Book of Abstracts: Albany 2003
June 17-21 2003
The Role of Both Negatively and Positively Charged Protein Residues on the Salt-Dependent Protein-Nucleic Acid Association Process
The long-range electrostatic forces associated with highly charged nucleic acid polyions typically provide a strong driving force for the interaction between proteins and nucleic acids. For many protein-DNA (RNA) systems a plot of log (Kobs) (observed binding constant) as a function of log(salt) is linear, at least in a limited range. The slope has commonly been interpreted as proportional to the number of ion (phosphate-cationic protein residue) pairs formed upon complexation. This model implies that only the positively charged protein residues influence the electrostatic potential surrounding the nucleic acid. We have performed a nonlinear Poisson-Boltzmann analysis of 30 different protein-DNA (RNA) recognition complexes. We find that the slopes δlog(ΔGel)/δlog(salt) in the presence and absence (with the charge on the negatively charged residues turned "off") of negatively charged protein residues are different. Therefore, our results suggest that both positively and negatively charged protein residues interact with the electrostatic field of the nucleic acid in the binding site region.
Marcia O. Fenley1,*
1Institute of Molecular Biophysics