Syllabus for
Protein 3D Structure Visualization & Structural Bioinformatics


Part of the Applied Molecular Biotechnology MS Program, Dept. Microbiology,
University of Massachusetts, Amherst.
2017: Tuesdays and Thursdays, January 10, 12, 17, 19 in Fine Arts Center 444.
1:00 to 4:00 PM each day.


Bringing A Laptop Computer Is Encouraged
but not required (lab mac & windows computers are available).


Taught by Eric Martz* and Jeffrey Kane.
*principal author of FirstGlance in Jmol ( buttons in the journal Nature) and MolviZ.Org,
team member of Proteopedia.Org, and coauthor of the ConSurf Server.
*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.) You may use Mac OS X or Windows, whichever you prefer. The software works the same in both.
  2. Use the Firefox (or Safari) browser. If you do not have either, take a few minutes to install Firefox (www.firefox.com). (Firefox or Safari will be faster/smoother than Chrome for this software. Internet Explorer and Edge are unusably slow with this software.)
  3. In the Firefox (or Safari) 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)

  2. Nikhil Malvankar (Physics) took this workshop in 2012. Published his homology model in 2015.
    I. Protein Data Bank & PDB Codes
    Crystallographic Resolution
    Proteopedia.Org
  1. The Protein Data Bank (PDB) -- World Wide: USA:RCSB -- Japan:PDBj -- Europe:PDBe. All 3 have the same data.
  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. Obtaining models for 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.
Standard amino acids.
Click to see details.

  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. In proteins, donor-acceptor distance can be 2.5 to 2.5 Å.
  6. Secondary Structure
  7. Folding: hydrophobic collapse
  8. Protein folds cannot be reliably predicted from sequence alone (using ab initio theory).
  9. Fold does not always equal function: 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. This is termed intrinsic disorder. Examples: 1jsu, 2rrl.

  10. Introduction to Structural Bioinformatics

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

  1. To start FirstGlance, google "firstglance" (no space), or go to FirstGlance.Jmol.Org. 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, use Isolate.. on each end of a helix or strand.)
      5. Compare with the Hydrophobic/Polar View of 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. (Red sidechain (-) touching blue sidechain (+)).
      5. Charges with Slab on.
      6. Sidechain distributions in Vines View (rings buried; charges on surface).
      7. Find (review Chart of AA): PHE, (VAL,LEU,ILE), ASN, THR

  3. Explore 9ins in FirstGlance.
    1. Tools tab
      1. Disulfides/S/Se

  4. Explore 3onz in FirstGlance. (Letter O not numeral zero!)
    1. Molecule Information 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. Tools tab
      1. Contacts
      2. Non-covalent interactions for HEM in chain A (blue chain).
    4. Resources tab
      1. Biological unit.

  5. Solution Nuclear Magnetic Resonance (NMR)
  6. 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. Identify Functional Sites In Your Molecule Using The ConSurf Server:
  2. Get your ConSurf calculation started while we discuss evolutionary conservation:

    1. Go to the ConSurf Server.
    2. Select Amino Acids.
    3. Check YES there is a known protein structure.
    4. Enter the PDB code, or upload your homology model.
    5. Select a chain for analysis. ConSurf can analyze only one chain at a time.
    6. Check NO, you will not be uploading a multiple sequence alignment. (ConSurf will create one for you.)
    7. OPTIONAL: If you want a research grade result, check "Let me select the sequences for the analysis manually out of BLAST results", and see Limiting ConSurf Analysis to Proteins of a Single Function.
    8. Leave all other parameters at their pre-set defaults.
    9. Enter your email address at the bottom of the form (this is important so you don't lose your results). Optionally enter a job title.
    10. Click the button Submit. It may take an hour or more to complete this calculation.
    11. When it is finished, under Final Results, click the link View ConSurf Results with FirstGlance in Jmol.
    12. Example: 4enl result in ConSurf.

  3. Background: see Introduction to Evolutionary Conservation.

  4. 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.

    1. Enzyme example: ConSurf-colored sequence -- 4enl ConSurf Result -- enolase in Wikipedia.
    2. Multiple sequence alignments reveal conservation: MSA for 4ENL in black and white.
    3. Detail of MSA with color. ConSurf does a much more sophisticated job of calculating evolutionary conservation scores than this simple example!
    4. On the less conserved side of the molecule, touch the isolated highly conserved residues to display the amino acid and sequence number. Gly236 and Pro290 are highly conserved. Why?.

  5. ConSurf Mechanism.   (Details of Mechanism).
  6. Note the Caveats in Proteopedia's Evolutionary Conservation.

  7. Atomic Coordinate Files
  8. Continue preparing slides to answer the Powerpoint Questions.

    VI. 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

    VII. 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. Animate customized molecular scenes easily with Polyview-3D.

    Animations are most easily saved from FirstGlance, but you are limited to the "canned" color schemes and renderings that it offers.

    If you wish to customize a molecular scene with arbitrary colors and renderings, there are two relatively easy options:

    1. Proteopedia.Org has molecular scene authoring tools: you use checkboxes and forms to customize the scene, and it is immediately online to share. "Export Animated Image" is under development but does not work well yet.

    2. Polyview-3D also allows customization of colors and renderings from forms and checkboxes. Its output is a high-quality animation (rendered with PyMOL) or publication-quality image.
      • Accepts PDB files obtained from ConSurf to color your figures or slides by evolutionary conservation. Under Advanced Structure Annotation check "Functional regions from ConSurf" and follow the displayed instructions.

    Once you have an animation from 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. Jmol in Scientific Journals
    1. FirstGlance in Jmol is used in Nature (3D buttons) and other journals.
    2. Jmolize your own figures: Frieda Reichsman -- MoleculesInMotion.Com
    3. Note that Proteopedia is easier than "Jmolizing": see Interactive 3D Complements in Proteopedia (similar to supplementary materials).


    Simplified SV40 Virus Capsid.


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

    For Teachers and Future Teachers

  3. BioMolecular Explorer 3D (for students ages 15-19).

  4. High School Teacher's Resources.

  5. MolviZ.Org
    1. DNA, Hemoglobin, Antibody
    2. Lipid Bilayers and Gramicidin Channel
    3. Collagen
    4. Water & Ice & hydrogen bonding
    5. Toobers in Science Education

  6. About Protein Structure
  7. Building a web page that shows your favorite molecules for research or teaching.


Keep in touch!