Reading and Web activities

Voet: Chp8: Sect 3C; Chp9: Sect 3A,B

Jmol Animation

In Class Activities

- Bioinformatics

• Swiss Institute of Bioinformatics
  • ExPASy (Expert Protein Analysis System)
    • ENZYME (repository of information relative to the nomenclature of enzymes)
    • Primary
      • pI, Titration Curve, e280nm
      • HelixWheel (analyze helix composed of res 92-112 of TOP)
    • Secondary
      • nnPredict - University of California at San Francisco (UCSF)
      • APSSP - Advanced Protein Secondary Structure Prediction Server
    • Tertiary structure analysis tools
• European Bioinformatics Institute
  • Tools for Multiple and pairwise protein stuctural comparison
    • SSM (Structure-Structure alignment of proteins) Formally called DALI
    • Pairwise comparison (DaliLite)
  • 3D Protein Structural Comparison
    • CE (Combinatorial Extension Method)

- Homology Modeling: A tutorial and exercise using Swiss-PDBviewer

Tutorial Assignment 2, exercise 4. Answer questions at end.

Problems

• Search Swiss-Prot/TrEMBL (top of ExPASy page) for the sequence of goose egg lysozyme from the Western graylag goose. This will bring up the UniProt page for this protein sequence.

1. What is the Primary accession number for this protein sequence?
2. Save the FASTA format of the sequence to your desktop.
3. Use the primary sequence tools to determine the pI, absorptivity at 280 nm, and molar mass for this protein.
4. Suppose you were purifying this protein by HPLC and monitoring the fractions eluted by absorption at 280nm. How many mg of this protein would be found in a 5 mL fraction with an absorbance of 0.035 at 280 nm?
5. Go back to the UniProt page for your goose egg lysozyme. Do a quick BlastP search (top right). Scroll down the page. What information is found from a BlastP search? Scroll down until you find the alignment of Western graylag goose with Ostrich lysozyme. Note the Primary accession number for Ostrich lysozyme then click on the word align? Note the symbols * . : used below the aligment. Based on your knowledge of the amino acids what do the symbols symbolize in the match?
6. Go back to the UniProt page for your goose egg lysozyme. Scroll down to the Features section. Select HELIX 49-59 by clicking on the numbers. Note the sequence of this helix. Enter the sequence in the HelixWheel. Draw the result of the wheel. Is the helix likely to be completely buried, partially solvent exposed, or completely solvent exposed?
7. Search the protein data bank for goose lysozyme. Note the pDB file name (remember Hen egg lysozyme is 1HEW). Go to the CE page and click on TWO CHAINS. Enter the pdb names for hen and goose lysozyme in the appropriate blanks. Click on Calculate Alignment button. Click the -Press to start protein compare- button. What is the RMSD (Root mean square deviation) of the backbones for these two structures?

See questions at end of Assignment 2, exercise 4 of the tutorial.

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

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