User:Eric Martz/Introduction to Structural Bioinformatics I

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Revision as of 19:29, 29 September 2012

Overview and Goals

In these two classes, you will

1. Be introduced to structural biology and structural bioinformatics.
2. Choose a protein molecule to work with (different for each student).
3. Learn how to use easy tools to visualize answers to questions about the structure of your molecule. The main tools are:
   1. Proteopedia.Org, a wiki encyclopedia of protein structure.
   2. FirstGlance in Jmol (FirstGlance.Jmol.Org), making it easy to see key structural features of a macromolecule.
4. Take snapshots of your molecule, and paste them into Powerpoint slides, along with your answers.
5. Email your .pptx file to emartz@microbio.umass.edu for grading.

Computer Lab Preparation (BCRC)

1. Log in
2. Run Firefox
3. Go to proteopedia.org (do NOT type www).
4. If you see inactive plug-in, click on it and ENABLE the plug-in.
5. Restart the browser and again go to proteopedia.org.
6. When you see a rotating 3D molecular structure, you are prepared.
7. Take a look around Proteopedia. Click on the PDB codes below, or the Random links to see other molecules.

Protein Structure and Structural Bioinformatics

1. Amino acid sequence + protein chain conformation = protein function.

A. Conformation can be a stable fold or intrinsically unstructured. Both commonly exist in the same protein molecule.

B. 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 domain destroys its function.

2. 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:

• X-ray crystallography, 88%.
• Nuclear magnetic resonance (NMR) in aqueous solution, 11%.

• NMR is limited to small proteins (30 kD or smaller).

• 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

• 1hho
• 1d66
• 2bbn
• 9ins

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.

Choose a Molecule to Explore

• Choose a molecule that includes protein and ligand. It may also include nucleic acid, but must have protein and ligand.
• 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" molecule that has ligand.
2. Structural View of Biology at the PDB.
3. Molecule of the Month at the PDB.
4. Topic Pages in Proteopedia.
5. Random PDB Entry in Proteopedia (see random box at top left of this page).
6. Search by molecule name or amino acid sequence at www.pdb.org, but remember that less than 10% of proteins have known structure.

Explore Your Molecule

Snapshot means you should take a snapshot to answer a question and paste into your Powerpoint report.

1. Start in Proteopedia.

A. Open Proteopedia in a new browser tab and enter your PDB code in the search slot at the left.

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.

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

Each question below may be answered in a single slide, or multiple slides. For example, Section # is complicated, so you might have the answer in two slides, labeled Section 1A and Section 1B.

This is not a test. It is to help you learn by doing. Ask for help!

Section 1

• 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 resolution or number of models (given in Proteopedia immediately under the molecule). The experimental method used to determine the structure.
  • A resolution usually implies that the method is X-ray crystallography.
  • A number of models usually implies that the method is NMR.
  • To double check, in Proteopedia, click on the link RCSB and at the RCSB PDB, look in the box at the lower right, Experimental Details.
• The number of polymer chains (protein or nucleic acid) present. (Given in Proteopedia in the section About this Structure.)
• A snapshot of your molecule. (See instructions for taking static snapshots, also linked at the bottom left in FirstGlance.)

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.