Syllabus for
Protein 3D Structure Visualization & Structural Bioinformatics


Part of the Applied Molecular Biotechnology MS Program, Dept. Microbiology,
University of Massachusetts, Amherst.
Tuesdays and Thursdays, January 6, 8, 13, 15 (2015).
1:00 to 4:00 PM each day, Integrated Sciences Building 321.


Bringing A Laptop Computer Is Encouraged
but not required (iMacs are available in ISB 321).


Taught by Eric Martz* and Jeffrey Kane.
*Principal author of FirstGlance in Jmol, MolviZ.Org and team member of Proteopedia.Org.
*Professor Emeritus, University of Massachusetts, Amherst -- Morrill IVN 2A --

This syllabus is on-line:
Workshops.MolviZ.Org

Goals: This course will prepare students to understand and incorporate 3D macromolecular structure into their research and teaching. The principles of protein structure will be reviewed, including noncovalent bonds. Structural bioinformatics and genomics will be introduced. Students will learn what percentage of proteins have known 3D structures, and the importance of crystallographic models compared to homology models, or theoretical models.

Using laptop computers, students will learn how to find 3D protein molecular models for proteins of interest, or how to construct homology models,
and how to use the FirstGlance in Jmol 3D visualization software (adopted by the journal Nature) to investigate key structural features.

Protein structure will be related to function, evolutionary conservation and multiple-sequence alignments, and drug design. Specific oligomers will be constructed and visualized. Students will learn how to prepare customized publication-quality molecular images and animations for Powerpoint slides. Each student will prepare a report, using Powerpoint slides to capture the concepts and skills they have learned. All the software is web browser-based, easy to use, works on Windows or Mac OS X, requires no installation, is free and open-source, and is expected to be available for years to come.

Get Started

Each student please get started:
  1. If you brought your own laptop, you are welcome use it. (iPads will be too slow.) Lab iMac login: ask instructor.
  2. Use the Chrome browser. If you do not have it, take a few minutes to install it (www.google.com/chrome). (Chrome will be faster/smoother than Safari, and Firefox is even slower for this software. Internet Explorer and Opera are unusably slow with this software.)
  3. In the Chrome browser, go to our syllabus: Workshops.MolviZ.Org.
  4. Now you can see this document in your browser. Go to Atlas.MolviZ.Org.
  5. In the Atlas, choose any molecule deemed Straightforward and click on the link to FirstGlance. After a minute or so to load, you should see a rotating molecule. Have a look around at the information, views and tools in FirstGlance.
  6. If you have any difficulty or the molecule does not appear, or does not rotate, ask for help!
Workshop Startup and Overview

  1. Workshop Startup & Overview (Powerpoint Slides)
    I. Protein Data Bank & PDB Codes
    Crystallographic Resolution
    Proteopedia.Org
  1. The Protein Data Bank (PDB) -- World Wide: -- USA:RCSB -- Japan:PDBj -- Europe:PDBe
  2. PDB identification code examples:
  3. Proteopedia.Org (Part I).
    1. Main page: green links connect text to molecular scenes.
    2. Molecules explained by users. Examples:
    3. Explanations of structural biology terms and concepts, e.g. asymmetric unit, Protein Data Bank, hydrogen bonds, temperature value, etc. all at About Macromolecular Structure.
    4. Pages in Spanish, Chinese, Russian, Arabic, Japanese, Turkish, etc.

    An electron density map at 2.5 Å resolution.
  4. X-Ray Crystallography and Resolution

    II. Finding published molecules of interest.
    Begin Powerpoint Slides.

  1. Finding molecular models of interest:
    Each student: please find a 3D model of a molecule related to your research or interests.
    You will use the model that you select for the rest of the class, and for your Powerpoint report.
    How To Find Models:
    Browsing: If you can't find a model for your protein, or you don't have a molecule in mind, look at one of these sites and pick one.
  2. Begin your Powerpoint Slides (Later, you will email them to Prof. Martz)

    III. Review of Protein Chemistry and Structure.
    Introduction to Structural Bioinformatics.

  1. Central Dogma: DNA mRNA Protein.     DNA structure in Jmol / Estructura del ADN
  2. 20 Amino acids
  3. Polypeptide chain geometry and steric restrictions
  4. Covalent and non-covalent chemical bonds
  5. Typical hydrogen bond within a protein: hydrogen donor atom is covalently bonded to hydrogen; acceptor atom is not.
  6. Secondary Structure
  7. Folding: hydrophobic collapse
  8. Protein folds cannot be reliably predicted from sequence alone (using ab initio theory).

  9. Introduction to Structural Bioinformatics

    IV. FirstGlance in Jmol for exploring any macromolecule.
    FirstGlance in Jmol (Part I).

  1. To start FirstGlance, go to FirstGlance.Jmol.Org and enter the PDB code, or upload your homology model.

    Unusually large models may take a long time to display and be sluggish to manipulate in FirstGlance. For such cases, using Java will enable much better performance in FirstGlance. Java is not needed for most models. Ask the instructor for advice. Here are instructions for Installing and Enabling Java.

