Kinetics of Desolvation-Mediated Protein–Protein Binding

Abstract

The role of desolvation in protein binding kinetics is investigated using Brownian dynamics simulations in complexes in which the electrostatic interactions are relatively weak. We find that partial desolvation, modeled by a short-range atomic contact potential, is not only a major contributor to the binding free energy but also substantially increases the diffusion-limited rate for complexes in which long-range electrostatics is weak. This rate enhancement is mostly due to weakly specific pathways leading to a low free-energy attractor, i.e., a precursor state before docking. For alpha-chymotrypsin and human leukocyte elastase, both interacting with turkey ovomucoid third domain, we find that the forward rate constant associated with a collision within a solid angle phi around their corresponding attractor approaches 10(7) and 10(6) M(-1)s(-1), respectively, in the limit phi approximately 2 degrees. Because these estimates agree well with experiments, we conclude that the final bound conformation must be preceded by a small set of well-defined diffusion-accessible precursor states. The inclusion of the otherwise repulsive desolvation interaction also explains the lack of aggregation in proteins by restricting nonspecific association times to approximately 4 ns. Under the same reaction conditions but without short range forces, the association rate would be only approximately 10(3) M(-1)s(-1). Although desolvation increases these rates by three orders of magnitude, desolvation-mediated association is still at least 100-fold slower than the electrostatically assisted binding in complexes such as barnase and barstar.

Solvent fluctuations in hydrophobic cavity–ligand binding kinetics

“…Theoretically, binding rates are often calculated using implicit approaches, where explicit solvent effects are neglected or only coarsely described (21)(22)(23)(24). In the typical view of diffusive encounter of the two reactants, binding kinetics is then governed not only by the free energy (potential of mean force) along the reaction path but also the local diffusivity (or friction) profile (25)(26)(27)(28)(29), which, however, is a priori unknown due to missing microscopic insights.…”

Thermodynamic evaluation and modeling of proton and water exchange associated with benzamidine and berenil binding to ß-trypsin

“…The degree of hydration seems to define states of higher or lower structural flexibility for the protein (17). It was proposed that about 300 water molecules are associated with trypsin (32).…”

“…The involvement of water molecules, helping to define conformational states of the protein through hydrogen bonds, is very important because intra-and intermolecular interactions can modulate the elasticity and plasticity of proteins, which are fundamental for their action (14)(15)(16). The involvement of hydration water molecules, by inclusion or exclusion, has been considered to be a driving force in the interactions involving low charge complementarities (17). Binding of water to hemoglobin, for example, is the determinant step in the mechanism of allosteric regulation (18).…”

Structural basis of RNA binding by leucine zipper GCN4

“…2(B,C)]. The helicity of glutamate and serine mutants remained largely unaffected; however those displayed increased stability since unfolding temperature was increased by 2.8-7.8 C. This effect may be due to the increased helical propensity of alanine, elimination of repulsive electrostatic interactions and/or elimination of charge desolvation penalty, [15][16][17] . S7) data suggested that the introduced mutations had only marginal effect on the overall integrity of LZ.…”

“…Transverse relaxation rates and corresponding errors were calculated employing CurveFit (A. G. Palmer, Columbia University, www. palmer.hs.columbia.edu) based on six relaxation delay values (8,16,32,64,96, and 128 ms).…”