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Protein Dynamics Simulations Using Coarse-Grained Models

  • Sebastian KmiecikEmail author
  • Jacek Wabik
  • Michal Kolinski
  • Maksim Kouza
  • Andrzej Kolinski
Chapter
Part of the Springer Series on Bio- and Neurosystems book series (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.

Notes

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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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Sebastian Kmiecik
    • 1
    Email author
  • Jacek Wabik
    • 1
  • Michal Kolinski
    • 2
  • Maksim Kouza
    • 1
  • Andrzej Kolinski
    • 1
  1. 1.Faculty of ChemistryBiological and Chemical Research Centre, University of WarsawWarsawPoland
  2. 2.Bioinformatics LaboratoryMossakowski Medical Research Centre Polish Academy of SciencesWarsawPoland

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