SIMULATION OF ELECTROSTATIC AND HYDRODYNAMIC PROPERTIES OF SERRATIA ENDONUCLEASE

We analyze the electrostatic and hydrodynamic properties of a nuclease from the pathogenic gram-negative bacterium Serratia marcescens using finite-difference Poisson-Boltzmann methods for electrostatic calcula tions and a bead-model approach for diffusion coefficient calculations . Electrostatic properties are analyzed for the enzyme in monomeric an d dimeric Sol ms and also in the context of DNA binging by the nucleas e. Our preliminary results show that binding of a double-stranded DNA dodecamer by nuclease causes an overall shift in the charge of the pro tein by approximately three units of elementary charge pet monomer, re sulting, in a positively charged protein? at physiologic pH. In these calculations,the free enzyme was found to have a negative (-1 e) charg e per monomer at pH 7. The most dramatic shift in pK(a) involves His 8 9 whose pK(a) increases by three pH units upon DNA binding. This shift leads to a protonated residue at pH 7, in contrast to the unprotonate d form in the free enzyme. DNA binding also leads to a decrease in the energetic distances between the most stable protonation states of the enzyme. Dimerization has no significant effect on the electrostatic p roperties of each of the monomers for both free enzyme and that bound to DNA. Results of hydrodynamic calculations are consistent with the d imeric form of the enzyme in solution. The computed translational diff usion coefficient for the dimer model of the enzyme is in very good ag reement with measurements from light scattering experiments. Prelimina ry electrooptical calculations indicate that the dimer should possess a large dipole moment (appr- oximately 600 Debye units) as well as sub stantial optical anisotropy (limiting reduced linear electric dichrois m of about 0.3). Therefore, this system may serve as a good model for investigation of electric and hydrodynamic properties by relaxation el ectrooptical experiments. (C) 1997 John Wiley & Sons, Inc.