Assignment 4
Structural bioinformatics
Function of a protein can be predicted based on its 3D structure as a particular domain may serve a particular function. Therefore, many structures of proteins have been solved by means of X-ray crystallography or NMR. Still, it has not been practicable to obtain structure of every protein through these approaches. Consequenlty, 3D structure of a protein can be modelled based on a protein with similar amino acid sequence in which the 3D structure is available.
1. BLAST the nucleotide sequence with “blastx” program that is available in http://blast.ncbi.nlm.nih.gov/Blast.cgi
This BLAST program will translate the nucleotide query to amino acid sequences in all reading frames and search in protein database.
Paste the nucleotide sequence in FASTA format. Then, choose database as “Non-redundant protein sequences (nr)”.
Then, Click on “BLAST” button on the left. The program may take a few minutes to finish. The result will be shown as following:
2. Identify the unknown nucleotide sequence
Scroll down to the description box. The best matching protein to the query will be on the top of the list based on the lowest E-value.
The unknown nucleotide sequence is corresponded to BRC1 protein after it had been translated into amino acid sequence.
3. 3D structure of BRC1
Click on the accession number of the top-list protein. The information page of this protein will show up. Now we know what kind of protein this nucleotide sequence is. Then, we can look for the structure of this protein by scrolling down the information page and go to “LinkOut” under the “All links for this record” box on the right.
The following page will appear. Click on “MODBASE” to go to the comparative modeling of this protein.
The 3D structure of BRC1 protein is generated based on comparative modeling.
The template is a crystal structure of BRCA1/BARD1 ring heterodimer in which the structure can be assessed through PDB code 1JM7A on RCSB database.
The 3D structure of BRC1 protein allows us to understand its function regarding to its template, BRCA1, that consists of domains in the structure such as the DNA binding domain. Simulation of the structure can be further investigated in silico to observe how it interacts with other compounds, etc.
