 (Ark protein, Drosophila)', '0 (Drosophila Proteins)', 'EC 3.4.22.- (Caspases)', 'EC 3.4.22.- (Ice protein, Drosophila)', 'EC 3.4.22.- (Nc protein, Drosophila)'], 'SB': 'IM', 'SI': ['PDB/1VT4', 'PDB/3IZ8', 'PDB/3IZA'], 'SO': 'Structure. 2011 Jan 12;19(1):128-40.', 'STAT': 'MEDLINE', 'TA': 'Structure', 'TI': 'Structure of the Drosophila apoptosome at 6.9 a resolution.', 'VI': '19'}, {'AB': 'Electron cryo-microscopy (cryoEM) is a rapidly maturing methodology in structural biology, which now enables the determination of 3D structures of molecules, macromolecular complexes and cellular components at resolutions as high as 3.5A, bridging the gap between light microscopy and X-ray crystallography/NMR. In recent years structures of many complex molecular machines have been visualized using this method. Single particle reconstruction, the most widely used technique in cryoEM, has recently demonstrated the capability of producing structures at resolutions approaching those of X-ray crystallography, with over a dozen structures at better than 5 A resolution published to date. This method represents a significant new source of experimental data for molecular modeling and simulation studies. CryoEM derived maps and models are archived through EMDataBank.org joint deposition services to the EM Data Bank (EMDB) and Protein Data Bank (PDB), respectively. CryoEM maps are now being routinely produced over the 3 - 30 A resolution range, and a number of computational groups are developing software for building coordinate models based on this data and developing validation techniques to better assess map and model accuracy. In this workshop we will present the results of the first cryoEM modeling challenge, in which computational groups were asked to apply their tools to a selected set of published cryoEM structures. We will also compare the results of the various applied methods, and discuss the current state of the art and how we can most productively move forward.', 'AD': 'Verna & Marrs McLean Dept. of Biochem. & Mol. Biology, Baylor College of Medicine, 1 Baylor Plaza , Houston, TX 77030, USA. sludtke@bcm.edu.', 'AID': ['9789814335058_0039 [pii]'], 'AU': ['Ludtke SJ', 'Lawson CL', 'Kleywegt GJ', 'Berman HM', 'Chiu W'], 'CRDT': ['2010/12/02 06:00'], 'DA': '20101201', 'DP': '2011', 'EDAT': '2010/12/02 06:00', 'FAU': ['Ludtke, Steven J', 'Lawson, Catherine L', 'Kleywegt, Gerard J', 'Berman, Helen M', 'Chiu, Wah'], 'GR': ['R01 GM079429-05/GM/NIGMS NIH HHS/United States'], 'IS': '1793-5091 (Print)', 'JID': '9711271', 'JT': 'Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing', 'LA': ['eng'], 'MHDA': '2010/12/02 06:00', 'OWN': 'NLM', 'PG': '369-73', 'PL': 'Singapore', 'PMID': '21121065', 'PST': 'ppublish', 'PT': ['Journal Article'], 'SB': 'IM', 'SO': 'Pac Symp Biocomput. 2011:369-73.', 'STAT': 'In-Data-Review', 'TA': 'Pac Symp Biocomput', 'TI': 'WORKSHOP ON THE VALIDATION AND MODELING OF ELECTRON CRYO-MICROSCOPY STRUCTURES OF BIOLOGICAL NANOMACHINES - Workshop Introduction.'}, {'AB': 'RNA folding occurs via a series of transitions between metastable intermediate states. It is unknown whether folding intermediates are discrete structures folding along defined pathways or heterogeneous ensembles folding along broad landscapes. We use cryo-electron microscopy and single-particle image reconstruction to determine the structure of the major folding intermediate of the specificity domain of a ribonuclease P ribozyme. Our results support the existence of a discrete conformation for this folding intermediate.', 'AD': 'Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States.', 'AID': ['10.1021/ja107492b [doi]'], 'AU': ['Baird NJ', 'Ludtke SJ', 'Khant H', 'Chiu W', 'Pan T', 'Sosnick TR'], 'CRDT': ['2010/11/03 06:00'], 'DA': '20101118', 'DCOM': '20110308', 'DEP': '20101101', 'DP': '2010 Nov 24', 'EDAT': '2010/11/03 06:00', 'FAU': ['Baird, Nathan J', 'Ludtke, Steven J', 'Khant, Htet', 'Chiu, Wah', 'Pan, Tao', 'Sosnick, Tobin R'], 'GR': ['GM57880/GM/NIGMS NIH HHS/United States', 'P41RR002250/RR/NCRR NIH HHS/United States', 'R01 GM057880-11/GM/NIGMS NIH HHS/United States', 'R01 GM057880-12/GM/NIGMS NIH HHS/United States'], 'IP': '46', 'IS': '1520-5126 (Electronic) 0002-7863 (Linking)', 'JID': '7503056', 'JT': 'Journal of the American Chemical Society', 'LA': ['eng'], 'LR': '20111221', 'MH': ['Amino Acid Sequence', 'Bacillus/enzymology', 'Circular Dichroism', '*Cryoelectron Microscopy', 'Models, Molecular', 'Molecular Sequence Data', 'Ribonuclease P/*chemistry/*metabolism'], 'MHDA': '2011/03/09 06:00', 'MID': ['NIHMS249915'], 'OID': ['NLM: NIHMS249915', 'NLM: PMC2988076'], 'OWN': 'NLM', 'PG': '16352-3', 'PHST': ['2010/11/01 [aheadofprint]'], 'PL': 'United States', 'PMC': 'PMC2988076', 'PMID': '21038867', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural'], 'RN': ['EC 3.1.26.5 (Ribonuclease P)'], 'SB': 'IM', 'SO': 'J Am Chem Soc. 2010 Nov 24;132(46):16352-3. Epub 2010 Nov 1.', 'STAT': 'MEDLINE', 'TA': 'J Am Chem Soc', 'TI': 'Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy.', 'VI': '132'}, {'AB': "Cryo-electron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and macromolecular complexes. EMDataBank.org, a joint effort of the Protein Data Bank in Europe (PDBe), the Research Collaboratory for Structural Bioinformatics (RCSB) and the National Center for Macromolecular Imaging (NCMI), is a global 'one-stop shop' resource for deposition and retrieval of cryoEM maps, models and associated metadata. The resource unifies public access to the two major archives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data of macromolecules and macromolecular complexes by the wider scientific community.", 'AD': 'Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA. cathy.lawson@rutgers.edu', 'AID': ['gkq880 [pii]', '10.1093/nar/gkq880 [doi]'], 'AU': ['Lawson CL', 'Baker ML', 'Best C', 'Bi C', 'Dougherty M', 'Feng P', 'van Ginkel G', 'Devkota B', 'Lagerstedt I', 'Ludtke SJ', 'Newman RH', 'Oldfield TJ', 'Rees I', 'Sahni G', 'Sala R', 'Velankar S', 'Warren J', 'Westbrook JD', 'Henrick K', 'Kleywegt GJ', 'Berman HM', 'Chiu W'], 'CRDT': ['2010/10/12 06:00'], 'DA': '20101223', 'DCOM': '20110428', 'DEP': '20101008', 'DP': '2011 Jan', 'EDAT': '2010/10/12 06:00', 'FAU': ['Lawson, Catherine L', 'Baker, Matthew L', 'Best, Christoph', 'Bi, Chunxiao', 'Dougherty, Matthew', 'Feng, Powei', 'van Ginkel, Glen', 'Devkota, Batsal', 'Lagerstedt, Ingvar', 'Ludtke, Steven J', 'Newman, Richard H', 'Oldfield, Tom J', 'Rees, Ian', 'Sahni, Gaurav', 'Sala, Raul', 'Velankar, Sameer', 'Warren, Joe', 'Westbrook, John D', 'Henrick, Kim', 'Kleywegt, Gerard J', 'Berman, Helen M', 'Chiu, Wah'], 'GR': ['BBG022577/Biotechnology and Biological Sciences Research Council/United Kingdom', 'R01 GM079429-05/GM/NIGMS NIH HHS/United States', 'R01GM079429/GM/NIGMS NIH HHS/United States'], 'IP': 'Database issue', 'IS': '1362-4962 (Electronic) 0305-1048 (Linking)', 'JID': '0411011', 'JT': 'Nucleic acids research', 'LA': ['eng'], 'LR': '20110720', 'MH': ['*Cryoelectron Microscopy', '*Databases, Factual', 'Databases, Protein', 'Macromolecular Substances/*chemistry/ultrastructure', 'Models, Molecular', 'Proteins/*chemistry/ultrastructure'], 'MHDA': '2011/04/29 06:00', 'OID': ['NLM: PMC3013769'], 'OWN': 'NLM', 'PG': 'D456-64', 'PHST': ['2010/10/08 [aheadofprint]'], 'PL': 'England', 'PMC': 'PMC3013769', 'PMID': '20935055', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural', "Research Support, Non-U.S. Gov't"], 'RN': ['0 (Macromolecular Substances)', '0 (Proteins)'], 'SB': 'IM', 'SO': 'Nucleic Acids Res. 2011 Jan;39(Database issue):D456-64. Epub 2010 Oct 8.', 'STAT': 'MEDLINE', 'TA': 'Nucleic Acids Res', 'TI': 'EMDataBank.org: unified data resource for CryoEM.', 'VI': '39'}, {'AB': 'Electron cryomicroscopy (cryo-EM) and single particle analysis is emerging as a powerful technique for determining the 3D structure of large biomolecules and biomolecular assemblies in close to their native solution environment. Over the last decade, this technology has improved, first to sub-nanometer resolution, and more recently beyond 0.5 nm resolution. Achieving sub-nanometer resolution is now readily approachable on mid-range microscopes with straightforward data processing, so long as the target specimen meets some basic requirements. Achieving resolutions beyond 0.5 nm currently requires a high-end microscope and careful data acquisition and processing, with much more stringent specimen requirements. This chapter will review and discuss the methodologies for determining high-resolution cryo-EM structures of nonvirus particles to sub-nanometer resolution and beyond, with a particular focus on the reconstruction strategy implemented in the EMAN software suite.', 'AD': 'National Center for Macromolecular Imaging, The Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA.', 'AID': ['S0076-6879(10)82009-9 [pii]', '10.1016/S0076-6879(10)82009-9 [doi]'], 'AU': ['Cong Y', 'Ludtke SJ'], 'CI': ['Copyright (c) 2010 Elsevier Inc. All rights reserved.'], 'CRDT': ['2010/10/05 06:00'], 'DA': '20101004', 'DCOM': '20110119', 'DP': '2010', 'EDAT': '2010/10/05 06:00', 'FAU': ['Cong, Yao', 'Ludtke, Steven J'], 'GR': ['P41RR02250/RR/NCRR NIH HHS/United States', 'PN1EY016525/EY/NEI NIH HHS/United States', 'R01GM080139/GM/NIGMS NIH HHS/United States'], 'IS': '1557-7988 (Electronic) 0076-6879 (Linking)', 'JID': '0212271', 'JT': 'Methods in enzymology', 'LA': ['eng'], 'MH': ['Cryoelectron Microscopy/*methods', 'Image Processing, Computer-Assisted/*methods', 'Imaging, Three-Dimensional/methods'], 'MHDA': '2011/01/20 06:00', 'OWN': 'NLM', 'PG': '211-35', 'PL': 'United States', 'PMID': '20888963', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural'], 'SB': 'IM', 'SO': 'Methods Enzymol. 2010;482:211-35.', 'STAT': 'MEDLINE', 'TA': 'Methods Enzymol', 'TI': 'Single particle analysis at high resolution.', 'VI': '482'}, {'AB': 'With single-particle electron cryomicroscopy (cryo-EM), it is possible to visualize large, macromolecular assemblies in near-native states. Although subnanometer resolutions have been routinely achieved for many specimens, state of the art cryo-EM has pushed to near-atomic (3.3-4.6 A) resolutions. At these resolutions, it is now possible to construct reliable atomic models directly from the cryo-EM density map. In this study, we describe our recently developed protocols for performing the three-dimensional reconstruction and modeling of Mm-cpn, a group II chaperonin, determined to 4.3 A resolution. This protocol, utilizing the software tools EMAN, Gorgon and Coot, can be adapted for use with nearly all specimens imaged with cryo-EM that target beyond 5 A resolution. Additionally, the feature recognition and computational modeling tools can be applied to any near-atomic resolution density maps, including those from X-ray crystallography.', 'AD': 'National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA.', 'AID': ['nprot.2010.126 [pii]', '10.1038/nprot.2010.126 [doi]'], 'AU': ['Baker ML', 'Zhang J', 'Ludtke SJ', 'Chiu W'], 'CRDT': ['2010/10/02 06:00'], 'DA': '20101004', 'DCOM': '20110408', 'DEP': '20100930', 'DP': '2010 Sep', 'EDAT': '2010/10/05 06:00', 'FAU': ['Baker, Matthew L', 'Zhang, Junjie', 'Ludtke, Steven J', 'Chiu, Wah'], 'GR': ['P41 RR002250-26/RR/NCRR NIH HHS/United States', 'P41RR002250/RR/NCRR NIH HHS/United States', 'PN1 EY016525-01/EY/NEI NIH HHS/United States', 'PN1EY016525/EY/NEI NIH HHS/United States', 'R01 GM079429-03/GM/NIGMS NIH HHS/United States', 'R01 GM079429-05/GM/NIGMS NIH HHS/United States', 'R01 GM080139-05/GM/NIGMS NIH HHS/United States', 'R01GM079429/GM/NIGMS NIH HHS/United States', 'R01GM080139/GM/NIGMS NIH HHS/United States', 'R90 DK071504-03/DK/NIDDK NIH HHS/United States', 'R90DK71504/DK/NIDDK NIH HHS/United States'], 'IP': '10', 'IS': '1750-2799 (Electronic) 1750-2799 (Linking)', 'JID': '101284307', 'JT': 'Nature protocols', 'LA': ['eng'], 'LR': '20110926', 'MH': ['Algorithms', 'Cryoelectron Microscopy/*methods', 'Crystallography, X-Ray', 'Group II Chaperonins/*ultrastructure', 'Macromolecular Substances', 'Models, Molecular', 'Protein Conformation', 'Protein Structure, Secondary', 'Protein Structure, Tertiary', '*Software'], 'MHDA': '2011/04/09 06:00', 'MID': ['NIHMS293473'], 'OID': ['NLM: NIHMS293473', 'NLM: PMC3107675'], 'OWN': 'NLM', 'PG': '1697-708', 'PHST': ['2010/09/30 [aheadofprint]'], 'PL': 'England', 'PMC': 'PMC3107675', 'PMID': '20885381', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural', "Research Support, U.S. Gov't, Non-P.H.S."], 'RN': ['0 (Macromolecular Substances)', 'EC 3.6.1.- (Group II Chaperonins)'], 'SB': 'IM', 'SO': 'Nat Protoc. 2010 Sep;5(10):1697-708. Epub 2010 Sep 30.', 'STAT': 'MEDLINE', 'TA': 'Nat Protoc', 'TI': 'Cryo-EM of macromolecular assemblies at near-atomic resolution.', 'VI': '5'}, {'AB': 'Single-particle reconstruction is a methodology whereby transmission electron microscopy (TEM) is used to record images of individual monodisperse molecules or macromolecular assemblies, then sets of images of individual particles are computationally combined to produce a 3-D volumetric reconstruction. Ideally the TEM specimen will be prepared in vitreous ice (electron cryomicroscopy), but negative stain preparations may be used for lower resolution work. This technique has been demonstrated to produce structures at resolutions as high as approximately 4 A, though this is not yet typical. The reconstruction process is quite computationally intensive, and several software packages are available for this task. EMAN is one of the easier to master software suites for single-particle analysis. This protocol explains how to perform an initial low-resolution reconstruction using EMAN.', 'AD': 'Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.', 'AID': ['10.1007/978-1-60761-842-3_9 [doi]'], 'AU': ['Ludtke SJ'], 'CRDT': ['2010/09/14 06:00'], 'DA': '20100913', 'DCOM': '20101222', 'DP': '2010', 'EDAT': '2010/09/14 06:00', 'FAU': ['Ludtke, Steven J'], 'IS': '1940-6029 (Electronic) 1064-3745 (Linking)', 'JID': '9214969', 'JT': 'Methods in molecular biology (Clifton, N.J.)', 'LA': ['eng'], 'MH': ['Chaperonin 60/ultrastructure', 'Image Processing, Computer-Assisted/*methods', 'Macromolecular Substances/*chemistry', '*Models, Molecular', '*Software', 'Vitrification'], 'MHDA': '2010/12/24 06:00', 'OWN': 'NLM', 'PG': '157-73', 'PL': 'United States', 'PMID': '20835797', 'PST': 'ppublish', 'PT': ['Journal Article'], 'RN': ['0 (Chaperonin 60)', '0 (Macromolecular Substances)'], 'SB': 'IM', 'SO': 'Methods Mol Biol. 2010;673:157-73.', 'STAT': 'MEDLINE', 'TA': 'Methods Mol Biol', 'TI': '3-D structures of macromolecules using single-particle analysis in EMAN.', 'VI': '673'}, {'AB': 'Apaf-1 coassembles with cytochrome c to form the apoptosome, which then binds and activates procaspase-9 (pc-9). We removed pc-9 catalytic domains from the holoapoptosome by site-directed thrombinolysis. A structure of the resulting apoptosome-pc-9 CARD complex was then determined at approximately 9.5 A resolution. In our model, the central hub is constructed like other AAA+ protein rings but also contains novel features. At higher radius, the regulatory region of each Apaf-1 is comprised of tandem seven and eight blade beta-propellers with cytochrome c docked between them. Remarkably, Apaf-1 CARDs are disordered in the ground state. During activation, each Apaf-1 CARD interacts with a pc-9 CARD and these heterodimers form a flexibly tethered "disk" that sits above the central hub. When taken together, the data reveal conformational changes during Apaf-1 assembly that allow pc-9 activation. The model also provides a plausible explanation for the effects of NOD mutations that have been mapped onto the central hub.', 'AD': 'Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118-2526, USA.', 'AID': ['S0969-2126(10)00134-6 [pii]', '10.1016/j.str.2010.04.001 [doi]'], 'AU': ['Yuan S', 'Yu X', 'Topf M', 'Ludtke SJ', 'Wang X', 'Akey CW'], 'CI': ['Copyright 2010 Elsevier Ltd. All rights reserved.'], 'CRDT': ['2010/05/14 06:00'], 'DA': '20100513', 'DCOM': '20100907', 'DP': '2010 May 12', 'EDAT': '2010/05/14 06:00', 'FAU': ['Yuan, Shujun', 'Yu, Xinchao', 'Topf, Maya', 'Ludtke, Steven J', 'Wang, Xiaodong', 'Akey, Christopher W'], 'GR': ['R01 GM063834-08/GM/NIGMS NIH HHS/United States', 'Howard Hughes Medical Institute/United States', 'Medical Research Council/United Kingdom'], 'IP': '5', 'IS': '1878-4186 (Electronic) 0969-2126 (Linking)', 'JID': '101087697', 'JT': 'Structure (London, England : 1993)', 'LA': ['eng'], 'LR': '20110728', 'MH': ['Apoptosomes/*metabolism', 'Caspase 9/*metabolism', 'Cytochrome c Group', 'Cytochromes c/chemistry/metabolism/pharmacology', 'Humans', 'Proteins/*chemistry/*metabolism/physiology'], 'MHDA': '2010/09/08 06:00', 'MID': ['NIHMS202397'], 'OID': ['NLM: NIHMS202397', 'NLM: PMC2874686'], 'OWN': 'NLM', 'PG': '571-83', 'PHST': ['2010/03/04 [received]', '2010/04/07 [revised]', '2010/04/16 [accepted]'], 'PL': 'United States', 'PMC': 'PMC2874686', 'PMID': '20462491', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural', "Research Support, Non-U.S. Gov't"], 'RN': ['0 (Apoptosomes)', '0 (Cytochrome c Group)', '0 (Proteins)', "116110-46-4 (cytochrome c'')", '9007-43-6 (Cytochromes c)', 'EC 3.4.22.- (Caspase 9)'], 'SB': 'IM', 'SO': 'Structure. 2010 May 12;18(5):571-83.', 'STAT': 'MEDLINE', 'TA': 'Structure', 'TI': 'Structure of an apoptosome-procaspase-9 CARD complex.', 'VI': '18'}, {'AB': "The essential double-ring eukaryotic chaperonin TRiC/CCT (TCP1-ring complex or chaperonin containing TCP1) assists the folding of approximately 5-10% of the cellular proteome. Many TRiC substrates cannot be folded by other chaperonins from prokaryotes or archaea. These unique folding properties are likely linked to TRiC's unique heterooligomeric subunit organization, whereby each ring consists of eight different paralogous subunits in an arrangement that remains uncertain. Using single particle cryo-EM without imposing symmetry, we determined the mammalian TRiC structure at 4.7-A resolution. This revealed the existence of a 2-fold axis between its two rings resulting in two homotypic subunit interactions across the rings. A subsequent 2-fold symmetrized map yielded a 4.0-A resolution structure that evinces the densities of a large fraction of side chains, loops, and insertions. These features permitted unambiguous identification of all eight individual subunits, despite their sequence similarity. Independent biochemical near-neighbor analysis supports our cryo-EM derived TRiC subunit arrangement. We obtained a Calpha backbone model for each subunit from an initial homology model refined against the cryo-EM density. A subsequently optimized atomic model for a subunit showed approximately 95% of the main chain dihedral angles in the allowable regions of the Ramachandran plot. The determination of the TRiC subunit arrangement opens the way to understand its unique function and mechanism. In particular, an unevenly distributed positively charged wall lining the closed folding chamber of TRiC differs strikingly from that of prokaryotic and archaeal chaperonins. These interior surface chemical properties likely play an important role in TRiC's cellular substrate specificity.", 'AD': 'National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemsitry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030.', 'AID': ['0913774107 [pii]', '10.1073/pnas.0913774107 [doi]'], 'AU': ['Cong Y', 'Baker ML', 'Jakana J', 'Woolford D', 'Miller EJ', 'Reissmann S', 'Kumar RN', 'Redding-Johanson AM', 'Batth TS', 'Mukhopadhyay A', 'Ludtke SJ', 'Frydman J', 'Chiu W'], 'CRDT': ['2010/03/03 06:00'], 'DA': '20100322', 'DCOM': '20100422', 'DEP': '20100301', 'DP': '2010 Mar 16', 'EDAT': '2010/03/03 06:00', 'FAU': ['Cong, Yao', 'Baker, Matthew L', 'Jakana, Joanita', 'Woolford, David', 'Miller, Erik J', 'Reissmann, Stefanie', 'Kumar, Ramya N', 'Redding-Johanson, Alyssa M', 'Batth, Tanveer S', 'Mukhopadhyay, Aindrila', 'Ludtke, Steven J', 'Frydman, Judith', 'Chiu, Wah'], 'GR': ['5PN2EY016525/EY/NEI NIH HHS/United States', 'P41RR02250/RR/NCRR NIH HHS/United States', 'PN1EY016525/EY/NEI NIH HHS/United States', 'R01 GM080139-03/GM/NIGMS NIH HHS/United States', 'R01 GM080139-04/GM/NIGMS NIH HHS/United States'], 'IP': '11', 'IS': '1091-6490 (Electronic) 0027-8424 (Linking)', 'JID': '7505876', 'JT': 'Proceedings of the National Academy of Sciences of the United States of America', 'LA': ['eng'], 'LR': '20110926', 'MH': ['Amino Acid Sequence', 'Animals', 'Cattle', 'Chaperonin Containing TCP-1/*chemistry', '*Cryoelectron Microscopy', 'Crystallography, X-Ray', 'Models, Molecular', 'Molecular Sequence Data', 'Protein Structure, Secondary', 'Protein Subunits/*chemistry', 'Reproducibility of Results', 'Static Electricity', 'Surface Properties'], 'MHDA': '2010/04/23 06:00', 'OID': ['NLM: PMC2841888'], 'OWN': 'NLM', 'PG': '4967-72', 'PHST': ['2010/03/01 [aheadofprint]'], 'PL': 'United States', 'PMC': 'PMC2841888', 'PMID': '20194787', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural', "Research Support, U.S. Gov't, Non-P.H.S."], 'RN': ['0 (Protein Subunits)', 'EC 3.6.1.