Coarse-Grained Molecular Dynamics Simulation of Lysozyme Protein Crystals
Author:
Farhadian Nafiseh,Shariaty-Niassar Mojtaba,Malek Kourosh,Maghari Ali
Abstract
Many biological phenomena of interest occur on a time scale that is too great to be studied by atomistic simulations. The use of coarse-graining methods to represent a system can alleviate this restriction by reducing the number of degrees of freedom thus extending the time and length scale in molecular modeling.
Coarse-grained molecular dynamics (CGMD) technique was employed to simulate diffusion of water in the nanopores of lysozyme protein crystals. Good agreement was obtained between the atomistic and CG simulations in view of the stability of the protein crystal structure and water transport properties. Our simulations demonstrate that the CG method is a suitable technique for simulation the solvent diffusion process in the lysozyme protein crystal and also can be a good technique to predict the behavior of solvent and solutes in the biological systems at longer length and time scales.
Publisher
Walter de Gruyter GmbH
Subject
Modelling and Simulation,General Chemical Engineering
Cited by
1 articles.
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