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ASSIGNMENT 6

The function of a protein being a direct consequence of its 3-D structure (shape),

the logical link was established.

Sequence >> Structure >> Function

It is now a central concept of molecular biology and bioinformatics. As a consequence, an increasing proportion of the bioinformatics pie is now devoted to the development of tools to navigate between sequences and 3-D structures. (This specialized area is called structural bioinformatics.)

Bioinformatic Assignment 6



ASSIGNMENT 6 The function of a protein being a direct consequence of its 3-D structure (shape), the logical link was established. Sequence >> Structure >> Function It is now a central concept of molecular biology and bioinformatics. As a consequence, an increasing proportion of the bioinformatics pie is now devoted to the development of tools to navigate between sequences and 3-D structures. (This specialized area is called structural bioinformatics.)
In this assignment, I will show some basic to find the structure and function of protein coded by specific DNA sequence. The steps to answer the question as following. Conversion of nucleotide sequences into amino acid sequences Structural and functional search in PDB

1. Conversion of nucleotide sequences into amino acid sequences The nucleotide sequences from the question were translated to protein sequences and blast by "translating BLAST" from NCBI.
We will use blastx (translated query vs. protein database) to find out what protein has similary DNA sequence compared with our sequence.

The program "translating BLAST" will open. Paste the nucleotide sequences into the search box and click "BLAST"



This is a graphical display showing alignments to the query sequence. Results show 23 Blasts Hits.

Select the first sequence that produce the significant alignments.



protien sequence in "FASTA" format

2.Structural and functional search in PDB The Protein Data Bank (PDB) PDB is a repository for 3-D structural data of proteins and nucleic acids. This data, typically obtained by x-ray crystallography or NMR spectroscopy, is submitted by biologists and biochemist from around the world, is released into the public domain, and can be accessed for free. The database is the central repository for biological structural data.
Find "PDB" homepage by using google.
It is found that our sequence coded for BRCA1 (Homo sapiens). Then open PDB webpage. In the search box, type "BRCA1 AND Homo sapiens" then click search.

From the result there are many stuctures of BRCA1 homo sapiens protein. I select the first one "1T2V ; Stuctural basis of phospho-peptide recognition by the BRCT domain of BRCA1,structure with phosphopeptide.

The data show the information of antitumer prtein such as Structure summary and 3D structure.





After clicking "Abstract", we can read the summary of this protein. This protien is the structural consequence of a cancer-causeing BRCA1-BRCT missense mutation.
conclusion the given DNA sequence is coded for a mutated BRCA1 tumor suppressor protein.