- (Chaperonin Containing TCP-1)'], 'SB': 'IM', 'SI': ['PDB/3IYG', 'PDB/3KTT'], 'SO': 'Proc Natl Acad Sci U S A. 2010 Mar 16;107(11):4967-72. Epub 2010 Mar 1.', 'STAT': 'MEDLINE', 'TA': 'Proc Natl Acad Sci U S A', 'TI': '4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement.', 'VI': '107'}, {'AB': 'Group II chaperonins are essential mediators of cellular protein folding in eukaryotes and archaea. These oligomeric protein machines, approximately 1 megadalton, consist of two back-to-back rings encompassing a central cavity that accommodates polypeptide substrates. Chaperonin-mediated protein folding is critically dependent on the closure of a built-in lid, which is triggered by ATP hydrolysis. The structural rearrangements and molecular events leading to lid closure are still unknown. Here we report four single particle cryo-electron microscopy (cryo-EM) structures of Mm-cpn, an archaeal group II chaperonin, in the nucleotide-free (open) and nucleotide-induced (closed) states. The 4.3 A resolution of the closed conformation allowed building of the first ever atomic model directly from the single particle cryo-EM density map, in which we were able to visualize the nucleotide and more than 70% of the side chains. The model of the open conformation was obtained by using the deformable elastic network modelling with the 8 A resolution open-state cryo-EM density restraints. Together, the open and closed structures show how local conformational changes triggered by ATP hydrolysis lead to an alteration of intersubunit contacts within and across the rings, ultimately causing a rocking motion that closes the ring. Our analyses show that there is an intricate and unforeseen set of interactions controlling allosteric communication and inter-ring signalling, driving the conformational cycle of group II chaperonins. Beyond this, we anticipate that our methodology of combining single particle cryo-EM and computational modelling will become a powerful tool in the determination of atomic details involved in the dynamic processes of macromolecular machines in solution.', 'AD': 'Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.', 'AID': ['nature08701 [pii]', '10.1038/nature08701 [doi]'], 'AU': ['Zhang J', 'Baker ML', 'Schroder GF', 'Douglas NR', 'Reissmann S', 'Jakana J', 'Dougherty M', 'Fu CJ', 'Levitt M', 'Ludtke SJ', 'Frydman J', 'Chiu W'], 'CRDT': ['2010/01/22 06:00'], 'DA': '20100121', 'DCOM': '20100303', 'DP': '2010 Jan 21', 'EDAT': '2010/01/22 06:00', 'FAU': ['Zhang, Junjie', 'Baker, Matthew L', 'Schroder, Gunnar F', 'Douglas, Nicholai R', 'Reissmann, Stefanie', 'Jakana, Joanita', 'Dougherty, Matthew', 'Fu, Caroline J', 'Levitt, Michael', 'Ludtke, Steven J', 'Frydman, Judith', 'Chiu, Wah'], 'GR': ['P41 RR002250-23/RR/NCRR NIH HHS/United States', 'P41 RR002250-237254/RR/NCRR NIH HHS/United States', 'P41 RR002250-24/RR/NCRR NIH HHS/United States', 'P41 RR002250-247897/RR/NCRR NIH HHS/United States', 'PN2 EY016525-02S1/EY/NEI NIH HHS/United States', 'PN2 EY016525-03/EY/NEI NIH HHS/United States', 'PN2 EY016525-04/EY/NEI NIH HHS/United States', 'PN2 EY016525-05/EY/NEI NIH HHS/United States', 'R01 GM063817-11/GM/NIGMS NIH HHS/United States', 'R01 GM079429-03/GM/NIGMS NIH HHS/United States', 'R01 GM080139-03/GM/NIGMS NIH HHS/United States', 'R01 GM080139-04/GM/NIGMS NIH HHS/United States', 'R90 DK071504-03/DK/NIDDK NIH HHS/United States', 'T32 GM007276-30/GM/NIGMS NIH HHS/United States', 'T32 GM007276-31/GM/NIGMS NIH HHS/United States'], 'IP': '7279', 'IS': '1476-4687 (Electronic) 0028-0836 (Linking)', 'JID': '0410462', 'JT': 'Nature', 'LA': ['eng'], 'LR': '20110926', 'MH': ['Adenosine Triphosphate/chemistry/metabolism/pharmacology', 'Allosteric Regulation', 'Binding Sites', 'Cryoelectron Microscopy', 'Group II Chaperonins/*chemistry/*metabolism/ultrastructure', 'Hydrolysis/drug effects', 'Methanococcus/*chemistry', 'Models, Molecular', 'Protein Binding', 'Protein Conformation/drug effects', '*Protein Folding', 'Protein Subunits/chemistry/metabolism', 'Structure-Activity Relationship'], 'MHDA': '2010/03/04 06:00', 'MID': ['NIHMS165702'], 'OID': ['NLM: NIHMS165702', 'NLM: PMC2834796'], 'OWN': 'NLM', 'PG': '379-83', 'PHST': ['2009/06/24 [received]', '2009/11/16 [accepted]'], 'PL': 'England', 'PMC': 'PMC2834796', 'PMID': '20090755', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, Non-P.H.S."], 'RN': ['0 (Protein Subunits)', '56-65-5 (Adenosine Triphosphate)', 'EC 3.6.1.- (Group II Chaperonins)'], 'SB': 'IM', 'SI': ['PDB/3IYE', 'PDB/3IYF'], 'SO': 'Nature. 2010 Jan 21;463(7279):379-83.', 'STAT': 'MEDLINE', 'TA': 'Nature', 'TI': 'Mechanism of folding chamber closure in a group II chaperonin.', 'VI': '463'}, {'AB': 'Human plasma low-density lipoproteins (LDL), a risk factor for cardiovascular disease, transfer cholesterol from plasma to liver cells via the LDL receptor (LDLr). Here, we report the structures of LDL and its complex with the LDL receptor extracellular domain (LDL.LDLr) at extracellular pH determined by cryoEM. Difference imaging between LDL.LDLr and LDL localizes the site of LDLr bound to its ligand. The structural features revealed from the cryoEM map lead to a juxtaposed stacking model of cholesteryl esters (CEs). High density in the outer shell identifies protein-rich regions that can be accounted for by a single apolipoprotein (apo B-100, 500 kDa) leading to a model for the distribution of its alpha-helix and beta-sheet rich domains across the surface. The structural relationship between the apo B-100 and CEs appears to dictate the structural stability and function of normal LDL.', 'AD': 'Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA. gren@msg.ucsf.edu', 'AID': ['0908004107 [pii]', '10.1073/pnas.0908004107 [doi]'], 'AU': ['Ren G', 'Rudenko G', 'Ludtke SJ', 'Deisenhofer J', 'Chiu W', 'Pownall HJ'], 'CRDT': ['2010/01/19 06:00'], 'DA': '20100205', 'DCOM': '20100326', 'DEP': '20091228', 'DP': '2010 Jan 19', 'EDAT': '2010/01/19 06:00', 'FAU': ['Ren, Gang', 'Rudenko, Gabby', 'Ludtke, Steven J', 'Deisenhofer, Johann', 'Chiu, Wah', 'Pownall, Henry J'], 'GR': ['HL-30914/HL/NHLBI NIH HHS/United States', 'HL-56865/HL/NHLBI NIH HHS/United States', 'P01GM99116/GM/NIGMS NIH HHS/United States', 'P41RR02250/RR/NCRR NIH HHS/United States', 'Howard Hughes Medical Institute/United States'], 'IP': '3', 'IS': '1091-6490 (Electronic) 0027-8424 (Linking)', 'JID': '7505876', 'JT': 'Proceedings of the National Academy of Sciences of the United States of America', 'LA': ['eng'], 'LR': '20100928', 'MH': ['Cryoelectron Microscopy/*methods', 'Humans', '*Models, Molecular', 'Protein Conformation', 'Receptors, LDL/*chemistry'], 'MHDA': '2010/03/27 06:00', 'OID': ['NLM: PMC2798884'], 'OWN': 'NLM', 'PG': '1059-64', 'PHST': ['2009/12/28 [aheadofprint]'], 'PL': 'United States', 'PMC': 'PMC2798884', 'PMID': '20080547', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural', "Research Support, Non-U.S. Gov't"], 'RN': ['0 (Receptors, LDL)'], 'SB': 'IM', 'SO': 'Proc Natl Acad Sci U S A. 2010 Jan 19;107(3):1059-64. Epub 2009 Dec 28.', 'STAT': 'MEDLINE', 'TA': 'Proc Natl Acad Sci U S A', 'TI': 'Model of human low-density lipoprotein and bound receptor based on cryoEM.', 'VI': '107'}, {'AB': "Magainin, a 23-residue antibiotic peptide, interacts directly with the lipid bilayer leading to cell lysis in a strongly concentration-dependent fashion. Utilizing cryo-electron microscopy, we have directly observed magainin interacting with synthetic DMPC/DMPG membranes. Visual examination shows that visibly unperturbed vesicles are often found adjacent to vesicles that are lysed or porous, demonstrating that magainin disruption is a highly stochastic process. Quantitatively, power spectra of large numbers of porous vesicles can be averaged together to produce the equivalent of an electron scattering curve, which can be related to theory, simulation, and published neutron scattering experiments. We demonstrate that magainin-induced pores in lipid vesicles have a mean diameter of approximately 80 A, compatible with earlier reported results in multilayer stacks. In addition to establishing a connection between experiments in multilayer stacks and vesicles, this also demonstrates that computed power spectra from windowed-out regions of cryo-EM images can be compared to neutron scattering data in a meaningful way, even though the pores of interest cannot yet be individually identified in images. Cryo-EM offers direct imaging of systems in configurations closely related to in vivo conditions, whereas neutron scattering has a greater variety of mechanisms for specific contrast variation via D2O and deuterated lipids. Combined, the two mechanisms support each other, and provide a clearer picture of such 'soft' systems than either could provide alone.", 'AD': 'Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA.', 'AID': ['S0006-3495(09)00905-9 [pii]', '10.1016/j.bpj.2009.04.039 [doi]'], 'AU': ['Han M', 'Mei Y', 'Khant H', 'Ludtke SJ'], 'CRDT': ['2009/07/08 09:00'], 'DA': '20090707', 'DCOM': '20091013', 'DP': '2009 Jul 8', 'EDAT': '2009/07/08 09:00', 'FAU': ['Han, Mikyung', 'Mei, Yuan', 'Khant, Htet', 'Ludtke, Steven J'], 'GR': ['P41RR02250/RR/NCRR NIH HHS/United States', 'R01 GM080139-02/GM/NIGMS NIH HHS/United States', 'R01 GM080139-03/GM/NIGMS NIH HHS/United States', 'R01 GM080139-04/GM/NIGMS NIH HHS/United States', 'R01GM080139/GM/NIGMS NIH HHS/United States'], 'IP': '1', 'IS': '1542-0086 (Electronic) 0006-3495 (Linking)', 'JID': '0370626', 'JT': 'Biophysical journal', 'LA': ['eng'], 'LR': '20111117', 'MH': ['Algorithms', 'Animals', 'Antimicrobial Cationic Peptides/*chemistry', 'Computer Simulation', 'Dimyristoylphosphatidylcholine/chemistry', 'Liposomes/*chemistry', 'Magainins', 'Microscopy, Electron/methods', 'Models, Theoretical', 'Neutrons', 'Phosphatidylglycerols/chemistry', 'Scattering, Radiation', 'Stochastic Processes', 'Temperature', 'Xenopus', 'Xenopus Proteins/*chemistry'], 'MHDA': '2009/10/14 06:00', 'OID': ['NLM: PMC2711362'], 'OWN': 'NLM', 'PG': '164-72', 'PHST': ['2008/10/29 [received]', '2009/04/24 [revised]', '2009/04/27 [accepted]'], 'PL': 'United States', 'PMC': 'PMC2711362', 'PMID': '19580754', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural'], 'RN': ['0 (Antimicrobial Cationic Peptides)', '0 (Liposomes)', '0 (Magainins)', '0 (Phosphatidylglycerols)', '0 (Xenopus Proteins)', '108433-95-0 (magainin 2 peptide, Xenopus)', '13699-48-4 (Dimyristoylphosphatidylcholine)', '61361-72-6 (dimyristoylphosphatidylglycerol)'], 'SB': 'IM', 'SO': 'Biophys J. 2009 Jul 8;97(1):164-72.', 'STAT': 'MEDLINE', 'TA': 'Biophys J', 'TI': 'Characterization of antibiotic peptide pores using cryo-EM and comparison to neutron scattering.', 'VI': '97'}, {'AB': 'Phenoloxidases (POs) occur in all organisms and are involved in skin and hair coloring in mammals, and initiating melanization in wound healing. Mutation or overexpression of PO can cause albinism or melanoma, respectively. SDS can convert inactive PO and the oxygen carrier hemocyanin (Hc) into enzymatically active PO. Here we present single-particle cryo-EM maps at subnanometer resolution and pseudoatomic models of the 24-oligomeric Hc from scorpion Pandinus imperator in resting and SDS-activated states. Our structural analyses led to a plausible mechanism of Hc enzyme PO activation: upon SDS activation, the intrinsically flexible Hc domain I twists away from domains II and III in each subunit, exposing the entrance to the active site; this movement is stabilized by enhanced interhexamer and interdodecamer interactions, particularly in the central linker subunits. This mechanism could be applicable to other type 3 copper proteins, as the active site is highly conserved.', 'AD': 'National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA.', 'AID': ['S0969-2126(09)00150-6 [pii]', '10.1016/j.str.2009.03.005 [doi]'], 'AU': ['Cong Y', 'Zhang Q', 'Woolford D', 'Schweikardt T', 'Khant H', 'Dougherty M', 'Ludtke SJ', 'Chiu W', 'Decker H'], 'CRDT': ['2009/05/19 09:00'], 'DA': '20090518', 'DCOM': '20090813', 'DP': '2009 May 13', 'EDAT': '2009/05/19 09:00', 'FAU': ['Cong, Yao', 'Zhang, Qinfen', 'Woolford, David', 'Schweikardt, Thorsten', 'Khant, Htet', 'Dougherty, Matthew', 'Ludtke, Steven J', 'Chiu, Wah', 'Decker, Heinz'], 'GR': ['2 PN2 EY016525/EY/NEI NIH HHS/United States', 'P41 RR002250-22/RR/NCRR NIH HHS/United States', 'P41 RR002250-23/RR/NCRR NIH HHS/United States', 'P41 RR002250-24/RR/NCRR NIH HHS/United States', 'P41 RR02250/RR/NCRR NIH HHS/United States', 'PN1 EY016525-01/EY/NEI NIH HHS/United States', 'PN2 EY016525-02/EY/NEI NIH HHS/United States', 'PN2 EY016525-03/EY/NEI NIH HHS/United States', 'PN2 EY016525-04/EY/NEI NIH HHS/United States', 'R01 GM080139-03/GM/NIGMS NIH HHS/United States', 'R01 GM08139/GM/NIGMS NIH HHS/United States'], 'IP': '5', 'IS': '0969-2126 (Print) 0969-2126 (Linking)', 'JID': '101087697', 'JT': 'Structure (London, England : 1993)', 'LA': ['eng'], 'LR': '20110926', 'MH': ['Animals', 'Binding Sites', 'Catalytic Domain', 'Cryoelectron Microscopy', 'Enzyme Activation', 'Hemocyanin/*chemistry/metabolism', 'Models, Molecular', 'Monophenol Monooxygenase/*chemistry/*metabolism', 'Protein Conformation', 'Protein Subunits/chemistry/metabolism', 'Scorpions/*metabolism', 'Sodium Dodecyl Sulfate/*pharmacology', 'Surface-Active Agents/*pharmacology'], 'MHDA': '2009/08/14 09:00', 'MID': ['NIHMS119397'], 'OID': ['NLM: NIHMS119397', 'NLM: PMC2705691'], 'OWN': 'NLM', 'PG': '749-58', 'PHST': ['2008/12/06 [received]', '2009/02/22 [revised]', '2009/03/13 [accepted]'], 'PL': 'United States', 'PMC': 'PMC2705691', 'PMID': '19446530', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural', "Research Support, Non-U.S. Gov't"], 'RN': ['0 (Protein Subunits)', '0 (Surface-Active Agents)', '151-21-3 (Sodium Dodecyl Sulfate)', '9013-72-3 (Hemocyanin)', 'EC 1.14.18.1 (Monophenol Monooxygenase)'], 'SB': 'IM', 'SI': ['PDB/3IXV', 'PDB/3IXW'], 'SO': 'Structure. 2009 May 13;17(5):749-58.', 'STAT': 'MEDLINE', 'TA': 'Structure', 'TI': 'Structural mechanism of SDS-induced enzyme activity of scorpion hemocyanin revealed by electron cryomicroscopy.', 'VI': '17'}, {'AB': "Alzheimer's disease is a neurodegenerative disorder characterized by the accumulation of amyloid plaques in the brain. This amyloid primarily contains amyloid-beta (Abeta), a 39- to 43-aa peptide derived from the proteolytic cleavage of the endogenous amyloid precursor protein. The 42-residue-length Abeta peptide (Abeta(1-42)), the most abundant Abeta peptide found in plaques, has a much greater propensity to self-aggregate into fibrils than the other peptides and is believed to be more pathogenic. Synthetic human Abeta(1-42) peptides self-aggregate into stable but poorly-ordered helical filaments. We determined their structure to approximately 10-A resolution by using cryoEM and the iterative real-space reconstruction method. This structure reveals 2 protofilaments winding around a hollow core. Previous hairpin-like NMR models for Abeta(17-42) fit well in the cryoEM density map and reveal that the juxtaposed protofilaments are joined via the N terminus of the peptide from 1 protofilament connecting to the loop region of the peptide in the opposite protofilament. This model of mature Abeta(1-42) fibrils is markedly different from previous cryoEM models of Abeta(1-40) fibrils. In our model, the C terminus of Abeta forms the inside wall of the hollow core, which is supported by partial proteolysis analysis.", 'AD': 'Graduate Program in Structural and Computational Biology and Molecular Biophysics, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.', 'AID': ['0901085106 [pii]', '10.1073/pnas.0901085106 [doi]'], 'AU': ['Zhang R', 'Hu X', 'Khant H', 'Ludtke SJ', 'Chiu W', 'Schmid MF', 'Frieden C', 'Lee JM'], 'CRDT': ['2009/03/07 09:00'], 'DA': '20090325', 'DCOM': '20090408', 'DEP': '20090305', 'DP': '2009 Mar 24', 'EDAT': '2009/03/07 09:00', 'FAU': ['Zhang, Rui', 'Hu, Xiaoyan', 'Khant, Htet', 'Ludtke, Steven J', 'Chiu, Wah', 'Schmid, Michael F', 'Frieden, Carl', 'Lee, Jin-Moo'], 'GR': ['DK13332/DK/NIDDK NIH HHS/United States', 'P01 NS032636/NS/NINDS NIH HHS/United States', 'P01 NS032636-139001/NS/NINDS NIH HHS/United States', 'P41RR02250/RR/NCRR NIH HHS/United States', 'PN1EY016525/EY/NEI NIH HHS/United States', 'R01 GM080139-03/GM/NIGMS NIH HHS/United States', 'R01 NS048283/NS/NINDS NIH HHS/United States', 'R01 NS048283-03/NS/NINDS NIH HHS/United States', 'R01 NS048283-04/NS/NINDS NIH HHS/United States'], 'IP': '12', 'IS': '1091-6490 (Electronic) 0027-8424 (Linking)', 'JID': '7505876', 'JT': 'Proceedings of the National Academy of Sciences of the United States of America', 'LA': ['eng'], 'LR': '20110926', 'MH': ['Amino Acid Sequence', 'Amyloid/*metabolism/*ultrastructure', 'Amyloid beta-Peptides/chemistry/*metabolism/*ultrastructure', 'Cryoelectron Microscopy', 'Humans', 'Models, Molecular', 'Molecular Sequence Data', 'Peptide Fragments/chemistry/*metabolism/*ultrastructure', 'Peptides/*metabolism', 'Protein Processing, Post-Translational', 'Static Electricity'], 'MHDA': '2009/04/09 09:00', 'OID': ['NLM: PMC2660777'], 'OWN': 'NLM', 'PG': '4653-8', 'PHST': ['2009/03/05 [aheadofprint]'], 'PL': 'United States', 'PMC': 'PMC2660777', 'PMID': '19264960', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural', "Research Support, Non-U.S. Gov't"], 'RN': ['0 (Amyloid)', '0 (Amyloid beta-Peptides)', '0 (Peptide Fragments)', '0 (Peptides)', '0 (amyloid beta-protein (1-42))'], 'SB': 'IM', 'SO': 'Proc Natl Acad Sci U S A. 2009 Mar 24;106(12):4653-8. Epub 2009 Mar 5.', 'STAT': 'MEDLINE', 'TA': 'Proc Natl Acad Sci U S A', 'TI': "Interprotofilament interactions between Alzheimer's Abeta1-42 peptides in amyloid fibrils revealed by cryoEM.", 'VI': '106'}, {'AB': 'Human plasma high-density lipoproteins (HDL), the primary vehicle for reverse cholesterol transport, are the target of serum opacity factor (SOF), a virulence determinant of Streptococcus pyogenes that turns serum opaque. HDL comprise a core of neutral lipidscholesteryl esters and some triglyceridesurrounded by a surface monolayer of cholesterol, phospholipids, and specialized proteins [apolipoproteins (apos) A-I and A-II]. A HDL is an unstable particle residing in a kinetic trap from which it can escape via chaotropic, detergent, or thermal perturbation. Recombinant (r) SOF catalyzes the transfer of nearly all neutral lipids of approximately 100,000 HDL particles (D approximately 8.5 nm) into a single, large cholesteryl ester-rich microemulsion (CERM; D > 100 nm), leaving a new HDL-like particle [neo HDL (D approximately 5.8 nm)] while releasing lipid-free (LF) apo A-I. CERM formation and apo A-I release have similar kinetics, suggesting parallel or rapid consecutive steps. By using complementary physicochemical methods, we have refined the mechanistic model for HDL opacification. According to size exclusion chromatography, a HDL containing nonlabile apo A-I resists rSOF-mediated opacification. On the basis of kinetic cryo-electron microscopy, rSOF (10 nM) catalyzes the conversion of HDL (4 microM) to neo HDL via a stepwise mechanism in which intermediate-sized particles are seen. Kinetic turbidimetry revealed opacification as a rising exponential reaction with a rate constant k of (4.400 +/- 0.004) x 10(-2) min(-1). Analysis of the kinetic data using transition state theory gave an enthalpy (DeltaH()), entropy (DeltaS(++)), and free energy (DeltaG()) of activation of 73.9 kJ/mol, -66.87 J/K, and 94.6 kJ/mol, respectively. The free energy of activation for opacification is nearly identical to that for the displacement of apo A-I from HDL by guanidine hydrochloride. We conclude that apo A-I lability is required for HDL opacification, LF apo A-I desorption is the rate-limiting step, and nearly all HDL particles contain at least one labile copy of apo A-I.', 'AD': 'Section of Atherosclerosis and Vascular Medicine, Department of Medicine, Baylor College of Medicine, Houston, Texas 77030, USA.', 'AID': ['10.1021/bi802287q [doi]', '10.1021/bi802287q [pii]'], 'AU': ['Han M', 'Gillard BK', 'Courtney HS', 'Ward K', 'Rosales C', 'Khant H', 'Ludtke SJ', 'Pownall HJ'], 'CRDT': ['2009/02/05 09:00'], 'DA': '20090217', 'DCOM': '20090310', 'DP': '2009 Feb 24', 'EDAT': '2009/02/05 09:00', 'FAU': ['Han, Mikyung', 'Gillard, Baiba K', 'Courtney, Harry S', 'Ward, Kathryn', 'Rosales, Corina', 'Khant, Htet', 'Ludtke, Steven J', 'Pownall, Henry J'], 'GR': ['HL-30914/HL/NHLBI NIH HHS/United States', 'HL-56865/HL/NHLBI NIH HHS/United States', 'P41RR02250/RR/NCRR NIH HHS/United States', 'R01 GM080139-03/GM/NIGMS NIH HHS/United States', 'R01 HL030914-17/HL/NHLBI NIH HHS/United States', 'R01 HL056865-09A2/HL/NHLBI NIH HHS/United States'], 'IP': '7', 'IS': '1520-4995 (Electronic) 0006-2960 (Linking)', 'JID': '0370623', 'JT': 'Biochemistry', 'LA': ['eng'], 'LR': '20110926', 'MH': ['Apolipoprotein A-I/isolation & purification/*physiology', 'Chromatography, Gel', 'Cryoelectron Microscopy', 'Humans', 'Kinetics', 'Lipoproteins, HDL/*blood/chemistry', 'Peptide Hydrolases/*physiology', 'Streptococcus pyogenes/*physiology', 'Thermodynamics'], 'MHDA': '2009/03/11 09:00', 'MID': ['NIHMS240090'], 'OID': ['NLM: NIHMS240090', 'NLM: PMC2962917'], 'OWN': 'NLM', 'PG': '1481-7', 'PL': 'United States', 'PMC': 'PMC2962917', 'PMID': '19191587', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural'], 'RN': ['0 (Apolipoprotein A-I)', '0 (Lipoproteins, HDL)', '0 (opacity factor)', 'EC 3.4.