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Title: The ONIOM molecular dynamics method for biochemical applications: cytidine deaminase

Abstract

Abstract We derived and implemented the ONIOM-molecular dynamics (MD) method for biochemical applications. The implementation allows the characterization of the functions of the real enzymes taking account of their thermal motion. In this method, the direct MD is performed by calculating the ONIOM energy and gradients of the system on the fly. We describe the first application of this ONOM-MD method to cytidine deaminase. The environmental effects on the substrate in the active site are examined. The ONIOM-MD simulations show that the product uridine is strongly perturbed by the thermal motion of the environment and dissociates easily from the active site. TM and MA were supported in part 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:
908947
Report Number(s):
PNNL-SA-53781
Journal ID: ISSN 0009-2614; CHPLBC; KC0302020; TRN: US200722%%827
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Chemical Physics Letters, 437(1-3):138-142; Journal Volume: 437; Journal Issue: 1-3
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; CYTIDINE; ENZYMES; MOLECULAR DYNAMICS METHOD; SUBSTRATES; URIDINE

Citation Formats

Matsubara, Toshiaki, Dupuis, Michel, and Aida, Misako. The ONIOM molecular dynamics method for biochemical applications: cytidine deaminase. United States: N. p., 2007. Web. doi:10.1016/j.cplett.2007.01.085.
Matsubara, Toshiaki, Dupuis, Michel, & Aida, Misako. The ONIOM molecular dynamics method for biochemical applications: cytidine deaminase. United States. doi:10.1016/j.cplett.2007.01.085.
Matsubara, Toshiaki, Dupuis, Michel, and Aida, Misako. Thu . "The ONIOM molecular dynamics method for biochemical applications: cytidine deaminase". United States. doi:10.1016/j.cplett.2007.01.085.
@article{osti_908947,
title = {The ONIOM molecular dynamics method for biochemical applications: cytidine deaminase},
author = {Matsubara, Toshiaki and Dupuis, Michel and Aida, Misako},
abstractNote = {Abstract We derived and implemented the ONIOM-molecular dynamics (MD) method for biochemical applications. The implementation allows the characterization of the functions of the real enzymes taking account of their thermal motion. In this method, the direct MD is performed by calculating the ONIOM energy and gradients of the system on the fly. We describe the first application of this ONOM-MD method to cytidine deaminase. The environmental effects on the substrate in the active site are examined. The ONIOM-MD simulations show that the product uridine is strongly perturbed by the thermal motion of the environment and dissociates easily from the active site. TM and MA were supported in part 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 = {10.1016/j.cplett.2007.01.085},
journal = {Chemical Physics Letters, 437(1-3):138-142},
number = 1-3,
volume = 437,
place = {United States},
year = {Thu Mar 22 00:00:00 EDT 2007},
month = {Thu Mar 22 00:00:00 EDT 2007}
}