Notes
Use pdb to analyze a selected protein and look at variance in structure due to non-synonymous SNPs.
Assignment
Due to the lack of SNPs in the previous proteins selected, transketolase and LL-37, I will be exploring the protein p53. This protein plays a critical role in tumor suppression as it is a part of the response mechanism to DNA damage within a cell.
As shown below from dbSNP, there is a large number of variations in this protein.
Using the genome browser from The 1000 Genomes Project, you can see the variation distributions.
From the Protein Data Base (PDB), many pathways and interactions with p53 are annotated.
The protein feature view of this molecule gives even more information.
Below is a 3D representation of the p53 complex bound to DNA.
Mutations to the DNA-binding domain of p53 can lead to persistence of DNA damage and can lead to cellular abnormalities such as cancer. Shown below is a single section of the DNA-binding domain of p53. The red highlighted residue is an arginine that is a common site of mutation. Other mutation sites are highlighted in pink (from http://www.rcsb.org/pdb/101/motm.do?momID=31).
Comments: Very well done! Super thorough.
