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Mechanostability of Virus Capsids and Their Proteins in Structure-Based Coarse-Grained Models

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Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes

Part of the book series: Springer Series on Bio- and Neurosystems ((SSBN,volume 8))

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Abstract

We outline a simple coarse-grained molecular dynamics model of proteins which is based on the knowledge of their native structures. We apply the model to study properties of selected proteins that are found in virus capsids, such as in CCMV and its mutant. We characterize their folding kinetics and force-displacement curves obtained during stretching. The stretching curves are shown to be sensitive to the mutations. We make a short review of possible mechanical clamps (motifs that are most resistant to stretching) that have been found in large scale surveys of mechanostability with the use of the model. We then discuss stretching of multimeric complexes of such proteins and demonstrate existence of strong dependence of the force-displacement curves on selection of a pair of termini involved in stretching. Finally, we consider nanoindentation processes in several virus capsids. We show that values of characteristic forces at which the capsids collapse are not correlated with mechanostabilities of the constituting proteins. We also show that the response to nanoindentation recognizes existence of single point mutations in the proteins but not in the initial stages of the process.

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Acknowledgements

M. Cieplak is grateful to M. Chwastyk, P. Cieplak, K. Modro, M. Sikora, and T. Włodarski for discussions and help with some figures and data. The computer resources were financed by the European Regional Development Fund under the Operational Programme Innovative Economy NanoFun POIG.02.02.00-00-025/09. The research on the revised version of this chapter has been supported by the Polish National Science Centre Grant No. 2014/15/B/ST3/01905.

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  1. Institute of Physics, Polish Academy of Sciences, Aleja Lotników 32/46, 02-668, Warsaw, Poland

    Marek Cieplak

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    Adam Liwo

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Cieplak, M. (2019). Mechanostability of Virus Capsids and Their Proteins in Structure-Based Coarse-Grained Models. In: Liwo, A. (eds) Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes. Springer Series on Bio- and Neurosystems, vol 8. Springer, Cham. https://doi.org/10.1007/978-3-319-95843-9_10

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