Skip to main content

Research Repository

Advanced Search

Electrostatic-consistent coarse-grained potentials for molecular simulations of proteins.

Spiga, E.; Alemani, D.; Degiacomi, M.T.; Cascella, M.; Peraro, M.D.

Authors

E. Spiga

D. Alemani

M. Cascella

M.D. Peraro



Abstract

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.

Citation

Spiga, E., Alemani, D., Degiacomi, M., Cascella, M., & Peraro, M. (2013). Electrostatic-consistent coarse-grained potentials for molecular simulations of proteins. Journal of Chemical Theory and Computation, 9(8), 3515-3526. https://doi.org/10.1021/ct400137q

Journal Article Type Article
Online Publication Date Jun 19, 2013
Publication Date 2013-08
Deposit Date Jul 26, 2017
Journal Journal of Chemical Theory and Computation
Print ISSN 1549-9618
Electronic ISSN 1549-9626
Publisher American Chemical Society
Peer Reviewed Peer Reviewed
Volume 9
Issue 8
Pages 3515-3526
DOI https://doi.org/10.1021/ct400137q
Public URL https://durham-repository.worktribe.com/output/1350955