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Multiscale virtual particle based elastic network model (MVP-ENM) for normal mode analysis of large-sized biomolecules

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Abstract

In this paper, a multiscale virtual particle based elastic network model (MVP-ENM) is proposed for the normal mode analysis of large-sized biomolecules. The multiscale virtual particle (MVP) model is proposed for the discretization of biomolecular density data. With this model, large-sized biomolecular structures can be coarse-grained into virtual particles such that a balance between model accuracy and computational cost can be achieved. An elastic network is constructed by assuming “connections” between virtual particles. The connection is described by a special harmonic potential function, which considers the influence from both the mass distributions and distance relations of the virtual particles. Two independent models, i.e., the multiscale virtual particle based Gaussian network model (MVP-GNM) and the multiscale virtual particle based anisotropic network model (MVP-ANM), are proposed. It has been found that in the Debye–Waller factor (B-factor) prediction, the results from our MVP-GNM with a high resolution are as good as the ones from GNM. Even with low resolutions, our MVP-GNM can still capture the global behavior of the B-factor very well with mismatches predominantly from the regions with large B-factor values. Further, it has been demonstrated that the low-frequency eigenmodes from our MVP-ANM are highly consistent with the ones from ANM even with very low resolutions and a coarse grid. Finally, the great advantage of MVP-ANM model for large-sized biomolecules has been demonstrated by using two poliovirus virus structures. The paper ends with a conclusion.

Graphical abstract: Multiscale virtual particle based elastic network model (MVP-ENM) for normal mode analysis of large-sized biomolecules

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Publication details

The article was received on 23 Oct 2017, accepted on 30 Nov 2017 and first published on 01 Dec 2017


Article type: Paper
DOI: 10.1039/C7CP07177A
Citation: Phys. Chem. Chem. Phys., 2018, Advance Article
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    Multiscale virtual particle based elastic network model (MVP-ENM) for normal mode analysis of large-sized biomolecules

    K. Xia, Phys. Chem. Chem. Phys., 2018, Advance Article , DOI: 10.1039/C7CP07177A

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