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Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes pp 61–87Cite as

Protein Dynamics Simulations Using Coarse-Grained Models

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

Abstract

Simulations of protein dynamics may work on different levels of molecular detail. The levels of simplification (coarse-graining) may concern different simulation aspects, including protein representation, interaction schemes or models of molecular motion. So-called coarse-grained (CG) models offer many advantages, unreachable by classical simulation tools, as demonstrated in numerous studies of protein dynamics. Followed by a brief introduction, we present example applications of CG models for efficient predictions of biophysical mechanisms. We discuss the following topics: mechanisms of chaperonin action, mechanical properties of proteins and their complexes, membrane proteins , protein-protein interactions and intrinsically unfolded proteins. These areas illustrate the opportunities for practical applications of CG simulations.

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Acknowledgements

We thank Dr. Joanna Sulkowska for critical reading of the section “Mechanical Unfolding and Refolding of Proteins and their Complexes” of the manuscript. We acknowledge partial support from: Foundation for Polish Science TEAM project (TEAM/2011-7/6) co-financed by the European Regional Development Fund operated within the Innovative Economy Operational Program; Polish National Science Center (NCN) on the basis of a decision DEC-2011/01/D/NZ2/05314; Polish National Science Center (NCN) Grant No. NN301071140, Polish Ministry of Science and Higher Education Grant No. IP2011024371, Polish National Science Center (NCN) Grant (MAESTRO 2014/14/A/ST6/00088). M. Kouza acknowledges the Polish Ministry of Science and Higher Education for financial support through ‘‘Mobilnosc Plus’’ Program No. 1287/MOB/IV/2015/0.

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    Sebastian Kmiecik, Jacek Wabik, Maksim Kouza & Andrzej Kolinski

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    Michal Kolinski

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Kmiecik, S., Wabik, J., Kolinski, M., Kouza, M., Kolinski, A. (2019). Protein Dynamics Simulations Using 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_3

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