title: Conformational properties of the Arg-Leu-Gly tripeptide--DMSO--water clusters with the combined use of molecular dynamics and energy minimization studies.
abstract: The Arg-Leu-Gly tripeptide is the repeating fragment of sequential arginine-rich polypeptides capable of interacting with DNA. The conformational influence of solvent molecules (DMSO/H2O) were investigated with the combined use of molecular dynamics and energy minimization. It was found that water molecules greatly contribute to the peptide structure by solvating all its hydrophylic sites even in the presence of DMSO excess, whereas one water molecule links the ammonium and carboxylic ends of the Arg-Leu-Gly. The persistence of residual water, which was confirmed by varying the computer simulation parameters, indicates that pretreatment of peptide segments in aqueous solutions should greatly affect their conformational properties in organic media. A satisfactory agreement between experimental data (1H-NMR and IR spectroscopy) and the presented computational study deserves also to be noted.
authors.affiliation: Department of Chemistry, University of Ioannina.
authors.forename: I
authors.initials: I
authors.lastname: Demetropoulos
authors.forename: A
authors.initials: A
authors.lastname: Tsibiris
authors.forename: V
authors.initials: V
authors.lastname: Tsikaris
authors.forename: M
authors.initials: M
authors.lastname: Sakarellos-Daitsiotis
authors.forename: C
authors.initials: C
authors.lastname: Sakarellos
mesh_terms: D000595:Amino Acid Sequence; D016000:Cluster Analysis; D003196:Computer Graphics; D003198:Computer Simulation; D004121:Dimethyl Sulfoxide / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008956:Models, Chemical; D008969:Molecular Sequence Data; D009842:Oligopeptides / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D012997:Solvents / Q000737:chemistry; D014867:Water / Q000737:chemistry*
chemical_list: D009842:Oligopeptides; D010455:Peptides; D012997:Solvents; C094047:arginyl-leucyl-glycine; D014867:Water; D004121:Dimethyl Sulfoxide