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Communication: Role of explicit water models in the helix folding/unfolding processes

Palazzesi, F; Salvalaglio, M; Barducci, A; Parrinello, M; (2016) Communication: Role of explicit water models in the helix folding/unfolding processes. The Journal of Chemical Physics , 145 (12) , Article 121101. 10.1063/1.4963340. Green open access

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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.

Type: Article
Title: Communication: Role of explicit water models in the helix folding/unfolding processes
Open access status: An open access version is available from UCL Discovery
DOI: 10.1063/1.4963340
Publisher version: http://dx.doi.org/10.1063/1.4963340
Language: English
Additional information: The following article appeared in the Journal of Chemical Physics [Palazzesi, F; Salvalaglio, M; Barducci, A; Parrinello, M; (2016) Communication: Role of explicit water models in the helix folding/unfolding processes. The Journal of Chemical Physics, 145 (12), Article 121101. 10.1063/1.4963340] and may be found at http://dx.doi.org/10.1063/1.4963340. This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing.
UCL classification: UCL
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Chemical Engineering
URI: https://discovery.ucl.ac.uk/id/eprint/1532141
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