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Microscopic theory of protein folding rates. I. Fine structure of the free energy profile and folding routes from a variational approach
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previousl...
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We propose a method to calculate time correlation functions using path integral formulation of quantum mechanics. The accuracy of the proposed method is examined by comparing the calculated result wit...

Microscopic theory of protein folding rates. II. Local reaction coordinates and chain dynamics

J. Chem. Phys. 114, 5082 (2001); doi:10.1063/1.1334663

Issue Date: 15 March 2001

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John J. Portman
Department of Physics, University of Illinois, Urbana, Illinois 61801

Shoji Takada
Department of Chemistry, Kobe University, Kobe 657-8501, Japan

Peter G. Wolynes
Department of Chemistry, University of Illinois, Urbana, Illinois 61801
The motions involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the preceding paper. Local reaction coordinates are identified as collective growth modes of the unstable fluctuations about the saddle points in the free energy surface. The description of the chain dynamics incorporates internal friction (independent of the solvent viscosity) arising from the elementary isomerization of the backbone dihedral angles. We find that the folding rate depends linearly on the solvent friction for high viscosity, but saturates at low viscosity because of internal friction. For lambda-repressor, the calculated folding rate prefactor, along with the free energy barrier from the variational theory, gives a folding rate that agrees well with the experimentally determined rate under highly stabilizing conditions, but the theory predicts too large a folding rate at the transition midpoint. This discrepancy obtained using a fairly complete quantitative theory inspires a new set of questions about chain dynamics, specifically detailed motions in individual contact formation. ©2001 American Institute of Physics.
History: Received 31 August 2000; accepted 30 October 2000
Permalink: http://link.aip.org/link/?JCPSA6/114/5082/1
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EDITORIALLY RELATED

  1. Microscopic theory of protein folding rates. I. Fine structure of the free energy profile and folding routes from a variational approach
    John J. Portman et al.
    J. Chem. Phys. 114, 5069 (2001)

KEYWORDS and PACS

Keywords
PACS
  • 87.14.Ee
    Biological and medical physics Biomolecules: types Proteins
  • 87.15.Cc
    Biological and medical physics Biomolecules: structure and physical properties Folding and sequence analysis
  • 87.15.Rn
    Biological and medical physics Biomolecules: structure and physical properties Reactions and kinetics; polymerization
  • 82.30.Qt
    Physical chemistry and chemical physics Specific chemical reactions; reaction mechanisms Isomerization and rearrangement
  • YEAR: 2001

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ISSN:
0021-9606 (print)   1089-7690 (online)
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