Discrete step model of helix-coil kinetics: Distribution of fluctuation times
A method is outlined for the computer simulation of the cooperative kinetics required to construct the distribution function for time intervals between fluctuations in conformational states in macromolecules. Using the helix-coil transition in polyamino acids as an example, we develop a Monte Carlo...
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1996
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Online Access: | http://dx.doi.org/10.1063/1.471965 https://pubs.aip.org/aip/jcp/article-pdf/105/3/1242/10781016/1242_1_online.pdf |
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craippubl:10.1063/1.471965 2024-04-07T07:56:03+00:00 Discrete step model of helix-coil kinetics: Distribution of fluctuation times Poland, Douglas 1996 http://dx.doi.org/10.1063/1.471965 https://pubs.aip.org/aip/jcp/article-pdf/105/3/1242/10781016/1242_1_online.pdf en eng AIP Publishing The Journal of Chemical Physics volume 105, issue 3, page 1242-1269 ISSN 0021-9606 1089-7690 Physical and Theoretical Chemistry General Physics and Astronomy journal-article 1996 craippubl https://doi.org/10.1063/1.471965 2024-03-08T00:06:06Z A method is outlined for the computer simulation of the cooperative kinetics required to construct the distribution function for time intervals between fluctuations in conformational states in macromolecules. Using the helix-coil transition in polyamino acids as an example, we develop a Monte Carlo cellular automata approximation of the kinetics of this system in discrete time. This approximation is tested against a number of exact solutions for homopolymers and is then used to calculate moments of the distribution function for the time intervals between switches in conformational state at a given site (e.g., given a switch from coil to helix at zero time, how long will it take before the state switches back). The maximum-entropy method is used to construct the very broad distribution function from the moments. In heteropolymers the diffusion of helix-coil boundaries is reduced, helix being more localized on strong helix-forming residues. We investigate the effect of a specific sequence of amino acid residues on conformational fluctuations by using the known σ and s values for the naturally occurring amino acids to simulate the kinetics of helix formation (limiting the range of cooperativity to the α-helix) in sperm whale myoglobin, giving the time evolution to the equilibrium probability profile in this system. Article in Journal/Newspaper Sperm whale AIP Publishing The Journal of Chemical Physics 105 3 1242 1269 |
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AIP Publishing |
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craippubl |
language |
English |
topic |
Physical and Theoretical Chemistry General Physics and Astronomy |
spellingShingle |
Physical and Theoretical Chemistry General Physics and Astronomy Poland, Douglas Discrete step model of helix-coil kinetics: Distribution of fluctuation times |
topic_facet |
Physical and Theoretical Chemistry General Physics and Astronomy |
description |
A method is outlined for the computer simulation of the cooperative kinetics required to construct the distribution function for time intervals between fluctuations in conformational states in macromolecules. Using the helix-coil transition in polyamino acids as an example, we develop a Monte Carlo cellular automata approximation of the kinetics of this system in discrete time. This approximation is tested against a number of exact solutions for homopolymers and is then used to calculate moments of the distribution function for the time intervals between switches in conformational state at a given site (e.g., given a switch from coil to helix at zero time, how long will it take before the state switches back). The maximum-entropy method is used to construct the very broad distribution function from the moments. In heteropolymers the diffusion of helix-coil boundaries is reduced, helix being more localized on strong helix-forming residues. We investigate the effect of a specific sequence of amino acid residues on conformational fluctuations by using the known σ and s values for the naturally occurring amino acids to simulate the kinetics of helix formation (limiting the range of cooperativity to the α-helix) in sperm whale myoglobin, giving the time evolution to the equilibrium probability profile in this system. |
format |
Article in Journal/Newspaper |
author |
Poland, Douglas |
author_facet |
Poland, Douglas |
author_sort |
Poland, Douglas |
title |
Discrete step model of helix-coil kinetics: Distribution of fluctuation times |
title_short |
Discrete step model of helix-coil kinetics: Distribution of fluctuation times |
title_full |
Discrete step model of helix-coil kinetics: Distribution of fluctuation times |
title_fullStr |
Discrete step model of helix-coil kinetics: Distribution of fluctuation times |
title_full_unstemmed |
Discrete step model of helix-coil kinetics: Distribution of fluctuation times |
title_sort |
discrete step model of helix-coil kinetics: distribution of fluctuation times |
publisher |
AIP Publishing |
publishDate |
1996 |
url |
http://dx.doi.org/10.1063/1.471965 https://pubs.aip.org/aip/jcp/article-pdf/105/3/1242/10781016/1242_1_online.pdf |
genre |
Sperm whale |
genre_facet |
Sperm whale |
op_source |
The Journal of Chemical Physics volume 105, issue 3, page 1242-1269 ISSN 0021-9606 1089-7690 |
op_doi |
https://doi.org/10.1063/1.471965 |
container_title |
The Journal of Chemical Physics |
container_volume |
105 |
container_issue |
3 |
container_start_page |
1242 |
op_container_end_page |
1269 |
_version_ |
1795673726888443904 |