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research article

Electrostatic-Consistent Coarse-Grained Potentials for Molecular Simulations of Proteins

Spiga, Enrico  
•
Alemani, Davide  
•
Degiacomi, Matteo T.
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2013
Journal of Chemical Theory and Computation

We present a new generation of coarse-grained (CG) potentials that account for a simplified electrostatic description of soluble proteins. The treatment of permanent electrostatic dipoles of the backbone and polar side-chains allows to simulate proteins, preserving an excellent structural and dynamic agreement with respective reference structures and all-atom molecular dynamics simulations. Moreover, multiprotein complexes can be well described maintaining their molecular interfaces thanks to the ability of this scheme to better describe the actual electrostatics at a CG level of resolution. An efficient and robust heuristic algorithm based on particle swarm optimization is used for the derivation of CG parameters via a force-matching procedure. The ability of this protocol to deal with high dimensional search spaces suggests that the extension of this optimization procedure to larger data sets may lead to the generation of a fully transferable CG force field. At the present stage, these electrostatic-consistent CG potentials are easily and efficiently parametrized, show a good degree of transferability, and can be used to simulate soluble proteins or, more interestingly, large macromolecular assemblies for which long all-atom simulations may not be easily affordable.

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Type
research article
DOI
10.1021/ct400137q
Web of Science ID

WOS:000323193500027

Author(s)
Spiga, Enrico  
Alemani, Davide  
Degiacomi, Matteo T.
Cascella, Michele  
Dal Peraro, Matteo  
Date Issued

2013

Publisher

Amer Chemical Soc

Published in
Journal of Chemical Theory and Computation
Volume

9

Issue

8

Start page

3515

End page

3526

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
UPDALPE  
Available on Infoscience
October 1, 2013
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/95656
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