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.
Revised: April 7, 2011 |
Published: February 15, 2007
Citation
Chen C., B.W. Beck, K. Krause, T.E. Weksberg, and B.M. Pettitt. 2007. "Effects of Dimerization of Serratia marcescens Endonuclease
on Water Dynamics." Biopolymers 85, no. 3:241-252. doi:10.1002/bip.20641