Biological Applications of Hybrid Quantum MechanicsMolecular Mechanics Calculation
Joint Authors
Kang, Jiyoung
Hagiwara, Yohsuke
Tateno, Masaru
Source
Journal of Biomedicine and Biotechnology
Issue
Vol. 2012, Issue 2012 (31 Dec. 2012), pp.1-11, 11 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2012-03-28
Country of Publication
Egypt
No. of Pages
11
Main Subjects
Abstract EN
Since in most cases biological macromolecular systems including solvent water molecules are remarkably large, the computational costs of performing ab initio calculations for the entire structures are prohibitive.
Accordingly, QM calculations that are jointed with MM calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules.
A UNIX-shell-based interface program connecting the quantum mechanics (QMs) and molecular mechanics (MMs) calculation engines, GAMESS and AMBER, was developed in our lab.
The system was applied to a metalloenzyme, azurin, and PU.1-DNA complex; thereby, the significance of the environmental effects on the electronic structures of the site of interest was elucidated.
Subsequently, hybrid QM/MM molecular dynamics (MD) simulation using the calculation system was employed for investigation of mechanisms of hydrolysis (editing reaction) in leucyl-tRNA synthetase complexed with the misaminoacylated tRNALeu, and a novel mechanism of the enzymatic reaction was revealed.
Thus, our interface program can play a critical role as a powerful tool for state-of-the-art sophisticated hybrid ab initio QM/MM MD simulations of large systems, such as biological macromolecules.
American Psychological Association (APA)
Kang, Jiyoung& Hagiwara, Yohsuke& Tateno, Masaru. 2012. Biological Applications of Hybrid Quantum MechanicsMolecular Mechanics Calculation. Journal of Biomedicine and Biotechnology،Vol. 2012, no. 2012, pp.1-11.
https://search.emarefa.net/detail/BIM-456126
Modern Language Association (MLA)
Kang, Jiyoung…[et al.]. Biological Applications of Hybrid Quantum MechanicsMolecular Mechanics Calculation. Journal of Biomedicine and Biotechnology No. 2012 (2012), pp.1-11.
https://search.emarefa.net/detail/BIM-456126
American Medical Association (AMA)
Kang, Jiyoung& Hagiwara, Yohsuke& Tateno, Masaru. Biological Applications of Hybrid Quantum MechanicsMolecular Mechanics Calculation. Journal of Biomedicine and Biotechnology. 2012. Vol. 2012, no. 2012, pp.1-11.
https://search.emarefa.net/detail/BIM-456126
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-456126