title: Communication: Role of explicit water models in the helix folding/unfolding processes.
abstract: In the last years, it has become evident that computer simulations can assume a relevant role in modelling protein dynamical motions for their ability to provide a full atomistic image of the processes under investigation. The ability of the current protein force-fields in reproducing the correct thermodynamics and kinetics systems behaviour is thus an essential ingredient to improve our understanding of many relevant biological functionalities. In this work, employing the last developments of the metadynamics framework, we compare the ability of state-of-the-art all-atom empirical functions and water models to consistently reproduce the folding and unfolding of a helix turn motif in a model peptide. This theoretical study puts in evidence that the choice of the water models can influence the thermodynamic and the kinetics of the system under investigation, and for this reason cannot be considered trivial.
authors: Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich, 8093 Zurich, Switzerland.
authors: Ferruccio
authors: F
authors: Palazzesi
authors: Department of Chemical Engineering, University College London, London WC1E 7JE, United Kingdom.
authors: Matteo
authors: M
authors: Salvalaglio
authors: Inserm, U1054 Montpellier, France.
authors: Alessandro
authors: A
authors: Barducci
authors: Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich, 8093 Zurich, Switzerland.
authors: Michele
authors: M
authors: Parrinello
mesh_terms: D007700:Kinetics; D056004:Molecular Dynamics Simulation; D000072756:Protein Conformation, alpha-Helical; D058767:Protein Unfolding; D011506:Proteins / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
chemical_list: D011506:Proteins; D014867:Water