Protein Structure

1. Do a BLAST search with human oncostatin
"AAIGSCSKEYRVLLGQLQKQTDLMQDTSRLLDPYIRIQGLDVPKLREHCRERPGAFPSE
ETLRGLGRRGFLQTLNATLGCVLHRLADLEQRLPKAQDLERSGLNIEDLEKLQMARPNIL
GLRNNIYCMAQLLDNSDTAEPTKAGRGASQPPTPTPASDAFQRKLEGCRFLHGYHRFMHS
VGRVFSKWGESPNRSRRHSPHQALRKGVRRTRPSRKGKRLMTRGQLPR"

A) Does your BLAST search identify OSM orthologs in other species that are present in the protein database? List the names, species of origin, E-values and accession numbers of potentia lorthologs.

B) Does BLAST identify any obvious paralog of the oncostatin M? If you detect a paralog provide the data and reasoning for your conclusion. If you don't detect a paralog describe the basis of your conclusion.

2. Use PSIPRED (quick GenTHREADER) or Phyre2 to identify protein folds within oncostatin M using.

A) Do either of these programs identify a protein with similar folds?

B) Would you consider one of these to be a paralog of oncostatin M? Provide your reasoning

3. Take the most probable paralog of on costatin M and do a protein-protein alignment. (10 points). Discuss the similarity identified in your alignment.

4. Go to the PDB database and look at the Onco statin M record - view the structure. In your own words briefly describe the structure

5. Go to the Conserved domain database and search with the oncostatin M sequence.

A) Is a conserved domain identified? If so, indicated which domain.

B) Look at the names and species origin of the sequences that were used to define the domain (hint-link to one of the PSSMs and click on the accession number of the sequence) (10 points). Are any of these sequences pot ential paralogs of OSM? Describe briefly?

C) Can you identify amino acid residues in the PSSMs that are conserved in all of the sequences that would substantia te the classification of this as a conserved domain? Very briefly describe.

D) Are there conserved cysteines that could contribute to structural conservation?

6. Go to the PDB database and view the structure of any potential paralog id