User:Eric Martz/Introduction to Structural Bioinformatics I, 2014

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How to visualize, understand and share/present 3D protein molecular structures
by Eric Martz, 2014
for Prof. Steven Sandler's course Microbiology 565: Laboratory in Molecular Genetics
University of Massachusetts, Amherst MA USA
Get here with 565.MolviZ.Org


Contents

I. Getting Started in the BCRC

  1. Log in using your Biology Dept. account. If you brought your own laptop, you are welcome to use it. (iPads will be too slow.)
  2. Use the Chrome browser: click Spotlight (Image:Spotlight-icon.png upper right corner of screen), enter "chrome" and click on the top hit, Google Chrome. (Chrome will be faster/smoother than Safari, and Firefox is even slower for this software. Internet Explorer and Opera are very slow with this software.)
  3. In the Chrome browser, go to our syllabus: 565.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.
  6. If you have any difficulty or the molecule does not appear, ask for help!

II. Goals

1. Review principles of protein 3D structure.

2. Choose an existing experimentally-determined 3D protein structure model to investigate.

3. Learn how FirstGlance in Jmol makes it easy to see structure-function relationships in the protein you chose.

4. Write a report including snapshots of your protein that answer questions it. (Your report will be a Powerpoint file emailed to emartz@microbio.umass.edu. You will not present your report in class.)

III. Protein Structure and Structural Bioinformatics

About this image
1. Amino acid sequence + protein chain conformation = protein function.
A. Why do we care about protein 3D structure?
B. Conformation can be a stable fold or intrinsically unstructured. Both commonly exist in the same protein molecule.
C. Conformation is specified by sequence.
  • Folded domains fold spontaneously (Anfinson, 1960's[1]), or with the help of chaperonins.
  • The denaturation (unfolding) of a folded protein domain destroys its function.


2. Backbone Representation.
A. Backbone Representations
B. Small Protein in FirstGlance (use the Views Tab: Vines, Cartoon)


3. Structure Knowledge.
A. Although sequence specifies fold, scientists cannot yet predict the fold from the sequence. Therefore, fold must be determined by empirical (experimental) methods. The most common methods for determining the 3D structure of a protein molecule are:
  • Result is a single model representing the average of the molecules in the crystal.
  • Resolution reflects the degree of order or disorder in the crystal.
  • X-ray crystallography gives no models for intrinsically unstructured loops or molecules.
  • NMR is limited to small proteins (30 kD or smaller; median NMR in PDB is 10K; median X-ray is 50K).
  • Result is an ensemble of models consistent with the data. Examples: 2bbn
  • High resolution cryo-electron microscopy, 0.5%.
B. These methods are difficult and expensive. Less than 10% of proteins have known structure.
C. All published, empirically determined 3D macromolecular structure models are available from the Protein Data Bank (PDB; pdb.org; About the PDB).
D. Each model has a unique, 4-character accession code called a PDB identification code, for example
E. Crystallographers publish the asymmetric unit of the crystal. It may be identical with the biological unit (the functional form of the molecule), or it may be only part of the biological unit, or it may contain multiple copies of the biological unit. See examples.
Interchain contacts that occur in the asymmetric unit that are absent in the biological unit are an artifact of crystallization, termed crystal contacts.

IV. Choose a Molecule to Explore

  • Choose a molecule to use for your report.
    • Each student should choose a different molecule.
    • It must have protein.
    • It will be more interesting if it contains some non-protein: DNA, RNA or ligand.
    • X-ray results should have resolution of 3 Å or better.
  • Be sure to note the 4-character PDB code of the molecule you choose. The PDB code makes it easy to retrieve the molecule and information about it. Here are some ways to find a protein with known structure:
  1. Atlas of Macromolecules (Atlas.MolviZ.Org). Choose a "Straightforward" or "Challenging" (not "Enormous") molecule that has protein and ligand.
  2. Structural View of Biology at the PDB. To get a PDB code, scroll to the bottom of an article and look for the boxes Discussed Structures.
  3. Molecule of the Month at the PDB. To get a PDB code, scroll to the bottom of an article and look for the boxes Discussed Structures.
  4. Topic Pages in Proteopedia, or its Table of Contents.
  5. Random PDB Entry in Proteopedia (see Random at top left of this page in the navigation box).
  6. Search by molecule name or amino acid sequence at www.pdb.org, but remember that less than 10% of proteins have known structure.

