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


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.

Publication DOI: https://doi.org/10.1063/1.1780152
Divisions: College of Engineering & Physical Sciences > Systems analytics research institute (SARI)
Additional Information: © 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
Uncontrolled Keywords: computer simulation,Leucine Enkephalin,chemical models,molecular models,motion,peptides,secondary protein structure,solutions,solvents,water
Publication ISSN: 1089-7690
Last Modified: 03 May 2024 07:08
Date Deposited: 24 Jul 2014 14:59
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Related URLs: http://scitatio ... .1063/1.1780152 (Publisher URL)
PURE Output Type: Article
Published Date: 2004-09-08
Published Online Date: 2004-08-23
Authors: Karvounis, George
Nerukh, Dmitry (ORCID Profile 0000-0001-9005-9919)
Glen, Robert C.



Version: Published Version

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