Water network dynamics at the critical moment of a peptide's beta-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 beta-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 beta-turns. These studies suggest that, when intramolecular hydrogen bonding between the first and fourth residue of the beta-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 beta-turn. Finally, we provide possible explanations and mechanisms for the formations of different kinds of beta-turns.
Karvounis
George
G
Unilever Centre for Molecular Informatics, Department of Chemistry, Cambridge University, Cambridge CB2 1EW, United Kingdom.
Nerukh
Dmitry
D
Glen
Robert C
RC
D003198:Computer Simulation; D004743:Enkephalin, Leucine / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D009038:Motion; D010455:Peptides / Q000737:chemistry; D017433:Protein Structure, Secondary; D012996:Solutions; D012997:Solvents / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
D010455:Peptides; D012996:Solutions; D012997:Solvents; D014867:Water; D004743:Enkephalin, Leucine