  2. Explore 1izh in FirstGlance.
    1. Introduction
    2. Molecule tab
      1. Year, Method.
      2. Resolution.
      3. Free R.
      4. Chain details.
      5. Sequences: Crystallized vs. Full Length. Alignment at UniProt (1d66).
      6. Abstract.
      7. Citations.
      8. Text contents of the PDB file.
    3. Views tab
      1. Top 3 rows of views:
        Secondary Structure / Cartoon / N->C Rainbow
        Composition / Hydrophobic/Polar / Charge..
        Local Uncertainty / Vines / Thin Backbone
      2. Buttons.
        Ligands+ / Water / Slab
      3. 1pgb: Hydrophobic core: Hydrophobic/Polar, then Slab.
      4. 1pgb: Amphipathic helices and strands. (In FirstGlance, Hide a range (the helix or strand) then invert.)
      5. Compare with 1bl8 or 7ahl.
    4. Resources tab
      1. See lipid bilayer boundaries (1bl8 or 7ahl).
    5. 1pgb: Tools tab with Views.
      1. Salt bridges.
      2. Cation-pi interactions.
      3. Distances.
      4. Salt bridges in Charge View.
      5. Charges with Slab on.
      6. Sidechain distributions in Vines View.
      7. Find (review Chart of AA): PHE, (VAL,LEU,ILE), ASN, THR

  3. Explore 2mcg in FirstGlance.
    1. Tools tab
      1. Disulfides/S/Se

  4. Explore 3onz in FirstGlance. (Letter O not numeral zero!)
    1. Molecule tab
      1. Two chains, not sequence identical.
      2. Missing residues.
      3. Ligands+ and non-standard residues
    2. Views tab
      1. Ligands button; smaller ligands.
      2. Hide (chain, toluene, isolated His).
      3. Contacts
      4. Non-covalent interactions for HEM in chain A (blue chain).
    3. Resources tab
      1. Biological unit.


  5. Continue preparing slides to answer the Powerpoint Questions.

    V. Introduction to Multiple Sequence Alignment (MSA) and Conservation
    ConSurf Server
    Structure of Atomic Coordinate ("PDB") Files
  1. Evolutionary conservation identifies functional sites in protein molecules.

    1. See Introduction to evolutionary conservation.

      Effect of mutation on protein function Genetic consequence Example
      Function LOST** CONSERVED:
      mutation LOST from gene pool
      R133C*
      None NOT conserved:
      mutation remains in gene pool
      E143?*
      * in methyl CpG binding protein 2 (MeCP2), 3c2i:

         ASASPKQRRS IIRDRGPMYD DPTLPEGWTR KLKQRKSGRS AGKYDVYLIN
         PQGKAFRSKV ELIMYFEKVG DTSLDPNDFD FTVTGRGSPS RHHHHHH
               ^          ^

      ** R133C causes Rett syndrome, a severe neurological disorder.
      Gray: disordered in crystal, absent in model 3c2i.

    2. In Proteopedia, show Evolutionary Conservation. Example: 3c2i
    3. Enzyme example: ConSurf-colored sequence -- enolase 4enl in Proteopedia -- 4enl ConSurf Result -- enolase in Wikipedia.

    4. Multiple sequence alignments reveal conservation: MSA for 4ENL in black and white (printed handout).
    5. Detail of MSA with color

    6. ConSurf Mechanism.   (Details of Mechanism).
    7. There are two ConSurf Servers:
      1. ConSurfDB (DataBase)
        • Pre-calculated for every chain in the PDB.
        • Results are shown in Proteopedia.
        • Multiple Sequence Alignments typically include proteins of more than one function, so some conservation may be hidden.
      2. ConSurf
        • Set up each job by hand.
        • Easily select sequences for a single protein function, revealing conservation (within a family of proteins performing a single function) that may be hidden in ConSurfDB.

  2. Atomic Coordinate Files

    VI. Evolutionary Conservation with ConSurf-DB
    Authoring Molecular Scenes in Proteopedia
    Publication-Quality Images & Animations for Powerpoint
    As you complete each section today, record your results in your Powerpoint Slides.

  1. Evolutionary Conservation: Follow the instructions for Question 14 to show conservation in your PDB code.
  2. If you have a serious research interest in the conservation pattern of your molecule (not required):
    1. You will want to do a ConSurf run where you limit the multiple sequence alignment to proteins with the same function as your molecule. Instructions.
    2. Using FirstGlance from ConSurf, you can see the conservation levels of amino acids contacting a moiety of interest.


  3. Author two scenes in Proteopedia.Org (Part II):
    1. See the help and movies under Want to Contribute? at the Main Page of Proteopedia.

