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| {{attachment:struct_bio.png||align="center",width=400}} | Structural biology overview {{attachment:struct_bio.png||align="right",width=400}} |
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| A. Example proteins. 1. Ribosomes such as this use the information encoded in ribonucleic acid (RNA) to assemble amino acids into chains, forming other protein structures. 2. Membrane transporters such as the TolC-AcrAB complex shown here move molecules across cellular membranes, helping maintain homeostatic conditions. 3. Enzymes. Shown here are a set of glycolytic enzymes that break down sugars to produce energy for cellular functions in the form of adenosine triphosphate (ATP) molecules. B. Length scales. Structural biology studies topics spanning a wide range of length scales from cells, which span multiple microns to atoms and small molecules, spanning only a few angstroms. While objects larger than ~200 nm can be examined using a light microscope, higher-resolution techniques such as X-ray crystallography (XRC), nuclear magnetic resonance (NMR), and electron microscopy are required to visualize features ranging from protein complexes to individual atoms. C. Taxonomy of protein structure elements superimposed on a structure of hemoglobin (PDB 2HHB). Protein structures are taxonomized according to their primary, secondary, tertiary, and quaternary structure elements. A protein’s primary structure corresponds to its sequence of amino acids. Secondary structure assigns spatial relationships between sequence elements, forming motifs such as the alpha-helix shown in this example. Tertiary structure describes how secondary structure elements conform within a single chain, and quaternary structure describes how multiple amino acid chains combine to form a complex. | Transmission electron microscopes (TEM) {{attachment:tem.png||align="right",width=400}} |
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| Protein illustrations in A and B are licensed under a Creative Commons Attribution 4.0 International license by David S. Goodsell and the RCSB PDB. | TEM grids {{attachment:grid.png||align="right",width=400}} |
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| {{attachment:tem.png||align="center",width=400}} | Movie-mode imaging {{attachment:movie.png||align="right",width=400}} |
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| {{attachment:grid.png||align="center",width=400}} | Basic image processing {{attachment:imgproc.png||align="right",width=400}} |
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| {{attachment:movie.png||align="center",width=400}} | Fourier transforms {{attachment:fft.png||align="right",width=400}} |
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| {{attachment:imgproc.png||align="center",width=400}} | Single particle analysis {{attachment:spa.png||align="right",width=400}} |
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| {{attachment:fft.png||align="center",width=400}} | Contrast transfer function (CTF) {{attachment:ctf.png||align="right",width=400}} |
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| {{attachment:spa.png||align="center",width=400}} | Resolution measurement via Fourier Shell Correlation (FSC) {{attachment:fsc.png||align="right",width=400}} |
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| {{attachment:ctf.png||align="center",width=400}} | Electron cryo-tomography (cryoET) {{attachment:cryoet.png||align="right",width=400}} |
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| {{attachment:fsc.png||align="center",width=400}} {{attachment:cryoet.png||align="center",width=400}} {{attachment:subtomoavg.png||align="center",width=400}} |
Subtomogram Averaging {{attachment:subtomoavg.png||align="right",width=400}} |
Michael Bell, Ludtke Lab (2014 - 2019)
All are welcome to use the materials provided here. Credit is appreciated but not required.
Thesis
Note: All protein illustrations in are licensed under a Creative Commons Attribution 4.0 International license by David S. Goodsell and the RCSB PDB.
Thesis Defense Presentation
Posters
cryoet_poster.pdf, cryoet_poster.pptx
Note, these posters are have been uploaded without modification. There may be typos.
Talks
microscopy_microanalysis_2018.ppt
Select Thesis Figures
Structural biology overview 
Transmission electron microscopes (TEM) 
TEM grids 
Movie-mode imaging 
Basic image processing 
Fourier transforms 
Single particle analysis 
Contrast transfer function (CTF) 
Resolution measurement via Fourier Shell Correlation (FSC) 
Electron cryo-tomography (cryoET) 
Subtomogram Averaging 