title: Structural and dynamical studies of all-trans and all-cis cyclo[(1R,3S)-gamma-Acc-Gly]3 peptides.
abstract: The quantum chemical and molecular dynamics studies have been performed to infer the structural changes of all-trans and all-cis forms of cyclo[(1R,3S)-3-aminocyclohexanecarboxylicacid(gamma-Acc)-alpha-Glycine(Gly)](3) hexapeptide. The backbone conformations of the above peptide have been analyzed using the valence and peptide deformation angles applying B3LYP/6-311G** level of theory. The conformational preference of the backbone of all-trans and all-cis cyclo[(1R,3S)-gamma-Acc-Gly](3) hexapeptides is found to depend on the puckering of cyclohexane rings. The non-uniform distribution of water inside the cavity is observed, where sometimes water molecules formed a chain like conformation through hydrogen bond networks while traversing the pore of all-cis cyclo[(1R,3S)-gamma-Acc-Gly](3) peptide. Larger relaxation times of the order of a hundred to two hundred pico seconds for active site...water hydrogen bond interactions were noticed. The hydrophobic nature of the cavity of all-trans cyclo[(1R,3S)-gamma-Acc-Gly](3) due to the presence of cyclohexane moiety has been analyzed. Further this investigation emphasized on the non-transport of molecules through the pore of all-trans cyclo[(1R,3S)-gamma-Acc-Gly](3) peptide due to the obstruction produced by cyclohexane groups.
authors.affiliation: Department of Physics, Bharathiar University, Coimbatore, India.
authors.forename: Gopalan
authors.initials: G
authors.lastname: Praveena
authors.forename: Ponmalai
authors.initials: P
authors.lastname: Kolandaivel
mesh_terms: D001665:Binding Sites; D020134:Catalytic Domain; D003198:Computer Simulation; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D007536:Isomerism; D008958:Models, Molecular; D009842:Oligopeptides / Q000737:chemistry*; D010456:Peptides, Cyclic / Q000737:chemistry*; D014867:Water / Q000737:chemistry
chemical_list: D009842:Oligopeptides; D010456:Peptides, Cyclic; C534494:cyclo(3-aminocyclohexanecarboxylicacid-glycyl)3 hexapeptide; D014867:Water
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