Rationale & Goals: In this day of exploding bioinformatics information from genomics and proteomics, it is ever more important to be conversant with macromolecular three-dimensional structure, and how it relates to protein and nucleic acid function and drug design. This workshop will enable participants to find published macromolecular structure data, and visualize and interpret 3D macromolecular structure. Participants will be enabled to incorporate computer visualization and qualitative analysis of 3D structure of protein, DNA, RNA, and protein-ligand interactions into their research.

Software: The central tool for this workshop is Protein Explorer (www.proteinexplorer.org). Protein Explorer is free, operates on Windows or Macintosh (also linux), and is much easier to use, yet much more powerful than RasMol. Protein Explorer has been adopted for visualization of macromolecular 3D structure by the Protein Data Bank (www.pdb.org) and several other bioinformatics resources.

Level & Pace: This workshop is designed for researchers familiar with basic biochemistry, but with no previous molecular visualization software experience. It progresses rapidly to powerful tools that will be of interest to specialists in protein structure and bioinformatics. Experienced participants are encouraged to work at their own speed, ahead of the group -- there is plenty of power to discover within Protein Explorer and its links to other resources!

First Day, July 9 or 10. Basics. How to use Protein Explorer to visualize structural features of proteins and protein-ligand interactions.

Netscape 4.8 is best, but Internet Explorer is OK.
Go to www.proteinexplorer.org

FirstView

1. Use of the mouse to rotate the molecule; clicking to identify atoms.
2. Identifying and becoming familiar with the computer representations for chains, backbones, disulfide bonds, solvent, and ligands.

   Features (PE Alpha version only)

3. Understanding and using information provided in the PDB file header by the authors of the structure.
4. The Help/Index/Glossary (green for "go"), a major component of PE's knowledge base.

   QuickViews

5. Selecting, emphasizing, and hiding portions of the molecule.
6. Selecting arbitrary atoms/chains/residues by clicking on them.
7. Saving/recalling selected sets.
8. Zooming, centering.
9. Backbone, trace, cartoon, stick, ball and stick, spacefill to van der Waals radii.
10. Coloring by element (Corey, Pauling, Koltun color scheme).
11. Coloring cartoons by secondary structure.
12. Identifying the amino and carboxy termini (5', 3' ends): N->C Rainbow (Group) color scheme.
13. Interpreting the distribution of hydrophobic, polar, and charged residues (Polarity color schemes).
    1. Potassium channel: 1bl8. Trp prefers lipid-water interface.
    2. Gramicidin in a lipid bilayer: bilagram.pdb
14. Coloring to distinguish A, T, G, C, U. How to distinguish DNA from RNA. (Cf. 104d)
15. Coloring by disorder: temperature factor coloring.

    Global Protein Structure Issues

16. How are 3D macromolecular structures obtained? Crystallography, NMR, and homology modeling.
17. What fraction of the human proteome has known structure? A few percent.
18. Is Structural Genomics the answer? Not in the next few years.
19. Intrinsicially unstructured proteins:
    About 10% of proteins are thought to be fully disordered to support their functions, and 40% of eukaryotic proteins have at least one long disordered region. Examples.

20. Finding published molecules of interest:
    Browsing
    1. Atlas of MacroMolecules: molvis.sdsc.edu/atlas/atlas.htm
    2. PDB at a Glance: cmm.info.nih.gov/modeling/pdb_at_a_glance.html

       Searching

    3. PDB Lite: www.pdblite.org
    4. SearchFields at the Protein Data Bank www.pdb.org
    5. Prilusky's OCA http://bioportal.weizmann.ac.il/oca-bin/ocamain

    Sequences

21. PE Site Map (PE Alpha version only)

    Residue ranges for the CDR's in the Fab of 1FDL are: Heavy chain (H) CDR1: 31-35 CDR2: 50-66 CDR3: 98-105 Light chain (L) CDR1: 24-34 CDR2: 50-56 CDR3: 90-97 For shortcuts and tricks in using PE to visualize epitope-paratope contacts, see step #35 in this Antibody Structure Tutorial.

22. OPTIONAL: Protein Explorer's Sequence display - finding gaps
    1. Insertions and non-physical gaps: 1igt.
    2. Physical gaps: 2ace, 1fod.
    3. Microheterogeneity: 1cbn.
23. Protein Explorer's clickable Seq3D
    1. Sequence to 3D structure mapping.
    2. Finding all instances of one amino acid (e.g. cysteine).
    3. Selecting and coloring an arbitrary range of residues (see example in box at right).

