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Biochem Biophys Res Commun. 2018 Mar 29;498(2):296-304. doi: 10.1016/j.bbrc.2017.08.165. Epub 2017 Sep 14.

Multi-scale simulations of biological systems using the OPEP coarse-grained model.

Author information

1
Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité, PSL Research University, IBPC, 13 Rue Pierre et Marie Curie, 75005, Paris, France.
2
Istituto Sistemi Complessi - ISC, Consiglio Nazionale delle Richerche, P.za A. Moro 2, 008185, Italy.
3
Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité, PSL Research University, IBPC, 13 Rue Pierre et Marie Curie, 75005, Paris, France. Electronic address: philippe.derreumaux@ibpc.fr.

Abstract

Biomolecules are complex machines that are optimized by evolution to properly fulfill or contribute to a variety of biochemical tasks in the cellular environment. Computer simulations based on quantum mechanics and atomistic force fields have been proven to be a powerful microscope for obtaining valuable insights into many biological, physical, and chemical processes. Many interesting phenomena involve, however, a time scale and a number of degrees of freedom, notably if crowding is considered, that cannot be explored at an atomistic resolution. To bridge the gap between reality and simulation, many different advanced computational techniques and coarse-grained (CG) models have been developed. Here, we report some applications of the CG OPEP protein model to amyloid fibril formation, the response of catch-bond proteins to two types of fluid flow, and interactive simulations to fold peptides with well-defined 3D structures or with intrinsic disorder.

KEYWORDS:

Amyloid and catch bond proteins; Coarse-grained model; Hydrodynamics; Interactive; On-lattice and off-lattice simulations

PMID:
28917842
DOI:
10.1016/j.bbrc.2017.08.165
[Indexed for MEDLINE]

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