title: Assessment of the intrinsic conformational preferences of dipeptide amino acids in aqueous solution by combined umbrella sampling/MBAR statistics. A comparison with experimental results.
abstract: The propensities of 19 amino acid dipeptides have been calculated by a distributed umbrella sampling molecular dynamics simulation procedure using the OPLS-AA force field. The potential of mean force maps was estimated with the multiple Bennett acceptance ratio statistics. The resulting propensities compare satisfactorily well with very recently published experimental data on equivalent systems. In particular, α conformation-probabilities for all of the dipeptides remain much lower than either β or P(II) propensities. This result is in agreement with most experimental data for dipeptides. However, it is also in contrast with most simulation studies performed so far with other force fields, where α conformations result even more probable than P(II) or β ones. We discuss the behavior of the OPLS-AA force field, which can be useful for the improvement of this model in reproducing the recent experimental observations on amino acid dipeptides.
authors.affiliation: BIOPHYM, Department of Macromolecular Physics, Instituto de Estructura de la Materia, CSIC Serrano 113-bis, Madrid, Spain. victor.cruz@iem.cfmac.csic.es
authors.forename: Victor L
authors.initials: VL
authors.lastname: Cruz
authors.forename: Javier
authors.initials: J
authors.lastname: Ramos
authors.forename: Javier
authors.initials: J
authors.lastname: Martinez-Salazar
mesh_terms: D000465:Algorithms; D000577:Amides / Q000737:chemistry; D004151:Dipeptides / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D014867:Water / Q000737:chemistry
chemical_list: D000577:Amides; D004151:Dipeptides; D014867:Water