- (Peptide Hydrolases)'], 'SB': 'IM', 'SO': 'Biochemistry. 2009 Feb 24;48(7):1481-7.', 'STAT': 'MEDLINE', 'TA': 'Biochemistry', 'TI': 'Disruption of human plasma high-density lipoproteins by streptococcal serum opacity factor requires labile apolipoprotein A-I.', 'VI': '48'}, {'AB': 'The skeletal muscle Ca(2+) release channel (RyR1), a homotetramer, regulates the release of Ca(2+) from the sarcoplasmic reticulum to initiate muscle contraction. In this work, we have delineated the RyR1 monomer boundaries in a subnanometer-resolution electron cryomicroscopy (cryo-EM) density map. In the cytoplasmic region of each RyR1 monomer, 36 alpha-helices and 7 beta-sheets can be resolved. A beta-sheet was also identified close to the membrane-spanning region that resembles the cytoplasmic pore structures of inward rectifier K(+) channels. Three structural folds, generated for amino acids 12-565 using comparative modeling and cryo-EM density fitting, localize close to regions implicated in communication with the voltage sensor in the transverse tubules. Eleven of the 15 disease-related residues for these domains are mapped to the surface of these models. Four disease-related residues are found in a basin at the interfaces of these regions, creating a pocket in which the immunophilin FKBP12 can fit. Taken together, these results provide a structural context for both channel gating and the consequences of certain malignant hyperthermia and central core disease-associated mutations in RyR1.', 'AD': 'National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.', 'AID': ['0803189105 [pii]', '10.1073/pnas.0803189105 [doi]'], 'AU': ['Serysheva II', 'Ludtke SJ', 'Baker ML', 'Cong Y', 'Topf M', 'Eramian D', 'Sali A', 'Hamilton SL', 'Chiu W'], 'CRDT': ['2008/07/16 09:00'], 'DA': '20080717', 'DCOM': '20080903', 'DEP': '20080710', 'DP': '2008 Jul 15', 'EDAT': '2008/07/16 09:00', 'FAU': ['Serysheva, Irina I', 'Ludtke, Steven J', 'Baker, Matthew L', 'Cong, Yao', 'Topf, Maya', 'Eramian, David', 'Sali, Andrej', 'Hamilton, Susan L', 'Chiu, Wah'], 'GR': ['P01GM064692/GM/NIGMS NIH HHS/United States', 'P01GM99116/GM/NIGMS NIH HHS/United States', 'P41 RR002250-22/RR/NCRR NIH HHS/United States', 'P41 RR002250-226483/RR/NCRR NIH HHS/United States', 'P41 RR002250-23/RR/NCRR NIH HHS/United States', 'P41 RR002250-237245/RR/NCRR NIH HHS/United States', 'P41RR02250/RR/NCRR NIH HHS/United States', 'PN2 EY016525-02S1/EY/NEI NIH HHS/United States', 'PN2 EY016525-03/EY/NEI NIH HHS/United States', 'PN2 EY016525-03S1/EY/NEI NIH HHS/United States', 'PN2 EY016525-04/EY/NEI NIH HHS/United States', 'PN2EY016525/EY/NEI NIH HHS/United States', 'R01 AR041802-14/AR/NIAMS NIH HHS/United States', 'R01 AR044864-10/AR/NIAMS NIH HHS/United States', 'R01 GM072804-01/GM/NIGMS NIH HHS/United States', 'R01 GM072804-02/GM/NIGMS NIH HHS/United States', 'R01 GM072804-03/GM/NIGMS NIH HHS/United States', 'R01 GM072804-04/GM/NIGMS NIH HHS/United States', 'R01 GM080139-02/GM/NIGMS NIH HHS/United States', 'R01 GM080139-03/GM/NIGMS NIH HHS/United States', 'R01AR41802/AR/NIAMS NIH HHS/United States', 'R01AR44864/AR/NIAMS NIH HHS/United States', 'R01GM072804/GM/NIGMS NIH HHS/United States'], 'IP': '28', 'IS': '1091-6490 (Electronic) 0027-8424 (Linking)', 'JID': '7505876', 'JT': 'Proceedings of the National Academy of Sciences of the United States of America', 'LA': ['eng'], 'LR': '20110926', 'MH': ['*Cryoelectron Microscopy', 'Cytoplasm', '*Models, Molecular', 'Muscle, Skeletal/chemistry', 'Protein Structure, Secondary', 'Protein Structure, Tertiary', 'Ryanodine Receptor Calcium Release Channel/*chemistry'], 'MHDA': '2008/09/04 09:00', 'OID': ['NLM: PMC2474495'], 'OWN': 'NLM', 'PG': '9610-5', 'PHST': ['2008/07/10 [aheadofprint]'], 'PL': 'United States', 'PMC': 'PMC2474495', 'PMID': '18621707', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, Non-P.H.S."], 'RN': ['0 (Ryanodine Receptor Calcium Release Channel)'], 'SB': 'IM', 'SO': 'Proc Natl Acad Sci U S A. 2008 Jul 15;105(28):9610-5. Epub 2008 Jul 10.', 'STAT': 'MEDLINE', 'TA': 'Proc Natl Acad Sci U S A', 'TI': 'Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel.', 'VI': '105'}, {'AB': 'All chaperonins mediate ATP-dependent polypeptide folding by confining substrates within a central chamber. Intriguingly, the eukaryotic chaperonin TRiC (also called CCT) uses a built-in lid to close the chamber, whereas prokaryotic chaperonins use a detachable lid. Here we determine the mechanism of lid closure in TRiC using single-particle cryo-EM and comparative protein modeling. Comparison of TRiC in its open, nucleotide-free, and closed, nucleotide-induced states reveals that the interdomain motions leading to lid closure in TRiC are radically different from those of prokaryotic chaperonins, despite their overall structural similarity. We propose that domain movements in TRiC are coordinated through unique interdomain contacts within each subunit and, further, these contacts are absent in prokaryotic chaperonins. Our findings show how different mechanical switches can evolve from a common structural framework through modification of allosteric networks.', 'AD': 'Graduate Program in Structural and Computational Biology and Molecular Biophysics, One Baylor Plaza, Baylor College of Medicine, Houston, Texas 77030, USA.', 'AID': ['nsmb.1436 [pii]', '10.1038/nsmb.1436 [doi]'], 'AU': ['Booth CR', 'Meyer AS', 'Cong Y', 'Topf M', 'Sali A', 'Ludtke SJ', 'Chiu W', 'Frydman J'], 'CRDT': ['2008/06/10 09:00'], 'DA': '20080703', 'DCOM': '20080804', 'DEP': '20080608', 'DP': '2008 Jul', 'EDAT': '2008/06/10 09:00', 'FAU': ['Booth, Christopher R', 'Meyer, Anne S', 'Cong, Yao', 'Topf, Maya', 'Sali, Andrej', 'Ludtke, Steven J', 'Chiu, Wah', 'Frydman, Judith'], 'GR': ['P41 RR002250-120007/RR/NCRR NIH HHS/United States', 'P41 RR002250-120009/RR/NCRR NIH HHS/United States', 'P41 RR002250-120010/RR/NCRR NIH HHS/United States', 'P41 RR002250-120011/RR/NCRR NIH HHS/United States', 'P41 RR002250-120029/RR/NCRR NIH HHS/United States', 'P41 RR002250-120030/RR/NCRR NIH HHS/United States', 'P41 RR002250-130010/RR/NCRR NIH HHS/United States', 'P41 RR002250-130018/RR/NCRR NIH HHS/United States', 'P41 RR002250-14/RR/NCRR NIH HHS/United States', 'P41 RR002250-140029/RR/NCRR NIH HHS/United States', 'P41 RR002250-150009/RR/NCRR NIH HHS/United States', 'P41 RR002250-160008/RR/NCRR NIH HHS/United States', 'P41 RR002250-190031/RR/NCRR NIH HHS/United States', 'P41 RR002250-190033/RR/NCRR NIH HHS/United States', 'P41 RR002250-190034/RR/NCRR NIH HHS/United States', 'P41 RR002250-190064/RR/NCRR NIH HHS/United States', 'P41 RR002250-190067/RR/NCRR NIH HHS/United States', 'P41 RR002250-190069/RR/NCRR NIH HHS/United States', 'P41 RR002250-190072/RR/NCRR NIH HHS/United States', 'P41 RR002250-190079/RR/NCRR NIH HHS/United States', 'P41 RR002250-200031/RR/NCRR NIH HHS/United States', 'P41 RR002250-200069/RR/NCRR NIH HHS/United States', 'P41 RR002250-200084/RR/NCRR NIH HHS/United States', 'P41 RR002250-200085/RR/NCRR NIH HHS/United States', 'P41 RR002250-217373/RR/NCRR NIH HHS/United States', 'P41 RR002250-217374/RR/NCRR NIH HHS/United States', 'P41 RR002250-217381/RR/NCRR NIH HHS/United States', 'P41 RR002250-217422/RR/NCRR NIH HHS/United States', 'PN1 EY016525-01/EY/NEI NIH HHS/United States', 'R01 GM074074-01/GM/NIGMS NIH HHS/United States', 'R01 GM074074-01S1/GM/NIGMS NIH HHS/United States', 'R01 GM074074-02/GM/NIGMS NIH HHS/United States', 'R01 GM074074-03/GM/NIGMS NIH HHS/United States', 'R01 GM074074-04/GM/NIGMS NIH HHS/United States', 'R01 GM080139-02/GM/NIGMS NIH HHS/United States', 'R01 GM080139-03/GM/NIGMS NIH HHS/United States'], 'IP': '7', 'IS': '1545-9985 (Electronic) 1545-9985 (Linking)', 'JID': '101186374', 'JT': 'Nature structural & molecular biology', 'LA': ['eng'], 'LR': '20110926', 'MH': ['Animals', 'Cattle', 'Chaperonin 60/chemistry/metabolism', 'Chaperonin Containing TCP-1', 'Chaperonins/*chemistry/metabolism/ultrastructure', 'Cryoelectron Microscopy', 'Crystallography, X-Ray', 'Models, Molecular', 'Protein Structure, Secondary', 'Protein Structure, Tertiary', 'Protein Subunits/chemistry/metabolism'], 'MHDA': '2008/08/05 09:00', 'MID': ['NIHMS53940'], 'OID': ['NLM: NIHMS53940', 'NLM: PMC2546500'], 'OWN': 'NLM', 'PG': '746-53', 'PHST': ['2007/09/18 [received]', '2008/04/28 [accepted]', '2008/06/08 [aheadofprint]'], 'PL': 'United States', 'PMC': 'PMC2546500', 'PMID': '18536725', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, Non-P.H.S."], 'RN': ['0 (Chaperonin 60)', '0 (Protein Subunits)', 'EC 3.6.1.- (Chaperonin Containing TCP-1)', 'EC 3.6.1.- (Chaperonins)'], 'SB': 'IM', 'SO': 'Nat Struct Mol Biol. 2008 Jul;15(7):746-53. Epub 2008 Jun 8.', 'STAT': 'MEDLINE', 'TA': 'Nat Struct Mol Biol', 'TI': 'Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT.', 'VI': '15'}, {'AB': 'In this work, we employ single-particle electron cryo-microscopy (cryo-EM) to reconstruct GroEL to approximately 4 A resolution with both D7 and C7 symmetry. Using a newly developed skeletonization algorithm and secondary structure element identification in combination with sequence-based secondary structure prediction, we demonstrate that it is possible to achieve a de novo Calpha trace directly from a cryo-EM reconstruction. The topology of our backbone trace is completely accurate, though subtle alterations illustrate significant differences from existing crystal structures. In the map with C7 symmetry, the seven monomers in each ring are identical; however, the subunits have a subtly different structure in each ring, particularly in the equatorial domain. These differences include an asymmetric salt bridge, density in the nucleotide-binding pocket of only one ring, and small shifts in alpha helix positions. This asymmetric conformation is different from previous asymmetric structures, including GroES-bound GroEL, and may represent a "primed state" in the chaperonin pathway.', 'AD': 'National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.', 'AID': ['S0969-2126(08)00072-5 [pii]', '10.1016/j.str.2008.02.007 [doi]'], 'AU': ['Ludtke SJ', 'Baker ML', 'Chen DH', 'Song JL', 'Chuang DT', 'Chiu W'], 'CRDT': ['2008/03/13 09:00'], 'DA': '20080312', 'DCOM': '20080610', 'DP': '2008 Mar', 'EDAT': '2008/03/13 09:00', 'FAU': ['Ludtke, Steven J', 'Baker, Matthew L', 'Chen, Dong-Hua', 'Song, Jiu-Li', 'Chuang, David T', 'Chiu, Wah'], 'GR': ['P01GM064692/GM/NIGMS NIH HHS/United States', 'P41RR02250/RR/NCRR NIH HHS/United States', 'PN2EY016525/EY/NEI NIH HHS/United States', 'R01 GM080139-02/GM/NIGMS NIH HHS/United States', 'R01DK26758/DK/NIDDK NIH HHS/United States', 'R01GM08139/GM/NIGMS NIH HHS/United States'], 'IP': '3', 'IS': '0969-2126 (Print) 0969-2126 (Linking)', 'JID': '101087697', 'JT': 'Structure (London, England : 1993)', 'LA': ['eng'], 'LR': '20110922', 'MH': ['Chaperonin 10/chemistry/metabolism', 'Chaperonin 60/*chemistry/metabolism', 'Dimerization', 'Escherichia coli', 'Imaging, Three-Dimensional', 'Microscopy, Electron/*methods', 'Models, Molecular', 'Molecular Chaperones/chemistry/physiology', 'Signal Transduction/physiology'], 'MHDA': '2008/06/11 09:00', 'OWN': 'NLM', 'PG': '441-8', 'PHST': ['2008/02/01 [received]', '2008/02/17 [revised]', '2008/02/19 [accepted]'], 'PL': 'United States', 'PMID': '18334219', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, Non-P.H.S."], 'RN': ['0 (Chaperonin 10)', '0 (Chaperonin 60)', '0 (Molecular Chaperones)'], 'SB': 'IM', 'SI': ['PDB/3C9V', 'PDB/3CAU'], 'SO': 'Structure. 2008 Mar;16(3):441-8.', 'STAT': 'MEDLINE', 'TA': 'Structure', 'TI': 'De novo backbone trace of GroEL from single particle electron cryomicroscopy.', 'VI': '16'}, {'AB': 'The SecY complex associates with the ribosome to form a protein translocation channel in the bacterial plasma membrane. We have used cryo-electron microscopy and quantitative mass spectrometry to show that a nontranslating E. coli ribosome binds to a single SecY complex. The crystal structure of an archaeal SecY complex was then docked into the electron density maps. In the resulting model, two cytoplasmic loops of SecY extend into the exit tunnel near proteins L23, L29, and L24. The loop between transmembrane helices 8 and 9 interacts with helices H59 and H50 in the large subunit RNA, while the 6/7 loop interacts with H7. We also show that point mutations of basic residues within either loop abolish ribosome binding. We suggest that SecY binds to this primary site on the ribosome and subsequently captures and translocates the nascent chain.', 'AD': 'Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118-2526, USA.', 'AID': ['S1097-2765(07)00825-8 [pii]', '10.1016/j.molcel.2007.10.034 [doi]'], 'AU': ['Menetret JF', 'Schaletzky J', 'Clemons WM Jr', 'Osborne AR', 'Skanland SS', 'Denison C', 'Gygi SP', 'Kirkpatrick DS', 'Park E', 'Ludtke SJ', 'Rapoport TA', 'Akey CW'], 'CRDT': ['2007/12/27 09:00'], 'DA': '20071226', 'DCOM': '20080211', 'DP': '2007 Dec 28', 'EDAT': '2007/12/27 09:00', 'FAU': ['Menetret, Jean-Francois', 'Schaletzky, Julia', 'Clemons, William M Jr', 'Osborne, Andrew R', 'Skanland, Sigrid S', 'Denison, Carilee', 'Gygi, Steven P', 'Kirkpatrick, Don S', 'Park, Eunyong', 'Ludtke, Steven J', 'Rapoport, Tom A', 'Akey, Christopher W'], 'IP': '6', 'IS': '1097-2765 (Print) 1097-2765 (Linking)', 'JID': '9802571', 'JT': 'Molecular cell', 'LA': ['eng'], 'MH': ['Archaeal Proteins/chemistry/genetics/metabolism', 'Cell Membrane/*metabolism', 'Cryoelectron Microscopy', 'Crystallization', 'Electrophoresis, Polyacrylamide Gel', 'Escherichia coli/genetics/metabolism', 'Escherichia coli Proteins/chemistry/genetics/*metabolism', 'Models, Molecular', 'Point Mutation', 'Protein Binding', 'Protein Structure, Tertiary', 'Protein Transport', 'RNA, Ribosomal/metabolism', 'Ribosomes/chemistry/*metabolism/ultrastructure'], 'MHDA': '2008/02/12 09:00', 'OWN': 'NLM', 'PG': '1083-92', 'PHST': ['2007/04/26 [received]', '2007/08/03 [revised]', '2007/10/04 [accepted]'], 'PL': 'United States', 'PMID': '18158904', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural', "Research Support, Non-U.S. Gov't"], 'RN': ['0 (Archaeal Proteins)', '0 (Escherichia coli Proteins)', '0 (RNA, Ribosomal)', '0 (SecY protein, E coli)'], 'SB': 'IM', 'SI': ['PDB/3BO0', 'PDB/3BO1'], 'SO': 'Mol Cell. 2007 Dec 28;28(6):1083-92.', 'STAT': 'MEDLINE', 'TA': 'Mol Cell', 'TI': 'Ribosome binding of a single copy of the SecY complex: implications for protein translocation.', 'VI': '28'}, {'AD': 'National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, Texas 77030, USA.', 'AID': ['S0091-679X(06)79016-1 [pii]', '10.1016/S0091-679X(06)79016-1 [doi]'], 'AU': ['Serysheva II', 'Chiu W', 'Ludtke SJ'], 'CRDT': ['2007/03/01 09:00'], 'DA': '20070228', 'DCOM': '20070419', 'DP': '2007', 'EDAT': '2007/03/01 09:00', 'FAU': ['Serysheva, Irina I', 'Chiu, Wah', 'Ludtke, Steven J'], 'GR': ['P01GM99116/GM/NIGMS NIH HHS/United States', 'P41RR02250/RR/NCRR NIH HHS/United States', 'R01AR44864/AR/NIAMS NIH HHS/United States', 'R01GM072804/GM/NIGMS NIH HHS/United States'], 'IS': '0091-679X (Print) 0091-679X (Linking)', 'JID': '0373334', 'JT': 'Methods in cell biology', 'LA': ['eng'], 'LR': '20071203', 'MH': ['Animals', 'Calcium Channels/*chemistry/*ultrastructure', 'Cryoelectron Microscopy/*methods', '*Muscle Contraction', 'Protein Conformation'], 'MHDA': '2007/04/20 09:00', 'OWN': 'NLM', 'PG': '407-35', 'PL': 'United States', 'PMID': '17327167', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural', "Research Support, Non-U.S. Gov't", 'Review'], 'RF': '110', 'RN': ['0 (Calcium Channels)'], 'SB': 'IM', 'SO': 'Methods Cell Biol. 2007;79:407-35.', 'STAT': 'MEDLINE', 'TA': 'Methods Cell Biol', 'TI': 'Single-particle electron cryomicroscopy of the ion channels in the excitation-contraction coupling junction.', 'VI': '79'}, {'AB': 'Electron cryomicroscopy reveals an unprecedented conformation of the single-ring mutant of GroEL (SR398) bound to GroES in the presence of Mg-ATP. This conformation exhibits a considerable expansion of the folding cavity, with approximately 80% more volume than the X-ray structure of the equivalent cis cavity in the GroEL-GroES-(ADP)(7) complex. This expanded conformation can encapsulate an 86 kDa heterodimeric (alphabeta) assembly intermediate of mitochondrial branched-chain alpha-ketoacid dehydrogenase, the largest substrate ever observed to be cis encapsulated. The SR398-GroES-Mg-ATP complex is found to exist as a mixture of standard and expanded conformations, regardless of the absence or presence of the substrate. However, the presence of even a small substrate causes a pronounced bias toward the expanded conformation. Encapsulation of the large assembly intermediate is supported by a series of electron cryomicroscopy studies as well as the protection of both alpha and beta subunits of the substrate from tryptic digestion.', 'AD': 'National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.', 'AID': ['S0969-2126(06)00396-0 [pii]', '10.1016/j.str.2006.09.010 [doi]'], 'AU': ['Chen DH', 'Song JL', 'Chuang DT', 'Chiu W', 'Ludtke SJ'], 'CIN': ['Structure. 2006 Nov;14(11):1599-600. PMID: 17098183'], 'CRDT': ['2006/11/14 09:00'], 'DA': '20061113', 'DCOM': '20070116', 'DP': '2006 Nov', 'EDAT': '2006/11/14 09:00', 'FAU': ['Chen, Dong-Hua', 'Song, Jiu-Li', 'Chuang, David T', 'Chiu, Wah', 'Ludtke, Steven J'], 'GR': ['DK26758/DK/NIDDK NIH HHS/United States', 'P01GM064692/GM/NIGMS NIH HHS/United States', 'P41RR02250/RR/NCRR NIH HHS/United States', 'PN2EY016525/EY/NEI NIH HHS/United States'], 'IP': '11', 'IS': '0969-2126 (Print) 0969-2126 (Linking)', 'JID': '101087697', 'JT': 'Structure (London, England : 1993)', 'LA': ['eng'], 'LR': '20091119', 'MH': ['Adenosine Triphosphate/chemistry', 'Chaperonin 10/*chemistry', 'Chaperonin 60/*chemistry', 'Cryoelectron Microscopy', 'Crystallography, X-Ray', 'Dimerization', 'Escherichia coli/*metabolism', 'Humans', 'Image Processing, Computer-Assisted', 'Ketone Oxidoreductases/chemistry', 'Models, Molecular', 'Molecular Conformation', 'Mutation', 'Protein Conformation', 'Trypsin/chemistry'], 'MHDA': '2007/01/17 09:00', 'OWN': 'NLM', 'PG': '1711-22', 'PHST': ['2005/05/18 [received]', '2006/09/14 [revised]', '2006/09/19 [accepted]'], 'PL': 'United States', 'PMID': '17098196', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural', "Research Support, Non-U.S. Gov't"], 'RN': ['0 (Chaperonin 10)', '0 (Chaperonin 60)', '56-65-5 (Adenosine Triphosphate)', 'EC 1.2.- (Ketone Oxidoreductases)', 'EC 3.4.21.4 (Trypsin)'], 'SB': 'IM', 'SO': 'Structure. 