Exploring the Free Energy Landscape and Thermodynamics of Protein-Protein AssociationAssociation: HIV-1 Integrase Multimerization Induced by an Allosteric Inhibitor

Abstract

We report the free energy landscape and thermodynamics of the protein-protein association responsible for the drug-induced multimerization of HIV-1 integrase (IN). Allosteric HIV-1 integrase inhibitors (ALLINIs) promote aberrant IN multimerization by bridging IN-IN intermolecular interactions. However, the thermodynamic driving forces and kinetics of the multimerization remain largely unknown. Here we explore the early steps in the IN multimerization by using umbrella sampling and unbiased molecular dynamics simulations in explicit solvent. In direct simulations, the two initially separated dimers spontaneously associate to form near-native complexes that resemble the crystal structure of the aberrant tetramer. Most strikingly, the effective interaction of the protein-protein association is very short-ranged: the two dimers associate rapidly within tens of nanoseconds when their binding surfaces are separated by d ≤ 4.3 Å (less than two water diameters). Beyond this distance, the oligomerization kinetics appears to be diffusion controlled with a much longer association time. The free energy profile also captured the crucial role of ALLINI in promoting multimerization, and explained why several CTD mutations are remarkably resistant to the drug-induced multimerization. The results also show that at small separation the protein-protein binding process contains two consecutive phases with distinct thermodynamic signatures. First, inter-protein water molecules are expelled to the bulk resulting in a small increase in entropy, as the solvent entropy gain from the water release is nearly cancelled by the loss of side chain entropies as the two proteins approach each other. At shorter distances, the two dry binding surfaces adapt to each other to optimize their interaction energy at the expense of further protein configurational entropy loss. While the binding interfaces feature clusters of hydrophobic residues, overall, the protein-protein association in this system is driven by enthalpy and opposed by entropy.Statement of Significance Elucidating the energetics and thermodynamic aspects of protein-protein association is important for understanding this fundamental biophysical process. This study provided a more complete physical picture of the protein-protein association responsible for the drug-induced HIV-1 integrase multimerization. The results captured the critical role of the inhibitor, and accounted for the effects of mutations on the protein association. Remarkably, the effective range of the protein-protein attractive funnel is found to be very short, at less than two layers of water, despite the fact that the two binding partners carry opposite net charges. Lastly, entropy/enthalpy decomposition shows that the solvent release from the inter-protein region into the bulk is more than offset by the loss of the solute configurational entropy due to complexation.View Full Text