NDLI: Probing the global and local dynamics of aminoacyl-tRNA synthetases using all-atom and coarse-grained simulations

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Probing the global and local dynamics of aminoacyl-tRNA synthetases using all-atom and coarse-grained simulations

Content Provider	PubMed Central
Author	Strom, Alexander M. Fehling, Samuel C. Bhattacharyya, Sudeep Hati, Sanchita
Abstract	Coarse-grained simulations have emerged as invaluable tools for studying conformational changes in biomolecules. To evaluate the effectiveness of computationally inexpensive coarse-grained models in studying global and local dynamics of large protein systems like aminoacyl-tRNA synthetases, we have performed coarse-grained normal mode analysis, as well as principle component analysis on trajectories of all-atom and coarse-grained molecular dynamics simulations for three aminoacyl-tRNA synthetases—Escherichia coli methionyl-tRNA synthetase, Thermus thermophilus leucyl-tRNA synthetase, and Enterococcus faecium prolyl-tRNA synthetase. In the present study, comparison of predicted dynamics based on B-factor and overlap calculations revealed that coarse-grained methods are comparable to the all-atom simulations in depicting the intrinsic global dynamics of the three enzymes. However, the principal component analyses of the motions obtained from the all-atom molecular dynamics simulations provide a superior description of the local fluctuations of these enzymes. In particular, the all-atom model was able to capture the functionally relevant substrate-induced dynamical changes in prolyl-tRNA synthetase. The alteration in the coupled dynamics between the catalytically important proline-binding loop and its neighboring structural elements due to substrate binding has been characterized and reported for the first time. Taken together, the study portrays comparable and contrasting situations in studying the functional dynamics of large multi-domain aminoacyl-tRNA synthetases using coarse-grained and all-atom simulation methods.
Related Links	http://dx.doi.org/10.1007/s00894-014-2245-1
Starting Page	2245
File Format	PDF
ISSN	16102940
e-ISSN	09485023
Journal	Journal of Molecular Modeling
Issue Number	5
Volume Number	20
Language	English
Publisher	Springer Berlin Heidelberg
Publisher Date	2014-05-01
Access Restriction	Open
Rights Holder	Springer Berlin Heidelberg
Subject Keyword	Physical and Theoretical Chemistry Inorganic Chemistry Organic Chemistry Computational Theory and Mathematics Catalysis Computer Science Applications Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Organic Chemistry Physical and Theoretical Chemistry Computational Theory and Mathematics Catalysis Inorganic Chemistry Computer Science Applications

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