2006 Nov;14(11):1711-22.', 'STAT': 'MEDLINE', 'TA': 'Structure', 'TI': 'An expanded conformation of single-ring GroEL-GroES complex encapsulates an 86 kDa substrate.', 'VI': '14'}, {'AB': 'SPARX (single particle analysis for resolution extension) is a new image processing environment with a particular emphasis on transmission electron microscopy (TEM) structure determination. It includes a graphical user interface that provides a complete graphical programming environment with a novel data/process-flow infrastructure, an extensive library of Python scripts that perform specific TEM-related computational tasks, and a core library of fundamental C++ image processing functions. In addition, SPARX relies on the EMAN2 library and cctbx, the open-source computational crystallography library from PHENIX. The design of the system is such that future inclusion of other image processing libraries is a straightforward task. The SPARX infrastructure intelligently handles retention of intermediate values, even those inside programming structures such as loops and function calls. SPARX and all dependencies are free for academic use and available with complete source.', 'AD': 'Lawrence Berkeley National Laboratory, Physical Bioscience Division, Berkeley, CA 94720, USA.', 'AID': ['S1047-8477(06)00212-7 [pii]', '10.1016/j.jsb.2006.07.003 [doi]'], 'AU': ['Hohn M', 'Tang G', 'Goodyear G', 'Baldwin PR', 'Huang Z', 'Penczek PA', 'Yang C', 'Glaeser RM', 'Adams PD', 'Ludtke SJ'], 'CRDT': ['2006/08/26 09:00'], 'DA': '20061215', 'DCOM': '20070321', 'DEP': '20060716', 'DP': '2007 Jan', 'EDAT': '2006/08/26 09:00', 'FAU': ['Hohn, Michael', 'Tang, Grant', 'Goodyear, Grant', 'Baldwin, P R', 'Huang, Zhong', 'Penczek, Pawel A', 'Yang, Chao', 'Glaeser, Robert M', 'Adams, Paul D', 'Ludtke, Steven J'], 'GR': ['P01GM064692/GM/NIGMS NIH HHS/United States', 'P41RR02250/RR/NCRR NIH HHS/United States', 'R01 GM080139-01/GM/NIGMS NIH HHS/United States', 'R01GM080139/GM/NIGMS NIH HHS/United States'], 'IP': '1', 'IS': '1047-8477 (Print) 1047-8477 (Linking)', 'JID': '9011206', 'JT': 'Journal of structural biology', 'LA': ['eng'], 'LR': '20110922', 'MH': ['Computational Biology', 'Cryoelectron Microscopy/*methods', 'Image Processing, Computer-Assisted/*methods', '*Software', 'Software Design', 'Systems Integration'], 'MHDA': '2007/03/22 09:00', 'OWN': 'NLM', 'PG': '47-55', 'PHST': ['2006/05/09 [received]', '2006/07/01 [revised]', '2006/07/07 [accepted]', '2006/07/16 [aheadofprint]'], 'PL': 'United States', 'PMID': '16931051', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural', "Research Support, U.S. Gov't, Non-P.H.S."], 'SB': 'IM', 'SO': 'J Struct Biol. 2007 Jan;157(1):47-55. Epub 2006 Jul 16.', 'STAT': 'MEDLINE', 'TA': 'J Struct Biol', 'TI': 'SPARX, a new environment for Cryo-EM image processing.', 'VI': '157'}, {'AB': 'The replication and packaging of the rotavirus genome, comprising 11 segments of double-stranded RNA, take place in specialized compartments called viroplasms, which are formed during infection and involve a coordinated interplay of multiple components. Two rotavirus nonstructural proteins, NSP2 (with nucleoside triphosphatase, single-stranded RNA [ssRNA] binding and helix-destabilizing activities) and NSP5, are essential in these events. Previous structural analysis of NSP2 showed that it is an octamer in crystals, obeying 4-2-2 crystal symmetry, with a large 35-A central hole along the fourfold axis and deep grooves at one of the twofold axes. To ascertain that the solution structure of NSP2 is the same as that in the crystals and investigate how NSP2 interacts with NSP5 and RNA, we carried out single-particle cryoelectron microscopy (cryo-EM) analysis of NSP2 alone and in complexes with NSP5 and ssRNA at subnanometer resolution. Because full-length NSP5 caused severe aggregation upon mixing with NSP2, the deletion construct NSP566-188 was used in these studies. Our studies show that the solution structure of NSP2 is same as the crystallographic octamer and that both NSP566-188 and ssRNA bind to the grooves in the octamer, which are lined by positively charged residues. The fitting of the NSP2 crystal structure to cryo-EM reconstructions of the complexes indicates that, in contrast to the binding of NSP566-188, the binding of RNA induces noticeable conformational changes in the NSP2 octamer. Consistent with the observation that both NSP5 and RNA share the same binding site on the NSP2 octamer, filter binding assays showed that NSP5 competes with ssRNA binding, indicating that one of the functions of NSP5 is to regulate NSP2-RNA interactions during genome replication.', 'AD': 'Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.', 'AID': ['JVI.01347-06 [pii]', '10.1128/JVI.01347-06 [doi]'], 'AU': ['Jiang X', 'Jayaram H', 'Kumar M', 'Ludtke SJ', 'Estes MK', 'Prasad BV'], 'CRDT': ['2006/08/25 09:00'], 'DA': '20061016', 'DCOM': '20061204', 'DEP': '20060823', 'DP': '2006 Nov', 'EDAT': '2006/08/25 09:00', 'FAU': ['Jiang, Xiaofang', 'Jayaram, Hariharan', 'Kumar, Mukesh', 'Ludtke, Steven J', 'Estes, Mary K', 'Prasad, B V Venkataram'], 'GR': ['AI-36040/AI/NIAID NIH HHS/United States', 'DK-30144/DK/NIDDK NIH HHS/United States', 'P41RR02250/RR/NCRR NIH HHS/United States'], 'IP': '21', 'IS': '0022-538X (Print) 0022-538X (Linking)', 'JID': '0113724', 'JT': 'Journal of virology', 'LA': ['eng'], 'LR': '20091118', 'MH': ['Binding Sites', 'Cryoelectron Microscopy', 'Genome, Viral', 'Image Processing, Computer-Assisted', 'Macromolecular Substances', 'Models, Molecular', 'Multiprotein Complexes', 'Nucleic Acid Conformation', 'Protein Conformation', 'Protein Structure, Quaternary', 'RNA, Viral/*chemistry/genetics/*ultrastructure', 'RNA-Binding Proteins/*chemistry/genetics/*ultrastructure', 'Recombinant Proteins/chemistry/genetics/ultrastructure', 'Rotavirus/*chemistry/genetics/physiology/*ultrastructure', 'Viral Nonstructural Proteins/*chemistry/genetics/*ultrastructure', 'Virus Assembly', 'Virus Replication', 'X-Ray Diffraction'], 'MHDA': '2006/12/09 09:00', 'OID': ['NLM: PMC1641785'], 'OWN': 'NLM', 'PG': '10829-35', 'PHST': ['2006/08/23 [aheadofprint]', '2006/08/24 [aheadofprint]'], 'PL': 'United States', 'PMC': 'PMC1641785', 'PMID': '16928740', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural', "Research Support, Non-U.S. Gov't"], 'RN': ['0 (Macromolecular Substances)', '0 (Multiprotein Complexes)', '0 (RNA, Viral)', '0 (RNA-Binding Proteins)', '0 (Recombinant Proteins)', '0 (Viral Nonstructural Proteins)', '138414-65-0 (NS35 protein, rotavirus)'], 'SB': 'IM', 'SO': 'J Virol. 2006 Nov;80(21):10829-35. Epub 2006 Aug 23.', 'STAT': 'MEDLINE', 'TA': 'J Virol', 'TI': 'Cryoelectron microscopy structures of rotavirus NSP2-NSP5 and NSP2-RNA complexes: implications for genome replication.', 'VI': '80'}, {'AB': "EMAN is a scientific image processing package with a particular focus on single particle reconstruction from transmission electron microscopy (TEM) images. It was first released in 1999, and new versions have been released typically 2-3 times each year since that time. EMAN2 has been under development for the last two years, with a completely refactored image processing library, and a wide range of features to make it much more flexible and extensible than EMAN1. The user-level programs are better documented, more straightforward to use, and written in the Python scripting language, so advanced users can modify the programs' behavior without any recompilation. A completely rewritten 3D transformation class simplifies translation between Euler angle standards and symmetry conventions. The core C++ library has over 500 functions for image processing and associated tasks, and it is modular with introspection capabilities, so programmers can add new algorithms with minimal effort and programs can incorporate new capabilities automatically. Finally, a flexible new parallelism system has been designed to address the shortcomings in the rigid system in EMAN1.", 'AD': 'National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.', 'AID': ['S1047-8477(06)00189-4 [pii]', '10.1016/j.jsb.2006.05.009 [doi]'], 'AU': ['Tang G', 'Peng L', 'Baldwin PR', 'Mann DS', 'Jiang W', 'Rees I', 'Ludtke SJ'], 'CRDT': ['2006/07/25 09:00'], 'DA': '20061215', 'DCOM': '20070321', 'DEP': '20060608', 'DP': '2007 Jan', 'EDAT': '2006/07/25 09:00', 'FAU': ['Tang, Guang', 'Peng, Liwei', 'Baldwin, Philip R', 'Mann, Deepinder S', 'Jiang, Wen', 'Rees, Ian', 'Ludtke, Steven J'], 'GR': ['P01AI055672/AI/NIAID NIH HHS/United States', 'P01GM064692/GM/NIGMS NIH HHS/United States', 'P41RR02250/RR/NCRR NIH HHS/United States', 'R01 GM080139-01/GM/NIGMS NIH HHS/United States', 'R01GM080139/GM/NIGMS NIH HHS/United States'], 'IP': '1', 'IS': '1047-8477 (Print) 1047-8477 (Linking)', 'JID': '9011206', 'JT': 'Journal of structural biology', 'LA': ['eng'], 'LR': '20110922', 'MH': ['Algorithms', 'Computational Biology', 'Image Processing, Computer-Assisted/*methods', 'Microscopy, Electron/*methods', '*Software', 'Software Design', 'Structural Homology, Protein'], 'MHDA': '2007/03/22 09:00', 'OWN': 'NLM', 'PG': '38-46', 'PHST': ['2006/05/02 [received]', '2006/05/29 [revised]', '2006/05/31 [accepted]', '2006/06/08 [aheadofprint]'], 'PL': 'United States', 'PMID': '16859925', 'PST': 'ppublish', 'PT': ['Evaluation Studies', 'Journal Article', 'Research Support, N.I.H., Extramural'], 'SB': 'IM', 'SO': 'J Struct Biol. 2007 Jan;157(1):38-46. Epub 2006 Jun 8.', 'STAT': 'MEDLINE', 'TA': 'J Struct Biol', 'TI': 'EMAN2: an extensible image processing suite for electron microscopy.', 'VI': '157'}, {'AB': 'Synaptotagmin acts as a Ca(2+) sensor in neurotransmitter release through its two C(2) domains. Ca(2+)-dependent phospholipid binding is key for synaptotagmin function, but it is unclear how this activity cooperates with the SNARE complex involved in release or why Ca(2+) binding to the C(2)B domain is more crucial for release than Ca(2+) binding to the C(2)A domain. Here we show that Ca(2+) induces high-affinity simultaneous binding of synaptotagmin to two membranes, bringing them into close proximity. The synaptotagmin C(2)B domain is sufficient for this ability, which arises from the abundance of basic residues around its surface. We propose a model wherein synaptotagmin cooperates with the SNAREs in bringing the synaptic vesicle and plasma membranes together and accelerates membrane fusion through the highly positive electrostatic potential of its C(2)B domain.', 'AD': 'Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA.', 'AID': ['nsmb1056 [pii]', '10.1038/nsmb1056 [doi]'], 'AU': ['Arac D', 'Chen X', 'Khant HA', 'Ubach J', 'Ludtke SJ', 'Kikkawa M', 'Johnson AE', 'Chiu W', 'Sudhof TC', 'Rizo J'], 'CIN': ['Nat Struct Mol Biol. 2006 Apr;13(4):301-3. PMID: 16715046'], 'CRDT': ['2006/02/24 09:00'], 'DA': '20060306', 'DCOM': '20060420', 'DEP': '20060219', 'DP': '2006 Mar', 'EDAT': '2006/02/24 09:00', 'FAU': ['Arac, Demet', 'Chen, Xiaocheng', 'Khant, Htet A', 'Ubach, Josep', 'Ludtke, Steven J', 'Kikkawa, Masahide', 'Johnson, Arthur E', 'Chiu, Wah', 'Sudhof, Thomas C', 'Rizo, Josep'], 'GR': ['GM26494/GM/NIGMS NIH HHS/United States', 'NS40944/NS/NINDS NIH HHS/United States', 'P41RR02250/RR/NCRR NIH HHS/United States'], 'IP': '3', 'IS': '1545-9993 (Print) 1545-9985 (Linking)', 'JID': '101186374', 'JT': 'Nature structural & molecular biology', 'LA': ['eng'], 'LR': '20071114', 'MH': ['Animals', 'Binding Sites', 'Calcium/metabolism/*pharmacology', 'Liposomes/chemistry/metabolism', 'Membrane Fusion/*drug effects', 'Models, Biological', 'Models, Molecular', 'Phospholipids/*metabolism', 'Pliability', 'Protein Binding/drug effects', 'Protein Structure, Secondary', 'Protein Structure, Tertiary', 'Rats', 'Spectrometry, Fluorescence', 'Synaptic Vesicles/drug effects/metabolism', 'Synaptotagmins/chemistry/*metabolism'], 'MHDA': '2006/04/21 09:00', 'OWN': 'NLM', 'PG': '209-17', 'PHST': ['2005/09/28 [received]', '2006/01/03 [accepted]', '2006/02/19 [aheadofprint]'], 'PL': 'United States', 'PMID': '16491093', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural', "Research Support, Non-U.S. Gov't"], 'RN': ['0 (Liposomes)', '0 (Phospholipids)', '134193-27-4 (Synaptotagmins)', '7440-70-2 (Calcium)'], 'SB': 'IM', 'SO': 'Nat Struct Mol Biol. 2006 Mar;13(3):209-17. Epub 2006 Feb 19.', 'STAT': 'MEDLINE', 'TA': 'Nat Struct Mol Biol', 'TI': 'Close membrane-membrane proximity induced by Ca(2+)-dependent multivalent binding of synaptotagmin-1 to phospholipids.', 'VI': '13'}, {'AB': "The anaphase-promoting complex/cyclosome (APC/C) is an E3 ubiquitin ligase composed of approximately 13 distinct subunits required for progression through meiosis, mitosis, and the G1 phase of the cell cycle. Despite its central role in these processes, information concerning its composition and structure is limited. Here, we determined the structure of yeast APC/C by cryo-electron microscopy (cryo-EM). Docking of tetratricopeptide repeat (TPR)-containing subunits indicates that they likely form a scaffold-like outer shell, mediating assembly of the complex and providing potential binding sites for regulators and substrates. Quantitative determination of subunit stoichiometry indicates multiple copies of specific subunits, consistent with a total APC/C mass of approximately 1.7 MDa. Moreover, yeast APC/C forms both monomeric and dimeric species. Dimeric APC/C is a more active E3 ligase than the monomer, with greatly enhanced processivity. Our data suggest that multimerisation and/or the presence of multiple active sites facilitates the APC/C's ability to elongate polyubiquitin chains.", 'AD': 'Section of Structural Biology, The Institute of Cancer Research, Chester Beatty Laboratories, London, UK. passmore@mrc-lmb.cam.ac.uk', 'AID': ['S1097-2765(05)01763-6 [pii]', '10.1016/j.molcel.2005.11.003 [doi]'], 'AU': ['Passmore LA', 'Booth CR', 'Venien-Bryan C', 'Ludtke SJ', 'Fioretto C', 'Johnson LN', 'Chiu W', 'Barford D'], 'CIN': ['Dev Cell. 2006 Jan;10(1):4-5. PMID: 16399071'], 'CRDT': ['2005/12/21 09:00'], 'DA': '20051220', 'DCOM': '20060223', 'DP': '2005 Dec 22', 'EDAT': '2005/12/21 09:00', 'FAU': ['Passmore, Lori A', 'Booth, Christopher R', 'Venien-Bryan, Catherine', 'Ludtke, Steven J', 'Fioretto, Celine', 'Johnson, Louise N', 'Chiu, Wah', 'Barford, David'], 'GR': ['P41RR02250/RR/NCRR NIH HHS/United States', 'Wellcome Trust/United Kingdom'], 'IP': '6', 'IS': '1097-2765 (Print) 1097-2765 (Linking)', 'JID': '9802571', 'JT': 'Molecular cell', 'LA': ['eng'], 'LR': '20071114', 'MH': ['Binding Sites', 'Cryoelectron Microscopy', 'Dimerization', 'Models, Molecular', 'Polyubiquitin/*metabolism', '*Protein Structure, Quaternary', 'Protein Subunits/*chemistry/genetics/metabolism', 'Saccharomyces cerevisiae Proteins/chemistry/genetics/metabolism', 'Ubiquitin-Protein Ligase Complexes/*chemistry/genetics/metabolism'], 'MHDA': '2006/02/24 09:00', 'OWN': 'NLM', 'PG': '855-66', 'PHST': ['2005/08/02 [received]', '2005/10/17 [revised]', '2005/11/02 [accepted]'], 'PL': 'United States', 'PMID': '16364911', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural', "Research Support, Non-U.S. Gov't"], 'RN': ['0 (Protein Subunits)', '0 (Saccharomyces cerevisiae Proteins)', '120904-94-1 (Polyubiquitin)', 'EC 6.3.2.19 (Ubiquitin-Protein Ligase Complexes)', 'EC 6.3.2.19 (anaphase-promoting complex)'], 'SB': 'IM', 'SO': 'Mol Cell. 2005 Dec 22;20(6):855-66.', 'STAT': 'MEDLINE', 'TA': 'Mol Cell', 'TI': 'Structural analysis of the anaphase-promoting complex reveals multiple active sites and insights into polyubiquitylation.', 'VI': '20'}, {'AB': 'Apaf-1 and cytochrome c coassemble in the presence of dATP to form the apoptosome. We have determined a structure of the apoptosome at 12.8 A resolution by using electron cryomicroscopy and single-particle methods. We then docked appropriate crystal structures into the map to create an accurate domain model. Thus, we found that seven caspase recruitment domains (CARDs) form a central ring within the apoptosome. At a larger radius, seven copies of the nucleotide binding and oligomerization domain (NOD) associate laterally to form the hub, which encircles the CARD ring. Finally, an arm-like helical domain (HD2) links each NOD to a pair of beta propellers, which bind a single cytochrome c. This model provides insights into the roles of dATP and cytochrome c in assembly. Our structure also reveals how a CARD ring and the central hub combine to create a platform for procaspase-9 activation.', 'AD': 'Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02118, USA.', 'AID': ['S0969-2126(05)00349-7 [pii]', '10.1016/j.str.2005.09.006 [doi]'], 'AU': ['Yu X', 'Acehan D', 'Menetret JF', 'Booth CR', 'Ludtke SJ', 'Riedl SJ', 'Shi Y', 'Wang X', 'Akey CW'], 'CRDT': ['2005/11/08 09:00'], 'DA': '20051107', 'DCOM': '20080710', 'DP': '2005 Nov', 'EDAT': '2005/11/08 09:00', 'FAU': ['Yu, Xinchao', 'Acehan, Devrim', 'Menetret, Jean-Francois', 'Booth, Christopher R', 'Ludtke, Steven J', 'Riedl, Stefan J', 'Shi, Yigong', 'Wang, Xiaodong', 'Akey, Christopher W'], 'IP': '11', 'IS': '0969-2126 (Print) 0969-2126 (Linking)', 'JID': '101087697', 'JT': 'Structure (London, England : 1993)', 'LA': ['eng'], 'MH': ['Apoptosis/*physiology', 'Apoptotic Protease-Activating Factor 1/*chemistry/metabolism', 'Caspase 9/metabolism', 'Cell Death/physiology', 'Crystallography, X-Ray', 'Cytochromes c/*chemistry/metabolism', 'Deoxyadenine Nucleotides/*metabolism', 'Humans', 'Protein Structure, Tertiary', 'Sequence Analysis, Protein'], 'MHDA': '2008/07/11 09:00', 'OWN': 'NLM', 'PG': '1725-35', 'PHST': ['2005/08/12 [received]', '2005/09/22 [revised]', '2005/09/26 [accepted]'], 'PL': 'United States', 'PMID': '16271896', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural', "Research Support, Non-U.S. Gov't"], 'RN': ['0 (Apoptotic Protease-Activating Factor 1)', '0 (Deoxyadenine Nucleotides)', '9007-43-6 (Cytochromes c)', 'EC 3.4.22.- (Caspase 9)'], 'SB': 'IM', 'SO': 'Structure. 2005 Nov;13(11):1725-35.', 'STAT': 'MEDLINE', 'TA': 'Structure', 'TI': 'A structure of the human apoptosome at 12.8 A resolution provides insights into this cell death platform.', 'VI': '13'}, {'AB': 'Electron cryomicroscopy and single-particle reconstruction have advanced substantially over the past two decades. There are now numerous examples of structures that have been solved using this technique to better than 10 A resolution. At such resolutions, direct identification of alpha helices is possible and, often, beta-sheet-containing regions can be identified. The most numerous subnanometer resolution structures are the icosahedral viruses, as higher resolution is easier to achieve with higher symmetry. Important non-icosahedral structures solved to subnanometer resolution include several ribosome structures, clathrin assemblies and, most recently, the Ca2+ release channel. There is now hope that, in the next few years, this technique will achieve resolutions approaching 4 A, permitting a complete trace of the protein backbone without reference to a crystal structure.', 'AD': 'National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.', 'AID': ['S0959-440X(05)00152-1 [pii]', '10.1016/j.sbi.2005.08.004 [doi]'], 'AU': ['Jiang W', 'Ludtke SJ'], 'CRDT': ['2005/09/06 09:00'], 'DA': '20051003', 'DCOM': '20060223', 'DP': '2005 Oct', 'EDAT': '2005/09/06 09:00', 'FAU': ['Jiang, Wen', 'Ludtke, Steven J'], 'IP': '5', 'IS': '0959-440X (Print) 0959-440X (Linking)', 'JID': '9107784', 'JT': 'Current opinion in structural biology', 'LA': ['eng'], 'LR': '20091119', 'MH': ['Animals', 'Chaperonin 60/chemistry/ultrastructure', 'Clathrin/chemistry/ultrastructure', 'Cryoelectron Microscopy/*methods', 'Humans', 'Models, Molecular', 'Nanostructures/*chemistry/ultrastructure', 'Ribosomes/chemistry/ultrastructure', 'Ryanodine Receptor Calcium Release Channel/chemistry', 'Viral Proteins/chemistry', 'Viruses/chemistry/ultrastructure'], 'MHDA': '2006/02/24 09:00', 'OWN': 'NLM', 'PG': '571-7', 'PHST': ['2005/05/27 [received]', '2005/07/09 [revised]', '2005/08/24 [accepted]'], 'PL': 'England', 'PMID': '16140524', 'PST': 'ppublish', 'PT': ['Journal Article', 'Review'], 'RF': '44', 'RN': ['0 (Chaperonin 60)', '0 (Clathrin)', '0 (Ryanodine Receptor Calcium Release Channel)', '0 (Viral Proteins)'], 'SB': 'IM', 'SO': 'Curr Opin Struct Biol. 2005 Oct;15(5):571-7.', 'STAT': 'MEDLINE', 'TA': 'Curr Opin Struct Biol', 'TI': 'Electron cryomicroscopy of single particles at subnanometer resolution.', 'VI': '15'}, {'AB': 'Using single particle electron cryomicroscopy, several helices in the membrane-spanning region of RyR1, including an inner transmembrane helix, a short pore helix, and a helix parallel to the membrane on the cytoplasmic side, have been clearly resolved. Our model places a highly conserved glycine (G4934) at the hinge position of the bent inner helix and two rings of negative charges at the luminal and cytoplasmic mouths of the pore. The kinked inner helix closely resembles the inner helix of the open MthK channel, suggesting that kinking alone does not open RyR1, as proposed for K+ channels.', 'AD': 'National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.', 'AID': ['S0969-2126(05)00215-7 [pii]', '10.1016/j.str.2005.06.005 [doi]'], 'AU': ['Ludtke SJ', 'Serysheva II', 'Hamilton SL', 'Chiu W'], 'CIN': ['Structure. 2005 Aug;13(8):1094-5. PMID: 16084381'], 'CRDT': ['2005/08/09 09:00'], 'DA': '20050808', 'DCOM': '20070919', 'DP': '2005 Aug', 'EDAT': '2005/08/09 09:00', 'FAU': ['Ludtke, Steven J', 'Serysheva, Irina I', 'Hamilton, Susan L', 'Chiu, Wah'], 'GR': ['P01GM99116/GM/NIGMS NIH HHS/United States', 'P41RR02250/RR/NCRR NIH HHS/United States', 'R01 GM072804-01/GM/NIGMS NIH HHS/United States', 'R01 GM072804-02/GM/NIGMS NIH HHS/United States', 'R01 GM072804-03/GM/NIGMS NIH HHS/United States', 'R01 GM072804-04/GM/NIGMS NIH HHS/United States', 'R01 GM072804-05/GM/NIGMS NIH HHS/United States', 'R01 GM072804-05S1/GM/NIGMS NIH HHS/United States', 'R01AR41729/AR/NIAMS NIH HHS/United States', 'R01AR44864/AR/NIAMS NIH HHS/United States', 'R01GM072804/GM/NIGMS NIH HHS/United States'], 'IP': '8', 'IS': '0969-2126 (Print) 0969-2126 (Linking)', 'JID': '101087697', 'JT': 'Structure (London, England : 1993)', 'LA': ['eng'], 'LR': '20101203', 'MH': ['Amino Acid Sequence', 'Animals', 'Cryoelectron Microscopy', 'Molecular Sequence Data', 'Muscle, Skeletal/metabolism', 'Protein Structure, Secondary', 'Protein Structure, Tertiary', 'Rabbits', 'Ryanodine Receptor Calcium Release Channel/*chemistry/metabolism', 'Structural Homology, Protein'], 'MHDA': '2007/09/20 09:00', 'MID': ['NIHMS248882'], 'OID': ['NLM: NIHMS248882', 'NLM: PMC2983469'], 'OWN': 'NLM', 'PG': '1203-11', 'PHST': ['2005/05/14 [received]', '2005/06/18 [revised]', '2005/06/20 [accepted]'], 'PL': 'United States', 'PMC': 'PMC2983469', 'PMID': '16084392', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['0 (Ryanodine Receptor Calcium Release Channel)'], 'SB': 'IM', 'SO': 'Structure. 