Syllabus for
Protein 3D Structure Visualization & Structural Bioinformatics

Part of the Applied Molecular Biotechnology MS Program, Dept. Microbiology,
University of Massachusetts, Amherst.
2020: Thursdays and a Monday, January 9, 13, 16 in Du Bois LIBR 720.
1:00 to 4:00 PM each day.

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

Taught by Eric Martz* and Jeffrey Kane.
*principal author of FirstGlance in Jmol and MolviZ.Org,
team member of Proteopedia.Org, and coauthor of the ConSurf Server.
*Professor Emeritus, University of Massachusetts, Amherst -- Morrill IVN 422B --

This syllabus is on-line:

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 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.
Licence: Creative Commons License This Syllabus for Protein 3D Structure Visualization & Structural Bioinformatics by Eric Martz is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

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 Chrome browser or Firefox or Opera. (Why?). If you do not have one of these, take a few minutes to install one (,
  3. Go to Workshops.MolviZ.Org and click on today's syllabus.
  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 brief time 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
  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
    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, Hindi, Russian, Arabic, Japanese, Turkish, etc.

  4. X-Ray Crystallography and Resolution
    X-ray crystallography generates an electron density map with resolution limited by the order in the protein crystal. The atomic model (shown as sticks below) must then be fitted into the map.
    (Technical: Endnote 1) (Technical: Endnote 2)
    C O N Electron Density Map
    (Technical: Endnote 3) Movie

  5. Electron Cryo-Microscopy is increasingly important

    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. Primary, Secondary, Tertiary, Quaternary Protein Structure
    Los cuatro niveles estructurales de las proteÝnas
  7. Secondary Structure
  8. Tertiary Structure: Folding & Hydrophobic Collapse
  9. Quaternary Structure
  10. Intrinsically Disordered Protein

  11. 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.

  2. Explore 1izh in FirstGlance.
    1. Introduction
    2. Molecule Information Tab
      1. Year, Method.
      2. Resolution.
      3. Free R. (1awq)
      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
      Enolase (4enl; a glycolytic enzyme) evolutionary conservation from ConSurf. Catalytic cleft is at the left. More..
  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. (If your PDB file has only one chain, it will be selected automatically.) 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. Leave all search parameters at their pre-set defaults.
    8. Select sequence homologs for ConSurf analysis:
      Check manually for a research-grade result.
      Check automatically for a quick but probably lower quality result.
    9. Leave the alignment method, calculation method, and evolutionary substitution model at their default settings.
    10. 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.
    11. Click the button Submit. It may take an hour or more to complete this calculation.
    12. If you are selecting sequences manually, you will see SELECT SEQUENCES.
      For instructions, see Limiting ConSurf Analysis to Proteins of a Single Function.
      Example: Sequences ready for selection (2vaa, Swiss-Prot).
    13. When it is finished, under Final Results, click the link View ConSurf Results with FirstGlance in Jmol.
    14. 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
    None NOT conserved:
    mutation remains in gene pool
    * in methyl CpG binding protein 2 (MeCP2), 3c2i:

             ^          ^

    ** 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. 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. It is easy to make a presentation-ready animation from your customized Proteopedia scene.

    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.

    Simplified SV40 Virus Capsid.

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

  2. 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. Structural Alignment of two or more chains or molecules, and how to view the alignment.

    For Teachers and Future Teachers

  4. High School Teacher's Resources.

  5. MolviZ.Org
    1. DNA (with quiz), Hemoglobin (with quiz)
    2. Atomic clashes: Ramachandran Principle (animated, interactive, with quiz)
    3. Lipid Bilayers and Gramicidin Channel
    4. Collagen
    5. Water & Ice & hydrogen bonding
    6. Toobers in Science Education

  6. About Macromolecular Structure

  7. Building a web page that shows your favorite molecules for research or teaching.

Keep in touch!


Endnote 1 (): Slabbed image from Electron Density at 1.0 σ showing Leu5 and Ala4 in 3hyd. Temperature factors in those two residues range from 3 to 12, average 5.

Endnote 2 (): Slabbed image from Electron Density Maps at 1.0 σ showing Leu425 and Ala426 in 1io1. Temperature factors in those two residues range from 12 to 17, average 15.

Endnote 3 (): Slabbed image with electron density map at 1.0 σ showing Ile98 and Val99 in 4cgf. Temperature factors in those two residues range from 32 to 45, average 37.