Literature DB >> 16302178

Low barrier kinetics: dependence on observables and free energy surface.

Hairong Ma1, Martin Gruebele.   

Abstract

Dynamics on free energy surfaces with high activation barriers are usually treated by few-state kinetics models, yielding characteristic rate coefficients and amplitudes depending on the connectivity of the states. When the barriers are low (< 3 kT), the assumption of instantaneous equilibration of the transition state, and hence, the few-state kinetics treatment, break down. Langevin dynamics is used here to explore the characteristic trends that occur in such cases, as a function of barrier height, number of barriers, dimensionality of the free energy surface, and switching functions that describe how spectroscopic probes vary from reactant to product. The result is a systematic phenomenological description of low barrier kinetics and dynamics. Copyright 2005 Wiley Periodicals, Inc.

Mesh:

Year:  2006        PMID: 16302178     DOI: 10.1002/jcc.20311

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  12 in total

1.  Protein folded states are kinetic hubs.

Authors:  Gregory R Bowman; Vijay S Pande
Journal:  Proc Natl Acad Sci U S A       Date:  2010-06-01       Impact factor: 11.205

Review 2.  Dynamics, energetics, and structure in protein folding.

Authors:  Athi N Naganathan; Urmi Doshi; Adam Fung; Mourad Sadqi; Victor Muñoz
Journal:  Biochemistry       Date:  2006-07-18       Impact factor: 3.162

3.  Site-specific collapse dynamics guide the formation of the cytochrome c' four-helix bundle.

Authors:  Tetsunari Kimura; Jennifer C Lee; Harry B Gray; Jay R Winkler
Journal:  Proc Natl Acad Sci U S A       Date:  2006-12-19       Impact factor: 11.205

4.  Protein folding kinetics: barrier effects in chemical and thermal denaturation experiments.

Authors:  Athi N Naganathan; Urmi Doshi; Victor Muñoz
Journal:  J Am Chem Soc       Date:  2007-04-10       Impact factor: 15.419

5.  An experimental survey of the transition between two-state and downhill protein folding scenarios.

Authors:  Feng Liu; Deguo Du; Amelia A Fuller; Jennifer E Davoren; Peter Wipf; Jeffery W Kelly; Martin Gruebele
Journal:  Proc Natl Acad Sci U S A       Date:  2008-02-11       Impact factor: 11.205

6.  A one-dimensional free energy surface does not account for two-probe folding kinetics of protein alpha(3)D.

Authors:  Feng Liu; Charles Dumont; Yongjin Zhu; William F DeGrado; Feng Gai; Martin Gruebele
Journal:  J Chem Phys       Date:  2009-02-14       Impact factor: 3.488

7.  Slowing down downhill folding: a three-probe study.

Authors:  Seung Joong Kim; Yoshitaka Matsumura; Charles Dumont; Hiroshi Kihara; Martin Gruebele
Journal:  Biophys J       Date:  2009-07-08       Impact factor: 4.033

Review 8.  The protein folding problem.

Authors:  Ken A Dill; S Banu Ozkan; M Scott Shell; Thomas R Weikl
Journal:  Annu Rev Biophys       Date:  2008       Impact factor: 12.981

9.  A molecular interpretation of 2D IR protein folding experiments with Markov state models.

Authors:  Carlos R Baiz; Yu-Shan Lin; Chunte Sam Peng; Kyle A Beauchamp; Vincent A Voelz; Vijay S Pande; Andrei Tokmakoff
Journal:  Biophys J       Date:  2014-03-18       Impact factor: 4.033

10.  Modeling conformational ensembles of slow functional motions in Pin1-WW.

Authors:  Faruck Morcos; Santanu Chatterjee; Christopher L McClendon; Paul R Brenner; Roberto López-Rendón; John Zintsmaster; Maria Ercsey-Ravasz; Christopher R Sweet; Matthew P Jacobson; Jeffrey W Peng; Jesús A Izaguirre
Journal:  PLoS Comput Biol       Date:  2010-12-02       Impact factor: 4.475

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