Computing in Molecular Biology
Protein Analysis
Exercises
1. Poliovirus RNA dependent RNA polymerase contains a conserved structural subdomain commonly found in many DNA and RNA binding proteins. Search the structure database in Entrez for this RNA dependent RNA polymerase.
a. What is its PDB accession?
b. How many domains does the structure contain? Which domain contains the conserved structural subdomain?
c. Display the neighbors in all of MMDB for this domain and sort by number of aligned residues. Which neighbor appears on top of the list? View the VAST alignment for this pair using Cn3D. Observe the alignment in both the sequence and structure windows.
d. Now do a single iteration of a PSI-BLAST search on the protein sequence for RNA dependent RNA polymerase. Does the top scoring neighbor from c appear as a PSI-BLAST hit? If yes, are the PSI-BLAST alignment and the VAST alignment similar or different? If no, explain why the two protein structures from part c are not PSI-BLAST neighbors of each other.
2. Amytrophic lateral sclerosis, commonly known as Lou Gehrig’s disease, is a neurodegerartive disorder characterized by the destruction of motor neurons in the central nervous system. Use the Structure database in Entrez to establish the link between protein structure and Lou Gehrig’s disease.
a. List the PDB accession of the structure associated with the disease?
b. Where is the mutation in the protein sequence?
c. Are the wild type and mutant structures VAST neighbors of each other? To answer this question, you must look at all the display options in VAST to answer this question.
d. Assuming they are neighbors, examine the VAST alignment between the wild type and mutant forms of the protein in Cn3D. Is the structure between the wild type and mutant forms very different? Is there anyway of answering this question without examining the alignments?
e. Can you explain why the mutation produces the result? Hint: think about side chain conformation and folding of a protein.