Dynamics and Thermodynamics of β-Hairpin Assembly: Insights from Various Simulation Techniques

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Title: Dynamics and Thermodynamics of β-Hairpin Assembly: Insights from Various Simulation Techniques
Author: Kolinski, Andrzej ; Ilkowski, Bartosz ; Skolnick, Jeffrey
Abstract: Small peptides that might have some features of globular proteins can provide important insights into the protein folding problem. Two simulation methods, Monte Carlo Dynamics (MCD), based on the Metropolis sampling scheme, and Entropy Sampling Monte Carlo (ESMC), were applied in a study of a high-resolution lattice model of the C-terminal fragment of the B1 domain of protein G. The results provide a detailed description of folding dynamics and thermodynamics and agree with recent experimental findings (Munoz et al., 1997. Nature. 390:196–197). In particular, it was found that the folding is cooperative and has features of an all-or-none transition. Hairpin assembly is usually initiated by turn formation; however, hydrophobic collapse, followed by the system rearrangement, was also observed. The denatured state exhibits a substantial amount of fluctuating helical conformations, despite the strong b-type secondary structure propensities encoded in the sequence.
Description: © 1999 by the Biophysical Society
Type: Article
URI: http://hdl.handle.net/1853/41943
ISSN: 0006-3495
Citation: Kolinski, A, Ilkowski B, Skolnick J. 1999. Dynamics and thermodynamics of beta-hairpin assembly: insights from various simulation techniques. Biophysical journal. 77(6):2942-52.
Date: 1999-12
Contributor: Uniwersytet Warszawski. Wydział Chemii
Scripps Research Institute. Dept. of Molecular Biology
Publisher: Georgia Institute of Technology
Biophysical Society
Subject: Globular proteins
Peptides
Simulation
Monte Carlo method
Protein folding

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