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- W2083753453 abstract "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. A CG model for CCMV (Cowpea Chlorotic Mottle Virus), a virus with an icosahedral shell of 180 identical proteins, 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 proteins. 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 aggregates. Here, aggregates of 20 and more capsid proteins are chosen that are possible intermediates in the assembly process or otherwise relevant for the mechanical stability of the CCMV virus shell. 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 elastic aspects of larger protein complexes from models that are carefully parametrized on smaller units, is achievable." @default.
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- W2083753453 date "2013-01-01" @default.
- W2083753453 modified "2023-10-18" @default.
- W2083753453 title "Optimization of an Elastic Network Augmented Coarse Grained Model to Study Ccmv Capsid Deformation" @default.
- W2083753453 doi "https://doi.org/10.1016/j.bpj.2012.11.2301" @default.
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