Peptide kinetics from picoseconds to microseconds using boxed molecular dynamics: Power law rate coefficients in cyclisation reactions

Dmitrii V. Shalashilin, Godfrey S. Beddard, Emanuele Paci, David R. Glowacki

Research output: Contribution to journalArticle (Academic Journal)peer-review

19 Citations (Scopus)

Abstract

Molecular dynamics (MD) methods are increasingly widespread, but simulation of rare events in complex molecular systems remains a challenge. We recently introduced the boxed molecular dynamics (BXD) method, which accelerates rare events, and simultaneously provides both kinetic and thermodynamic information. We illustrate how the BXD method may be used to obtain high-resolution kinetic data from explicit MD simulations, spanning picoseconds to microseconds. The method is applied to investigate the loop formation dynamics and kinetics of cyclisation for a range of polypeptides, and recovers a power law dependence of the instantaneous rate coefficient over six orders of magnitude in time, in good agreement with experimental observations. Analysis of our BXD results shows that this power law behaviour arises when there is a broad and nearly uniform spectrum of reaction rate coefficients. For the systems investigated in this work, where the free energy surfaces have relatively small barriers, the kinetics is very sensitive to the initial conditions: strongly non-equilibrium conditions give rise to power law kinetics, while equilibrium initial conditions result in a rate coefficient with only a weak dependence on time. These results suggest that BXD may offer us a powerful and general algorithm for describing kinetics and thermodynamics in chemical and biochemical systems. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4759088]

Original languageEnglish
Article number165102
Pages (from-to)-
Number of pages9
JournalJournal of Chemical Physics
Volume137
Issue number16
DOIs
Publication statusPublished - 28 Oct 2012

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