Literature DB >> 15994895

Quantifying kinetic paths of protein folding.

Jin Wang1, Kun Zhang, Hongyang Lu, Erkang Wang.   

Abstract

We propose a new approach to activated protein folding dynamics via a diffusive path integral framework. The important issues of kinetic paths in this situation can be directly addressed. This leads to the identification of the kinetic paths of the activated folding process, and provides a direct tool and language for the theoretical and experimental community to understand the problem better. The kinetic paths giving the dominant contributions to the long-time folding activation dynamics can be quantitatively determined. These are shown to be the instanton paths. The contributions of these instanton paths to the kinetics lead to the "bell-like" shape folding rate dependence on temperature, which is in good agreement with folding kinetic experiments and simulations. The connections to other approaches as well as the experiments of the protein folding kinetics are discussed.

Mesh:

Substances:

Year:  2005        PMID: 15994895      PMCID: PMC1366665          DOI: 10.1529/biophysj.104.055186

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  31 in total

1.  Towards a consistent modeling of protein thermodynamic and kinetic cooperativity: how applicable is the transition state picture to folding and unfolding?

Authors:  Hüseyin Kaya; Hue Sun Chan
Journal:  J Mol Biol       Date:  2002-01-25       Impact factor: 5.469

2.  Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding.

Authors:  Jin Wang; Gennady M Verkhivker
Journal:  Phys Rev Lett       Date:  2003-05-06       Impact factor: 9.161

3.  Diffusion dynamics, moments, and distribution of first-passage time on the protein-folding energy landscape, with applications to single molecules.

Authors:  Chi-Lun Lee; Chien-Ting Lin; George Stell; Jin Wang
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2003-04-17

4.  Single-molecule measurement of protein folding kinetics.

Authors:  Everett A Lipman; Benjamin Schuler; Olgica Bakajin; William A Eaton
Journal:  Science       Date:  2003-08-29       Impact factor: 47.728

Review 5.  Intermediates in the folding reactions of small proteins.

Authors:  P S Kim; R L Baldwin
Journal:  Annu Rev Biochem       Date:  1990       Impact factor: 23.643

6.  Contact order, transition state placement and the refolding rates of single domain proteins.

Authors:  K W Plaxco; K T Simons; D Baker
Journal:  J Mol Biol       Date:  1998-04-10       Impact factor: 5.469

7.  Submillisecond protein folding kinetics studied by ultrarapid mixing.

Authors:  C K Chan; Y Hu; S Takahashi; D L Rousseau; W A Eaton; J Hofrichter
Journal:  Proc Natl Acad Sci U S A       Date:  1997-03-04       Impact factor: 11.205

8.  Protein folding intermediates: native-state hydrogen exchange.

Authors:  Y Bai; T R Sosnick; L Mayne; S W Englander
Journal:  Science       Date:  1995-07-14       Impact factor: 47.728

9.  Ultrafast thermally induced unfolding of RNase A.

Authors:  C M Phillips; Y Mizutani; R M Hochstrasser
Journal:  Proc Natl Acad Sci U S A       Date:  1995-08-01       Impact factor: 11.205

10.  Global analysis of the effects of temperature and denaturant on the folding and unfolding kinetics of the N-terminal domain of the protein L9.

Authors:  B Kuhlman; D L Luisi; P A Evans; D P Raleigh
Journal:  J Mol Biol       Date:  1998-12-18       Impact factor: 5.469

View more
  9 in total

1.  Kinetic definition of protein folding transition state ensembles and reaction coordinates.

Authors:  Christopher D Snow; Young Min Rhee; Vijay S Pande
Journal:  Biophys J       Date:  2006-04-14       Impact factor: 4.033

2.  Exact low-force kinetics from high-force single-molecule unfolding events.

Authors:  Jeremiah Nummela; Ioan Andricioaei
Journal:  Biophys J       Date:  2007-08-17       Impact factor: 4.033

3.  Minimal folding pathways for coarse-grained biopolymer fragments.

Authors:  Ali R Mohazab; Steven S Plotkin
Journal:  Biophys J       Date:  2008-09-26       Impact factor: 4.033

4.  Quantifying the landscape and kinetic paths for epithelial-mesenchymal transition from a core circuit.

Authors:  Chunhe Li; Tian Hong; Qing Nie
Journal:  Phys Chem Chem Phys       Date:  2016-06-21       Impact factor: 3.676

Review 5.  Perspectives on the landscape and flux theory for describing emergent behaviors of the biological systems.

Authors:  Jin Wang
Journal:  J Biol Phys       Date:  2021-11-25       Impact factor: 1.365

6.  Temperature-dependent folding pathways of Pin1 WW domain: an all-atom molecular dynamics simulation of a Gō model.

Authors:  Zhonglin Luo; Jiandong Ding; Yaoqi Zhou
Journal:  Biophys J       Date:  2007-05-18       Impact factor: 4.033

7.  The dominant folding route minimizes backbone distortion in SH3.

Authors:  Heiko Lammert; Jeffrey K Noel; José N Onuchic
Journal:  PLoS Comput Biol       Date:  2012-11-15       Impact factor: 4.475

8.  Multi-scaled explorations of binding-induced folding of intrinsically disordered protein inhibitor IA3 to its target enzyme.

Authors:  Jin Wang; Yong Wang; Xiakun Chu; Stephen J Hagen; Wei Han; Erkang Wang
Journal:  PLoS Comput Biol       Date:  2011-04-07       Impact factor: 4.475

9.  MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape.

Authors:  Joel Franklin; Patrice Koehl; Sebastian Doniach; Marc Delarue
Journal:  Nucleic Acids Res       Date:  2007-06-01       Impact factor: 16.971

  9 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.