User:Eric Martz/Introduction to Structural Bioinformatics I
From Proteopedia
How to find, visualize, and understand 3D protein molecular structures
by Eric Martz, October 2 and 4, 2012
for Prof. Steven Sandler's course Microbiology 565: Laboratory in Molecular Genetics
University of Massachusetts, Amherst MA USA
Get here with 565.MolviZ.Org
Computer Lab Preparation (BCRC)
- Log in
- Run Firefox
- Go to proteopedia.org (do NOT type www)
- If you see inactive plug-in, click on it and ENABLE the plug-in.
- Restart the browser and again go to proteopedia.org.
- When you see a rotating 3D molecular structure, you are prepared.
- Take a look around. Click on the PDB codes below, or the Random links to see other molecules.
Protein Structure
- 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 sequece. 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
- A. Although sequence specifies fold, scientists cannot yet predict the fold from the sequece. Therefore, fold must be determined by empirical (experimental) methods. The most common methods for determining the 3D structure of a protein molecule are:
Notes and References
- ↑ For a brief overview of Anfinson's protein folding experiments in the 1960's, see the first paragraph at Intrinsically Disordered Protein.
