Simulation of electrostatic and hydrodynamic properties of Serratia endonuclease.

摘要: We analyze the electrostatic and hydrodynamic properties of a nuclease from pathogenic gram-negative bacterium Serratia marcescens using finite-difference Poisson-Boltzmann methods for calculations bead-model approach diffusion coefficient calculations. Electrostatic are analyzed enzyme in monomeric dimeric forms also context DNA binding by nuclease. Our preliminary results show that double-stranded dodecamer causes an overall shift charge protein approximately three units elementary per monomer, resulting positively charged at physiologic pH. In these calculations, free was found to have negative (-1 e) monomer pH 7. The most dramatic pKa involves His 89 whose increases upon binding. This leads protonated residue 7, contrast unprotonated form enzyme. decrease energetic distances between stable protonation states Dimerization has no significant effect on each monomers both bound DNA. Results consistent with solution. computed translational dimer model is very good agreement measurements light scattering experiments. Preliminary electrooptical indicate should possess large dipole moment (approximately 600 Debye units) as well substantial optical anisotropy (limiting reduced linear electric dichroism about 0.3). Therefore, this system may serve investigation relaxation