V. Explore Your Molecule

FirstGlance in Jmol

The main tool we will use is FirstGlance in Jmol: FirstGlance.Jmol.Org. (To google it later, use the single word (no space) firstglance.)

  • Enter your 4-character PDB code at FirstGlance, and you should see the molecule you have chosen.
  • Get familiar with what the molecule information tab tells you. Ask about anything you don't understand.
  • In the Views tab, there are 10 links at the top that show you different aspects of the molecule. Try them all, as well as any of the other tools in FirstGlance that interest you.


FirstGlance does NOT use Java unless you tell it to. Larger proteins will be slow to load and rotate, and to change the view, unless you use Java. Use Safari (or Firefox) for Java on Macs because Chrome does not support Java on Macs. On Windows, Internet Explorer is good for Java. In your Java-compatible browser, display a molecule in FirstGlance, and then click on the Preferences tab in FirstGlance. Java is installed and working in the BCRC. Simply give it permission when asked (several times).

Here are two Views in FirstGlance that will be used in your Powerpoint report:

A. Hydrophobic/Polar

  • Water-soluble proteins have polar/charged amino acids nearly everywhere on their surfaces (Examples: small 2hhd, large 1igy). Patches of hydrophobic amino acids on the surfaces of soluble proteins are usually less than ~10 å in their smaller diameter, and usually recessed.
  • Hydrophobic surface patches may be buried in chain-to-chain contacts -- check the biological unit (example: lac repressor homodimer).
  • Large, protruding hydrophobic surface areas (>25 Å in their smaller diameter) may indicate transmembrane proteins (insoluble). Examples:

B. Charge

Most proteins have roughly equal numbers of positive and negative charges intermixed on their surfaces. Surface patches of exclusively positive charge often bind nucleic acids (negatively charged because of their phosphates). For example, examine the protein surface charges where the gal4 transcriptional regulator binds DNA (1d66).

VI. Powerpoint Report

Save your report with the filename yourLastName-565.pptx, for example sandler-565.pptx. When completed, your Powerpoint report is to be emailed to emartz@microbio.umass.edu for grading. You will not be asked to present your report in class.

Each slide MUST be labeled at the top with its section number, e.g. Section 1.

Each Section below may be answered in a single slide, or multiple slides. For example, suppose you want to show two snapshots for Section 3, and make separate comments. You may choose to use two slides, labeled Section 3A and Section 3B.

This is not a test. It is to help you learn by doing. Ask for help!
Sample Completed Powerpoint Assignment (You may download it, rename the file, and use it as a template.)

Section 1: Identity

  • The label Section 1 at the top (and so forth for every slide).
  • Your name.
  • Your major; grad students, give the name of your grad program (Micro, MCB, etc.) and whose lab you work in.
  • Your PDB identification code.
  • The name of your molecule.
  • The function of your molecule.
  • The experimental method and resolution (or number of models for NMR). Available in the molecule information tab in FirstGlance.
  • A snapshot of your molecule.

How to make a snapshot,
is also linked at the bottom left in FirstGlance.

Section 2: Composition

  • The number of
    • Protein chains
    • DNA chains
    • RNA chains
      • Available in the molecule information tab in FirstGlance: Chain Details. You can identify a residue in any chain by touching it with the mouse (spinning off!). DNA residues are DA, DG, DC, DT while RNA residues are A, G, C and U.
  • Ligands and Non-Standard Residues: Give the 3-letter abbreviations and full names for all ligands and non-standard residues. If none, so state. (Standard residues)
The molecule information tab in FirstGlance lists the 1 to 3-letter abbreviations for each ligand and non-standard residue, and their full names. Click on an abbreviation to locate that entity in the model. See also Composition in FirstGlance's Views tab.

Section 3: Evolutionary Conservation

See Introduction to Evolutionary Conservation.

Does your molecule have a highly conserved region? If so, what is its function? If there is no highly conserved region, is there a highly variable region? Show a snapshot illustrating a highly conserved (or variable) region.

See How to see conserved regions.

If Proteopedia lacks a pre-calculated Evolutionary Conservation for your molecule, and you do your own calculation at the ConSurf Server, be sure to include the address of the ConSurf result in your Powerpoint slide!.

Section 4: Hydrophobic/Polar

Do you think your molecule is water soluble? Support your conclusion with a snapshot. Be sure to use the Hydrophobic/Polar view from FirstGlance in a snapshot. Optionally, you may show other views in other snapshots.

