vsns.gif Assignment 3 vsns.gif

VSNS-PPS Main Index.... last updated 15th.Feb'95

Finding out about Proteins

It is EXTREMELY important to be able to understand the molecular composition of the protein(s) that you are dealing with. Although genomes code for proteins, the composition of the final protein(s) cannot be uniquely determined from the genomic data. In this exercise , which should take about 2 weeks, you should investigate the composition of your given protein (the 4-character Brookhaven code) as closely as possible.

DO NOT WORRY ABOUT ANALYSING OR DESCRIBING THE 3-D STRUCTURE OF YOUR PROTEIN AT THIS STAGE. COMPOSITION IS VERY IMPORTANT.

SOME OF THE EXAMPLES WE HAVE GIVEN TO COURSE MEMBERS WILL BE VERY STRAIGHTFORWARD, AND OTHERS WILL BE QUITE COMPLEX. GROUPS MAY LIKE TO COMPARE THEIR INDIVIDUAL ANSWERS AND COLLATE THEM.

(******DO NOT MAIL THE COURSE ADMIN OR ANY LISTS WITH ANSWERS**********)

Start by inspecting/retrieving the relevant file(s) from Brookhaven/PDB

  1. Do there appear to be other codes in PDB which are closely related? (Often there are entries of the form 1ABC, 3ABC, etc.)

  2. Are there other proteins in PDB of the same name/functionality, but from different species? Or mutants? Are there any with the same protein composition by different non-protein constituents?

  3. Does your protein contain:

  4. Does your protein have any non-protein molecule bound to it? How?

  5. Does your protein contain any disulphide bridges? Or any free -SH groups?

  6. Is there any ambiguity in your protein's composition in the PDB file?

  7. How many molecules are there in your protein? Are there more reported in PDB?

  8. Does it have a SEQRES record? Does this correspond to the ATOM cards?

  9. Is the crystal structure composed of discrete molecules? Or is there evidence of oligomerisation? What symmetry does any oligomer have?

  10. Is there any evidence **in the crystal** that the protein is not homogeneous?

  11. Is there a picture of your protein in PDB?

    (******DO NOT MAIL THE COURSE ADMIN OR ANY LISTS WITH ANSWERS**********)

    Crystallography

  12. What is the resolution of your crystal structure? The R-factor? Were all atoms located? (Roughly) What are your temperature factors? Why do they matter? What is the spacegroup? (DON'T WORRY about understanding it).

    Find the corresponding entry in SWISSPROT (species is important!)

  13. Does the SWISSPROT sequence correspond to the PDB sequence(s)? If not, why?

  14. Does the protein have an entry in PROSITE?

  15. Is there an entry in SWISS3DIMAGE?

  16. What are the pI and MWt of your protein? (HINT: Use ExPAsY).

  17. Has your protein undergone any processing?

    (******DO NOT MAIL THE COURSE ADMIN OR ANY LISTS WITH ANSWERS**********)

    Find the corresponding entry in a nucleic acid database

  18. Is your entry genomic or cDNA? Does it matter? Does it relate directly to the SWISSPROT sequence?

    From all databases

  19. What is known about the function of your protein? Are the databases consistent? (Do not worry about relating function to structure at this stage).

    (******DO NOT MAIL THE COURSE ADMIN OR ANY LISTS WITH ANSWERS**********)

    VSNS-PPS Main Index
    PM-R
    Feb05 1995