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Please use this identifier to cite or link to this item: http://dspace.library.iitb.ac.in/jspui/handle/10054/7159

Title: beta-Hairpins with native-like and non-native hydrogen bonding patterns could form during the refolding of staphylococcal nuclease
Authors: PATEL, S
SISTA, P
BALAJI, PV
SASIDHAR, YU
Keywords: molecular-dynamics simulations
polyproline ii helix
short linear peptide
particle mesh ewald
protein-g
folding simulations
aqueous-solution
atom depth
exchange
water
Issue Date: 2006
Publisher: ELSEVIER SCIENCE INC
Citation: JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 25(1), 103-115
Abstract: Refolding of staphylococcal nuclease has been studied recently by hydrogen-deuterium exchange and NMR spectroscopy. These studies infer that beta-hairpin formed by strand 2 and strand 3 connected by reverse turn forms early during the refolding of nuclease. Typically, hydrogen-deuterium exchange NMR techniques are usually carried out on a time scale of milliseconds whereas beta-hairpins are known to fold on a much shorter time scale. It follows that in the experiments, the hydrogen-deuterium exchange protection patterns could be arising from a significant population of fully formed hairpins. In order to demonstrate it is the fully formed hairpins which gives rise to the hydrogen-deuterium exchange protection patterns, we have considered molecular dynamics simulation of the peptide (21)DTVKLMYKGQPMTFR(35) from staphylococcal nuclease corresponding to the beta-hairpin region, using GROMOS96 force field under NVT conditions. Starting from unfolded conformational states, the peptide folds into hairpin conformations with native-like and non-native hydrogen bonding patterns. Subsequent to folding, equilibrium conditions prevail. The computed protection factors and atom depth values, at equilibrium, of the various amide protons agree qualitatively with experimental observations. A collection of molecules following the trajectories observed in the simulations can account for experimental observations. These simulations provide a molecular picture of the formed hairpins and their conformational features during the refolding experiments on nuclease, monitored by hydrogen-deuterium exchange. (c) 2005
URI: http://dx.doi.org/10.1016/j.jmgm.2005.11.007
http://dspace.library.iitb.ac.in/xmlui/handle/10054/7159
http://hdl.handle.net/10054/7159
ISSN: 1093-3263
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