2005 Aug;13(8):1203-11.', 'STAT': 'MEDLINE', 'TA': 'Structure', 'TI': 'The pore structure of the closed RyR1 channel.', 'VI': '13'}, {'AB': 'We report the nanoscale loading and confinement of aquated Gd3+n-ion clusters within ultra-short single-walled carbon nanotubes (US-tubes); these Gd3+n@US-tube species are linear superparamagnetic molecular magnets with Magnetic Resonance Imaging (MRI) efficacies 40 to 90 times larger than any Gd3+-based contrast agent (CA) in current clinical use.', 'AD': 'Department of Chemistry, the Center for Nanoscale Science and Technology, and the Center for Biological and Environmental Nanotechnology MS 60, Rice University, Houston, Texas 77251-1892, USA.', 'AID': ['10.1039/b504435a [doi]'], 'AU': ['Sitharaman B', 'Kissell KR', 'Hartman KB', 'Tran LA', 'Baikalov A', 'Rusakova I', 'Sun Y', 'Khant HA', 'Ludtke SJ', 'Chiu W', 'Laus S', 'Toth E', 'Helm L', 'Merbach AE', 'Wilson LJ'], 'CRDT': ['2005/08/03 09:00'], 'DA': '20050802', 'DCOM': '20070427', 'DEP': '20050708', 'DP': '2005 Aug 21', 'EDAT': '2005/08/03 09:00', 'FAU': ['Sitharaman, B', 'Kissell, K R', 'Hartman, K B', 'Tran, L A', 'Baikalov, A', 'Rusakova, I', 'Sun, Y', 'Khant, H A', 'Ludtke, S J', 'Chiu, W', 'Laus, S', 'Toth, E', 'Helm, L', 'Merbach, A E', 'Wilson, L J'], 'GR': ['1-R01-EB000703/EB/NIBIB NIH HHS/United States', 'P41RR02250/RR/NCRR NIH HHS/United States'], 'IP': '31', 'IS': '1359-7345 (Print) 1359-7345 (Linking)', 'JID': '9610838', 'JT': 'Chemical communications (Cambridge, England)', 'LA': ['eng'], 'LR': '20071203', 'MH': ['*Contrast Media', 'Gadolinium/*chemistry', 'Magnetic Resonance Imaging/*methods', '*Nanotubes'], 'MHDA': '2007/04/28 09:00', 'OWN': 'NLM', 'PG': '3915-7', 'PHST': ['2005/07/08 [aheadofprint]', '2005/08/01 [epublish]'], 'PL': 'England', 'PMID': '16075070', 'PST': 'ppublish', 'PT': ['Journal Article', 'Research Support, N.I.H., Extramural', "Research Support, Non-U.S. Gov't"], 'RN': ['0 (Contrast Media)', '7440-54-2 (Gadolinium)'], 'SB': 'IM', 'SO': 'Chem Commun (Camb). 2005 Aug 21;(31):3915-7. Epub 2005 Jul 8.', 'STAT': 'MEDLINE', 'TA': 'Chem Commun (Camb)', 'TI': 'Superparamagnetic gadonanotubes are high-performance MRI contrast agents.'}, {'AB': 'The mammalian Sec61 complex forms a protein translocation channel whose function depends upon its interaction with the ribosome and with membrane proteins of the endoplasmic reticulum (ER). To study these interactions, we determined structures of "native" ribosome-channel complexes derived from ER membranes. We find that the ribosome is linked to the channel by seven connections, but the junction may still provide a path for domains of nascent membrane proteins to move into the cytoplasm. In addition, the native channel is significantly larger than a channel formed by the Sec61 complex, due to the presence of a second membrane protein. We identified this component as TRAP, the translocon-associated protein complex. TRAP interacts with Sec61 through its transmembrane domain and has a prominent lumenal domain. The presence of TRAP in the native channel indicates that it may play a general role in translocation. Crystal structures of two Sec61 homologues were used to model the channel. This analysis indicates that there are four Sec61 complexes and two TRAP molecules in each native channel. Thus, we suggest that a single Sec61 complex may form a conduit for translocating polypeptides, while three copies of Sec61 play a structural role or recruit accessory factors such as TRAP.', 'AD': 'Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany St., Boston, MA 02118-2526, USA.', 'AID': ['S0022-2836(05)00229-9 [pii]', '10.1016/j.jmb.2005.02.053 [doi]'], 'AU': ['Menetret JF', 'Hegde RS', 'Heinrich SU', 'Chandramouli P', 'Ludtke SJ', 'Rapoport TA', 'Akey CW'], 'CRDT': ['2005/04/07 09:00'], 'DA': '20050406', 'DCOM': '20050512', 'DP': '2005 Apr 29', 'EDAT': '2005/04/07 09:00', 'FAU': ['Menetret, Jean-Francois', 'Hegde, Ramanujan S', 'Heinrich, Sven U', 'Chandramouli, Preethi', 'Ludtke, Steven J', 'Rapoport, Tom A', 'Akey, Christopher W'], 'IP': '2', 'IS': '0022-2836 (Print) 0022-2836 (Linking)', 'JID': '2985088R', 'JT': 'Journal of molecular biology', 'LA': ['eng'], 'LR': '20061115', 'MH': ['Animals', 'Dogs', 'Endoplasmic Reticulum/*chemistry/metabolism', 'Intracellular Membranes/*chemistry/metabolism', 'Ion Channels/chemistry/*metabolism', 'Membrane Proteins/*chemistry/*metabolism', 'Models, Molecular', 'Protein Binding', 'Protein Structure, Quaternary', 'Ribosomes/*chemistry/*metabolism'], 'MHDA': '2005/05/13 09:00', 'OWN': 'NLM', 'PG': '445-57', 'PHST': ['2004/12/06 [received]', '2005/02/13 [revised]', '2005/02/21 [accepted]'], 'PL': 'England', 'PMID': '15811380', 'PST': 'ppublish', 'PT': ['Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['0 (Ion Channels)', '0 (Membrane Proteins)', '0 (SEC61 protein)'], 'SB': 'IM', 'SO': 'J Mol Biol. 2005 Apr 29;348(2):445-57.', 'STAT': 'MEDLINE', 'TA': 'J Mol Biol', 'TI': 'Architecture of the ribosome-channel complex derived from native membranes.', 'VI': '348'}, {'AB': 'The 14 A resolution structure of the 2.3 MDa Ca2+ release channel (also known as RyR1) was determined by electron cryomicroscopy and single particle reconstruction. This structure was produced using collected data used for our previous published structures at 22-30 A resolution, but now taking advantage of recent algorithmic improvements in the EMAN software suite. This improved map clearly exhibits more structural detail and allows better defined docking of computationally predicted structural domain folds. Using sequence-based fold recognition, the N-terminal region of RyR1, residues 216-572, was predicted to have significant structural similarity with the IP3-binding core region of the type 1 IP3R. This putative structure was computationally localized to the clamp-shaped region of RyR1, which has been implicated to have a regulatory role in the channel activity.', 'AD': 'National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.', 'AID': ['S0022-2836(04)01379-8 [pii]', '10.1016/j.jmb.2004.10.073 [doi]'], 'AU': ['Serysheva II', 'Hamilton SL', 'Chiu W', 'Ludtke SJ'], 'CRDT': ['2004/12/08 09:00'], 'DA': '20041207', 'DCOM': '20050307', 'DP': '2005 Jan 21', 'EDAT': '2004/12/08 09:00', 'FAU': ['Serysheva, Irina I', 'Hamilton, Susan L', 'Chiu, Wah', 'Ludtke, Steven J'], 'GR': ['P01GM99116/GM/NIGMS NIH HHS/United States', 'P41RR02250/RR/NCRR NIH HHS/United States', 'R01 GM072804-01/GM/NIGMS NIH HHS/United States', 'R01 GM072804-02/GM/NIGMS NIH HHS/United States', 'R01 GM072804-03/GM/NIGMS NIH HHS/United States', 'R01 GM072804-04/GM/NIGMS NIH HHS/United States', 'R01 GM072804-05/GM/NIGMS NIH HHS/United States', 'R01 GM072804-05S1/GM/NIGMS NIH HHS/United States', 'R01AR41729/AR/NIAMS NIH HHS/United States', 'R01AR44864/AR/NIAMS NIH HHS/United States'], 'IP': '3', 'IS': '0022-2836 (Print) 0022-2836 (Linking)', 'JID': '2985088R', 'JT': 'Journal of molecular biology', 'LA': ['eng'], 'LR': '20101203', 'MH': ['Algorithms', 'Models, Molecular', 'Protein Conformation', 'Ryanodine Receptor Calcium Release Channel/*chemistry'], 'MHDA': '2005/03/08 09:00', 'MID': ['NIHMS236329'], 'OID': ['NLM: NIHMS236329', 'NLM: PMC2978512'], 'OWN': 'NLM', 'PG': '427-31', 'PHST': ['2004/06/30 [received]', '2004/10/11 [revised]', '2004/10/25 [accepted]'], 'PL': 'England', 'PMC': 'PMC2978512', 'PMID': '15581887', 'PST': 'ppublish', 'PT': ['Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['0 (Ryanodine Receptor Calcium Release Channel)'], 'SB': 'IM', 'SO': 'J Mol Biol. 2005 Jan 21;345(3):427-31.', 'STAT': 'MEDLINE', 'TA': 'J Mol Biol', 'TI': 'Structure of Ca2+ release channel at 14 A resolution.', 'VI': '345'}, {'AB': 'Mammalian formiminotransferase cyclodeaminase (FTCD), a 0.5 million Dalton homo-octameric enzyme, plays important roles in coupling histidine catabolism with folate metabolism and integrating the Golgi complex with the vimentin intermediate filament cytoskeleton. It is also linked to two human diseases, autoimmune hepatitis and glutamate formiminotransferase deficiency. Determination of the FTCD structure by X-ray crystallography and electron cryomicroscopy revealed that the eight subunits, each composed of distinct FT and CD domains, are arranged like a square doughnut. A key finding indicates that coupling of three subunits governs the octamer-dependent sequential enzyme activities, including channeling of intermediate and conformational change. The structure further shed light on the molecular nature of two strong antigenic determinants of FTCD recognized by autoantibodies from patients with autoimmune hepatitis and on the binding of thin vimentin filaments to the FTCD octamer.', 'AD': 'Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.', 'AID': ['10.1038/sj.emboj.7600327 [doi]', '7600327 [pii]'], 'AU': ['Mao Y', 'Vyas NK', 'Vyas MN', 'Chen DH', 'Ludtke SJ', 'Chiu W', 'Quiocho FA'], 'CRDT': ['2004/07/24 05:00'], 'DA': '20040804', 'DCOM': '20050614', 'DEP': '20040722', 'DP': '2004 Aug 4', 'EDAT': '2004/07/24 05:00', 'FAU': ['Mao, Yuxin', 'Vyas, Nand K', 'Vyas, Meenakshi N', 'Chen, Dong-Hua', 'Ludtke, Steven J', 'Chiu, Wah', 'Quiocho, Florante A'], 'IP': '15', 'IS': '0261-4189 (Print) 0261-4189 (Linking)', 'JID': '8208664', 'JT': 'The EMBO journal', 'LA': ['eng'], 'LR': '20091118', 'MH': ['Amino Acid Sequence', 'Ammonia-Lyases/*chemistry/*metabolism', 'Animals', 'Autoantigens/immunology', 'Binding Sites', 'Cryoelectron Microscopy', 'Crystallography, X-Ray', 'Epitopes/immunology', 'Golgi Apparatus/*enzymology', 'Hepatitis/immunology', 'Humans', 'Models, Molecular', 'Molecular Sequence Data', 'Movement', 'Protein Binding', 'Protein Structure, Quaternary', 'Protein Structure, Secondary', 'Protein Structure, Tertiary', 'Protein Subunits/chemistry/metabolism', 'Rats', 'Sequence Alignment', 'Vimentin/chemistry/metabolism'], 'MHDA': '2005/06/15 09:00', 'OID': ['NLM: PMC514939'], 'OWN': 'NLM', 'PG': '2963-71', 'PHST': ['2004/05/10 [received]', '2004/06/21 [accepted]', '2004/07/22 [aheadofprint]'], 'PL': 'England', 'PMC': 'PMC514939', 'PMID': '15272307', 'PST': 'ppublish', 'PT': ['Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['0 (Autoantigens)', '0 (Epitopes)', '0 (Protein Subunits)', '0 (Vimentin)', 'EC 4.3.1.- (Ammonia-Lyases)', 'EC 4.3.1.4 (Ftcd protein, rat)', 'EC 4.3.1.4 (formiminotetrahydrofolate cyclodeaminase)'], 'SB': 'IM', 'SI': ['PDB/1TT9'], 'SO': 'EMBO J. 2004 Aug 4;23(15):2963-71. Epub 2004 Jul 22.', 'STAT': 'MEDLINE', 'TA': 'EMBO J', 'TI': 'Structure of the bifunctional and Golgi-associated formiminotransferase cyclodeaminase octamer.', 'VI': '23'}, {'AB': 'We present a reconstruction of native GroEL by electron cryomicroscopy (cryo-EM) and single particle analysis at 6 A resolution. alpha helices are clearly visible and beta sheet density is also visible at this resolution. While the overall conformation of this structure is quite consistent with the published X-ray data, a measurable shift in the positions of three alpha helices in the intermediate domain is observed, not consistent with any of the 7 monomeric structures in the Protein Data Bank model (1OEL). In addition, there is evidence for slight rearrangement or flexibility in parts of the apical domain. The 6 A resolution cryo-EM GroEL structure clearly demonstrates the veracity and expanding scope of cryo-EM and the single particle reconstruction technique for macromolecular machines.', 'AD': 'National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA.', 'AID': ['10.1016/j.str.2004.05.006 [doi]', 'S0969212604001698 [pii]'], 'AU': ['Ludtke SJ', 'Chen DH', 'Song JL', 'Chuang DT', 'Chiu W'], 'CRDT': ['2004/07/10 05:00'], 'DA': '20040709', 'DCOM': '20050209', 'DP': '2004 Jul', 'EDAT': '2004/07/10 05:00', 'FAU': ['Ludtke, Steven J', 'Chen, Dong-Hua', 'Song, Jiu-Li', 'Chuang, David T', 'Chiu, Wah'], 'GR': ['DK 26758/DK/NIDDK NIH HHS/United States', 'P01 GM 064692/GM/NIGMS NIH HHS/United States', 'P41 RR 02250/RR/NCRR NIH HHS/United States'], 'IP': '7', 'IS': '0969-2126 (Print) 0969-2126 (Linking)', 'JID': '101087697', 'JT': 'Structure (London, England : 1993)', 'LA': ['eng'], 'LR': '20091119', 'MH': ['Chaperonin 60/*chemistry', 'Cryoelectron Microscopy/*methods', 'Crystallography, X-Ray', 'Protein Structure, Quaternary', 'Protein Structure, Secondary'], 'MHDA': '2005/02/11 09:00', 'OWN': 'NLM', 'PG': '1129-36', 'PL': 'United States', 'PMID': '15242589', 'PST': 'ppublish', 'PT': ['Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['0 (Chaperonin 60)'], 'SB': 'IM', 'SO': 'Structure. 2004 Jul;12(7):1129-36.', 'STAT': 'MEDLINE', 'TA': 'Structure', 'TI': 'Seeing GroEL at 6 A resolution by single particle electron cryomicroscopy.', 'VI': '12'}, {'AB': 'Sub-nanometer resolution structure determination is becoming a common practice in electron cryomicroscopy of macromolecular assemblies. The data for these studies have until now been collected on photographic film. Using cytoplasmic polyhedrosis virus (CPV), a previously determined structure, as a test specimen, we show the feasibility of obtaining a 9 angstroms structure from images acquired from a 4 k x 4 k Gatan CCD on a 200 kV electron cryomicroscope. The match of the alpha-helices in the protein components of the CPV with the previous structure of the same virus validates the suitability of this type of camera as the recording media targeted for single particle reconstructions at sub-nanometer resolution.', 'AD': 'Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.', 'AID': ['10.1016/j.jsb.2004.02.004 [doi]', 'S104784770400036X [pii]'], 'AU': ['Booth CR', 'Jiang W', 'Baker ML', 'Zhou ZH', 'Ludtke SJ', 'Chiu W'], 'CRDT': ['2004/06/15 05:00'], 'DA': '20040614', 'DCOM': '20050126', 'DP': '2004 Aug', 'EDAT': '2004/06/15 05:00', 'FAU': ['Booth, Christopher R', 'Jiang, Wen', 'Baker, Matthew L', 'Zhou, Z Hong', 'Ludtke, Steven J', 'Chiu, Wah'], 'GR': ['P41RR02250/RR/NCRR NIH HHS/United States', 'R01AI38469/AI/NIAID NIH HHS/United States', 'R01AI46420/AI/NIAID NIH HHS/United States', 'R01CA94809/CA/NCI NIH HHS/United States', 'R21AI053737/AI/NIAID NIH HHS/United States', 'T15LM07093/LM/NLM NIH HHS/United States'], 'IP': '2', 'IS': '1047-8477 (Print) 1047-8477 (Linking)', 'JID': '9011206', 'JT': 'Journal of structural biology', 'LA': ['eng'], 'LR': '20071114', 'MH': ['Cryoelectron Microscopy/*methods', 'Imaging, Three-Dimensional/*methods', 'Reoviridae/chemistry/ultrastructure', 'Virion/*chemistry/*ultrastructure'], 'MHDA': '2005/01/27 09:00', 'OWN': 'NLM', 'PG': '116-27', 'PHST': ['2003/11/12 [received]', '2004/02/03 [revised]'], 'PL': 'United States', 'PMID': '15193640', 'PST': 'ppublish', 'PT': ['Evaluation Studies', 'Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, P.H.S."], 'SB': 'IM', 'SO': 'J Struct Biol. 2004 Aug;147(2):116-27.', 'STAT': 'MEDLINE', 'TA': 'J Struct Biol', 'TI': 'A 9 angstroms single particle reconstruction from CCD captured images on a 200 kV electron cryomicroscope.', 'VI': '147'}, {'AB': 'The terminal steps involved in making ATP in mitochondria require an ATP synthase (F(0)F(1)) comprised of two motors, a phosphate carrier (PIC), and an adenine nucleotide carrier (ANC). Under mild conditions, these entities sub-fractionate as an ATP synthase/PIC/ANC complex or "ATP synthasome" (Ko, Y.H., Delannoy, M, Hullihen, J., Chiu, W., and Pedersen, P.L. (2003) J. Biol. Chem. 278, 12305-12309). As a first step toward obtaining three-dimensional information about this large complex or "metabolon" and the locations of PIC and ANC therein, we dispersed ATP synthasomes into single complexes and visualized negatively stained images by electron microscopy (EM) that showed clearly the classical headpiece, central stalk, and basepiece. Parallel immuno-EM studies revealed the presence of PIC and ANC located non-centrally in the basepiece, and other studies implicated an ATP synthase/PIC/ANC stoichiometry near 1:1:1. Single ATP synthasome images (7506) were boxed, and, using EMAN software, a three-dimensional model was obtained at a resolution of 23 A. Significantly, the basepiece is oblong and contains two domains, the larger of which connects to the central stalk, whereas the smaller appears as an extension. Docking studies with known structures together with the immuno-EM studies suggest that PIC or ANC may be located in the smaller domain, whereas the other transporter resides nearby in the larger domain. Collectively, these finding support a mechanism in which the entry of the substrates ADP and P(i) into mitochondria, the synthesis of ATP on F(1), and the release and exit of ATP are very localized and highly coordinated events.', 'AD': 'Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185, USA.', 'AID': ['10.1074/jbc.M401353200 [doi]', 'M401353200 [pii]'], 'AU': ['Chen C', 'Ko Y', 'Delannoy M', 'Ludtke SJ', 'Chiu W', 'Pedersen PL'], 'CRDT': ['2004/05/29 05:00'], 'DA': '20040719', 'DCOM': '20040921', 'DEP': '20040527', 'DP': '2004 Jul 23', 'EDAT': '2004/05/29 05:00', 'FAU': ['Chen, Chen', 'Ko, Young', 'Delannoy, Michael', 'Ludtke, Steven J', 'Chiu, Wah', 'Pedersen, Peter L'], 'GR': ['CA 10951/CA/NCI NIH HHS/United States', 'P41RR02250/RR/NCRR NIH HHS/United States'], 'IP': '30', 'IS': '0021-9258 (Print) 0021-9258 (Linking)', 'JID': '2985121R', 'JT': 'The Journal of biological chemistry', 'LA': ['eng'], 'LR': '20071114', 'MH': ['Animals', 'Macromolecular Substances', 'Male', 'Microscopy, Electron', 'Mitochondria, Liver/chemistry', 'Mitochondrial ADP, ATP Translocases/*chemistry/*ultrastructure', 'Mitochondrial Proton-Translocating ATPases/*chemistry/*ultrastructure', 'Models, Molecular', 'Molecular Motor Proteins/chemistry/ultrastructure', 'Phosphate Transport Proteins/*chemistry/*ultrastructure', 'Rats', 'Rats, Sprague-Dawley'], 'MHDA': '2004/09/24 05:00', 'OWN': 'NLM', 'PG': '31761-8', 'PHST': ['2004/05/27 [aheadofprint]'], 'PL': 'United States', 'PMID': '15166242', 'PST': 'ppublish', 'PT': ['In Vitro', 'Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['0 (Macromolecular Substances)', '0 (Molecular Motor Proteins)', '0 (Phosphate Transport Proteins)', '9068-80-8 (Mitochondrial ADP, ATP Translocases)', 'EC 3.6.3.- (Mitochondrial Proton-Translocating ATPases)'], 'SB': 'IM', 'SO': 'J Biol Chem. 2004 Jul 23;279(30):31761-8. Epub 2004 May 27.', 'STAT': 'MEDLINE', 'TA': 'J Biol Chem', 'TI': 'Mitochondrial ATP synthasome: three-dimensional structure by electron microscopy of the ATP synthase in complex formation with carriers for Pi and ADP/ATP.', 'VI': '279'}, {'AB': 'Manual selection of single particles in images acquired using cryo-electron microscopy (cryoEM) will become a significant bottleneck when datasets of a hundred thousand or even a million particles are required for structure determination at near atomic resolution. Algorithm development of fully automated particle selection is thus an important research objective in the cryoEM field. A number of research groups are making promising new advances in this area. Evaluation of algorithms using a standard set of cryoEM images is an essential aspect of this algorithm development. With this goal in mind, a particle selection "bakeoff" was included in the program of the Multidisciplinary Workshop on Automatic Particle Selection for cryoEM. Twelve groups participated by submitting the results of testing their own algorithms on a common dataset. The dataset consisted of 82 defocus pairs of high-magnification micrographs, containing keyhole limpet hemocyanin particles, acquired using cryoEM. The results of the bakeoff are presented in this paper along with a summary of the discussion from the workshop. It was agreed that establishing benchmark particles and using bakeoffs to evaluate algorithms are useful in promoting algorithm development for fully automated particle selection, and that the infrastructure set up to support the bakeoff should be maintained and extended to include larger and more varied datasets, and more criteria for future evaluations.', 'AD': 'Center for Integrative Molecular Biosciences and Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.', 'AU': ['Zhu Y', 'Carragher B', 'Glaeser RM', 'Fellmann D', 'Bajaj C', 'Bern M', 'Mouche F', 'de Haas F', 'Hall RJ', 'Kriegman DJ', 'Ludtke SJ', 'Mallick SP', 'Penczek PA', 'Roseman AM', 'Sigworth FJ', 'Volkmann N', 'Potter CS'], 'CRDT': ['2004/04/07 05:00'], 'DA': '20040406', 'DCOM': '20041005', 'DP': '2004 Jan-Feb', 'EDAT': '2004/04/07 05:00', 'FAU': ['Zhu, Yuanxin', 'Carragher, Bridget', 'Glaeser, Robert M', 'Fellmann, Denis', 'Bajaj, Chandrajit', 'Bern, Marshall', 'Mouche, Fabrice', 'de Haas, Felix', 'Hall, Richard J', 'Kriegman, David J', 'Ludtke, Steven J', 'Mallick, Satya P', 'Penczek, Pawel A', 'Roseman, Alan M', 'Sigworth, Fred J', 'Volkmann, Niels', 'Potter, Clinton S'], 'GR': ['P41 RR17573/RR/NCRR NIH HHS/United States'], 'IP': '1-2', 'IS': '1047-8477 (Print) 1047-8477 (Linking)', 'JID': '9011206', 'JT': 'Journal of structural biology', 'LA': ['eng'], 'LR': '20071114', 'MH': ['*Algorithms', 'Animals', 'Automatic Data Processing/methods', 'Cryoelectron Microscopy/*methods', 'Hemocyanin/chemistry/ultrastructure', 'Image Processing, Computer-Assisted/*methods', 'Imaging, Three-Dimensional', 'Mollusca', 'Protein Conformation'], 'MHDA': '2004/10/06 09:00', 'OWN': 'NLM', 'PG': '3-14', 'PL': 'United States', 'PMID': '15065668', 'PST': 'ppublish', 'PT': ['Comparative Study', 'Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['0 (keyhole-limpet hemocyanin)', '9013-72-3 (Hemocyanin)'], 'SB': 'IM', 'SO': 'J Struct Biol. 2004 Jan-Feb;145(1-2):3-14.', 'STAT': 'MEDLINE', 'TA': 'J Struct Biol', 'TI': 'Automatic particle selection: results of a comparative study.', 'VI': '145'}, {'AB': 'Fatty acid synthase (FAS) is a 550 kDa homodimeric enzyme with multiple functional and structural domains. Normal mode analysis of a previously determined 19 A structure of FAS suggested that this enzyme might assume different conformational states with several distinct hinge movements. We have used a simultaneous multiple-model refinement method to search for the presence of the structural conformers from the electron images of FAS. We have demonstrated that the resulting models observed in the electron images are consistent with the predicted conformational changes. This technique demonstrates the potential of the combination of normal mode analysis with multiple model refinement to elucidate the multiple conformations of flexible proteins. Since each of these structures is based on a more homogeneous particle set, this technique has the potential, provided that sufficient references are used, to improve the resolution of the final reconstructions of single particles from electron cryomicroscopy.', 'AD': 'National Center for Macromolecular Imaging, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.', 'AID': ['10.1016/j.str.2004.01.015 [doi]', 'S0969212604000036 [pii]'], 'AU': ['Brink J', 'Ludtke SJ', 'Kong Y', 'Wakil SJ', 'Ma J', 'Chiu W'], 'CIN': ['Structure. 