The ONIOM molecular dynamics method for biochemical applications: cytidine deaminase

Journal Article · Thu Mar 22 04:00:00 EDT 2007 · Chemical Physics Letters, 437(1-3):138-142

DOI:https://doi.org/10.1016/j.cplett.2007.01.085· OSTI ID:908947

Matsubara, Toshiaki; Dupuis, Michel; Aida, Misako

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.

• Research Organization: Pacific Northwest National Laboratory (PNNL), Richland, WA (US)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 908947
• Report Number(s): PNNL-SA-53781; KC0302020
• Journal Information: Chemical Physics Letters, 437(1-3):138-142, Journal Name: Chemical Physics Letters, 437(1-3):138-142 Journal Issue: 1-3 Vol. 437; ISSN CHPLBC; ISSN 0009-2614
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
CYTIDINE
ENZYMES
MOLECULAR DYNAMICS METHOD
SUBSTRATES
URIDINE