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Please use this identifier to cite or link to this item: http://dspace.library.iitb.ac.in/jspui/handle/10054/5100

Title: A small tripeptide AFA undergoes two state cooperative conformational transitions: Implications for conformational biases in unfolded states
Authors: PATEL, S
TAIMNI, R
SASIDHAR, YU
Keywords: molecular-dynamics simulations
particle mesh ewald
polypeptide-chains
aqueous-solution
denatured state
ribonuclease-a
cytochrome-c
drug design
protein
water
Issue Date: 2007
Publisher: BENTHAM SCIENCE PUBL LTD
Citation: PROTEIN AND PEPTIDE LETTERS, 14(6), 581-589
Abstract: It is important to understand the conformational biases that are present in unfolded states to understand protein folding. In this context, it is surprising that even a short tripeptide like AFA samples folded/ordered conformation as demonstrated recently by NMR experiments of the peptide in Aqueous solution at 280 K. In this paper, we present molecular dynamics simulation of the peptide in explicit water using OPLS-AA/L all-atom force field. The results are in overall agreement with NMR results and provide some further insights. The peptide samples turn and extended conformational forms corresponding to minima in free energy landscape. Frequent transitions between the minima are observed due to modest free energy barriers. The turn conformation seems to be stabilized by hydrophobic interactions and possibly by bridging water molecules between backbone donors and acceptors. Thus the peptide does not sample conformations randomly, but samples well defined conformations. The peptide served as a model for folding-unfolding equilibrium in the context of peptide folding. Further, implications for drug design are also discussed.
URI: http://dspace.library.iitb.ac.in/xmlui/handle/10054/5100
http://hdl.handle.net/10054/5100
ISSN: 0929-8665
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