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Non-Gaussian dynamics from a simulation of a short peptide: Loop closure rates and effective diffusion coefficients

J. Chem. Phys. 118, 2381 (2003); doi:10.1063/1.1532728

Issue Date: 1 February 2003

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John J. Portman
Center for Nonlinear Studies and Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
Intrachain contact formation rates, fundamental to the dynamics of biopolymer self-organization such as protein folding, can be monitored in the laboratory through fluorescence quenching measurements. The common approximations for the intrachain contact rate given by the theory of Szabo, Schulten, and Schulten (SSS) [J. Chem. Phys. 72, 4350 (1980)] and Wilemski–Fixman (WF) [J. Chem. Phys. 60, 878 (1973)] are shown to be complementary variational bounds: The SSS and WF approximations are lower and upper bounds, respectively, on the mean first contact times. As reported in the literature, the SSS approximation requires an effective diffusion coefficient 10 to 100 times smaller than expected to fit experimentally measured quenching rates. An all atom molecular dynamics simulation of an eleven residue peptide sequence in explicit water is analyzed to investigate the source of this surprising parameter value. The simulated diffusion limited contact time is [approximate]6 ns for a reaction radius of 4 Å for solvent viscosity corresponding to that of water at 293 K and 1 atm (eta= 1.0 cP). In analytical work, the polymer is typically modeled by a Gaussian chain of effective monomers. Compared to Gaussian dynamics, the simulated end-to-end distance autocorrelation has a much slower relaxation. The long time behavior of the distance autocorrelation function can be approximated by a Gaussian model in which the monomer diffusion coefficient D0 is reduced to D0/6. This value of the diffusion coefficient brings the mean end-to-end contact time from analytical approximations and simulation into agreement in the sense that the SSS and WF approximations bracket the simulated mean first contact time. ©2003 American Institute of Physics.
History: Received 30 July 2002; accepted 4 November 2002
Permalink: http://link.aip.org/link/?JCPSA6/118/2381/1
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KEYWORDS and PACS

Keywords
PACS
  • 87.14.Ee
    Proteins
  • 87.15.He
    Biomolecular dynamics and conformational changes
  • 87.15.Mi
    Spectra, photodissociation, and photoionization of biomolecules; bioluminescence
  • 33.50.Hv
    Molecular radiationless transitions, quenching
  • YEAR: 2003

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PUBLICATION DATA

ISSN:
0021-9606 (print)   1089-7690 (online)
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REFERENCES (55)
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