24. Noncovalent Bonds: Contact surfaces. Example: Gal4 contacting DNA (1d66), showing:
    1. Sequence specific recognition DNA bases by zinc finger domain of protein
    2. Hydrophobic protein-protein interaction
    3. Nonspecific charge interactions at DNA backbone phosphates

External Resources (via PE Site Map in Alpha version; via Mol Info in PE Beta)

25. FUNDAMENTAL
    1. Probable Quaternary Structures (Specific Oligomers)
    2. Conserved Regions (Evolution: ConSurf)
26. OPTIONAL
    1. Crystal Contacts
    2. Fewer or Single Chains
    3. Model Quality (& examples of errors in published PDB files)
    4. RCSB's Structure Explorer
    5. NCBI's Entrez Structure

27. Animations.
    1. Multiple-model NMR PDB files: simulation of thermal motion.
    2. Morphs of conformational changes.

28. Protein Comparator.
29. Preferences in Protein Explorer.
30. Aliases for RasMol/Chime commands.

31. Visualizing cation-pi interactions and salt bridges (QuickViews, DISPLAY)
32. QuickViews Plus (scroll down in the QuickViews frame).
    1. Example: Display contacts to lysozyme by Fab in 1FDL, then overlay a cartoon display of all protein. Color the cartoon by chain, then by structure.

    Advanced Explorer

33. The Noncovalent Bond Finder
34. Rolling probe surfaces and molecular electrostatic potential coloring
35. Including ligands in displays of cation-pi interactions and salt bridges

36. Searching by structure without reference to sequence: (Try the bacterial cell division protein 1FSZ^§.)
    Structure is more conserved than sequence! (Chothia et al., 2003; Precis)
    1. Shindyalov & Bourne's Combinatorial Extension cl.sdsc.edu/ce.html
    2. NCBI's Vector Alignment Search Tool (VAST) www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml

37. World Index of Molecular Visualization Resources molvisindex.org
    1. Tutorials on hundreds of specific macromolecules
    2. Tools for creating tutorials
    3. Deutsch? ¿Español? Français? Italiano? Português?
    4. SwissPDB-Viewer Resources
    5. Sources of atomic coordinate (PDB) files (metabolites, inorganic crystals, lipid micelles, etc.)
    6. EMail Lists
    7. Galleries
    8. Software

38. Martz Chime Resources www.umass.edu/microbio/chime
    1. Amino Acid Quizzer
    2. DNA, Hemoglobin, Antibody, MHC
    3. Lipid Bilayers and Gramicidin Channel
    4. IR Spectra with animated vibrations
    5. Protein Morpher
    6. Toobers in Science Education
    7. History of Visualization of Biological Macromolecules
       Where did Chime come from? What about Fred's Folly and Byron's Bender? See early computer images, physical models including the latest by computer-driven laser-powered rapid-prototype engineering, and the latest molecular sculpture.
    8. Knots in Proteins

39. Morphing conformational changes to view as animations in PE: see Protein Morpher.

40. Homology (comparative) modeling: Introduction.

41. Aligning two or more chains or molecules, and how to view the alignment.
    1. The CE site cl.sdsc.edu/ce.html will align any two protein chains quickly and easily (but hetero atoms are discarded).
    2. DeepView www.expasy.ch/spdbv/mainpage.html can align anything (one or more than one chains), selecting any subset of atoms for the alignment (other atoms following), and retaining hetero atoms. The results can be saved as a PDB file, but will need manual editing to separate models with MODEL [N] and ENDMDL records so that Protein Explorer can distinguish the models. Gale Rhodes provides a DeepView tutorial: click on the section Comparing Proteins.

42. Mutating your model:
    1. Changing residue sidechains and rotamer minimization with DeepView
    2. DeepView beginners should start with the superb Molecular Modeling for Beginners by Gale Rhodes, Univ. Southern Maine.
    3. DeepView resources are indexed at molvisindex.org.

43. Building a web page with hyperlinks to Protein Explorer that prespecify molecules for your teaching or research. Methods.

44. Presenting molecular structures in Chime websites:
    1. A well tested and debugged template (but will soon be obsolete) www.umass.edu/microbio/chime/prsswc/template.htm
    2. Script recorder (under development) so you can play back views acheived in PE.
    3. Examples of Presentations in Protein Explorer (PIPE) www.umass.edu/microbio/chime/pipe. Support for PIPE is not yet released.

• RasMol/Molecular Visualization Freeware/Education email list: www.umass.edu/microbio/rasmol/raslist.htm
• PDB email discussion: www.rcsb.org/pdb/forum.html
• Yours truly: emartz@microbio.umass.edu (But please direct questions about RasMol or Chime or Protein Explorer to the RasMol list, first item above.)
• Collaborations are invited that use Protein Explorer to display information about macromolecular structure, particularly information which may be the result of your research. The only example to date involving customization of PE is ConSurf. PE is used without modification by several other databases.