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Thermodynamic control and dynamical regimes in protein folding
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Faisca, P. F. N. and Ball, Robin (2002) Thermodynamic control and dynamical regimes in protein folding. Journal of Chemical Physics, Vol.116 (No.16). pp. 7231-7237. doi:10.1063/1.1466833 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 | ||||
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Subjects: | Q Science > QC Physics | ||||
Divisions: | Faculty of Science, Engineering and Medicine > 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 | ||||
Official Date: | 22 April 2002 | ||||
Dates: |
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Volume: | Vol.116 | ||||
Number: | No.16 | ||||
Number of Pages: | 7 | ||||
Page Range: | pp. 7231-7237 | ||||
DOI: | 10.1063/1.1466833 | ||||
Status: | Peer Reviewed | ||||
Publication Status: | Published | ||||
Access rights to Published version: | Open Access (Creative Commons) | ||||
Date of first compliant deposit: | 5 December 2015 | ||||
Date of first compliant Open Access: | 5 December 2015 |
Data sourced from Thomson Reuters' Web of Knowledge
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