title: Understanding the connection between conformational changes of peptides and equilibrium thermal fluctuations.
abstract: Despite the increasing evidence that conformational transitions in peptides and proteins are driven by specific vibrational energy pathways along the molecule, the current experimental techniques of analysis do as yet not allow to study these biophysical processes in terms of anisotropic energy flows. Computational methods offer a complementary approach to obtain a more detailed understanding of the vibrational and conformational dynamics of these systems. Accordingly, in this work we investigate jointly the vibrational energy distribution and the conformational dynamics of trialanine peptide in water solution at room temperature by applying the Instantaneous Normal Mode analysis to the results derived from equilibrium molecular dynamics simulations. It is shown that conformational changes in trialanine are triggered by the vibrational energy accumulated in the low-frequency modes of the molecule, and that excitation is caused exclusively by thermal fluctuations of the solute-solvent system, thus excluding the possibility of an intramolecular vibrational energy redistribution process.
authors.affiliation: Department of Medical and Biological Sciences, University of Udine, 33100 Udine, Italy. miguelangel.solerbastida@uniud.it.
authors.forename: Miguel A
authors.identifier: http://orcid.org/0000-0002-5780-9949
authors.initials: MA
authors.lastname: Soler
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 Química Física, Universidad de Murcia, 30100 Murcia, Spain.
authors.forename: Adolfo
authors.initials: A
authors.lastname: Bastida
mesh_terms: D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D012997:Solvents; D013816:Thermodynamics; D014732:Vibration; D014867:Water / Q000737:chemistry
chemical_list: D009842:Oligopeptides; D010455:Peptides; D012997:Solvents; D014867:Water; C039944:alanyl-alanyl-alanine