title: Water-mediated conformations of the alanine dipeptide as revealed by distributed umbrella sampling simulations, quantum mechanics based calculations, and experimental data.
abstract: An exhaustive umbrella sampling simulation of the alanine dipeptide in solution is reported. The presence of stable Y conformations in solution is assessed by both quantum calculations and experimental data from X-ray and NMR protein-solved structures available in the protein coil library. The agreement between experimental and simulation Ramachandran plots of the dipeptide in solution is excellent. A suitable explanation of the stabilization of the Y conformation mediated by water for the alanine dipeptide is discussed on the basis of Car-Parrinello MD calculations of the dipeptide in water.
authors.affiliation: BIOPHYM, Instituto de Estructura de la Materia, CSIC, Madrid, Spain. victor.cruz@iem.cfmac.csic.es
authors.forename: Víctor
authors.initials: V
authors.lastname: Cruz
authors.forename: Javier
authors.initials: J
authors.lastname: Ramos
authors.forename: Javier
authors.initials: J
authors.lastname: Martínez-Salazar
mesh_terms: D000409:Alanine / Q000737:chemistry*; D000465:Algorithms; D004151:Dipeptides / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D056004:Molecular Dynamics Simulation; D011789:Quantum Theory; D014867:Water / Q000737:chemistry*
chemical_list: D004151:Dipeptides; D014867:Water; D000409:Alanine