Section 4A: Hydrophobic Core

Is there a hydrophobic core in your molecule? Support your conclusion with a snapshot. Be sure to use the Hydrophobic/Polar view from FirstGlance and turn on the Slab button.

Section 5: Charge

Are there any areas on the surface of your molecule with only positive (or negative) charges? Show snapshots illustrating your conclusions. Be sure to use the Charge view from FirstGlance in a snapshot.

Section 5A: Cation-Pi Interactions

Show a snapshot of an energetically significant cation-pi interaction. Include a distance monitor in your snapshot. Also paste in the report from CaPTURE confirming its energetic significance. The cation-pi interaction tool, and instructions for measuring distances, are in the Tools Tab.

Section 6: Biological Unit

In FirstGlance, in the molecule information tab click Biological Unit. (It is also in the Resources Tab.)

How many total polymer chains (protein + DNA + RNA) are in the asymmetric unit? The Biological unit?

Show side-by-side two snapshots comparing the asymmetric unit with the biological unit. The Cartoon representation in FirstGlance is best for these snapshots. Make sure to label which is which.

Section 7: Animation from Polyview-3D

Minimal steps to make an animation:

  1. Go to Polyview-3D.
  2. Enter your PDB code in the PDB ID slot near the top. (If the slot is not visible, open the section Source of Structural Data.)
  3. Change "Type of request" from "Single slide" to "Animation". It is under the Image Settings section near the bottom.
  4. Click any "Preview" link.
  5. Optional: If you want to modify the orientation or zoom of the molecule, click on View by Jmol / Set orientation under Quick links at the upper left of the page. Use the mouse to rotate and zoom in Jmol. Then click the Set and close button.
  6. Optional: If you want to change the colors, hide portions of the molecule, emphasize certain residues, etc. feel free to try out these options in the form, using Preview to check your results.
  7. In the "Animation Settings" section at the bottom of the page, set Delay to 10/100.
  8. Change "Angle step" to 5 degrees.
  9. Check "Rocking".
  10. Change "angle range" for rocking to 30 degrees.
  11. Click "Submit".

The above steps are the minimum for an animation that avoids putting a heavy load on the server. Feel free to try other options, but while the class is in session, please don't make a large (>300 pixel) animation, or increase the angle range, or decrease the angle step size. Otherwise, the server may get overloaded and take a very long time to produce results. Optional: After class is over, feel free to submit more demanding jobs. If you highlight specific residues, please explain why.

In Powerpoint, animations move only when the slides are projected (full-screen).

Windows Powerpoint: Simply drag the animation directly from the Polyview-3D web page and drop it into a Powerpoint slide. If the result does not animate when you project the slide, try the instructions for Mac below.

Mac Powerpoint: The method below produces a slide that will animate continuously. Other methods we have tried do not.

  1. Control-Click on the animation in the Polyview-3D web page, and select Save Image As ...
  2. Save the image to the Desktop.
  3. Drag the image file (filename ending in .gif) from the Desktop and drop it into a Powerpoint slide.
  4. As stated above, the animation will run only when the saved .ppt file is projected (full screen).

Powerpoint Slides with Polyview-3D Animations (These slides are only to show you what is possible. These are not in your assignment.)


Section 8 - Contacts/Non-covalent Bonds

  1. Click Contacts in the Tools Tab in FirstGlance.
  2. Change target selection to Residues/Groups.
  3. Click on something small to select it as a "target", such as a ligand, or a single amino acid. Choose an amino acid with an uncharged polar side chain, such as Ser, Thr, Asn, Gln, Tyr, His.
  4. Click the link to Show atoms contacting target.
  5. Click Center contacts.
  6. Uncheck Backbones.
  7. Click the 4th thumbnail image Image:Contact4.gif to display the contacts as balls and sticks colored by element. The element color key is at the bottom of the Contacts help panel in FirstGlance.
  8. Zoom in (and click Return to Contacts if necessary).
  9. Uncheck all categories of non-covalent bonds.
  10. Check hydrogen-bonded non-water. (Review hydrogen bonds.)
  11. Double click the hydrogen bond donor and acceptor atoms to insert a distance monitor.

Describe the moiety you selected as a target. Include a snapshot showing a hydrogen bond.

VII. See Also

VIII. Notes and References

  1. ↑ For a brief overview of Anfinson's protein folding experiments in the 1960's, see the first paragraph at Intrinsically Disordered Protein.

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Jaime Prilusky

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