2004 Feb;12(2):170-1. PMID: 14962375'], 'CRDT': ['2004/02/14 05:00'], 'DA': '20040213', 'DCOM': '20040921', 'DP': '2004 Feb', 'EDAT': '2004/02/14 05:00', 'FAU': ['Brink, Jacob', 'Ludtke, Steven J', 'Kong, Yifei', 'Wakil, Salih J', 'Ma, Jianpeng', 'Chiu, Wah'], 'GR': ['P41RR02250/RR/NCRR NIH HHS/United States', 'R01GM063115/GM/NIGMS NIH HHS/United States', 'R01GM067801/GM/NIGMS NIH HHS/United States'], 'IP': '2', 'IS': '0969-2126 (Print) 0969-2126 (Linking)', 'JID': '101087697', 'JT': 'Structure (London, England : 1993)', 'LA': ['eng'], 'LR': '20081121', 'MH': ['Cryoelectron Microscopy', 'Crystallography, X-Ray', 'Fatty Acid Synthetase Complex/*chemistry', 'Genetic Variation/*physiology', 'Humans', '*Models, Molecular', 'Protein Conformation'], 'MHDA': '2004/09/24 05:00', 'OWN': 'NLM', 'PG': '185-91', 'PHST': ['2003/07/16 [received]', '2003/10/23 [revised]', '2003/10/29 [accepted]'], 'PL': 'United States', 'PMID': '14962379', 'PST': 'ppublish', 'PT': ['Journal Article', "Research Support, U.S. Gov't, Non-P.H.S.", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['EC 6.- (Fatty Acid Synthetase Complex)'], 'SB': 'IM', 'SO': 'Structure. 2004 Feb;12(2):185-91.', 'STAT': 'MEDLINE', 'TA': 'Structure', 'TI': 'Experimental verification of conformational variation of human fatty acid synthase as predicted by normal mode analysis.', 'VI': '12'}, {'AB': 'As high-resolution biological transmission electron microscopy (TEM) has increased in popularity over recent years, the volume of data and number of projects underway has risen dramatically. A robust tool for effective data management is essential to efficiently process large data sets and extract maximum information from the available data. We present the Electron Microscopy Electronic Notebook (EMEN), a portable, object-oriented, web-based tool for TEM data archival and project management. EMEN has several unique features. First, the database is logically organized and annotated so multiple collaborators at different geographical locations can easily access and interpret the data without assistance. Second, the database was designed to provide flexibility to the user, so it can be used much as a lab notebook would be, while maintaining a structure suitable for data mining and direct interaction with data-processing software. Finally, as an object-oriented database, the database structure is dynamic and can be easily extended to incorporate information not defined in the original database specification.', 'AD': 'National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.', 'AID': ['10.1017/S1431927603030575 [doi]', 'S1431927603030575 [pii]'], 'AU': ['Ludtke SJ', 'Nason L', 'Tu H', 'Peng L', 'Chiu W'], 'CRDT': ['2004/01/31 05:00'], 'DA': '20040130', 'DCOM': '20040315', 'DP': '2003 Dec', 'EDAT': '2004/01/31 05:00', 'FAU': ['Ludtke, Steven J', 'Nason, Laurie', 'Tu, Haili', 'Peng, Liwei', 'Chiu, Wah'], 'GR': ['P41 RR02250/RR/NCRR NIH HHS/United States'], 'IP': '6', 'IS': '1431-9276 (Print) 1431-9276 (Linking)', 'JID': '9712707', 'JT': 'Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada', 'LA': ['eng'], 'LR': '20071114', 'MH': ['*Databases, Factual', '*Electronics', 'Microscopy, Electron/*methods', 'Sensitivity and Specificity', 'Software'], 'MHDA': '2004/03/17 05:00', 'OWN': 'NLM', 'PG': '556-65', 'PHST': ['3000/09/23 [received]'], 'PL': 'United States', 'PMID': '14750990', 'PST': 'ppublish', 'PT': ['Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, Non-P.H.S.", "Research Support, U.S. Gov't, P.H.S."], 'SB': 'IM', 'SO': 'Microsc Microanal. 2003 Dec;9(6):556-65.', 'STAT': 'MEDLINE', 'TA': 'Microsc Microanal', 'TI': 'Object oriented database and electronic notebook for transmission electron microscopy.', 'VI': '9'}, {'AB': 'A common technique in transmission electron microscopy is the collection of a focal pair, in which the first, close to focus image contains higher resolution information at lower contrast, and the second, far from focus image has high contrast but less reliable high-resolution information. Typically these second micrographs are used for purposes of particle selection, orientation estimate or micrograph evaluation. We introduce a technique for merging the information from both images, including signal to noise ratio weighting, contrast transfer function correction, and optional Weiner filtration. This produces a composite image with reduced contrast transfer function artifacts and optimized contrast. This technique is useful in numerous cases where low-contrast images are produced, such as small particles, proteins solubilized in detergent or projects with high-resolution goals when the first image is taken very close to focus.', 'AD': 'National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.', 'AID': ['S1047847703002259 [pii]'], 'AU': ['Ludtke SJ', 'Chiu W'], 'CRDT': ['2003/12/04 05:00'], 'DA': '20031203', 'DCOM': '20040719', 'DP': '2003 Oct-Nov', 'EDAT': '2003/12/04 05:00', 'FAU': ['Ludtke, Steven J', 'Chiu, Wah'], 'GR': ['P41RR02250/RR/NCRR NIH HHS/United States'], 'IP': '1-2', 'IS': '1047-8477 (Print) 1047-8477 (Linking)', 'JID': '9011206', 'JT': 'Journal of structural biology', 'LA': ['eng'], 'LR': '20091119', 'MH': ['Algorithms', 'Chaperonin 60/chemistry', 'Cryoelectron Microscopy/*methods', 'Fatty Acid Synthetase Complex/chemistry', 'Image Processing, Computer-Assisted/*methods', 'Models, Theoretical', 'Proteins/chemistry'], 'MHDA': '2004/07/20 05:00', 'OWN': 'NLM', 'PG': '73-8', 'PL': 'United States', 'PMID': '14643210', 'PST': 'ppublish', 'PT': ['Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['0 (Chaperonin 60)', '0 (Proteins)', 'EC 6.- (Fatty Acid Synthetase Complex)'], 'SB': 'IM', 'SO': 'J Struct Biol. 2003 Oct-Nov;144(1-2):73-8.', 'STAT': 'MEDLINE', 'TA': 'J Struct Biol', 'TI': 'Focal pair merging for contrast enhancement of single particles.', 'VI': '144'}, {'AB': 'The three-dimensional structure of the type 1 inositol 1,4,5-trisphosphate receptor (InsP3R1) has been determined by electron cryomicroscopy and single-particle reconstruction. The receptor was immunoaffinity-purified and formed functional InsP3- and heparin-sensitive channels with a unitary conductance similar to native InsP3Rs. The channel structure exhibits the expected 4-fold symmetry and comprises two morphologically distinct regions: a large pinwheel and a smaller square. The pinwheel region has four radial curved spokes interconnected by a central core. The InsP3-binding core domain has been localized within each spoke of the pinwheel region by fitting its x-ray structure into our reconstruction. A structural mapping of the amino acid sequences to several functional domains is deduced within the structure of the InsP3R1 tetramer.', 'AD': 'Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA. irinas@bcm.tmc.edu', 'AID': ['10.1074/jbc.C300148200 [doi]', 'C300148200 [pii]'], 'AU': ['Serysheva II', 'Bare DJ', 'Ludtke SJ', 'Kettlun CS', 'Chiu W', 'Mignery GA'], 'CRDT': ['2003/04/26 05:00'], 'DA': '20030609', 'DCOM': '20030722', 'DEP': '20030424', 'DP': '2003 Jun 13', 'EDAT': '2003/04/26 05:00', 'FAU': ['Serysheva, Irina I', 'Bare, Dan J', 'Ludtke, Steven J', 'Kettlun, Claudia S', 'Chiu, Wah', 'Mignery, Gregory A'], 'GR': ['MH 53367/MH/NIMH NIH HHS/United States', 'P41 RR 02250/RR/NCRR NIH HHS/United States'], 'IP': '24', 'IS': '0021-9258 (Print) 0021-9258 (Linking)', 'JID': '2985121R', 'JT': 'The Journal of biological chemistry', 'LA': ['eng'], 'LR': '20071114', 'MH': ['Animals', 'Calcium Channels/*chemistry/ultrastructure', 'Cattle', 'Cryoelectron Microscopy', 'Crystallography, X-Ray', 'Electrophoresis, Polyacrylamide Gel', 'Electrophysiology', 'Endoplasmic Reticulum/metabolism', 'Inositol 1,4,5-Trisphosphate Receptors', 'Models, Biological', 'Protein Binding', 'Protein Conformation', 'Protein Structure, Tertiary', 'Receptors, Cytoplasmic and Nuclear/*chemistry/ultrastructure', 'X-Rays'], 'MHDA': '2003/07/23 05:00', 'OWN': 'NLM', 'PG': '21319-22', 'PHST': ['2003/04/24 [aheadofprint]'], 'PL': 'United States', 'PMID': '12714606', 'PST': 'ppublish', 'PT': ['Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['0 (Calcium Channels)', '0 (Inositol 1,4,5-Trisphosphate Receptors)', '0 (Receptors, Cytoplasmic and Nuclear)'], 'SB': 'IM', 'SO': 'J Biol Chem. 2003 Jun 13;278(24):21319-22. Epub 2003 Apr 24.', 'STAT': 'MEDLINE', 'TA': 'J Biol Chem', 'TI': 'Structure of the type 1 inositol 1,4,5-trisphosphate receptor revealed by electron cryomicroscopy.', 'VI': '278'}, {'AB': 'We used a combination of bioinformatics, electron cryomicroscopy, and biochemical techniques to identify an oxidoreductase-like domain in the skeletal muscle Ca2+ release channel protein (RyR1). The initial prediction was derived from sequence-based fold recognition for the N-terminal region (41-420) of RyR1. The putative domain was computationally localized to the clamp domain in the cytoplasmic region of a 22A structure of RyR1. This localization was subsequently confirmed by difference imaging with a sequence specific antibody. Consistent with the prediction of an oxidoreductase domain, RyR1 binds [3H]NAD+, supporting a model in which RyR1 has a oxidoreductase-like domain that could function as a type of redox sensor.', 'AD': 'Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.', 'AID': ['10.1073/pnas.182058899 [doi]', '182058899 [pii]'], 'AU': ['Baker ML', 'Serysheva II', 'Sencer S', 'Wu Y', 'Ludtke SJ', 'Jiang W', 'Hamilton SL', 'Chiu W'], 'CRDT': ['2002/09/10 10:00'], 'DA': '20020918', 'DCOM': '20021028', 'DEP': '20020906', 'DP': '2002 Sep 17', 'EDAT': '2002/09/10 10:00', 'FAU': ['Baker, Matthew L', 'Serysheva, Irina I', 'Sencer, Serap', 'Wu, Yili', 'Ludtke, Steven J', 'Jiang, Wen', 'Hamilton, Susan L', 'Chiu, Wah'], 'IP': '19', 'IS': '0027-8424 (Print) 0027-8424 (Linking)', 'JID': '7505876', 'JT': 'Proceedings of the National Academy of Sciences of the United States of America', 'LA': ['eng'], 'LR': '20091118', 'MH': ['Amino Acid Sequence', 'Animals', 'Biophysical Phenomena', 'Biophysics', 'Computer Simulation', 'Cryoelectron Microscopy', 'Models, Molecular', 'Molecular Sequence Data', 'Muscle, Skeletal/metabolism', 'NAD/metabolism', 'Oxidation-Reduction', 'Oxidoreductases/*chemistry/genetics/metabolism', 'Protein Structure, Tertiary', 'Rabbits', 'Ryanodine Receptor Calcium Release Channel/*chemistry/genetics/metabolism', 'Sequence Homology, Amino Acid'], 'MHDA': '2002/10/29 04:00', 'OID': ['NLM: PMC129414'], 'OT': ['Non-programmatic'], 'OTO': ['NASA'], 'OWN': 'NLM', 'PG': '12155-60', 'PHST': ['2002/09/06 [aheadofprint]'], 'PL': 'United States', 'PMC': 'PMC129414', 'PMID': '12218169', 'PST': 'ppublish', 'PT': ['In Vitro', 'Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['0 (Ryanodine Receptor Calcium Release Channel)', '53-84-9 (NAD)', 'EC 1.- (Oxidoreductases)'], 'SB': 'IM S', 'SO': 'Proc Natl Acad Sci U S A. 2002 Sep 17;99(19):12155-60. Epub 2002 Sep 6.', 'STAT': 'MEDLINE', 'TA': 'Proc Natl Acad Sci U S A', 'TI': 'The skeletal muscle Ca2+ release channel has an oxidoreductase-like domain.', 'VI': '99'}, {'AB': 'Voltage-dependent L-type Ca(2+) channels play important functional roles in many excitable cells. We present a three-dimensional structure of an L-type Ca(2+) channel. Electron cryomicroscopy in conjunction with single-particle processing was used to determine a 30-A resolution structure of the channel protein. The asymmetrical channel structure consists of two major regions: a heart-shaped region connected at its widest end with a handle-shaped region. A molecular model is proposed for the arrangement of this skeletal muscle L-type Ca(2+) channel structure with respect to the sarcoplasmic reticulum Ca(2+)-release channel, the physical partner of the L-type channel for signal transduction during the excitation-contraction coupling in muscle.', 'AD': 'Department of Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.', 'AID': ['10.1073/pnas.162363499 [doi]', '162363499 [pii]'], 'AU': ['Serysheva II', 'Ludtke SJ', 'Baker MR', 'Chiu W', 'Hamilton SL'], 'CRDT': ['2002/08/01 10:00'], 'DA': '20020807', 'DCOM': '20020923', 'DEP': '20020729', 'DP': '2002 Aug 6', 'EDAT': '2002/08/01 10:00', 'FAU': ['Serysheva, I I', 'Ludtke, S J', 'Baker, M R', 'Chiu, W', 'Hamilton, S L'], 'GR': ['AR41802/AR/NIAMS NIH HHS/United States', 'AR44864/AR/NIAMS NIH HHS/United States', 'P41RR02250/RR/NCRR NIH HHS/United States'], 'IP': '16', 'IS': '0027-8424 (Print) 0027-8424 (Linking)', 'JID': '7505876', 'JT': 'Proceedings of the National Academy of Sciences of the United States of America', 'LA': ['eng'], 'LR': '20091118', 'MH': ['Animals', 'Calcium Channels, L-Type/*chemistry/isolation & purification', 'Cryoelectron Microscopy/methods', 'Ion Channel Gating', 'Muscle, Skeletal/chemistry', 'Protein Structure, Tertiary', 'Rabbits'], 'MHDA': '2002/09/24 06:00', 'OID': ['NLM: PMC124921'], 'OT': ['Non-programmatic'], 'OTO': ['NASA'], 'OWN': 'NLM', 'PG': '10370-5', 'PHST': ['2002/07/29 [aheadofprint]'], 'PL': 'United States', 'PMC': 'PMC124921', 'PMID': '12149473', 'PST': 'ppublish', 'PT': ['Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['0 (Calcium Channels, L-Type)'], 'SB': 'IM S', 'SO': 'Proc Natl Acad Sci U S A. 2002 Aug 6;99(16):10370-5. Epub 2002 Jul 29.', 'STAT': 'MEDLINE', 'TA': 'Proc Natl Acad Sci U S A', 'TI': 'Structure of the voltage-gated L-type Ca2+ channel by electron cryomicroscopy.', 'VI': '99'}, {'AB': "We present the first three-dimensional reconstruction of human fatty acid synthase obtained by electron cryomicroscopy and single-particle image processing. The structure shows that the synthase is composed of two monomers, arranged in an antiparallel orientation, which is consistent with biochemical data. The monomers are connected to each other at their middle by a bridge of density, a site proposed to be the combination of the interdomain regions of the two monomers. Each monomer subunit appears to be subdivided into three structural domains. With this reconstruction of the synthase, we propose a location for the enzyme's two fatty acid synthesis sites.", 'AD': 'Verna and Marrs McLean Department of Biochemistry and Molecular Biology and National Center for Macromolecular Imaging, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.', 'AID': ['10.1073/pnas.012589499 [doi]', '012589499 [pii]'], 'AU': ['Brink J', 'Ludtke SJ', 'Yang CY', 'Gu ZW', 'Wakil SJ', 'Chiu W'], 'CRDT': ['2002/01/05 10:00'], 'DA': '20020109', 'DCOM': '20020415', 'DEP': '20011226', 'DP': '2002 Jan 8', 'EDAT': '2002/01/05 10:00', 'FAU': ['Brink, Jacob', 'Ludtke, Steven J', 'Yang, Chao-Yuh', 'Gu, Zei-Wei', 'Wakil, Salih J', 'Chiu, Wah'], 'GR': ['GMS19091/GM/NIGMS NIH HHS/United States', 'P41RR012109/RR/NCRR NIH HHS/United States', 'P41RR02250/RR/NCRR NIH HHS/United States'], 'IP': '1', 'IS': '0027-8424 (Print) 0027-8424 (Linking)', 'JID': '7505876', 'JT': 'Proceedings of the National Academy of Sciences of the United States of America', 'LA': ['eng'], 'LR': '20091118', 'MH': ['Binding Sites', 'Cryoelectron Microscopy', 'Electrophoresis, Polyacrylamide Gel', 'Fatty Acid Synthetase Complex/*chemistry', 'Humans', 'Protein Structure, Quaternary', 'Protein Structure, Tertiary', 'Scattering, Radiation', 'Tumor Cells, Cultured', 'X-Rays'], 'MHDA': '2002/04/16 10:01', 'OID': ['NLM: PMC117528'], 'OWN': 'NLM', 'PG': '138-43', 'PHST': ['2001/12/26 [aheadofprint]'], 'PL': 'United States', 'PMC': 'PMC117528', 'PMID': '11756679', 'PST': 'ppublish', 'PT': ['Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['EC 6.- (Fatty Acid Synthetase Complex)'], 'SB': 'IM', 'SO': 'Proc Natl Acad Sci U S A. 2002 Jan 8;99(1):138-43. Epub 2001 Dec 26.', 'STAT': 'MEDLINE', 'TA': 'Proc Natl Acad Sci U S A', 'TI': 'Quaternary structure of human fatty acid synthase by electron cryomicroscopy.', 'VI': '99'}, {'AB': 'Single-particle analysis has become an increasingly important method for structural determination of large macromolecular assemblies. GroEL is an 800 kDa molecular chaperone, which, along with its co-chaperonin GroES, promotes protein folding both in vitro and in the bacterial cell. EMAN is a single-particle analysis software package, which was first publicly distributed in 2000. We present a three-dimensional reconstruction of native naked GroEL to approximately 11.5 A performed entirely with EMAN. We demonstrate that the single-particle reconstruction, X-ray scattering data and X-ray crystal structure all agree well at this resolution. These results validate the specific methods of image restoration, reconstruction and evaluation techniques implemented in EMAN. It also demonstrates that the single-particle reconstruction technique and X-ray crystallography will yield consistent structure factors, even at low resolution, when image restoration is performed correctly. A detailed comparison of the single-particle and X-ray structures exhibits some small variations in the equatorial domain of the molecule, likely due to the absence of crystal packing forces in the single-particle reconstruction.', 'AD': 'National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.', 'AID': ['10.1006/jmbi.2001.5133 [doi]', 'jmbi.2001.5133 [pii]'], 'AU': ['Ludtke SJ', 'Jakana J', 'Song JL', 'Chuang DT', 'Chiu W'], 'CI': ['Copyright 2001 Academic Press.'], 'CRDT': ['2001/11/24 10:00'], 'DA': '20011123', 'DCOM': '20011227', 'DP': '2001 Nov 23', 'EDAT': '2001/11/24 10:00', 'FAU': ['Ludtke, S J', 'Jakana, J', 'Song, J L', 'Chuang, D T', 'Chiu, W'], 'GR': ['P41RR02250/RR/NCRR NIH HHS/United States'], 'IP': '2', 'IS': '0022-2836 (Print) 0022-2836 (Linking)', 'JID': '2985088R', 'JT': 'Journal of molecular biology', 'LA': ['eng'], 'LR': '20091119', 'MH': ['Chaperonin 60/*chemistry', '*Computer Simulation', 'Cryoelectron Microscopy', 'Escherichia coli Proteins/*chemistry', 'Models, Molecular', 'Protein Conformation', 'Reproducibility of Results', '*Software', 'X-Ray Diffraction'], 'MHDA': '2002/01/05 10:01', 'OWN': 'NLM', 'PG': '253-62', 'PL': 'England', 'PMID': '11718559', 'PST': 'ppublish', 'PT': ['Journal Article', "Research Support, U.S. Gov't, Non-P.H.S.", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['0 (Chaperonin 60)', '0 (Escherichia coli Proteins)'], 'SB': 'IM', 'SO': 'J Mol Biol. 2001 Nov 23;314(2):253-62.', 'STAT': 'MEDLINE', 'TA': 'J Mol Biol', 'TI': 'A 11.5 A single particle reconstruction of GroEL using EMAN.', 'VI': '314'}, {'AB': 'Several factors, including spatial and temporal coherence of the electron microscope, specimen movement, recording medium, and scanner optics, contribute to the decay of the measured Fourier amplitude in electron image intensities. We approximate the combination of these factors as a single Gaussian envelope function, the width of which is described by a single experimental B-factor. We present an improved method for estimating this B-factor from individual micrographs by combining the use of X-ray solution scattering and numerical fitting to the average power spectrum of particle images. A statistical estimation from over 200 micrographs of herpes simplex virus type-1 capsids was used to estimate the spread in the experimental B-factor of the data set. The B-factor is experimentally shown to be dependent on the objective lens defocus setting of the microscope. The average B-factor, the X-ray scattering intensity of the specimen, and the number of particles required to determine the structure at a lower resolution can be used to estimate the minimum fold increase in the number of particles that would be required to extend a single particle reconstruction to a specified higher resolution. We conclude that microscope and imaging improvements to reduce the experimental B-factor will be critical for obtaining an atomic resolution structure.', 'AD': 'National Center for Macromolecular Imaging, McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.', 'AID': ['10.1006/jsbi.2001.4330 [doi]', 'S1047-8477(01)94330-8 [pii]'], 'AU': ['Saad A', 'Ludtke SJ', 'Jakana J', 'Rixon FJ', 'Tsuruta H', 'Chiu W'], 'CI': ['Copyright 2001 Academic Press.'], 'CRDT': ['2001/05/18 10:00'], 'DA': '20010517', 'DCOM': '20010802', 'DP': '2001 Jan', 'EDAT': '2001/05/18 10:00', 'FAU': ['Saad, A', 'Ludtke, S J', 'Jakana, J', 'Rixon, F J', 'Tsuruta, H', 'Chiu, W'], 'GR': ['P41 RR01209/RR/NCRR NIH HHS/United States', 'P41 RR02250/RR/NCRR NIH HHS/United States', 'R01 AI38469/AI/NIAID NIH HHS/United States'], 'IP': '1', 'IS': '1047-8477 (Print) 1047-8477 (Linking)', 'JID': '9011206', 'JT': 'Journal of structural biology', 'LA': ['eng'], 'LR': '20071114', 'MH': ['Capsid/chemistry/ultrastructure', 'Computer Simulation', 'Cryoelectron Microscopy/*methods', '*Fourier Analysis', 'Herpesvirus 1, Human/chemistry/ultrastructure', 'Image Processing, Computer-Assisted/*methods', 'Protein Structure, Quaternary', 'Sensitivity and Specificity', 'Solutions', 'X-Ray Diffraction'], 'MHDA': '2001/08/03 10:01', 'OWN': 'NLM', 'PG': '32-42', 'PL': 'United States', 'PMID': '11356062', 'PST': 'ppublish', 'PT': ['Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, Non-P.H.S.", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['0 (Solutions)'], 'SB': 'IM', 'SO': 'J Struct Biol. 2001 Jan;133(1):32-42.', 'STAT': 'MEDLINE', 'TA': 'J Struct Biol', 'TI': 'Fourier amplitude decay of electron cryomicroscopic images of single particles and effects on structure determination.', 'VI': '133'}, {'AB': "Due to large sizes and complex nature, few large macromolecular complexes have been solved to atomic resolution. This has lead to an under-representation of these structures, which are composed of novel and/or homologous folds, in the library of known structures and folds. While it is often difficult to achieve a high-resolution model for these structures, X-ray crystallography and electron cryomicroscopy are capable of determining structures of large assemblies at low to intermediate resolutions. To aid in the interpretation and analysis of such structures, we have developed two programs: helixhunter and foldhunter. Helixhunter is capable of reliably identifying helix position, orientation and length using a five-dimensional cross-correlation search of a three-dimensional density map followed by feature extraction. Helixhunter's results can in turn be used to probe a library of secondary structure elements derived from the structures in the Protein Data Bank (PDB). From this analysis, it is then possible to identify potential homologous folds or suggest novel folds based on the arrangement of alpha helix elements, resulting in a structure-based recognition of folds containing alpha helices. Foldhunter uses a six-dimensional cross-correlation search allowing a probe structure to be fitted within a region or component of a target structure. The structural fitting therefore provides a quantitative means to further examine the architecture and organization of large, complex assemblies. These two methods have been successfully tested with simulated structures modeled from the PDB at resolutions between 6 and 12 A. With the integration of helixhunter and foldhunter into sequence and structural informatics techniques, we have the potential to deduce or confirm known or novel folds in domains or components within large complexes.", 'AD': 'Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, TX 77030, USA.', 'AID': ['10.1006/jmbi.2001.4633 [doi]', 'S0022-2836(01)94633-9 [pii]'], 'AU': ['Jiang W', 'Baker ML', 'Ludtke SJ', 'Chiu W'], 'CI': ['Copyright 2001 Academic Press.'], 'CRDT': ['2001/05/16 10:00'], 'DA': '20010515', 'DCOM': '20010614', 'DP': '2001 May 18', 'EDAT': '2001/05/16 10:00', 'FAU': ['Jiang, W', 'Baker, M L', 'Ludtke, S J', 'Chiu, W'], 'GR': ['2T15LM07093/LM/NLM NIH HHS/United States', 'P41RR02250/RR/NCRR NIH HHS/United States', 'R01AI38469/AI/NIAID NIH HHS/United States', 'R01AI43656/AI/NIAID NIH HHS/United States'], 'IP': '5', 'IS': '0022-2836 (Print) 0022-2836 (Linking)', 'JID': '2985088R', 'JT': 'Journal of molecular biology', 'LA': ['eng'], 'LR': '20071115', 'MH': ['Algorithms', 'Computational Biology/instrumentation/*methods', '*Computer Simulation', 'Databases as Topic', 'Internet', '*Models, Molecular', 'Molecular Weight', 'Protein Folding', 'Protein Structure, Secondary', 'Protein Structure, Tertiary', 'Proteins/*chemistry/metabolism', '*Software'], 'MHDA': '2001/06/23 10:01', 'OWN': 'NLM', 'PG': '1033-44', 'PL': 'England', 'PMID': '11352589', 'PST': 'ppublish', 'PT': ['Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, Non-P.H.S.", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['0 (Proteins)'], 'SB': 'IM', 'SO': 'J Mol Biol. 2001 May 18;308(5):1033-44.', 'STAT': 'MEDLINE', 'TA': 'J Mol Biol', 'TI': 'Bridging the information gap: computational tools for intermediate resolution structure interpretation.', 'VI': '308'}, {'AB': "We present EMAN (Electron Micrograph ANalysis), a software package for performing semiautomated single-particle reconstructions from transmission electron micrographs. The goal of this project is to provide software capable of performing single-particle reconstructions beyond 10 A as such high-resolution data become available. A complete single-particle reconstruction algorithm is implemented. Options are available to generate an initial model for particles with no symmetry, a single axis of rotational symmetry, or icosahedral symmetry. Model refinement is an iterative process, which utilizes classification by model-based projection matching. CTF (contrast transfer function) parameters are determined using a new paradigm in which data from multiple micrographs are fit simultaneously. Amplitude and phase CTF correction is then performed automatically as part of the refinement loop. A graphical user interface is provided, so even those with little image processing experience will be able to begin performing reconstructions. Advanced users can directly use the lower level shell commands and even expand the package utilizing EMAN's extensive image-processing library. The package was written from scratch in C++ and is provided free of charge on our Web site. We present an overview of the package as well as several conformance tests with simulated data.", 'AD': 'Verna and Marrs McLean Department of Biochemistry, National Center for Macromolecular Imaging, Houston, Texas 77030, USA.', 'AID': ['10.1006/jsbi.1999.4174 [doi]', 'S1047-8477(99)94174-6 [pii]'], 'AU': ['Ludtke SJ', 'Baldwin PR', 'Chiu W'], 'CI': ['Copyright 1999 Academic Press.'], 'CRDT': ['1999/12/22 00:00'], 'DA': '20000127', 'DCOM': '20000127', 'DP': '1999 Dec 1', 'EDAT': '1999/12/22', 'FAU': ['Ludtke, S J', 'Baldwin, P R', 'Chiu, W'], 'GR': ['F32AR08474/AR/NIAMS NIH HHS/United States', 'NLM2T15LM07093/LM/NLM NIH HHS/United States', 'P41RR02250/RR/NCRR NIH HHS/United States', 'etc.'], 'IP': '1', 'IS': '1047-8477 (Print) 1047-8477 (Linking)', 'JID': '9011206', 'JT': 'Journal of structural biology', 'LA': ['eng'], 'LR': '20071114', 'MH': ['Algorithms', 'Bluetongue virus', 'Capsid/ultrastructure', '*Cryoelectron Microscopy', 'Image Processing, Computer-Assisted', 'Internet', 'Models, Molecular', 'Programming Languages', 'Protein Structure, Secondary', '*Software'], 'MHDA': '1999/12/22 00:01', 'OWN': 'NLM', 'PG': '82-97', 'PL': 'UNITED STATES', 'PMID': '10600563', 'PST': 'ppublish', 'PT': ['Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, P.H.S."], 'SB': 'IM', 'SO': 'J Struct Biol. 1999 Dec 1;128(1):82-97.', 'STAT': 'MEDLINE', 'TA': 'J Struct Biol', 'TI': 'EMAN: semiautomated software for high-resolution single-particle reconstructions.', 'VI': '128'}, {'AB': 'Adsorption of amphiphilic peptides to the headgroup region of a lipid bilayer is a common mode of protein-membrane interactions. Previous studies have shown that adsorption causes membrane thinning. The degree of the thinning depends on the degree of the lateral expansion caused by the peptide adsorption. If this simple molecular mechanism is correct, the degree of lateral expansion and consequently the membrane thinning should depend on the size of the headgroup relative to the cross section of the hydrocarbon chains. Previously we have established the connection between the alamethicin insertion transition and the membrane thinning effect. In this paper we use oriented circular dichroism to study the effect of varying the size of the headgroup, while maintaining a constant cross section of the lipid chains, on the insertion transition. A simple quantitative prediction agrees very well with the experiment.', 'AD': 'Physics Department, Rice University, Houston, Texas 77005-1892, USA.', 'AID': ['S0006-3495(97)78064-0 [pii]', '10.1016/S0006-3495(97)78064-0 [doi]'], 'AU': ['Heller WT', 'He K', 'Ludtke SJ', 'Harroun TA', 'Huang HW'], 'CRDT': ['1997/07/01 00:00'], 'DA': '19970827', 'DCOM': '19970827', 'DP': '1997 Jul', 'EDAT': '1997/07/01', 'FAU': ['Heller, W T', 'He, K', 'Ludtke, S J', 'Harroun, T A', 'Huang, H W'], 'GR': ['AI34367/AI/NIAID NIH HHS/United States', 'GM08280/GM/NIGMS NIH HHS/United States'], 'IP': '1', 'IS': '0006-3495 (Print) 0006-3495 (Linking)', 'JID': '0370626', 'JT': 'Biophysical journal', 'LA': ['eng'], 'LR': '20100910', 'MH': ['Adsorption', 'Alamethicin/*chemistry', 'Circular Dichroism', 'Lipid Bilayers/*chemistry', 'Models, Chemical', 'Phosphatidylcholines/chemistry', 'Phosphatidylethanolamines/chemistry', '*Protein Conformation'], 'MHDA': '1997/07/01 00:01', 'OID': ['NLM: PMC1180925'], 'OWN': 'NLM', 'PG': '239-44', 'PL': 'UNITED STATES', 'PMC': 'PMC1180925', 'PMID': '9199788', 'PST': 'ppublish', 'PT': ['Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, Non-P.H.S.", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['0 (Lipid Bilayers)', '0 (Phosphatidylcholines)', '0 (Phosphatidylethanolamines)', '0 (diphytanoylphosphatidylethanolamine)', '27061-78-5 (Alamethicin)', '32448-32-1 (1,2-diphytanoylphosphatidylcholine)'], 'SB': 'IM', 'SO': 'Biophys J. 1997 Jul;73(1):239-44.', 'STAT': 'MEDLINE', 'TA': 'Biophys J', 'TI': 'Effect of changing the size of lipid headgroup on peptide insertion into membranes.', 'VI': '73'}, {'AB': 'Alamethicin adsorbs on the membrane surface at low peptide concentrations. However, above a critical peptide-to-lipid ratio (P/L), a fraction of the peptide molecules insert in the membrane. This critical ratio is lipid dependent. For diphytanoyl phosphatidylcholine it is about 1/40. At even higher concentrations P/L > or = 1/15, all of the alamethicin inserts into the membrane and forms well-defined pores as detected by neutron in-plane scattering. A previous x-ray diffraction measurement showed that alamethicin adsorbed on the surface has the effect of thinning the bilayer in proportion to the peptide concentration. A theoretical study showed that the energy cost of membrane thinning can indeed lead to peptide insertion. This paper extends the previous studies to the high-concentration region P/L > 1/40. X-ray diffraction shows that the bilayer thickness increases with the peptide concentration for P/L > 1/23 as the insertion approaches 100%. The thickness change with the percentage of insertion is consistent with the assumption that the hydrocarbon region of the bilayer matches the hydrophobic region of the inserted peptide. The elastic energy of a lipid bilayer including both adsorption and insertion of peptide is discussed. The Gibbs free energy is calculated as a function of P/L and the percentage of insertion phi in a simplified one-dimensional model. The model exhibits an insertion phase transition in qualitative agreement with the data. We conclude that the membrane deformation energy is the major driving force for the alamethicin insertion transition.', 'AD': 'Physics Department, Rice University, Houston, Texas 77005-1892, USA.', 'AID': ['S0006-3495(96)79458-4 [pii]', '10.1016/S0006-3495(96)79458-4 [doi]'], 'AU': ['He K', 'Ludtke SJ', 'Heller WT', 'Huang HW'], 'CRDT': ['1996/11/01 00:00'], 'DA': '19970303', 'DCOM': '19970303', 'DP': '1996 Nov', 'EDAT': '1996/11/01', 'FAU': ['He, K', 'Ludtke, S J', 'Heller, W T', 'Huang, H W'], 'GR': ['AI34367/AI/NIAID NIH HHS/United States', 'GM08280/GM/NIGMS NIH HHS/United States'], 'IP': '5', 'IS': '0006-3495 (Print) 0006-3495 (Linking)', 'JID': '0370626', 'JT': 'Biophysical journal', 'LA': ['eng'], 'LR': '20100913', 'MH': ['Adsorption', 'Alamethicin/*chemistry', 'Circular Dichroism', 'Ion Channels/*chemistry', 'Ionophores/*chemistry', '*Lipid Bilayers', 'Membrane Proteins/*chemistry', 'Micelles', 'Models, Biological', 'Phosphatidylcholines/*chemistry', 'Water/chemistry', 'X-Ray Diffraction'], 'MHDA': '1996/11/01 00:01', 'OID': ['NLM: PMC1233753'], 'OWN': 'NLM', 'PG': '2669-79', 'PL': 'UNITED STATES', 'PMC': 'PMC1233753', 'PMID': '8913604', 'PST': 'ppublish', 'PT': ['Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, Non-P.H.S.", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['0 (Ion Channels)', '0 (Ionophores)', '0 (Lipid Bilayers)', '0 (Membrane Proteins)', '0 (Micelles)', '0 (Phosphatidylcholines)', '27061-78-5 (Alamethicin)', '7732-18-5 (Water)'], 'SB': 'IM', 'SO': 'Biophys J. 1996 Nov;71(5):2669-79.', 'STAT': 'MEDLINE', 'TA': 'Biophys J', 'TI': 'Mechanism of alamethicin insertion into lipid bilayers.', 'VI': '71'}, {'AB': 'Magainin, found in the skin of Xenopus laevis, belongs to a broad class of antimicrobial peptides which kill bacteria by permeabilizing the cytoplasmic membrane but do not lyse eukaryotic cells. The 23-residue peptide has been shown to form an amphiphilic helix when associated with membranes. However, its molecular mechanism of action has been controversial. Oriented circular dichroism has detected helical magainin oriented perpendicular to the plane of the membrane at high peptide concentrations, but Raman, fluorescence, differential scanning calorimetry, and NMR all indicate that the peptide is associated with the head groups of the lipid bilayer. Here we show that neutron in-plane scattering detects pores formed by magainin 2 in membranes only when a substantial fraction of the peptide is oriented perpendicular to the membrane. The pores are almost twice as large as the alamethicin pores. On the basis of the in-plane scattering data, we propose a toroidal (or wormhole) model, which differs from the barrel-stave model of alamethicin in that the lipid bends back on itself like the inside of a torus. The bending requires a lateral expansion in the head group region of the bilayer. Magainin monomers play the role of fillers in the expansion region thereby stabilizing the pore. This molecular configuration is consistent with all published magainin data.', 'AD': 'Physics Department, Rice University, Houston, Texas 77005-1892, USA.', 'AID': ['10.1021/bi9620621 [doi]', 'bi9620621 [pii]'], 'AU': ['Ludtke SJ', 'He K', 'Heller WT', 'Harroun TA', 'Yang L', 'Huang HW'], 'CRDT': ['1996/10/29 00:00'], 'DA': '19961203', 'DCOM': '19961203', 'DP': '1996 Oct 29', 'EDAT': '1996/10/29', 'FAU': ['Ludtke, S J', 'He, K', 'Heller, W T', 'Harroun, T A', 'Yang, L', 'Huang, H W'], 'GR': ['AI34367/AI/NIAID NIH HHS/United States', 'GM08280/GM/NIGMS NIH HHS/United States'], 'IP': '43', 'IS': '0006-2960 (Print) 0006-2960 (Linking)', 'JID': '0370623', 'JT': 'Biochemistry', 'LA': ['eng'], 'LR': '20111117', 'MH': ['Alamethicin/pharmacology', 'Animals', '*Antimicrobial Cationic Peptides', 'Cell Membrane/drug effects/*metabolism', 'Deuterium Oxide', 'Lipid Bilayers/metabolism', 'Magainins', 'Membrane Lipids/metabolism', 'Models, Biological', 'Molecular Conformation', 'Neutrons', 'Peptides/*pharmacology', 'Phospholipids/metabolism', 'Scattering, Radiation', 'Skin/chemistry', '*Xenopus Proteins', 'Xenopus laevis'], 'MHDA': '1996/10/29 00:01', 'OWN': 'NLM', 'PG': '13723-8', 'PL': 'UNITED STATES', 'PMID': '8901513', 'PST': 'ppublish', 'PT': ['Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, Non-P.H.S.", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['0 (Antimicrobial Cationic Peptides)', '0 (Lipid Bilayers)', '0 (Magainins)', '0 (Membrane Lipids)', '0 (Peptides)', '0 (Phospholipids)', '0 (Xenopus Proteins)', '108433-95-0 (magainin 2 peptide, Xenopus)', '27061-78-5 (Alamethicin)', '7789-20-0 (Deuterium Oxide)'], 'SB': 'IM', 'SO': 'Biochemistry. 1996 Oct 29;35(43):13723-8.', 'STAT': 'MEDLINE', 'TA': 'Biochemistry', 'TI': 'Membrane pores induced by magainin.', 'VI': '35'}, {'AB': 'A technique of neutron in-plane scattering for studying the structures of peptide pores in membranes is described. Alamethicin in the inserted state was prepared and undeuterated and deuterated dilauroyl phosphatidylcholine (DLPC) hydrated with D2O or H2O. Neutron in-plane scattering showed a strong dependence on deuteration, clearly indicating that water is a part of the high-order structure of inserted alamethicin. The data are consistent with the simple barrel-stave model originally proposed by Baumann and Mueller. The theoretical curves computed with this model at four different deuteration conditions agree with the data in all cases. Both the diameter of the water pore and the effective outside diameter of the channel are determined accurately. Alamethicin forms pores in a narrow range of size. In a given sample condition, > 70% of the peptide forms pores of n and n +/- 1 monomers. The pore size varies with hydration and with lipid. In DLPC, the pores are made of n = 8-9 monomers, with a water pore approximately 18 A in diameter and with an effective outside diameter of approximately 40 A. In diphytanoyl phosphatidylcholine, the pores are made of n approximately 11 monomers, with a water pore approximately 26 A in diameter, with an effective outside diameter of approximately 50 A.', 'AD': 'Physics Department, Rice University, Houston, Texas 77005-1892, USA.', 'AID': ['S0006-3495(96)79835-1 [pii]', '10.1016/S0006-3495(96)79835-1 [doi]'], 'AU': ['He K', 'Ludtke SJ', 'Worcester DL', 'Huang HW'], 'CRDT': ['1996/06/01 00:00'], 'DA': '19961210', 'DCOM': '19961210', 'DP': '1996 Jun', 'EDAT': '1996/06/01', 'FAU': ['He, K', 'Ludtke, S J', 'Worcester, D L', 'Huang, H W'], 'GR': ['AI34367/AI/NIAID NIH HHS/United States', 'GM08280/GM/NIGMS NIH HHS/United States'], 'IP': '6', 'IS': '0006-3495 (Print) 0006-3495 (Linking)', 'JID': '0370626', 'JT': 'Biophysical journal', 'LA': ['eng'], 'LR': '20100913', 'MH': ['Alamethicin/*chemistry', 'Amino Acid Sequence', 'Biophysical Phenomena', 'Biophysics', 'Computer Simulation', 'Data Interpretation, Statistical', 'Ion Channels/chemistry', 'Membranes, Artificial', 'Models, Chemical', 'Molecular Sequence Data', 'Molecular Structure', 'Neutrons', 'Scattering, Radiation'], 'MHDA': '1996/06/01 00:01', 'OID': ['NLM: PMC1225245'], 'OWN': 'NLM', 'PG': '2659-66', 'PL': 'UNITED STATES', 'PMC': 'PMC1225245', 'PMID': '8744303', 'PST': 'ppublish', 'PT': ['Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, Non-P.H.S.", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['0 (Ion Channels)', '0 (Membranes, Artificial)', '27061-78-5 (Alamethicin)'], 'SB': 'IM', 'SO': 'Biophys J. 1996 Jun;70(6):2659-66.', 'STAT': 'MEDLINE', 'TA': 'Biophys J', 'TI': 'Neutron scattering in the plane of membranes: structure of alamethicin pores.', 'VI': '70'}, {'AB': 'Antimicrobial peptides isolated from the host defense systems of animals have been shown to exert their activity directly on the lipid bilayer of cell membranes, but the antimicrobial mechanisms are not clear, due chiefly to the difficulty of discerning the high-order structures formed by these peptides in membranes. Previously we have shown that these peptides insert into the membrane when their concentrations exceed a lipid-dependent critical value. With neutron in-plane scattering we now show that inserted alamethicin creates aqueous pores approximately greater than 18 A in diameter. The density of pores is consistent with the assumption that all of the alamethicin is involved in pore formation. Pores were not detected below the critical concentration. Thus concentration-dependent pore formation appears to be the molecular mechanism of antimicrobial action.', 'AD': 'Physics Department, Rice University, Houston, Texas 77251-1892, USA.', 'AU': ['He K', 'Ludtke SJ', 'Huang HW', 'Worcester DL'], 'CRDT': ['1995/12/05 00:00'], 'DA': '19960118', 'DCOM': '19960118', 'DP': '1995 Dec 5', 'EDAT': '1995/12/05', 'FAU': ['He, K', 'Ludtke, S J', 'Huang, H W', 'Worcester, D L'], 'GR': ['GM08280/GM/NIGMS NIH HHS/United States'], 'IP': '48', 'IS': '0006-2960 (Print) 0006-2960 (Linking)', 'JID': '0370623', 'JT': 'Biochemistry', 'LA': ['eng'], 'LR': '20071114', 'MH': ['Alamethicin/*chemistry', 'Anti-Bacterial Agents/*chemistry', 'Cell Membrane/chemistry', 'Lipid Bilayers', 'Neutrons', 'Scattering, Radiation'], 'MHDA': '1995/12/05 00:01', 'OWN': 'NLM', 'PG': '15614-8', 'PL': 'UNITED STATES', 'PMID': '7495788', 'PST': 'ppublish', 'PT': ['Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, Non-P.H.S.", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['0 (Anti-Bacterial Agents)', '0 (Lipid Bilayers)', '27061-78-5 (Alamethicin)'], 'SB': 'IM', 'SO': 'Biochemistry. 