Do electrostatic interactions destabilize protein–nucleic acid binding?

✍ Scribed by Sanbo Qin; Huan-Xiang Zhou

• Publisher: Wiley (John Wiley & Sons)
• Year: 2007
• Tongue: English
• Weight: 271 KB
• Volume: 86
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/bip.20708

✦ Synopsis

Abstract

The negatively charged phosphates of nucleic acids are often paired with positively charged residues upon binding proteins. It was thus counter‐intuitive when previous Poisson–Boltzmann (PB) calculations gave positive energies from electrostatic interactions, meaning that they destabilize protein–nucleic acid binding. Our own PB calculations on protein–protein binding have shown that the sign and the magnitude of the electrostatic component are sensitive to the specification of the dielectric boundary in PB calculations. A popular choice for the boundary between the solute low dielectric and the solvent high dielectric is the molecular surface; an alternative is the van der Waals (vdW) surface. In line with results for protein–protein binding, in this article, we found that PB calculations with the molecular surface gave positive electrostatic interaction energies for two protein–RNA complexes, but the signs are reversed when the vdW surface was used. Therefore, whether destabilizing or stabilizing effects are predicted depends on the choice of the dielectric boundary. The two calculation protocols, however, yielded similar salt effects on the binding affinity. Effects of charge mutations differentiated the two calculation protocols; PB calculations with the vdW surface had smaller deviations overall from experimental data. © 2007 Wiley Periodicals, Inc. Biopolymers 86: 112–118, 2007.

This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at [email protected]