Solvent participation in Serratia marcescens endonuclease complexes

Area of Science:

• Biochemistry
• Molecular Biology
• Computational Biology

Background:

• Serratia marcescens endonuclease (SMnase) exists as active monomers and dimers.
• Interfacial water molecules are hypothesized to influence SMnase stability and function.

Purpose of the Study:

• To investigate the role of hydration sites in the catalytic mechanism of SMnase.
• To analyze the impact of DNA binding on SMnase hydration properties.

Main Methods:

• Molecular dynamics simulations of SMnase monomer and its DNA complex.
• Analysis of hydration site occupancy and water residence times.
• Investigation of magnesium ion coordination and ligand exchange.

Main Results:

• DNA binding minimally affects global protein hydration.
• Protein-DNA recognition primarily involves direct hydrogen bond and hydrophobic interactions.
• A conserved water cluster near the active site stabilizes DNA cleavage, transition states, and leaving groups.
• Magnesium ion undergoes ligand exchange upon DNA binding, involving protein and DNA residues.

Conclusions:

• Water molecules are integral to SMnase's catalytic mechanism, beyond just DNA cleavage.
• Specific water clusters play a crucial role in stabilizing the enzyme-DNA complex and the reaction.
• SMnase's hydration dynamics are key to its enzymatic activity and stability.