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Thermodynamic control and dynamical regimes in protein folding

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Faisca, P. F. N. and Ball, R. C.. (2002) Thermodynamic control and dynamical regimes in protein folding. Journal of Chemical Physics, Vol.116 (No.16). pp. 7231-7237. ISSN 0021-9606

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Official URL: http://dx.doi.org/10.1063/1.1466833

Abstract

Monte Carlo simulations of a simple lattice model of protein folding show two distinct regimes depending on the chain length. The first regime well describes the folding of small protein sequences and its kinetic counterpart appears to be single exponential in nature, while the second regime is typical of sequences longer than 80 amino acids and the folding performance achievable is sensitive to target conformation. The extent to which stability, as measured by the energy of a sequence in the target, is an essential requirement and affects the folding dynamics of protein molecules in the first regime is investigated. The folding dynamics of sequences whose design stage was restricted to a certain fraction of randomly selected amino acids shows that while some degree of stability is a necessary and sufficient condition for successful folding, designing sequences that provide the lowest energy in the target seems to be a superfluous constraint. By studying the dynamics of under annealed but otherwise freely designed sequences we explore the relation between stability and kinetic accessibility. We find that there is no one-to-one correspondence between having low energy and folding quickly to the target, as only a small fraction of the most stable sequences were also found to fold relatively quickly.

Item Type:	Journal Article
Subjects:	Q Science > QC Physics
Divisions:	Faculty of Science > Physics
Library of Congress Subject Headings (LCSH):	Protein folding , Thermodynamics, Biophysics, Monte Carlo method
Journal or Publication Title:	Journal of Chemical Physics
Publisher:	American Institute of Physics
ISSN:	0021-9606
Date:	22 April 2002
Volume:	Vol.116
Number:	No.16
Number of Pages:	7
Page Range:	pp. 7231-7237
Identification Number:	10.1063/1.1466833
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Open Access
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URI:	http://wrap.warwick.ac.uk/id/eprint/11065