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Title: A shorter peptide model from staphylococcal nuclease for the folding-unfolding equilibrium of a beta-hairpin shows that unfolded state has significant contribution from compact conformational states
Authors: PATEL, S
Keywords: Molecular-Dynamics Simulations
Headpiece Helical Subdomain
Free-Energy Landscape
Particle Mesh Ewald
Denatured State
Explicit Water
Nondenaturing Conditions
Secondary Structure
Issue Date: 2008
Citation: JOURNAL OF STRUCTURAL BIOLOGY, 164(1), 60-74
Abstract: It is important to understand the conformational features of the unfolded state in equilibrium with folded state under physiological. In this paper, we consider a short peptide model LMYKGQPM from staphylococcal nuclease to model the conformational equilibrium between a hairpin conformation and its unfolded state using molecular dynamics simulation under NVT conditions at 300 K Using GROMOS96 force held. The free energy landscape has overall funnel-like shape with hairpin conformations sampling the minima. The "unfolded" state has a higher free energy of similar to 12 kJ/mol with respect to native hairpin mininium and occupies a plateau region. We find that the unfolded state has significant contributions from compact conformations. Many of these conformations have hairpin-like topology. Further, these compact conformational forms are stabilized by hydrophobic interactions. Conversion between native and non-native hairpins occurs via unfolded states. Frequent conversions between folded and Unfolded hairpins are observed with single exponential kinetics. We compare our results With the emerging picture of unfolded state from both experimental and theoretical studies. (c) 2008
ISSN: 1047-8477
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