Prediction of salt and mutational effects on the association rate of U1A protein and U1 small nuclear RNA stem/loop II

Abstract

We have developed a computational approach for predicting protein-protein association rates (Alsallaq and Zhou, Structure 2007, 15, 215). Here we expand the range of applicability of this approach to protein-RNA binding and report the first results for protein-RNA binding rates predicted from atomistic modeling. The system studied is the U1A protein and stem/loop II of the U1 small nuclear RNA. Experimentally it was observed that the binding rate is significantly reduced by increasing salt concentration while the dissociation changes little with salt concentration, and charges distant from the binding site make marginal contribution to the binding rate. These observations are rationalized. Moreover, predicted effects of salt and charge mutations are found to be in quantitative agreement with experimental results.

Figure 1

The native complex of U1A and U1SLII. (a) Locations of mutated residues. (b) Electrostatic surface of U1A.

Figure 2

Representative configurations in the transient complex of U1A and U1SLII.

Figure 3

Comparison of predicted and experimental ionic-strength dependences of the U1A-U1SLII binding rate.

Figure 4

Comparison of predicted and experimental results for the binding rates of wild-type U1A and seven mutants with U1SLII. The ionic strength was 160 mM.

Figure 5

Comparison of rate enhancements for compact and diffuse transient-complex ensembles. For the spherical target with radius R, the interaction potential is given by U = U* for R < r < 4R and 0 elsewhere (r: radial distance). The binding site is either a patch with an area fraction of 2.5 × 10⁻⁵ or is the whole surface. The cylindrical target features a binding site on an infinite cylinder with radius R. The binding site length is either 0.02R or 200R. The interaction potential is given by U = U* for R < ρ < 7R and 0 elsewhere (ρ: distance to the cylinder axis). The results were obtained from analytical solutions given by Zhou and Szabo.