Optimization of an Elastic Network Augmented Coarse Grained Model to Study CCMV Capsid Deformation

Globisch, Christoph; Krishnamani, Venkatramanan; Deserno, Markus; Peter, Christine

Optimization of an Elastic Network Augmented Coarse Grained Model to Study CCMV Capsid Deformation

Dateien

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Datum

2013

Autor:innen

Globisch, Christoph

Krishnamani, Venkatramanan

Deserno, Markus

Peter, Christine

Open Access-Veröffentlichung

Open Access Gold

Sammlungen

Chemie

Publikationstyp

Zeitschriftenartikel

Publikationsstatus

Published

Erschienen in

PLoS ONE. 2013, 8(4), e60582. eISSN 1932-6203. Available under: doi: 10.1371/journal.pone.0060582

Zusammenfassung

The major protective coat of most viruses is a highly symmetric protein capsid that forms spontaneously from many copies of identical proteins. Structural and mechanical properties of such capsids, as well as their self-assembly process, have been studied experimentally and theoretically, including modeling efforts by computer simulations on various scales. Atomistic models include specific details of local protein binding but are limited in system size and accessible time, while coarse grained (CG) models do get access to longer time and length scales but often lack the specific local interactions. Multi-scale models aim at bridging this gap by systematically connecting different levels of resolution. Here, a CG model for CCMV (Cowpea Chlorotic Mottle Virus), a virus with an icosahedral shell of 180 identical protein monomers, is developed, where parameters are derived from atomistic simulations of capsid protein dimers in aqueous solution. In particular, a new method is introduced to combine the MARTINI CG model with a supportive elastic network based on structural fluctuations of individual monomers. In the parametrization process, both network connectivity and strength are optimized. This elastic-network optimized CG model, which solely relies on atomistic data of small units (dimers), is able to correctly predict inter-protein conformational flexibility and properties of larger capsid fragments of 20 and more subunits. Furthermore, it is shown that this CG model reproduces experimental (Atomic Force Microscopy) indentation measurements of the entire viral capsid. Thus it is shown that one obvious goal for hierarchical modeling, namely predicting mechanical properties of larger protein complexes from models that are carefully parametrized on elastic properties of smaller units, is achievable.

Fachgebiet (DDC)

540 Chemie

Zitieren

ISO 690

GLOBISCH, Christoph, Venkatramanan KRISHNAMANI, Markus DESERNO, Christine PETER, 2013. Optimization of an Elastic Network Augmented Coarse Grained Model to Study CCMV Capsid Deformation. In: PLoS ONE. 2013, 8(4), e60582. eISSN 1932-6203. Available under: doi: 10.1371/journal.pone.0060582

BibTex

@article{Globisch2013Optim-25194,
  year={2013},
  doi={10.1371/journal.pone.0060582},
  title={Optimization of an Elastic Network Augmented Coarse Grained Model to Study CCMV Capsid Deformation},
  number={4},
  volume={8},
  journal={PLoS ONE},
  author={Globisch, Christoph and Krishnamani, Venkatramanan and Deserno, Markus and Peter, Christine},
  note={Article Number: e60582}
}

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Universitätsbibliographie

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