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Title: Effects of Dimerization of Serratia marcescens Endonuclease on Water Dynamics.

Abstract

The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The dynamics and structure of Serratia marcescens endonuclease and its neighboring solvent are investigated by molecular dynamics (MD). Comparisons are made with structural and biochemical experiments. The dimer form is physiologic and functions more processively than the monomer. We previously found a channel formed by connected clusters of waters from the active site to the dimer interface. Here, we show that dimerization clearly changes correlations in the water structure and dynamics in the active site not seen in the monomer. Our results indicate that water at the active sites of the dimer is less affected compared with bulk solvent than in the monomer where it has much slower characteristic relaxation times. Given that water is a required participant in the reaction, this gives a clear advantage to dimerization in the absence of an apparent ability to use both active sites simultaneously.

Authors:
; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
921370
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Biopolymers, 85(3):241-252; Journal Volume: 85; Journal Issue: 3
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; DIMERIZATION; DIMERS; ENDONUCLEASES; MONOMERS; RELAXATION TIME; SERRATIA; SOLVENTS; WATER; Environmental Molecular Sciences Laboratory

Citation Formats

Chen, Chuanying, Beck, Brian W., Krause, Kurt, Weksberg, Tiffany E., and Pettitt, Bernard M. Effects of Dimerization of Serratia marcescens Endonuclease on Water Dynamics.. United States: N. p., 2007. Web. doi:10.1002/bip.20641.
Chen, Chuanying, Beck, Brian W., Krause, Kurt, Weksberg, Tiffany E., & Pettitt, Bernard M. Effects of Dimerization of Serratia marcescens Endonuclease on Water Dynamics.. United States. doi:10.1002/bip.20641.
Chen, Chuanying, Beck, Brian W., Krause, Kurt, Weksberg, Tiffany E., and Pettitt, Bernard M. Thu . "Effects of Dimerization of Serratia marcescens Endonuclease on Water Dynamics.". United States. doi:10.1002/bip.20641.
@article{osti_921370,
title = {Effects of Dimerization of Serratia marcescens Endonuclease on Water Dynamics.},
author = {Chen, Chuanying and Beck, Brian W. and Krause, Kurt and Weksberg, Tiffany E. and Pettitt, Bernard M.},
abstractNote = {The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The dynamics and structure of Serratia marcescens endonuclease and its neighboring solvent are investigated by molecular dynamics (MD). Comparisons are made with structural and biochemical experiments. The dimer form is physiologic and functions more processively than the monomer. We previously found a channel formed by connected clusters of waters from the active site to the dimer interface. Here, we show that dimerization clearly changes correlations in the water structure and dynamics in the active site not seen in the monomer. Our results indicate that water at the active sites of the dimer is less affected compared with bulk solvent than in the monomer where it has much slower characteristic relaxation times. Given that water is a required participant in the reaction, this gives a clear advantage to dimerization in the absence of an apparent ability to use both active sites simultaneously.},
doi = {10.1002/bip.20641},
journal = {Biopolymers, 85(3):241-252},
number = 3,
volume = 85,
place = {United States},
year = {Thu Feb 15 00:00:00 EST 2007},
month = {Thu Feb 15 00:00:00 EST 2007}
}