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Title: Application of conventional molecular dynamics simulation in evaluating the stability of apomyoglobin in urea solution
Authors: Zhang, Dawei
Lazim, Raudah
Keywords: Mutation
Issue Date: 2017
Source: Zhang, D., & Lazim, R. (2017). Application of conventional molecular dynamics simulation in evaluating the stability of apomyoglobin in urea solution. Scientific Reports, 7, 44651-.
Series/Report no.: Scientific Reports
Abstract: In this study, we had exploited the advancement in computer technology to determine the stability of four apomyoglobin variants namely wild type, E109A, E109G and G65A/G73A by conducting conventional molecular dynamics simulations in explicit urea solution. Variations in RMSD, native contacts and solvent accessible surface area of the apomyoglobin variants during the simulation were calculated to probe the effect of mutation on the overall conformation of the protein. Subsequently, the mechanism leading to the destabilization of the apoMb variants was studied through the calculation of correlation matrix, principal component analyses, hydrogen bond analyses and RMSF. The results obtained here correlate well with the study conducted by Baldwin and Luo which showed improved stability of apomyoglobin with E109A mutation and contrariwise for E109G and G65A/G73A mutation. These positive observations showcase the feasibility of exploiting MD simulation in determining protein stability prior to protein expression.
ISSN: 2045-2322
DOI: 10.1038/srep44651
Schools: School of Physical and Mathematical Sciences 
Rights: © 2017 The Author(s) (Nature Publishing Group). This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit
Fulltext Permission: open
Fulltext Availability: With Fulltext
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