study of protein

The following is a translation of: http://www-esbs.u-strasbg.fr/notes-de-cours/2eme-annee/bioinfo/gaston.html

Study of a human protein

Your friend Gaston, a novice in molecular biology, stops by after an unsuccessful cloning experiment. Can you help him, based on your knowledge in tools in bioinformatics, to understand what's going on.

mystery.dna>

CAGGCTGCGC AACTGTTGGG AAGGGCGATC GGTGCGGGCC TCTTCGCTATTACGCCAGCT GGCGAAAGGG GGATGTGCTG CAAGGCGATT AAGTTGGGTAACGCCAGGGT TTTCCCAGTC ACGACGTTGT AAAACGACGG CCAGTGAATTCGAGCTCGGT ACCCGGGGAT CCGCTGACCA ACTGACTGAA GAGCAGATTGCAGAATTCAA AGAAGCTTTT TCATTATTTG ACAAAGATGG TGATGGCACTATAACAACAA AGGAACTTGG GACTGTAATG AGATCTCTTG GGCAGAATCCCACAGAAGCA GAGTTACAGG ACATGATTAA TGAAGTAGAT GCTGATGGTAATGGCACAAT TGACTTTCCT GAATTTCTGA CAATGATGGC AAGAAAATGAAAGACACAGA CAGTGAAGAA GAAATTAGAG AAGCATTCCG TGTGTTTGACAAGGATGGCA ATGGCTATAT TAGTGCTGCA GAACTTCGCC ATGTGATGACAAACCTTGGA GAGAAGTTAA CAGATGAAGA AGTTGATGAA AATGATCAGGGAAGCAGATA TTGATGGTGA TGGTCAAGTA AACTATGAAG AGTTTGTACAAATGATGACA GCAAAGTGAA GGGATCCTCT AGAGTCGACC TGCAGGCATGCAAGCTTGGC GTAATCATGG TCATAGCTGT TTCCTGTGTG AAATTGTTAT CCGCTCACAA TTCCACACAA CATACGAGCC GGAAGCATAA AGTGTAAAGC CTGGG

1. What can you say, analyzing the above sequence?

• What is the name of the protein studied by Gaston?

• Can you give the name and the type of the vector used by Gaston ?

• What is the selection method that was chosen for the cloning experiment ?

• What restriction enzyme was used for inserting the gene into the vector?

• The sequence has an error, can you decide which one and suggest a correct one?

• Can you explain the difference between the results given by BLAST and FASTA ?

2. Analysis of the protein.

• With the help of a dotplot show that Gaston's protein is composed of several repetitive domains; decide the number of repeats.

• What is the name and the function of these domains?

• Give the name of the four other human proteins that possess this type of domain.

• Indicate the charge of the protein at pH 7.

• Make an alignment that shows the residues that are important for the fixation of the substrate.

• Is the 3D structure of this domain known? What is the type of secondary structure (alpha, beta, alpha/beta, alpha+beta) ?