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

• DOI: 10.20944/preprints201810.0329.v1
• Publication Date: 2018-10-18T03:03:13Z
• Authors: Sebastian Kmiecik; Maksim Kouza; Aleksandra Elzbie...; Andrzej Kloczkowski; Andrzej Kolinski
• Keywords: Models, Molecular; 0301 basic medicine; molecular_biology; Protein Conformation; Proteins; Review; Molecular Dynamics Simulation; 01 natural sciences; 03 medical and health sciences; 0103 physical sciences; Peptides; Monte Carlo Method

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 mini-review, 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, on other hand, highly simplified structure-based Elastic Network Models of protein flexibility. In contrast to classical Molecular Dynamics the modeling strategies discussed here allow 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.