Classification of Protein Structure

RasMol: A free program to display three-dimensional structures on computers running Windows, Mac Classic, or Unix. Click on the RasMol link for information on downloading and using the program. Unfortunately there is no version of RasMol for Mac OS-X, however there is a Mac OS-X version of PyMOL, MacPyMOL.

PyMOL: Is free for students and teachers after you receive approval of your application. It is more sophisticated than RasMol at the cost of a steeper learning curve. Versions are available for Linux/Unix, Mac OS-X, and Windows.

Chime: A free Internet Browser plugin that allows you to view and manipulate protein structures from within your browser. Click on the Chime link to down load the plugin: http://www.mdlchime.com/chime/

Retrieve Protein Structure Coordinates: http://www.rcsb.org/pdb/

Or click on the name or picture of the example proteins shown below, and you will be asked if you want to save the file. If you are downloading the files in the Biology Student Computer Lab in LS 126, be sure to save the file into a folder on the Hard Disk and Not on the Desktop.

Other Structure Databases:

Small Molecules from Okanagan Univ.: http://www.okanagan.bc.ca/chem/molecule/molecule.html

Entrez (National Center for Biotechnology Information): http://www.ncbi.nlm.nih.gov/Entrez/index.html


Protein Secondary Structure

Alpha Helix - 3.6 amino acid residues per turn x 1.5 Å per amino acid ==> pitch = 5.4 Å

Beta Sheet (Antiparallel)


1. All a-Helix

a. Parallel a-helices / 4 helix bundles: Cytochrome b 562

b. Globin Fold: Myoglobin

c. DNA-Binding / 3 helix bundle: Engrailed homeodomain

Two proteins in aqua and blue bound to double stranded DNA displayed in spacefill with CPK colors


2. All b-Sheet

Fab-Immunoglobulin / b-sandwich


3. a / b Structures

a. b-barrel surrounded by a-helices:

TIM (Triose Phosephate Isomerase)

central domain of Pyruvate Kinase

b. b -sheet sandwiched between a -helices: Flavodoxin


4. a + b

Ribonuclease A

RuBisCo Small Subunit


Membrane Proteins

1. Transmembrane a-helices

a. Bacteriorhodopsin

Acidic Residues-Green; Basic Residues-Red; RetinalBlue

b. Bacterial Photosynthetic Reaction Center

H-Subunit-Yellow; M-Subunit-Green; L-Subunit-Aqua; Cytochrome-Blue

c. K+ Channel from Streptomyces lividans

Four identical polypeptides in green, blue, and aqua, four K+ in red

2. b-Barrels-bacterial outermembrane porins