| Go to the Protein Data Bank and obtain the record for the p53
crystal structure (1TSR). There are three identical polypeptides in the
record. They are named A, B and C. Choose one of the polypeptides for
this exercise. In the remarks section of the record you will find an assignment of secondary structure to several ranges of amino acids.
These will either be named "helix" or "sheet". For amino acids
in the structure that were not assigned to "helix" or "sheet" assume that
they adopt a "coil" structure. Create a line graph that places the amino
acid sequence in one row and the known secondary structure of that amino
acid in the next row. Next, obtain the PSIPRED predicted secondary
structure of p53. Create a third row on the line graph that shows
the predicted structure. If you can, try to obtain other portions of p53
where the structure has been solved from the Protein Data Bank (PDB) and fill
in those p53 sequences in the second row that were not obtained in the 1TSR record.
You will have to search for other PDB records with with p53 sequences. Turn in the hard copy of the line figure and calculate the percent accuracy (Q3)
of the PSIPRED prediction. A hypothetical example is shown below
Sequence:
MEETHAPYRGVCNNM
Actual Structure: CCCCCHHHHHHEEEE
PSIPRED Predict.: CCCCCHHHHHHEEEH
Percent accuracy: 14/15 X 100 |