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Systematic hierarchical coarse-graining with the inverse Monte Carlo method
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). University of Namur, Belgium .
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Stockholm University, Science for Life Laboratory (SciLifeLab).
Number of Authors: 4
2015 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 143, no 24, 243120Article in journal (Refereed) Published
Abstract [en]

We outline our coarse-graining strategy for linking micro-and mesoscales of soft matter and biological systems. The method is based on effective pairwise interaction potentials obtained in detailed ab initio or classical atomistic Molecular Dynamics (MD) simulations, which can be used in simulations at less accurate level after scaling up the size. The effective potentials are obtained by applying the inverse Monte Carlo (IMC) method [A. P. Lyubartsev and A. Laaksonen, Phys. Rev. E 52(4), 3730-3737 (1995)] on a chosen subset of degrees of freedom described in terms of radial distribution functions. An in-house software package MagiC is developed to obtain the effective potentials for arbitrary molecular systems. In this work we compute effective potentials to model DNA-protein interactions (bacterial LiaR regulator bound to a 26 base pairs DNA fragment) at physiological salt concentration at a coarse-grained (CG) level. Normally the IMC CG pair-potentials are used directly as look-up tables but here we have fitted them to five Gaussians and a repulsive wall. Results show stable association between DNA and the model protein as well as similar position fluctuation profile.

Place, publisher, year, edition, pages
2015. Vol. 143, no 24, 243120
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Chemical Sciences Physical Sciences
Identifiers
URN: urn:nbn:se:su:diva-128012DOI: 10.1063/1.4934095ISI: 000370412900026PubMedID: 26723605OAI: oai:DiVA.org:su-128012DiVA: diva2:913290
Available from: 2016-03-21 Created: 2016-03-15 Last updated: 2016-03-21Bibliographically approved

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Lyubartsev, Alexander P.Naomé, AymericLaaksonen, Aatto
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Department of Materials and Environmental Chemistry (MMK)Science for Life Laboratory (SciLifeLab)
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