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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}
}
  • We applied the ONIOM-molecular dynamics (MD) method to the hydrolytic deamination of cytidine by cytidine deaminase, which is an essential step of the activation process of the anticancer drug inside the human body. The direct MD simulations were performed for the realistic model of cytidine deaminase calculating the energy and its gradient by the ab initio ONIOM method on the fly. The ONIOM-MD calculations including the thermal motion show that the neighboring amino acid residue is an important factor of the environmental effects and significantly affects not only the geometry and energy of the substrate trapped in the pocket ofmore » the active site but also the elementary step of the catalytic reaction. We successfully simulate the second half of the catalytic cycle, which has been considered to involve the rate-determining step, and reveal that the rate-determing step is the release of the NH3 molecule. 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.« less
  • 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 frommore » 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.« less
  • The enzyme cytidine deaminase (EC 3.5.4.12; CDA) catalyzes the hydrolytic deamination of cytidine or deoxycytidine to uridine or deoxyuridine, respectively. It can also catalyze the deamination of cytosine nucleoside analogues such as cytosine arabinoside and 5-azacytidine, which results in a loss of their cytotoxic and antitumor activity. Cytosine arabinoside is used in the treatment of acute myeloid leukemia, and the antileukemic activity of the drug is dependent on phosphorylation by deoxycytidine kinase. The occurrence of clinical cytosine arabinoside resistance is one of the main problems in the successful treatment of acute myeloid leukemia. Resistance to the drug has been ascribedmore » to functional deoxycytidine kinase deficiency and to increased expression of the CDA gene. In this study, we report on the isolation of a CDA genomic fragment and its use as a probe for the chromosomal localization of the human CDA gene by in situ hybridization. 9 refs., 1 fig.« less
  • All canonical transfer RNAs (tRNAs) have a uridine at position 8, involved in maintaining tRNA tertiary structure. However, the hyperthermophilic archaeon Methanopyrus kandleri harbors 30 (out of 34) tRNA genes with cytidine at position 8. Here, we demonstrate C-to-U editing at this location in the tRNA's tertiary core, and present the crystal structure of a tRNA-specific cytidine deaminase, CDAT8, which has the cytidine deaminase domain linked to a tRNA-binding THUMP domain. CDAT8 is specific for C deamination at position 8, requires only the acceptor stem hairpin for activity, and belongs to a unique family within the cytidine deaminase-like superfamily. Themore » presence of this C-to-U editing enzyme guarantees the proper folding and functionality of all M. kandleri tRNAs.« less