Literature DB >> 15764665

Determination of barrier heights and prefactors from protein folding rate data.

S S Plotkin1.   

Abstract

We determine both barrier heights and prefactors for protein folding by applying constraints determined from experimental rate measurements to a Kramers theory for folding rate. The theoretical values are required to match the experimental values at two conditions of temperature and denaturant that induce the same stability. Several expressions for the prefactor in the Kramers rate equation are examined: a random energy approximation, a correlated energy approximation, and an approximation using a single Arrhenius activation energy. Barriers and prefactors are generally found to be large as a result of implementing this recipe, i.e., the folding landscape is cooperative and smooth. Interestingly, a prefactor with a single Arrhenius activation energy admits no formal solution.

Mesh:

Substances:

Year:  2005        PMID: 15764665      PMCID: PMC1305610          DOI: 10.1529/biophysj.104.052548

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


  24 in total

Review 1.  Understanding protein folding with energy landscape theory. Part II: Quantitative aspects.

Authors:  Steven S Plotkin; José N Onuchic
Journal:  Q Rev Biophys       Date:  2002-08       Impact factor: 5.318

2.  Folding a protein in a computer: an atomic description of the folding/unfolding of protein A.

Authors:  Angel E García; José N Onuchic
Journal:  Proc Natl Acad Sci U S A       Date:  2003-11-17       Impact factor: 11.205

3.  Complete change of the protein folding transition state upon circular permutation.

Authors:  Magnus Lindberg; Jeanette Tångrot; Mikael Oliveberg
Journal:  Nat Struct Biol       Date:  2002-11

4.  The nature of the free energy barriers to two-state folding.

Authors:  Arya Akmal; Victor Muñoz
Journal:  Proteins       Date:  2004-10-01

5.  Three-body interactions improve the prediction of rate and mechanism in protein folding models.

Authors:  M R Ejtehadi; S P Avall; S S Plotkin
Journal:  Proc Natl Acad Sci U S A       Date:  2004-10-06       Impact factor: 11.205

6.  Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition.

Authors:  S E Jackson; A R Fersht
Journal:  Biochemistry       Date:  1991-10-29       Impact factor: 3.162

7.  Cytochrome c folding triggered by electron transfer.

Authors:  G A Mines; T Pascher; S C Lee; J R Winkler; H B Gray
Journal:  Chem Biol       Date:  1996-06

8.  Funnels, pathways, and the energy landscape of protein folding: a synthesis.

Authors:  J D Bryngelson; J N Onuchic; N D Socci; P G Wolynes
Journal:  Proteins       Date:  1995-03

9.  Computation of the sterically allowed conformations of peptides.

Authors:  S J Leach; G Némethy; H A Scheraga
Journal:  Biopolymers       Date:  1966 Apr-May       Impact factor: 2.505

10.  The magnitude of the backbone conformational entropy change in protein folding.

Authors:  J A D'Aquino; J Gómez; V J Hilser; K H Lee; L M Amzel; E Freire
Journal:  Proteins       Date:  1996-06
View more
  5 in total

1.  Resolving the complex role of enzyme conformational dynamics in catalytic function.

Authors:  Urmi Doshi; Lauren C McGowan; Safieh Tork Ladani; Donald Hamelberg
Journal:  Proc Natl Acad Sci U S A       Date:  2012-03-26       Impact factor: 11.205

2.  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

3.  Excluded volume, local structural cooperativity, and the polymer physics of protein folding rates.

Authors:  Xianghong Qi; John J Portman
Journal:  Proc Natl Acad Sci U S A       Date:  2007-06-14       Impact factor: 11.205

4.  Comparing the energy landscapes for native folding and aggregation of PrP.

Authors:  Derek R Dee; Michael T Woodside
Journal:  Prion       Date:  2016-05-03       Impact factor: 3.931

5.  Mutations as trapdoors to two competing native conformations of the Rop-dimer.

Authors:  Alexander Schug; Paul C Whitford; Yaakov Levy; José N Onuchic
Journal:  Proc Natl Acad Sci U S A       Date:  2007-10-29       Impact factor: 11.205

  5 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.