Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations
Articolo
Data di Pubblicazione:
2015
Citazione:
Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations / P. Kukic, A. Kannan, M.J..J. Dijkstra, S. Abeln, C. Camilloni, M. Vendruscolo. - In: PLOS COMPUTATIONAL BIOLOGY. - ISSN 1553-734X. - 11:10(2015), pp. e1004435.1-e1004435.19. [10.1371/journal.pcbi.1004435]
Abstract:
It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a ‘tube model’ approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the ‘CamTube’ force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost.
Tipologia IRIS:
01 - Articolo su periodico
Keywords:
Programming Languages; Protein Conformation; Proteins; Software; Stress, Mechanical; Algorithms; Models, Chemical; Molecular Dynamics Simulation; Protein Folding; Computational Theory and Mathematics; Modeling and Simulation; Ecology, Evolution, Behavior and Systematics; Genetics; Molecular Biology; Ecology; Cellular and Molecular Neuroscience
Elenco autori:
P. Kukic, A. Kannan, M.J..J. Dijkstra, S. Abeln, C. Camilloni, M. Vendruscolo
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