Next Article in Journal
A Comparison of Proteins Expressed between Human and Mouse Adipose-Derived Mesenchymal Stem Cells by a Proteome Analysis through Liquid Chromatography with Tandem Mass Spectrometry
Next Article in Special Issue
Transient Secondary Structures as General Target-Binding Motifs in Intrinsically Disordered Proteins
Previous Article in Journal
AMP-Activated Protein Kinase and Host Defense against Infection
Previous Article in Special Issue
Revealing Unknown Protein Structures Using Computational Conformational Sampling Guided by Experimental Hydrogen-Exchange Data
Open AccessReview

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

1
Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
2
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)
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 protein dynamics; coarse-grained simulation; Monte Carlo dynamics; structural flexibility; large-scale dynamics; elastic network model
Show Figures

Graphical abstract

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.

Show more citation formats Show less citations formats
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map

1
Back to TopTop