Biological Applications of Hybrid Quantum Mechanics/Molecular Mechanics Calculation.
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 eval...
| Publicado en: | Journal of Biomedicine & Biotechnology Vol. 2012; pp. 1 - 12 |
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| Autores principales: | , , |
| Formato: | equations & formulas pictorial review Journal Article |
| Publicado: |
Wiley-Blackwell
2012
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=104298111&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 104298111 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 11107243 137K jtl: Journal of Biomedicine & Biotechnology issn: 11107243 maglogo: N pubinfo: dt: 2012 vid: 2012 pid: 480 pub: Wiley-Blackwell place: Malden, Massachusetts artinfo: ui: 104298111 104298111 2011907033 NLM22536015 PMC3321478 104298111 ppf: 1 ppct: 11 formats: fmt: @attributes: type: P tig: atl: Biological Applications of Hybrid Quantum Mechanics/Molecular Mechanics Calculation. aug: au: Kang, Jiyoung Hagiwara, Yohsuke Tateno, Masaru affil: Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba Science City, Tsukuba 305-857, Japan sug: subj: Bioinformatics Methods Biophysics Molecular Structure Metalloproteins Metabolism Binding Sites Amino Acids Computer Simulation Mathematics Metalloproteins Analysis Leucine Metabolism ab: 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. pubtype: Academic Journal doctype: equations & formulas pictorial review Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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