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 β-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 β-turns. These studies suggest that, when intramolecular hydrogen bonding between the first and fourth residue of the β-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 β-turn. Finally, we provide possible explanations and mechanisms for the formations of different kinds of β-turns.
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8 September 2004
Research Article|
September 08 2004
Water network dynamics at the critical moment of a peptide’s β-turn formation: A molecular dynamics study
George Karvounis;
George Karvounis
Unilever Centre for Molecular Informatics, Department of Chemistry, Cambridge University, Cambridge CB2 1EW, United Kingdom
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Dmitry Nerukh;
Dmitry Nerukh
Unilever Centre for Molecular Informatics, Department of Chemistry, Cambridge University, Cambridge CB2 1EW, United Kingdom
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Robert C. Glen
Robert C. Glen
Unilever Centre for Molecular Informatics, Department of Chemistry, Cambridge University, Cambridge CB2 1EW, United Kingdom
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George Karvounis
Dmitry Nerukh
Robert C. Glen
Unilever Centre for Molecular Informatics, Department of Chemistry, Cambridge University, Cambridge CB2 1EW, United Kingdom
J. Chem. Phys. 121, 4925–4935 (2004)
Article history
Received:
May 07 2004
Accepted:
June 15 2004
Citation
George Karvounis, Dmitry Nerukh, Robert C. Glen; Water network dynamics at the critical moment of a peptide’s β-turn formation: A molecular dynamics study. J. Chem. Phys. 8 September 2004; 121 (10): 4925–4935. https://doi.org/10.1063/1.1780152
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