Effects of dimerization of Serratia marcescens endonuclease on water dynamics

Chuanying Chen, Brian W. Beck, Kurt Krause, Tiffany E. Weksberg, B. Montgomery Pettitt

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)241-252
Number of pages12
JournalBiopolymers
Volume85
Issue number3
DOIs
StatePublished - Feb 15 2007

Keywords

  • Computer simulation
  • Molecular dynamics
  • Protein-DNA recognition

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Biomaterials
  • Organic Chemistry

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