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

Dmitry Nerukh, Makoto Taiji

Research output: Contribution to journalArticle

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 languageEnglish
Pages (from-to)124-127
Number of pages4
JournalJournal of Molecular Liquids
Volume147
Issue number1-2
Early online date19 Nov 2008
DOIs
Publication statusPublished - 20 Jul 2009

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Peptides
peptides
Water
perturbation
Atoms
Interfacial energy
Molecular dynamics
Dynamical systems
water
Molecules
Computer simulation
surface energy
atoms
molecular dynamics
molecules
simulation

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

Cite this

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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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21-residue peptide's dynamics at and between elementary structural transitions. / Nerukh, Dmitry; Taiji, Makoto.

In: Journal of Molecular Liquids, Vol. 147, No. 1-2, 20.07.2009, p. 124-127.

Research output: Contribution to journalArticle

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