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Title: An Insight into the Environmental Effects of the Pocket of the Active Site of the Enzyme. Ab initio ONIOM-Molecular Dynamics (MD) Study on Cytosine Deaminase

Abstract

We applied the ONIOM-molecular dynamics (MD) method to cytosine deaminase to examine the environmental effects of the amino acid residues in the pocket of the active site on the substrate taking account of their thermal motion. The ab initio ONIOM-MD simulations show that the substrate uracil is strongly perturbed by the amino acid residue Ile33, which sandwiches the uracil with His62, through the steric contact due to the thermal motion. As a result, the magnitude of the thermal oscillation of the potential energy and structure of the substrate uracil significantly increases. TM and MA were partly supported by grants from the Ministry of Education, Culture, Sports, Science and Technology of Japan.MD was supported by the Division of Chemical Sciences, Office of Basic Energy Sciences, and by the Office of Biological and Environmental Research of the U.S. Department of Energy DOE. Battelle operates Pacific Northwest National Laboratory for DOE.

Authors:
; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
924664
Report Number(s):
PNNL-SA-56280
KC0301020; TRN: US0802924
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Journal of Computational Chemistry, 29(3):458-465
Additional Journal Information:
Journal Volume: 29; Journal Issue: 3
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; AMINO ACIDS; CYTOSINE; EDUCATION; ENVIRONMENTAL EFFECTS; OSCILLATIONS; POTENTIAL ENERGY; RESIDUES; SUBSTRATES; URACILS; ab initio ONIOM-molecular dynamics (MD) method; cytosine deaminase; active site; environmental effects; thermal motion

Citation Formats

Matsubara, Toshiaki, Dupuis, Michel, and Aida, Misako. An Insight into the Environmental Effects of the Pocket of the Active Site of the Enzyme. Ab initio ONIOM-Molecular Dynamics (MD) Study on Cytosine Deaminase. United States: N. p., 2008. Web. doi:10.1002/jcc.20805.
Matsubara, Toshiaki, Dupuis, Michel, & Aida, Misako. An Insight into the Environmental Effects of the Pocket of the Active Site of the Enzyme. Ab initio ONIOM-Molecular Dynamics (MD) Study on Cytosine Deaminase. United States. https://doi.org/10.1002/jcc.20805
Matsubara, Toshiaki, Dupuis, Michel, and Aida, Misako. 2008. "An Insight into the Environmental Effects of the Pocket of the Active Site of the Enzyme. Ab initio ONIOM-Molecular Dynamics (MD) Study on Cytosine Deaminase". United States. https://doi.org/10.1002/jcc.20805.
@article{osti_924664,
title = {An Insight into the Environmental Effects of the Pocket of the Active Site of the Enzyme. Ab initio ONIOM-Molecular Dynamics (MD) Study on Cytosine Deaminase},
author = {Matsubara, Toshiaki and Dupuis, Michel and Aida, Misako},
abstractNote = {We applied the ONIOM-molecular dynamics (MD) method to cytosine deaminase to examine the environmental effects of the amino acid residues in the pocket of the active site on the substrate taking account of their thermal motion. The ab initio ONIOM-MD simulations show that the substrate uracil is strongly perturbed by the amino acid residue Ile33, which sandwiches the uracil with His62, through the steric contact due to the thermal motion. As a result, the magnitude of the thermal oscillation of the potential energy and structure of the substrate uracil significantly increases. TM and MA were partly supported by grants from the Ministry of Education, Culture, Sports, Science and Technology of Japan.MD was supported by the Division of Chemical Sciences, Office of Basic Energy Sciences, and by the Office of Biological and Environmental Research of the U.S. Department of Energy DOE. Battelle operates Pacific Northwest National Laboratory for DOE.},
doi = {10.1002/jcc.20805},
url = {https://www.osti.gov/biblio/924664}, journal = {Journal of Computational Chemistry, 29(3):458-465},
number = 3,
volume = 29,
place = {United States},
year = {Fri Feb 01 00:00:00 EST 2008},
month = {Fri Feb 01 00:00:00 EST 2008}
}