Advantage of being a dimer for Serratia marcescens endonuclease

Chuanying Chen, Kurt Krause, Bernard Pettitt

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

The monomer and dimer of the bacterium Serratia marcescens endonuclease (SMnase) are each catalytically active, and the two subunits of the dimer function independently of each other. Nature, however, chooses the dimer form instead of the monomer. In order to explain this, we performed molecular dynamics (MD) simulations of both model-built complexes of a subunit of SMnase and the dimer with DNA in aqueous solution. We estimated the electrostatic binding energy, analyzed the distribution and dynamics of water around the complexes, identified water clusters in the protein, and related the dynamics of water to the protein's function. We find that the dimer form has an electrostatic advantage over the monomer to associate with DNA. Although Mg 2+ remains hexa-coordinated during the simulation, the binding pathway of DNA to Mg2+ changes from inner-sphere binding in the monomer to outer-sphere in the dimer, which may be more energetically favorable. In addition, two water clusters in the active site of each monomer and in the dimer complex were identified and localized in two regions, named the "stabilizing" and "working" regions. Water in the "working" region in the dimer complex has larger fluctuations than that in the monomer.

Original languageEnglish (US)
Pages (from-to)511-521
Number of pages11
JournalJournal of Physical Chemistry B
Volume113
Issue number2
DOIs
StatePublished - Jan 15 2009
Externally publishedYes

Fingerprint

Serratia marcescens nuclease
serratia
Dimers
dimers
monomers
Monomers
Water
DNA
deoxyribonucleic acid
water
Electrostatics
electrostatics
proteins
Proteins
Endonucleases
Binding energy
bacteria

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Materials Chemistry
  • Surfaces, Coatings and Films

Cite this

Advantage of being a dimer for Serratia marcescens endonuclease. / Chen, Chuanying; Krause, Kurt; Pettitt, Bernard.

In: Journal of Physical Chemistry B, Vol. 113, No. 2, 15.01.2009, p. 511-521.

Research output: Contribution to journalArticle

Chen, Chuanying ; Krause, Kurt ; Pettitt, Bernard. / Advantage of being a dimer for Serratia marcescens endonuclease. In: Journal of Physical Chemistry B. 2009 ; Vol. 113, No. 2. pp. 511-521.
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