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

Pre-Assignment

  • 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.

Problems

Extra Problem

Voet 3rd ed (note that DALI is now SSM)
Chp8: 10
Chp9: 10, 12

Nomenclature, Sequence and Structure Problems

Web Resources

-Bioinformatics

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)
  • Secondary
    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

In Class Activities

Discussion of Structural Informatics Tools

Review

3D Structure of Proteins
- Berg 5th ed: Chp2: 2.3-2.6 Protein 3D Structure
- Cox 5th ed Chp 4.2, 4.3