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Communication: Role of explicit water models in the helix folding/unfolding processes
D. E. Shaw, P. Maragakis, K. Lindorff-Larsen, S. Piana, R. O. Dror, M. P. Eastwood, J. A. Bank, J. M. Jumper, J. K. Salmon, Y. Shan, and W. Willy, Science 330, 341 (2010).
, P. Tiwary
, M. Mazzotti
, and M. Parrinello
, preprint arXiv:1508.01642
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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.
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