1995 Dec 5;34(48):15614-8.', 'STAT': 'MEDLINE', 'TA': 'Biochemistry', 'TI': 'Antimicrobial peptide pores in membranes detected by neutron in-plane scattering.', 'VI': '34'}, {'AB': "A variety of amphiphilic helical peptides have been shown to exhibit a transition from adsorbing parallel to a membrane surface at low concentrations to inserting perpendicularly into the membrane at high concentrations. Furthermore, this transition has been correlated to the peptides' cytolytic activities. X-ray lamellar diffraction of diphytanoyl phosphatidylcholine-alamethicin mixtures revealed the changes of the bilayer structure with alamethicin concentration. In particular, the bilayer thickness decreases with increasing peptide concentration in proportion to the peptide-lipid molar ratio from as low as 1:150 to 1:47; the latter is near the threshold of the critical concentration for insertion. From the decreases of the bilayer thickness, one can calculate the cross sectional expansions of the lipid chains. For all of the peptide concentrations studied, the area expansion of the chain region for each adsorbed peptide is a constant 280 +/- 20 A2, which is approximately the cross sectional area of an adsorbed alamethicin. This implies that the peptide is adsorbed at the interface of the hydrocarbon region, separating the lipid headgroups laterally. Interestingly, the chain disorder caused by a peptide adsorption tends to spread over a large area, as much as 100 A in diameter. The theoretical basis of the long range nature of bilayer deformation is discussed.", 'AD': 'Physics Department, Rice University, Houston, Texas 77251-1892, USA.', 'AID': ['S0006-3495(95)80418-2 [pii]', '10.1016/S0006-3495(95)80418-2 [doi]'], 'AU': ['Wu Y', 'He K', 'Ludtke SJ', 'Huang HW'], 'CRDT': ['1995/06/01 00:00'], 'DA': '19950925', 'DCOM': '19950925', 'DP': '1995 Jun', 'EDAT': '1995/06/01', 'FAU': ['Wu, Y', 'He, K', 'Ludtke, S J', 'Huang, H W'], 'GR': ['AI34367/AI/NIAID NIH HHS/United States', 'GM08280/GM/NIGMS NIH HHS/United States'], 'IP': '6', 'IS': '0006-3495 (Print) 0006-3495 (Linking)', 'JID': '0370626', 'JT': 'Biophysical journal', 'LA': ['eng'], 'LR': '20100913', 'MH': ['Alamethicin/*chemistry', 'Circular Dichroism', 'Lipid Bilayers/*chemistry', 'Mathematics', 'Models, Structural', 'Molecular Conformation', 'Phosphatidylcholines/*chemistry', '*Protein Conformation', 'X-Ray Diffraction/methods'], 'MHDA': '1995/06/01 00:01', 'OID': ['NLM: PMC1282146'], 'OWN': 'NLM', 'PG': '2361-9', 'PL': 'UNITED STATES', 'PMC': 'PMC1282146', 'PMID': '7647240', 'PST': 'ppublish', 'PT': ['Comparative Study', 'Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, Non-P.H.S.", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['0 (Lipid Bilayers)', '0 (Phosphatidylcholines)', '27061-78-5 (Alamethicin)', '32448-32-1 (1,2-diphytanoylphosphatidylcholine)'], 'SB': 'IM', 'SO': 'Biophys J. 1995 Jun;68(6):2361-9.', 'STAT': 'MEDLINE', 'TA': 'Biophys J', 'TI': 'X-ray diffraction study of lipid bilayer membranes interacting with amphiphilic helical peptides: diphytanoyl phosphatidylcholine with alamethicin at low concentrations.', 'VI': '68'}, {'AB': "Using oriented circular dichroism, we have found that magainin adopts an alpha-helical conformation with two distinct orientations when interacting with a lipid bilayer. At low concentrations, magainin is absorbed parallel to the membrane surface. However, at high concentrations, magainin is inserted into the membrane. This transition occurs at roughly the same critical concentration required for cytolytic activity, implying that the membrane insertion is responsible for magainin's cell-lysing activity.", 'AD': 'Physics Department, Rice University, Houston, TX 77251-1892.', 'AID': ['0005-2736(94)90050-7 [pii]'], 'AU': ['Ludtke SJ', 'He K', 'Wu Y', 'Huang HW'], 'CRDT': ['1994/02/23 00:00'], 'DA': '19940328', 'DCOM': '19940328', 'DP': '1994 Feb 23', 'EDAT': '1994/02/23', 'FAU': ['Ludtke, S J', 'He, K', 'Wu, Y', 'Huang, H W'], 'GR': ['AI34367/AI/NIAID NIH HHS/United States', 'GM08280/GM/NIGMS NIH HHS/United States'], 'IP': '1', 'IS': '0006-3002 (Print) 0006-3002 (Linking)', 'JID': '0217513', 'JT': 'Biochimica et biophysica acta', 'LA': ['eng'], 'LR': '20071114', 'MH': ['Anti-Infective Agents/chemistry/*pharmacology', '*Antimicrobial Cationic Peptides', 'Cell Membrane Permeability/drug effects', 'Cell Survival/drug effects', 'Circular Dichroism', 'Dimyristoylphosphatidylcholine/chemistry', 'Lipid Bilayers/*chemistry', 'Peptides/chemistry/*pharmacology', 'Phosphatidylglycerols/chemistry', 'Protein Conformation', '*Xenopus Proteins'], 'MHDA': '1994/02/23 00:01', 'OWN': 'NLM', 'PG': '181-4', 'PL': 'NETHERLANDS', 'PMID': '8110813', 'PST': 'ppublish', 'PT': ['Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, Non-P.H.S.", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['0 (Anti-Infective Agents)', '0 (Antimicrobial Cationic Peptides)', '0 (Lipid Bilayers)', '0 (Peptides)', '0 (Phosphatidylglycerols)', '0 (Xenopus Proteins)', '108433-99-4 (magainin 1 peptide, Xenopus)', '13699-48-4 (Dimyristoylphosphatidylcholine)', '61361-72-6 (dimyristoylphosphatidylglycerol)'], 'SB': 'IM', 'SO': 'Biochim Biophys Acta. 1994 Feb 23;1190(1):181-4.', 'STAT': 'MEDLINE', 'TA': 'Biochim Biophys Acta', 'TI': 'Cooperative membrane insertion of magainin correlated with its cytolytic activity.', 'VI': '1190'}, {'AB': 'An analogue of gramicidin A (gA) was synthesized with the formyl group replaced by a BOC group. The analogue (BOC-gA) exhibited single channel conduction, but the channel is 5-order-of-magnitude destabilized relative to the gA channel. Hydrated mixtures of gramicidin and dilauroyl phosphatidylcholine in the molar ratio of 1:10 were prepared into uniformly aligned multiple bilayers, and X-ray scattering with the momentum transfer in the plane of the membrane was measured. Analysis with the help of computer simulations showed that 70% of BOC-gA are monomers. Thus for the first time it was shown that gramicidin monomers are stable inside the monolayers of a lipid membrane. Furthermore, the monomers have the same beta helical conformation as the dimeric channel. The result suggests the possibility that when a gramicidin channel is closed, it dissociates into two monomers floating in opposite monolayers.', 'AD': 'Physics Department, Rice University, Houston, TX 77251.', 'AID': ['0301-4622(93)E0085-J [pii]'], 'AU': ['He K', 'Ludtke SJ', 'Wu Y', 'Huang HW', 'Andersen OS', 'Greathouse D', 'Koeppe RE 2nd'], 'CRDT': ['1994/02/01 00:00'], 'DA': '19940421', 'DCOM': '19940421', 'DP': '1994 Feb', 'EDAT': '1994/02/01', 'FAU': ['He, K', 'Ludtke, S J', 'Wu, Y', 'Huang, H W', 'Andersen, O S', 'Greathouse, D', 'Koeppe, R E 2nd'], 'GR': ['GM08280/GM/NIGMS NIH HHS/United States'], 'IP': '1', 'IS': '0301-4622 (Print) 0301-4622 (Linking)', 'JID': '0403171', 'JT': 'Biophysical chemistry', 'LA': ['eng'], 'LR': '20071114', 'MH': ['Computer Simulation', 'Formic Acid Esters/chemistry', 'Gramicidin/*chemistry', 'Ion Channels/*chemistry', 'Lipid Bilayers/chemistry', 'Models, Biological', 'Scattering, Radiation', 'X-Ray Diffraction', 'X-Rays'], 'MHDA': '2001/03/28 10:01', 'OWN': 'NLM', 'PG': '83-9', 'PL': 'NETHERLANDS', 'PMID': '7510532', 'PST': 'ppublish', 'PT': ['Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, Non-P.H.S.", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['0 (Formic Acid Esters)', '0 (Ion Channels)', '0 (Lipid Bilayers)', '0 (t-butyloxycarbonyl group)', '1405-97-6 (Gramicidin)'], 'SB': 'IM', 'SO': 'Biophys Chem. 1994 Feb;49(1):83-9.', 'STAT': 'MEDLINE', 'TA': 'Biophys Chem', 'TI': 'Closed state of gramicidin channel detected by X-ray in-plane scattering.', 'VI': '49'}, {'AB': 'We demonstrate a technique for measuring x-ray (or neutron) scattering with the momentum transfer confined in the plane of membrane, for the purpose of studying lateral organization of proteins and peptides in membrane. Unlike freeze-fracture electron microscopy or atomic force microscopy which requires the membrane to be frozen or fixed, in-plane x-ray scattering can be performed with the membrane maintained in the liquid crystalline state. As an example, the controversial question of whether gramicidin forms aggregates in membrane was investigated. We used dilauroylphosphatidylcholine (DLPC) bilayers containing gramicidin in the molar ratio of 10:1. Very clear scattering curves reflecting gramicidin channel-channel correlation were obtained, even for the sample containing no heavy atoms. Thallium ions bound to gramicidin channels merely increase the magnitude of the scattering curve. Analysis of the data shows that the channels were randomly distributed in the membrane, similar to a computer simulation of freely moving disks in a plane. We suggest that oriented proteins may provide substantial x-ray contrast against the lipid background without requiring heavy-atom labeling. This should open up many possible new experiments.', 'AD': 'Physics Department, Rice University, Houston, Texas 77251-1892.', 'AID': ['S0006-3495(93)81350-X [pii]', '10.1016/S0006-3495(93)81350-X [doi]'], 'AU': ['He K', 'Ludtke SJ', 'Wu Y', 'Huang HW'], 'CRDT': ['1993/01/01 00:00'], 'DA': '19930317', 'DCOM': '19930317', 'DP': '1993 Jan', 'EDAT': '1993/01/01', 'FAU': ['He, K', 'Ludtke, S J', 'Wu, Y', 'Huang, H W'], 'GR': ['GM08280/GM/NIGMS NIH HHS/United States'], 'IP': '1', 'IS': '0006-3495 (Print) 0006-3495 (Linking)', 'JID': '0370626', 'JT': 'Biophysical journal', 'LA': ['eng'], 'LR': '20100910', 'MH': ['Biophysical Phenomena', 'Biophysics', 'Computer Simulation', 'Gramicidin/*chemistry', 'Ion Channels/chemistry', 'Lipid Bilayers/chemistry', 'Membrane Proteins/chemistry', '*Membranes, Artificial', 'Phosphatidylcholines/chemistry', 'Scattering, Radiation'], 'MHDA': '1993/01/01 00:01', 'OID': ['NLM: PMC1262312'], 'OWN': 'NLM', 'PG': '157-62', 'PL': 'UNITED STATES', 'PMC': 'PMC1262312', 'PMID': '7679294', 'PST': 'ppublish', 'PT': ['Journal Article', "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, Non-P.H.S.", "Research Support, U.S. Gov't, P.H.S."], 'RN': ['0 (Ion Channels)', '0 (Lipid Bilayers)', '0 (Membrane Proteins)', '0 (Membranes, Artificial)', '0 (Phosphatidylcholines)', '1405-97-6 (Gramicidin)', '18285-71-7 (1,2-dilauroylphosphatidylcholine)'], 'SB': 'IM', 'SO': 'Biophys J. 1993 Jan;64(1):157-62.', 'STAT': 'MEDLINE', 'TA': 'Biophys J', 'TI': 'X-ray scattering with momentum transfer in the plane of membrane. Application to gramicidin organization.', 'VI': '64'}] In [46]: Do you really want to exit ([y]/n)? odd-2% cd .. odd-2% ls Extra8.pdf Lecture11.key Lecture5.pdf lec12 Extra_5.pdf Lecture11.pdf Lecture6.key lec13 Extra_6.pdf Lecture11.txt Lecture6.pdf lec3 Extra_7.pdf Lecture12.key Lecture7.key lec4 Homework10.pdf Lecture12.pdf Lecture7.pdf lec5 Homework2.pdf Lecture13.key Lecture8.key lec6 Homework3.pdf Lecture13.pdf Lecture8.pdf lec7 Homework4.pdf Lecture2.key Lecture8.txt lec8 Homework6.pdf Lecture2.pdf Lecture_6.txt lecture10.key Homework7.pdf Lecture3.key day1handout.pages lecture10.pdf Homework8.pdf Lecture3.pdf grades.numbers lecture12.txt Homework_5.pdf Lecture4.key john_grades.xls terminal7.txt Lecture1.key Lecture4.pdf lec10 terminal_5.txt Lecture10.txt Lecture5.key lec11 odd-2% cd lec4 odd-2% ls Scrabble.zip scrabble2.py scrabble_recur.py x.py arg_demo.py scrabble_enum.py test.txt x.pyc scrabble.py scrabble_enum_2.py words.scrabble odd-2% vi scrabble.py odd-2% python scrabble.py Enter letters: abcdefg Traceback (most recent call last): File "scrabble.py", line 16, in words=[i.strp() for i in words] AttributeError: 'str' object has no attribute 'strp' odd-2% odd-2% !vi vi scrabble.py odd-2% python scrabble.py Enter letters: abcdefg Traceback (most recent call last): File "scrabble.py", line 18, in goodwords=[(len(x),x) for x in words if goodword(x,letters)] File "scrabble.py", line 5, in goodword tmp.remoe(letter) AttributeError: 'list' object has no attribute 'remoe' odd-2% python scrabble.py Enter letters: ^CTraceback (most recent call last): File "scrabble.py", line 13, in letters=raw_input("Enter letters: ") KeyboardInterrupt odd-2% vi scrabble.py odd-2% vi scrabble.py odd-2% python scrabble.py Enter letters: abcdefg Traceback (most recent call last): File "scrabble.py", line 16, in try : words=fie("words.scrabble","r").readlines() NameError: name 'fie' is not defined fadge faced decaf debag caged cadge begad badge gaed gade fade face egad ecad deaf dace cage cafe cade bead bade aged aced abed ged gae gad gab feg fed fag fae fad fab deg def deb dag dae dab cag cad cab beg bed bag bad bac age ace fe fa ef ed ea de da be ba ag ae ad ab odd-2% odd-2% !vi vi scrabble.py odd-2% idle 0 odd-2% python -m pudb.run scrabble.py Enter letters: abcdefg odd-2% python -mcProfile scrabble.py Enter letters: abcdefg fadge faced decaf debag caged cadge begad badge gaed gade fade face egad ecad deaf dace cage cafe cade bead bade aged aced abed ged gae gad gab feg fed fag fae fad fab deg def deb dag dae dab cag cad cab beg bed bag bad bac age ace fe fa ef ed ea de da be ba ag ae ad ab 671203 function calls in 4.360 seconds Ordered by: standard name ncalls tottime percall cumtime percall filename:lineno(function) 1 0.185 0.185 4.360 4.360 scrabble.py:1() 267751 0.358 0.000 0.379 0.000 scrabble.py:2(goodword) 1 0.000 0.000 0.000 0.000 traceback.py:1() 63 0.000 0.000 0.000 0.000 {len} 1 0.000 0.000 0.000 0.000 {method 'disable' of '_lsprof.Profiler' objects} 1 0.024 0.024 0.024 0.024 {method 'readlines' of 'file' objects} 135632 0.021 0.000 0.021 0.000 {method 'remove' of 'list' objects} 267751 0.041 0.000 0.041 0.000 {method 'strip' of 'str' objects} 1 3.731 3.731 3.731 3.731 {raw_input} 1 0.000 0.000 0.000 0.000 {sorted} odd-2% ls Scrabble.zip scrabble2.py scrabble_recur.py x.py arg_demo.py scrabble_enum.py test.txt x.pyc scrabble.py scrabble_enum_2.py words.scrabble odd-2% python -mcProfile scrabble_enum.py Enter letters: abcdefg fadge faced decaf debag caged cadge begad badge gaed gade fade face egad ecad deaf dace cage cafe cade bead bade aged aced abed ged gae gad gab feg fed fag fae fad fab deg def deb dag dae dab cag cad cab beg bed bag bad bac age ace fe fa ef ed ea de da be ba ag ae ad ab 618598 function calls in 66.480 seconds Ordered by: standard name ncalls tottime percall cumtime percall filename:lineno(function) 1 64.650 64.650 66.480 66.480 scrabble_enum.py:1() 60676 0.010 0.000 0.010 0.000 {len} 63 0.000 0.000 0.000 0.000 {method 'append' of 'list' objects} 1 0.000 0.000 0.000 0.000 {method 'disable' of '_lsprof.Profiler' objects} 13692 0.013 0.000 0.013 0.000 {method 'join' of 'str' objects} 267751 0.060 0.000 0.060 0.000 {method 'lower' of 'str' objects} 1 0.024 0.024 0.024 0.024 {method 'readlines' of 'file' objects} 267751 0.036 0.000 0.036 0.000 {method 'strip' of 'str' objects} 8660 0.049 0.000 0.049 0.000 {range} 1 1.639 1.639 1.639 1.639 {raw_input} 1 0.000 0.000 0.000 0.000 {sorted} odd-2% more scrabble_enum.py letters=raw_input("Enter letters: ") words=file("words.scrabble","r").readlines() words=[i.strip().lower() for i in words] # This generates all possible words and checks each to see if it's in the words list goodwords=[] n=[0]*7 for n[0] in range(7): w=letters[n[0]] if w in words : goodwords.append((len(w),w)) # 1 letter words for n[1] in range(7): if len(set(n[:2]))!=2 : continue # we skip possibilities with duplicates w="".join([letters[j] for j in n[:2]]) # 2 letter words if w in words : goodwords.append((len(w),w)) for n[2] in range(7): if len(set(n[:3]))!=3 : continue # we skip possibilities with duplicates w="".join([letters[j] for j in n[:3]]) # 3 letter words if w in words : goodwords.append((len(w),w)) for n[3] in range(7): if len(set(n[:4]))!=4 : continue # we skip possibilities with duplicates w="".join([letters[j] for j in n[:4]]) # 4 letter words if w in words : goodwords.append((len(w),w)) for n[4] in range(7): if len(set(n[:5]))!=5 : continue # we skip possibilities with duplicates w="".join([letters[j] for j in n[:5]]) # 5 letter words if w in words : goodwords.append((len(w)odd-2% odd-2% ls Scrabble.zip scrabble2.py scrabble_recur.py x.py arg_demo.py scrabble_enum.py test.txt x.pyc scrabble.py scrabble_enum_2.py words.scrabble odd-2% vi scrabble_enum_2.py odd-2% kernprof.py scrabble_enum_2.py Wrote profile results to scrabble_enum_2.py.prof Traceback (most recent call last): File "/usr/local/bin/kernprof.py", line 5, in pkg_resources.run_script('line-profiler==1.0b3', 'kernprof.py') File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 489, in run_script self.require(requires)[0].run_script(script_name, ns) File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 1214, in run_script exec script_code in namespace, namespace File "/Library/Python/2.7/site-packages/line_profiler-1.0b3-py2.7-macosx-10.7-intel.egg/EGG-INFO/scripts/kernprof.py", line 233, in File "/Library/Python/2.7/site-packages/line_profiler-1.0b3-py2.7-macosx-10.7-intel.egg/EGG-INFO/scripts/kernprof.py", line 223, in main File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/cProfile.py", line 140, in runctx exec cmd in globals, locals File "", line 1, in File "scrabble_enum_2.py", line 1, in @profile NameError: name 'profile' is not defined odd-2% kernprof.py -l scrabble_enum_2.py Enter letters: abcde Wrote profile results to scrabble_enum_2.py.lprof Traceback (most recent call last): File "/usr/local/bin/kernprof.py", line 5, in pkg_resources.run_script('line-profiler==1.0b3', 'kernprof.py') File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 489, in run_script self.require(requires)[0].run_script(script_name, ns) File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 1214, in run_script exec script_code in namespace, namespace File "/Library/Python/2.7/site-packages/line_profiler-1.0b3-py2.7-macosx-10.7-intel.egg/EGG-INFO/scripts/kernprof.py", line 233, in File "/Library/Python/2.7/site-packages/line_profiler-1.0b3-py2.7-macosx-10.7-intel.egg/EGG-INFO/scripts/kernprof.py", line 221, in main File "scrabble_enum_2.py", line 42, in main() File "build/bdist.macosx-10.7-intel/egg/line_profiler.py", line 92, in f File "scrabble_enum_2.py", line 32, in main w="".join([letters[j] for j in n[:6]]) # 6 letter words IndexError: string index out of range odd-2% kernprof.py -l scrabble_enum_2.py Enter letters: abcdefg fadge faced decaf debag caged cadge begad badge gaed gade fade face egad ecad deaf dace cage cafe cade bead bade aged aced abed ged gae gad gab feg fed fag fae fad fab deg def deb dag dae dab cag cad cab beg bed bag bad bac age ace fe fa ef ed ea de da be ba ag ae ad ab Wrote profile results to scrabble_enum_2.py.lprof odd-2% python -m line_profiler scrabble_enum_2.py.lprof Timer unit: 1e-06 s File: scrabble_enum_2.py Function: main at line 1 Total time: 69.9343 s Line # Hits Time Per Hit % Time Line Contents ============================================================== 1 @profile 2 def main(): 3 1 4281588 4281588.0 6.1 letters=raw_input("Enter letters: ") 4 5 1 24857 24857.0 0.0 words=file("words.scrabble","r").readlines() 6 267752 367469 1.4 0.5 words=[i.strip().lower() for i in words] 7 8 # This generates all possible words and checks each to see if it's in the words list 9 1 5 5.0 0.0 goodwords=[] 10 1 7 7.0 0.0 n=[0]*7 11 8 15 1.9 0.0 for n[0] in range(7): 12 7 11 1.6 0.0 w=letters[n[0]] 13 7 31982 4568.9 0.0 if w in words : goodwords.append((len(w),w)) # 1 letter words 14 56 154 2.8 0.0 for n[1] in range(7): 15 49 135 2.8 0.0 if len(set(n[:2]))!=2 : continue # we skip possibilities with duplicates 16 126 267 2.1 0.0 w="".join([letters[j] for j in n[:2]]) # 2 letter words 17 42 142844 3401.0 0.2 if w in words : goodwords.append((len(w),w)) 18 336 794 2.4 0.0 for n[2] in range(7): 19 294 714 2.4 0.0 if len(set(n[:3]))!=3 : continue # we skip possibilities with duplicates 20 840 1559 1.9 0.0 w="".join([letters[j] for j in n[:3]]) # 3 letter words 21 210 849839 4046.9 1.2 if w in words : goodwords.append((len(w),w)) 22 1680 4333 2.6 0.0 for n[3] in range(7): 23 1470 3793 2.6 0.0 if len(set(n[:4]))!=4 : continue # we skip possibilities with duplicates 24 4200 7312 1.7 0.0 w="".join([letters[j] for j in n[:4]]) # 4 letter words 25 840 3754455 4469.6 5.4 if w in words : goodwords.append((len(w),w)) 26 6720 17977 2.7 0.0 for n[4] in range(7): 27 5880 16915 2.9 0.0 if len(set(n[:5]))!=5 : continue # we skip possibilities with duplicates 28 15120 28376 1.9 0.0 w="".join([letters[j] for j in n[:5]]) # 5 letter words 29 2520 11631338 4615.6 16.6 if w in words : goodwords.append((len(w),w)) 30 20160 53708 2.7 0.1 for n[5] in range(7): 31 17640 58675 3.3 0.1 if len(set(n[:6]))!=6 : continue # we skip possibilities with duplicates 32 35280 63112 1.8 0.1 w="".join([letters[j] for j in n[:6]]) # 6 letter words 33 5040 23842177 4730.6 34.1 if w in words : goodwords.append((len(w),w)) 34 40320 135769 3.4 0.2 for n[6] in range(7): 35 35280 127713 3.6 0.2 if len(set(n))!=7 : continue # we skip possibilities with duplicates 36 40320 67210 1.7 0.1 w="".join([letters[j] for j in n]) # 7 letter words 37 5040 24418947 4845.0 34.9 if w in words : goodwords.append((len(w),w)) 38 39 40 64 266 4.2 0.0 for x in reversed(sorted(set(goodwords))): print x[1] odd-2% odd-2%