Coarse-Grained Modeling of Protein Dynamics

  • Sebastian Kmiecik
  • Jacek Wabik
  • Michal Kolinski
  • Maksim Kouza
  • Andrzej Kolinski
Part of the Springer Series in Bio-/Neuroinformatics book series (SSBN, volume 1)

Abstract

Simulations of protein dynamics may work on different levels of molecular detail. The levels of simplification (coarse-graining) can range from very low to atomic resolution and 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, membrane proteins, protein-protein interactions and intrinsically unfolded proteins. Presently, these areas represent emerging application fields of CG simulation models.

Abbreviations

CG coarse-grained MD Molecular Dynamics MC Monte Carlo 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Sebastian Kmiecik
    • 1
  • Jacek Wabik
    • 1
  • Michal Kolinski
    • 2
  • Maksim Kouza
    • 1
  • Andrzej Kolinski
    • 1
  1. 1.Laboratory of Theory of Biopolymers, Faculty of ChemistryUniversity of WarsawWarsawPoland
  2. 2.Bioinformatics LaboratoryMossakowski Medical Research Centre Polish Academy of SciencesWarsawPoland

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