21-residue peptide's dynamics at and between elementary structural transitions

Dmitry Nerukh; Makoto Taiji

doi:10.1016/j.molliq.2008.10.015

21-residue peptide's dynamics at and between elementary structural transitions

Research output: Contribution to journal › Article › peer-review

Abstract

Elementary conformational changes of the backbone of a 21-residue peptide A5(A3RA)3A are studied using molecular dynamics simulations in explicit water. The processes of the conformational transitions and the regimes of stationary fluctuations between them are investigated using minimal perturbations of the system. The perturbations consist of a few degrees rotation of the velocity of one of the systems' atoms and keep the system on the same energy surface. It is found that (i) the system dynamics is insignificantly changed by the perturbations in the regimes between the transitions; (ii) it is very sensitive to the perturbations just before the transitions that prevents the peptide from making the transitions; and (iii) the perturbation of any atom of the system, including distant water molecules is equally effective in preventing the transition. The latter implies strongly collective dynamics of the peptide and water during the transitions.

Original language	English
Pages (from-to)	124-127
Number of pages	4
Journal	Journal of Molecular Liquids
Volume	147
Issue number	1-2
Early online date	19 Nov 2008
DOIs	https://doi.org/10.1016/j.molliq.2008.10.015
Publication status	Published - 20 Jul 2009

Bibliographical note

NOTICE: this is the author’s version of a work that was accepted for publication in e's dynamics at and between elementary structural transitions', Journal of molecular liquids. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Nerukh, D & Taiji, M, '21-residue peptide's dynamics at and between elementary structural transitions', Journal of molecular liquids, vol 147, no. 1-2, (2009). DOI http://dx.doi.org/10.1016/j.molliq.2008.10.015

Keywords

conformational changes
elementary transitions
collective dynamics
trajectory perturbations
phase space flow

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10.1016/j.molliq.2008.10.015

21-residue peptide's dynamics
NOTICE: this is the author’s version of a work that was accepted for publication in e's dynamics at and between elementary structural transitions', Journal of molecular liquids. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Nerukh, D & Taiji, M, '21-residue peptide's dynamics at and between elementary structural transitions', Journal of molecular liquids, vol 147, no. 1-2, (2009). DOI http://dx.doi.org/10.1016/j.molliq.2008.10.015
Accepted author manuscript, 1.34 MB

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title = "21-residue peptide's dynamics at and between elementary structural transitions",

abstract = "Elementary conformational changes of the backbone of a 21-residue peptide A5(A3RA)3A are studied using molecular dynamics simulations in explicit water. The processes of the conformational transitions and the regimes of stationary fluctuations between them are investigated using minimal perturbations of the system. The perturbations consist of a few degrees rotation of the velocity of one of the systems' atoms and keep the system on the same energy surface. It is found that (i) the system dynamics is insignificantly changed by the perturbations in the regimes between the transitions; (ii) it is very sensitive to the perturbations just before the transitions that prevents the peptide from making the transitions; and (iii) the perturbation of any atom of the system, including distant water molecules is equally effective in preventing the transition. The latter implies strongly collective dynamics of the peptide and water during the transitions.",

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author = "Dmitry Nerukh and Makoto Taiji",

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N1 - NOTICE: this is the author’s version of a work that was accepted for publication in e's dynamics at and between elementary structural transitions', Journal of molecular liquids. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Nerukh, D & Taiji, M, '21-residue peptide's dynamics at and between elementary structural transitions', Journal of molecular liquids, vol 147, no. 1-2, (2009). DOI http://dx.doi.org/10.1016/j.molliq.2008.10.015

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N2 - Elementary conformational changes of the backbone of a 21-residue peptide A5(A3RA)3A are studied using molecular dynamics simulations in explicit water. The processes of the conformational transitions and the regimes of stationary fluctuations between them are investigated using minimal perturbations of the system. The perturbations consist of a few degrees rotation of the velocity of one of the systems' atoms and keep the system on the same energy surface. It is found that (i) the system dynamics is insignificantly changed by the perturbations in the regimes between the transitions; (ii) it is very sensitive to the perturbations just before the transitions that prevents the peptide from making the transitions; and (iii) the perturbation of any atom of the system, including distant water molecules is equally effective in preventing the transition. The latter implies strongly collective dynamics of the peptide and water during the transitions.

AB - Elementary conformational changes of the backbone of a 21-residue peptide A5(A3RA)3A are studied using molecular dynamics simulations in explicit water. The processes of the conformational transitions and the regimes of stationary fluctuations between them are investigated using minimal perturbations of the system. The perturbations consist of a few degrees rotation of the velocity of one of the systems' atoms and keep the system on the same energy surface. It is found that (i) the system dynamics is insignificantly changed by the perturbations in the regimes between the transitions; (ii) it is very sensitive to the perturbations just before the transitions that prevents the peptide from making the transitions; and (iii) the perturbation of any atom of the system, including distant water molecules is equally effective in preventing the transition. The latter implies strongly collective dynamics of the peptide and water during the transitions.

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21-residue peptide's dynamics at and between elementary structural transitions

Abstract

Bibliographical note

Keywords

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