Analysis of individual sequences

Exercises

1. Hydrophobicity scales
   • What are applications of a hydrophobicity scale?
   • Obtain the SWISSPROT-entry of human Rhodopsin and discuss the above hydrophobicity plot in the Introduction in the context of the annotated domains.
   
   
   
   theory
   
   
2. Amphipatic helices, helical wheels and Leucine Zipper
   • What are amphipatic helices? How do you recognise them?
   • Access the Swissprot-entry of X BOX BINDING PROTEIN-1 (ac P17861 or XBP1_HUMAN).
   • Follow the link to prosite and explore the function of the protein and the familiy it belongs to.
   • There is a Leucine Zipper domain annotated in the Swissprot-entry (where?). Follow the link to PDB and download the correspinding pdb-file containing 3D-structure information (PDB-id 1FOS).
   • Visualize the Leucine Zipper domain by means of rasmol (see also section on Protein Structure).
   • Obtain a helical wheel presentation by means of this helical wheel applet of the Leucine Zipper domain you visualized.
     Think about the function of the Leucine Zipper in the context of amphipaticity and hydrophobicity of the residues.
   
   
   
   theory