    2. Login as "Student". Ask for the password.
    3. Go to the page Sandbox Reserved NN, where NN is the number assigned to you. For example, if you are assigned number 12, go to the page titled Sandbox Reserved 12.
    4. Click the tab, at the top, edit this page.
    5. Keep the {{Template:...}} at the top, but delete anything else that you did not put in this page.

    6. Click the 3D button (above the box) to insert a Jmol.
    7. Put your PDB code in the load parameter of the applet tag.
    8. Save the page (click Save page twice). You should see your molecule.

    9. Edit again, and show the Scene authoring tools.
    10. Use the load molecule tab to load your PDB code.
    11. Customize your scene: select, represent (display), color, label as you wish.
    12. Option: If you wish, you may copy a scene from FirstGlance into Proteopedia: Instructions.
    13. Use the save scene tab to save your scene.
    14. Paste the scene tag into the box above (the page text).
    15. Save the page (click Save page twice).

    16. Try the green link you made.
    17. Put a snapshot into a Powerpoint slide.
    18. Create a second scene and green link for your second Proteopedia Powerpoint slide.

      If you would like to contribute permanent content to Proteopedia, please apply for an account and password: click on request account.

  4. Continue preparing slides to answer the Powerpoint Questions.

    VII. FirstGlance in Jmol -- Part II
    Solution NMR
    Isoelectric Point
    Intrinsically Unstructured Proteins
    FirstGlance in Jmol (Part II)
  1. Solution Nuclear Magnetic Resonance (NMR)
  2. Charge:
  3. Intrinsicially Unstructured / Natively Disordered Proteins

    VIII. Structural Bioinformatics and Genomics.
    Homology (Comparative) Modeling

  1. Structural Genomics: Worldwide Protein 3D Structure Knowledge
    1. How are 3D macromolecular structures obtained? Crystallography, NMR, and homology modeling.
    2. What fraction of the human proteome has known structure? A few percent.
    3. Is Structural Genomics the answer? Not in the next few years.
    4. Intrinsicially unstructured proteins.


  2. Homology (comparative) modeling: Introduction.
    1. Automated homology modeling: submit sequences (after removing any His tag!) to Swiss-Model (click on Automated Mode).
    2. Compare homology models from various methods at LOMETS. Here is an example study comparing multiple homology models. See especially comparisions in supplementary figures S4-S6.
    3. See if a structure of your molecule is in the Structural Genomics pipeline. Submit your sequence to the SG TargetDB. (Ask for help interpreting the results.)

    IX. Publication Quality Images and Animations with Polyview-3D
    Finishing Powerpoint Questions
    Animation from Polyview-3D.
    Click on the above image for
    a larger view and explanation.
  1. Make Animated PowerPoint Slides and Publication-Quality Images easily with Polyview-3D.
  2. You are now prepared to finish your Powerpoint Questions. Please email the completed PPT file to
    emartz AT microbio DOT umass DOT edu.


Additional Resources.
    Probably we will not have time in class to spend on these resources. Links are provided here in case you are interested to look at these later.
  1. Save any molecule you see! (as a PDB file)
  2. Example: Gramicidin channel in a lipid bilayer.

  3. Jmol in Scientific Journals
    1. FirstGlance in Jmol is used in Nature Structure & Molecular Biology and other journals.
    2. "Jmolized" Interactive Journal Figures: Biochemical Journal and ACS Chemical Biology.
    3. Jmolize your own figures: Frieda Reichsman -- MoleculesInMotion.Com
    4. Toolkit for Jmolizing journal figures provided by the International Union of Crystallography.
    5. Note that Proteopedia is easier than "Jmolizing": see Interactive 3D Complements in Proteopedia (similar to supplementary materials).


    Simplified SV40 Virus Capsid.
  4. Specific Oligomers vs. Crystal Contacts

    Lac repressor bending the DNA operon. If this image is not moving, reload the page.
  5. Animations & Morphing

    For Teachers and Future Teachers

  6. BioMolecular Explorer 3D (for students ages 15-19). All Jmol!

  7. High School Teacher's Resources.

  8. Bird Flu: N1 vs. Tamiflu Lesson Plan:
  9. MolviZ.Org
    1. DNA, Hemoglobin, Antibody
    2. Lipid Bilayers and Gramicidin Channel
    3. Collagen
    4. Water & Ice & hydrogen bonding
    5. Toobers in Science Education

  10. World Index of Molecular Visualization Resources   MolVisIndex.org
    1. Hundreds of tutorials indexed by macromolecule (most in Chime, some in Jmol)
    2. Sources of atomic coordinate (PDB) files (metabolites, inorganic crystals, lipid micelles, etc.)
    3. Galleries, Molecular Sculpture and Physical Models, Software

  11. About Protein Structure
  12. Building a web page that shows your favorite molecules for research or teaching.
  13. T shirts and mugs!                  
    (Click images for more information.)


Keep in touch!