Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models

Kmiecik, Sebastian; Kouza, Maksim; Badaczewska-Dawid, Aleksandra E.; Kloczkowski, Andrzej; Kolinski, Andrzej

doi:10.3390/ijms19113496

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Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models

Sebastian Kmiecik

¹,

Maksim Kouza

Aleksandra E. Badaczewska-Dawid

¹,

Andrzej Kloczkowski

^2,* and

Andrzej Kolinski

^1,*

Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland

Nationwide Children’s Hospital, Columbus, OH 43205, USA

Authors to whom correspondence should be addressed.

Int. J. Mol. Sci. 2018, 19(11), 3496; https://doi.org/10.3390/ijms19113496

Received: 15 October 2018 / Revised: 29 October 2018 / Accepted: 31 October 2018 / Published: 6 November 2018

(This article belongs to the Special Issue Protein Structural Dynamics)

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Abstract

Fluctuations of protein three-dimensional structures and large-scale conformational transitions are crucial for the biological function of proteins and their complexes. Experimental studies of such phenomena remain very challenging and therefore molecular modeling can be a good alternative or a valuable supporting tool for the investigation of large molecular systems and long-time events. In this minireview, we present two alternative approaches to the coarse-grained (CG) modeling of dynamic properties of protein systems. We discuss two CG representations of polypeptide chains used for Monte Carlo dynamics simulations of protein local dynamics and conformational transitions, and highly simplified structure-based elastic network models of protein flexibility. In contrast to classical all-atom molecular dynamics, the modeling strategies discussed here allow the quite accurate modeling of much larger systems and longer-time dynamic phenomena. We briefly describe the main features of these models and outline some of their applications, including modeling of near-native structure fluctuations, sampling of large regions of the protein conformational space, or possible support for the structure prediction of large proteins and their complexes. View Full-Text

Keywords: protein dynamics; coarse-grained simulation; Monte Carlo dynamics; structural flexibility; large-scale dynamics; elastic network model

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MDPI and ACS Style

Kmiecik, S.; Kouza, M.; Badaczewska-Dawid, A.E.; Kloczkowski, A.; Kolinski, A. Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models. Int. J. Mol. Sci. 2018, 19, 3496. https://doi.org/10.3390/ijms19113496

AMA Style

Kmiecik S, Kouza M, Badaczewska-Dawid AE, Kloczkowski A, Kolinski A. Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models. International Journal of Molecular Sciences. 2018; 19(11):3496. https://doi.org/10.3390/ijms19113496

Chicago/Turabian Style

Kmiecik, Sebastian, Maksim Kouza, Aleksandra E. Badaczewska-Dawid, Andrzej Kloczkowski, and Andrzej Kolinski. 2018. "Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models" International Journal of Molecular Sciences 19, no. 11: 3496. https://doi.org/10.3390/ijms19113496

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Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models

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