Reading (to be completed before class!)
Berg 5th ed: Chp3: 3.6 The Amino Acid Sequence Determines 3D Structure
Review Voet B. Tertiary Structure, p245 - p256
Voet: Chp8: Sect 3C; Chp9: Sect 3A,B
- Go to the protein data bank and find a PDB file for Thimet Oligopetidase
- "Play" with the page. In other words, analyse the information and tools provided.
For instance, try to view the structure in 3D. Determine CATH and SCOP classification of the enzyme.
- Your text and Voet have information of SCOP and CATH
- Find a protein or enzyme of interest to you. Bring a summary of your findings to share in class.
Voet 3rd ed (note that DALI is now SSM)
Chp9: 10, 12
Nomenclature, Sequence and Structure Problems
1) Swiss Institute of Bioinformatics
ExPASy (Expert Protein Analysis System) Tools
(the tools can be accessed by category or by resources A-Z)
- Sequence Alignment tools
- BLAST (BLASTp)
- ENZYME (repository of information relative to the nomenclature of enzymes)
- Compute pI/MW and ProtParam (calculate pI, % composition, e280nm, etc)
- HelixWheel (this is no longer on the ExPASy site, use Helical Wheel)
ProtScale - allows you to compute and represent the profile produced by any
amino acid scale on a selected protein. For instance, you can enter the Accession
number for a protein and predict the secondary structure content based on the
amino acid sequence using Chou-Fasman parameters.
-----Use the following Excel file to assist in the prediction of secondary structure using Chou-Fasman parameters
----- Compare the actual secondary structure of Goose Lysozyme to that prediced using Chou-Fasman parameters within ProtScale
- Tertiary structure analysis tools - http://expasy.org/structural_bioinformatics
2) European Bioinformatics Institute
Tools for Multiple and pairwise protein stuctural comparison and sequence alignment