Water network dynamics at the critical moment of a peptide's ß-turn formation: a molecular dynamics study

George Karvounis; Dmitry Nerukh; Robert C. Glen

doi:10.1063/1.1780152

Water network dynamics at the critical moment of a peptide's ß-turn formation: a molecular dynamics study

George Karvounis, Dmitry Nerukh, Robert C. Glen

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

Abstract

All-atom molecular dynamics simulations for a single molecule of Leu-Enkephalin in aqueous solution have been used to study the role of the water network during the formation of ß-turns. We give a detailed account of the intramolecular hydrogen bonding, the water-peptide hydrogen bonding, and the orientation and residence times of water molecules focusing on the short critical periods of transition to the stable ß-turns. These studies suggest that, when intramolecular hydrogen bonding between the first and fourth residue of the ß-turn is not present, the disruption of the water network and the establishment of water bridges constitute decisive factors in the formation and stability of the ß-turn. Finally, we provide possible explanations and mechanisms for the formations of different kinds of ß-turns.

Original language	English
Pages (from-to)	4925-4935
Number of pages	11
Journal	Journal of Chemical Physics
Volume	121
Issue number	10
Early online date	23 Aug 2004
DOIs	https://doi.org/10.1063/1.1780152
Publication status	Published - 8 Sept 2004

Bibliographical note

© 2004 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. The following article appeared in J. Chem. Phys. 121, 4925 (2004) and may be found at https://doi.org/10.1063/1.1780152

Keywords

computer simulation
Leucine Enkephalin
chemical models
molecular models
motion
peptides
secondary protein structure
solutions
solvents
water

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10.1063/1.1780152

Water network dynamics at the critical moment
© 2004 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. The following article appeared in J. Chem. Phys. 121, 4925 (2004) and may be found at https://doi.org/10.1063/1.1780152
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title = "Water network dynamics at the critical moment of a peptide's {\ss}-turn formation: a molecular dynamics study",

abstract = "All-atom molecular dynamics simulations for a single molecule of Leu-Enkephalin in aqueous solution have been used to study the role of the water network during the formation of {\ss}-turns. We give a detailed account of the intramolecular hydrogen bonding, the water-peptide hydrogen bonding, and the orientation and residence times of water molecules focusing on the short critical periods of transition to the stable {\ss}-turns. These studies suggest that, when intramolecular hydrogen bonding between the first and fourth residue of the {\ss}-turn is not present, the disruption of the water network and the establishment of water bridges constitute decisive factors in the formation and stability of the {\ss}-turn. Finally, we provide possible explanations and mechanisms for the formations of different kinds of {\ss}-turns.",

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T2 - a molecular dynamics study

AU - Karvounis, George

AU - Nerukh, Dmitry

AU - Glen, Robert C.

N1 - © 2004 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. The following article appeared in J. Chem. Phys. 121, 4925 (2004) and may be found at https://doi.org/10.1063/1.1780152

PY - 2004/9/8

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N2 - All-atom molecular dynamics simulations for a single molecule of Leu-Enkephalin in aqueous solution have been used to study the role of the water network during the formation of ß-turns. We give a detailed account of the intramolecular hydrogen bonding, the water-peptide hydrogen bonding, and the orientation and residence times of water molecules focusing on the short critical periods of transition to the stable ß-turns. These studies suggest that, when intramolecular hydrogen bonding between the first and fourth residue of the ß-turn is not present, the disruption of the water network and the establishment of water bridges constitute decisive factors in the formation and stability of the ß-turn. Finally, we provide possible explanations and mechanisms for the formations of different kinds of ß-turns.

AB - All-atom molecular dynamics simulations for a single molecule of Leu-Enkephalin in aqueous solution have been used to study the role of the water network during the formation of ß-turns. We give a detailed account of the intramolecular hydrogen bonding, the water-peptide hydrogen bonding, and the orientation and residence times of water molecules focusing on the short critical periods of transition to the stable ß-turns. These studies suggest that, when intramolecular hydrogen bonding between the first and fourth residue of the ß-turn is not present, the disruption of the water network and the establishment of water bridges constitute decisive factors in the formation and stability of the ß-turn. Finally, we provide possible explanations and mechanisms for the formations of different kinds of ß-turns.

KW - computer simulation

KW - Leucine Enkephalin

KW - chemical models

KW - molecular models

KW - motion

KW - peptides

KW - secondary protein structure

KW - solutions

KW - solvents

KW - water

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DO - 10.1063/1.1780152

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SN - 0021-9606

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JO - Journal of Chemical Physics

JF - Journal of Chemical Physics

IS - 10

ER -

Water network dynamics at the critical moment of a peptide's ß-turn formation: a molecular dynamics study

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