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Classification of ProteinStructure
RasMol:A free program to display three-dimensional structures oncomputers running Windows, Mac Classic, or Unix. Click on theRasMollink for information on downloading and using the program. Unfortunately thereis no version of RasMol for Mac OS-X, however there is a Mac OS-X version ofPyMOL, 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 manipulateprotein structures from within your browser. Click on the Chime linkto down load the plugin: http://www.mdlchime.com/chime/
Retrieve Protein StructureCoordinates:http://www.rcsb.org/pdb/
Or click on the name or pictureof the example proteins shown below, and you will be asked if youwant to save the file. If you are downloading the files in theBiology Student Computer Lab in LS 126, be sure to save the file intoa folder on the Hard Disk andNot on theDesktop.
Other StructureDatabases:
Small Molecules from OkanaganUniv.:http://www.okanagan.bc.ca/chem/molecule/molecule.html
Entrez (National Center forBiotechnology Information): http://www.ncbi.nlm.nih.gov/Entrez/index.html
Protein SecondaryStructure
AlphaHelix -3.6 amino acid residues perturn x 1.5 Å per amino acid > pitch = 5.4Å
BetaSheet (Antiparallel)
1. Alla-Helix
a. Parallel a-helices / 4 helix bundles: Cytochrome b 562
b. Globin Fold: Myoglobin
c. DNA-Binding / 3 helix bundle: Engrailed homeodomain
Intermediate french book pdf. 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
- b-barrel domain of bacterial outer membrane porin
3. a/ b Structures
a. b-barrel surrounded by a-helices:
b. b -sheet sandwiched between a -helices: Flavodoxin
4. a+ b
MembraneProteins
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1. Transmembranea-helices
a. Bacteriorhodopsin
Acidic Residues-Green; Basic Residues-Red; RetinalBlue
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b. Bacterial Photosynthetic Reaction Center
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H-Subunit-Yellow; M-Subunit-Green; L-Subunit-Aqua; Cytochrome-Blue
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c. K+ Channel from Streptomyces lividansAutomation studio software.
Four identical polypeptides in green, blue, and aqua, four K+ in red