title: Conformational Changes of Trialanine in Water Induced by Vibrational Relaxation of the Amide I Mode.
abstract: Most of the protein-based diseases are caused by anomalies in the functionality and stability of these molecules. Experimental and theoretical studies of the conformational dynamics of proteins are becoming in this respect essential to understand the origin of these anomalies. However, a description of the conformational dynamics of proteins based on mechano-energetic principles still remains elusive because of the intrinsic high flexibility of the peptide chains, the participation of weak noncovalent interactions, and the role of the ubiquitous water solvent. In this work, the conformational dynamics of trialanine dissolved in water (D2O) is investigated through Molecular Dynamics (MD) simulations combined with instantaneous normal modes (INMs) analysis both at equilibrium and after the vibrational excitation of the C-terminal amide I mode. The conformational equilibrium between α and pPII conformers is found to be altered by the intramolecular relaxation of the amide I mode as a consequence of the different relaxation pathways of each conformer which modify the amount of vibrational energy stored in the torsional motions of the tripeptide, so the α → pPII and pPII → α conversion rates are increased differently. The selectivity of the process comes from the shifts of the vibrational frequencies with the conformational changes that modify the resonance conditions driving the intramolecular energy flows.
authors.affiliation: Departamento de Química Física, Universidad de Murcia , 30100 Murcia, Spain.
authors.forename: Adolfo
authors.initials: A
authors.lastname: Bastida
authors.affiliation: Departamento de Química Física, Universidad de Murcia , 30100 Murcia, Spain.
authors.forename: José
authors.initials: J
authors.lastname: Zúñiga
authors.affiliation: Departamento de Química Física, Universidad de Murcia , 30100 Murcia, Spain.
authors.forename: Alberto
authors.initials: A
authors.lastname: Requena
authors.affiliation: Departamento de Ingeniería Química y Ambiental, Universidad Politécnica de Cartagena , 30203 Cartagena, Spain.
authors.forename: Beatriz
authors.initials: B
authors.lastname: Miguel
authors.affiliation: Departamento de Biología Vegetal, Universidad de Murcia , 30100 Murcia, Spain.
authors.forename: María Emilia
authors.initials: ME
authors.lastname: Candela
authors.affiliation: Department of Medical and Biological Sciences, University of Udine , 33100 Udine, Italy.
authors.forename: Miguel Angel
authors.initials: MA
authors.lastname: Soler
mesh_terms: D000577:Amides / Q000737:chemistry*; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation; D014867:Water / Q000737:chemistry
chemical_list: D000577:Amides; D009842:Oligopeptides; D014867:Water; C039944:alanyl-alanyl-alanine