Literature DB >> 11904417

How the folding rate constant of simple, single-domain proteins depends on the number of native contacts.

Dmitrii E Makarov1, Craig A Keller, Kevin W Plaxco, Horia Metiu.   

Abstract

Experiments have shown that the folding rate constants of two dozen structurally unrelated, small, single-domain proteins can be expressed in terms of one quantity (the contact order) that depends exclusively on the topology of the folded state. Such dependence is unique in chemical kinetics. Here we investigate its physical origin and derive the approximate formula ln(k) = ln(N) + a + bN, were N is the number of contacts in the folded state, and a and b are constants whose physical meaning is understood. This formula fits well the experimentally determined folding rate constants of the 24 proteins, with single values for a and b.

Entities:  

Mesh:

Substances:

Year:  2002        PMID: 11904417      PMCID: PMC122558          DOI: 10.1073/pnas.052713599

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  20 in total

1.  A simple model for calculating the kinetics of protein folding from three-dimensional structures.

Authors:  V Muñoz; W A Eaton
Journal:  Proc Natl Acad Sci U S A       Date:  1999-09-28       Impact factor: 11.205

Review 2.  First principles prediction of protein folding rates.

Authors:  D A Debe; W A Goddard
Journal:  J Mol Biol       Date:  1999-12-03       Impact factor: 5.469

Review 3.  Fast kinetics and mechanisms in protein folding.

Authors:  W A Eaton; V Muñoz; S J Hagen; G S Jas; L J Lapidus; E R Henry; J Hofrichter
Journal:  Annu Rev Biophys Biomol Struct       Date:  2000

4.  Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: application of long-range order to folding rate prediction.

Authors:  M M Gromiha; S Selvaraj
Journal:  J Mol Biol       Date:  2001-06-29       Impact factor: 5.469

Review 5.  Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics.

Authors:  K W Plaxco; K T Simons; I Ruczinski; D Baker
Journal:  Biochemistry       Date:  2000-09-19       Impact factor: 3.162

Review 6.  Pathways for protein folding: is a new view needed?

Authors:  V S Pande; T Tanaka; D S Rokhsar
Journal:  Curr Opin Struct Biol       Date:  1998-02       Impact factor: 6.809

Review 7.  Theory of protein folding: the energy landscape perspective.

Authors:  J N Onuchic; Z Luthey-Schulten; P G Wolynes
Journal:  Annu Rev Phys Chem       Date:  1997       Impact factor: 12.703

8.  Diffusion-limited contact formation in unfolded cytochrome c: estimating the maximum rate of protein folding.

Authors:  S J Hagen; J Hofrichter; A Szabo; W A Eaton
Journal:  Proc Natl Acad Sci U S A       Date:  1996-10-15       Impact factor: 11.205

9.  Measuring the rate of intramolecular contact formation in polypeptides.

Authors:  L J Lapidus; W A Eaton; J Hofrichter
Journal:  Proc Natl Acad Sci U S A       Date:  2000-06-20       Impact factor: 11.205

10.  Fast events in protein folding initiated by nanosecond laser photolysis.

Authors:  C M Jones; E R Henry; Y Hu; C K Chan; S D Luck; A Bhuyan; H Roder; J Hofrichter; W A Eaton
Journal:  Proc Natl Acad Sci U S A       Date:  1993-12-15       Impact factor: 11.205

View more
  35 in total

1.  Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations.

Authors:  Eric J Sorin; Young Min Rhee; Bradley J Nakatani; Vijay S Pande
Journal:  Biophys J       Date:  2003-08       Impact factor: 4.033

Review 2.  The topomer search model: A simple, quantitative theory of two-state protein folding kinetics.

Authors:  Dmitrii E Makarov; Kevin W Plaxco
Journal:  Protein Sci       Date:  2003-01       Impact factor: 6.725

3.  Critical nucleation size in the folding of small apparently two-state proteins.

Authors:  Yawen Bai; Hongyi Zhou; Yaoqi Zhou
Journal:  Protein Sci       Date:  2004-04-09       Impact factor: 6.725

4.  Universality in the timescales of internal loop formation in unfolded proteins and single-stranded oligonucleotides.

Authors:  Ryan R Cheng; Takanori Uzawa; Kevin W Plaxco; Dmitrii E Makarov
Journal:  Biophys J       Date:  2010-12-15       Impact factor: 4.033

5.  Characterization of the folding landscape of monomeric lactose repressor: quantitative comparison of theory and experiment.

Authors:  Payel Das; Corey J Wilson; Giovanni Fossati; Pernilla Wittung-Stafshede; Kathleen S Matthews; Cecilia Clementi
Journal:  Proc Natl Acad Sci U S A       Date:  2005-10-03       Impact factor: 11.205

6.  A critical assessment of the topomer search model of protein folding using a continuum explicit-chain model with extensive conformational sampling.

Authors:  Stefan Wallin; Hue Sun Chan
Journal:  Protein Sci       Date:  2005-06       Impact factor: 6.725

Review 7.  Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet.

Authors:  Eugene Shakhnovich
Journal:  Chem Rev       Date:  2006-05       Impact factor: 60.622

8.  Folding transition-state and denatured-state ensembles of FSD-1 from folding and unfolding simulations.

Authors:  Hongxing Lei; Shubhra Ghosh Dastidar; Yong Duan
Journal:  J Phys Chem B       Date:  2006-11-02       Impact factor: 2.991

Review 9.  Protein folding in confined and crowded environments.

Authors:  Huan-Xiang Zhou
Journal:  Arch Biochem Biophys       Date:  2007-08-01       Impact factor: 4.013

10.  How long does it take to equilibrate the unfolded state of a protein?

Authors:  Ronald M Levy; Wei Dai; Nan-Jie Deng; Dmitrii E Makarov
Journal:  Protein Sci       Date:  2013-09-17       Impact factor: 6.725

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.