Protein Modeling on the Internet A group of patients with Crohn disease (an infl

Question

Protein Modeling on the Internet A group of patients with Crohn disease (an inflammatory bowel disease) underwent biopsies of their intestinal mucosa in an attempt to identify the causative agent. Researchers identified a protein that was present at higher levels in patients with Crohn disease than in patients with an unrelated inflammatory bowel disease or in unaffected controls. The protein was isolated, and the following partial amino acid sequence was obtained (reads left to right):

EAELCPDRCI HSFQNLGIQC VKKRDLEQAI

SQRIQTNNNP FQVPIEEQRG DYDLNAVRLC

FQVTVRDPSG RPLRLPPVLP HPIFDNRAPN

TAELKICRVN RNSGSCLGGD EIFLLCDKVQ

KEDIEVYFTG PGWEARGSFS QADVHRQVAI

VFRTPPYADP SLQAPVRVSM QLRRPSDREL

SEPMEFQYLP DTDDRHRIEE KRKRTYETFK

SIMKKSPFSG PTDPRPPPRR IAVPSRSSAS

VPKPAPQPYP

(a) You can identify this protein using a protein database on the Internet. Some good places to start include Protein Information Resource (PIR; http://pir.georgetown.edu), Structural Classification of Proteins (SCOP; http://scop.mrc-lmb.cam.ac.uk/scop), and Prosite (http://prosite.expasy.org). At your selected database site, follow links to the sequence comparison engine. Enter about 30 residues from the protein sequence in the appropriate search field and submit it for analysis. What does this analysis tell you about the identity of the protein?

(b) Try using different portions of the amino acid sequence. Do you always get the same result?

(c) A variety of websites provide information about the three-dimensional structure of proteins. Find information about the protein’s secondary, tertiary, and quaternary structure using database sites such as the Protein Data Bank (PDB;www.pdb.org) or SCOP.

(d) In the course of your Web searches, what did you learn about the cellular function of the protein?

Explanation / Answer

First sequence tried out:

SQRIQTNNNPFQVPIEEQRGDYDLNAVRLCFQVTVRDPSGRPLRLPPVLPHPIFDNRAPN

on (http://prosite.expasy.org) showed result: REL-2(it is an active site)- (as per inetrnet search) It is A Gene encoding an unknown function protein which contains DUF630 and DUF632 domains controls leaf rolling in Rice.

Tested other sequences but with no hits as the result.

Unable to get data from www.pdb.org -for the secondary, tertiary and quartenary structures.

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