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Title:Are peptides good two-state folders?
Authors:Alexander M. Berezhkovskii, Florentina Tofoleanu, and Nicolae-Viorel Buchete, 2011
Abstract: The folding kinetics of proteins is frequently single-exponential, as basins of folded and unfolded conformations are well separated by a high barrier. However, for relatively short peptides, a two-state character of folding is rather the exception than the rule. In this work, we use a Zwanzig-type model of protein conformational dynamics to study the dependence of folding kinetics on the protein chain length, M. The analysis is focused on the gap in the eigenvalue spectrum of the rate matrix that describes the protein's conformational dynamics. When there is a large gap between the two smallest in magnitude nonzero eigenvalues, the corresponding relaxation times have qualitatively different physical interpretations. The longest of these two times characterizes the interbasin equilibration (i.e., folding), whereas the second time characterizes the intrabasin relaxation. We derive approximate analytical solutions for the two eigenvalues that show how they depend on M. From these solutions, we infer that there is a large gap between the two, and thus, the kinetics is essentially single-exponential when M is large enough such that 2M+1 is much larger than M2.
ICHEC Project:Multiscale Study of Molecular Aggregation Processes
Publication:J. Chem. Theory Comput.,7 (2011) 2370–2375
URL: http://pubs.acs.org/doi/abs/10.1021/ct200281d
Keywords: Protein folding, Molecular Dynamics
Status: Published

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