Rationale: 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 rational drug design. This workshop will enable participants to find published molecular structure data, and visualize and interpret 3D molecular structure. Participants will be enabled to incorporate computer visualization of protein, DNA, and RNA into their teaching and 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).

Level & Pace: This workshop is designed for educators and biological scientists familiar with basic biochemistry, but with no previous molecular visualization software experience. It progresses rapidly to powerful tools that will be of interest to researchers, including 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 in Protein Explorer to discover!

Monday June 11. Basics. How to use Protein Explorer to visualize structural features of proteins and nucleic acids. Observations may be recorded on a form provided.

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.

   QuickViews

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

    Sequences

12. Protein Explorer's clickable Seq3D
    • Sequence to 3D structure mapping.
    • Finding all instances of one amino acid (e.g. cysteine).
    • Selecting and coloring an arbitrary range of residues.

    Crystallography, NMR, Finding Molecules of Interest

13. Overview of origin, nature, and limitations of molecular structure data (X-ray crystallography, nuclear magnetic resonance).
    • www.rcsb.org/pdb/experimental_methods.html
    • Glossary of Terms from Crystallography, NMR, and Homology Modeling (Gale Rhodes, U Southern Maine).
14. The Protein Data Bank
    • www.rcsb.org
15. Finding molecules of interest.
    • PDB Lite: www.pdblite.org
    • RCSB's SearchFields www.pdb.org
    • Prilusky's OCA bioinfo.weizmann.ac.il:8500

    Oligomers, Single Chains, & Other Information about Your Molecule

16. Getting information about your molecule.
    • Protein Explorer's Molecule Information Window:
      • PDB File Header
      • Probable Quaternary Structures (Oligomers)
      • Fewer or Single Chains
      • Crystal Contacts
      • Model Quality (& examples of errors in published PDB files)
      • RCSB's Structure Explorer.
    • NCBI Entrez, PubMed www.ncbi.nlm.nih.gov

Wednesday June 13: Introduction to homology modeling and submission of sequences. Contact surfaces reveal noncovalent bonds. Cation-pi interactions and salt bridges. Coloring a 3D protein by conservation/mutation from a multiple protein sequence alignment (MSA3D).

9:00-10:00 Homology Modeling
17. Introduction to homology modeling.
18. Submission of sequences to SWISS MODEL.

    10:00-17:00 Protein Explorer, continued.

19. Contact surfaces. Example: Gal4 contacting DNA (1d66), showing:
    • Nonspecific charge interactions at DNA backbone phosphates,
    • Sequence specific recognition DNA bases by zinc finger domain of protein,
    • Hydrophobic protein-protein interaction.
20. Visualizing cation-pi interactions and salt bridges.
21. Preferences in Protein Explorer.

22. Demonstration of Protein Explorer's MSA3D.
23. Building a multiple protein sequence alignment.
    • Biology Workbench workbench.sdsc.edu
24. Locating and coloring regions of conservation or mutation with Protein Explorer's MSA3D.

Friday June 15: Animations, structure searching and alignments. DeepView: Constructing models with mutations, and homology modeling. Participants' requests.

25. Animations.
    • Multiple-model NMR PDB files: simulation of thermal motion.
    • Morphs of conformational changes.

26. Searching by structure without reference to sequence: (Try the bacterial cell division protein 1FSZ^§.)
    • Shindyalov & Bourne's Combinatorial Extension cl.sdsc.edu/ce.html
    • NCBI's Vector Alignment Search Tool (VAST) www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml

27. Aligning two or more chains or molecules, and how to view the alignment.
    • The CE site cl.sdsc.edu/ce.html will align any two protein chains quickly and easily (but hetero atoms are discarded).
    • 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.

28. Modeling: mutation and homology modeling in DeepView.
    • DeepView beginners should start with the superb Molecular Modeling for Beginners by Gale Rhodes, Univ. Southern Maine. Included are tutorials on
      • Basic use of DeepView.
      • Mutatiing and changing sidechain conformations.
      • Using the Ramachandran plot (interactively!).
      • Judging model quality.
      • Comparing proteins by alignment.
      • Homology modeling.
      He also provides a series of exercises to assess your command of DeepView.
    • You will probably find useful Rhodes' Glossary of Terms from Crystallography, NMR, and Homology Modeling.
    • DeepView (aka SwissPDBViewer) www.expasy.ch/spdbv is free, and does mutations very easily. It is very powerful but its many keystroke shortcuts and generally abbreviate documentation make it difficult unless you use it often.
    • DeepView resources are indexed at molvisindex.org.

    The following topics could be discussed on request, time permitting.

29. Hydrogen bonds.
30. The Noncovalent Bond Finder.
31. Introduction to using the RasMol/Chime Command Language.
    • Command aliases.
32. Rolling probe surfaces and molecular electrostatic potential coloring.

33. Building a web page with hyperlinks to Protein Explorer that prespecify molecules for your teaching or research.
34. Ready-to-use tutorials in Chime for teaching
    • World Index of Chime Resources www.umass.edu/microbio/rasmol/tutbymol.htm
    • Presentations in Protein Explorer www.umass.edu/microbio/chime/pipe
35. Building Chime presentation websites.
    • A well tested and debugged template (but will soon be obsolete) www.umass.edu/microbio/chime/prsswc/template.htm
    • Presentations in Protein Explorer (not yet available for general use) www.umass.edu/microbio/chime/pipe

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    Keep in touch!
    • 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.