Abstract
Virtually all biological processes depend on the interaction between proteins at some point. The correct prediction of biomolecular binding free-energies has many interesting applications in both basic and applied pharmaceutical research. While recent advances in the field of molecular dynamics (MD) simulations have proven the feasibility of the calculation of protein–protein binding free energies, the large conformational freedom of proteins and complex free energy landscapes of binding processes make such calculations a difficult task. Moreover, convergence and reversibility of resulting free-energy values remain poorly described. In this work, an easy-to-use, yet robust approach for the calculation of standard-state protein–protein binding free energies using perturbed distance restraints is described. In the binding process the conformations of the proteins were restrained, as suggested earlier. Two approaches to avoid end-state problems upon release of the conformational restraints were compared. The method was evaluated by practical application to a small model complex of ubiquitin and the very flexible ubiquitin-binding domain of human DNA polymerase ι (UBM2). All computed free energy differences were closely monitored for convergence, and the calculated binding free energies had a mean unsigned deviation of only 1.4 or 2.5 kJ·mol–1 from experimental values. Statistical error estimates were in the order of thermal noise. We conclude that the presented method has promising potential for broad applicability to quantitatively describe protein–protein and various other kinds of complex formation.
Highlights
All biological processes rely on the interaction between macromolecules at some point
For the calculation of the unbinding free energy of the proteins restrained to their bound conformations (ΔGurensbind), the binding and unbinding process was simulated in a Hamiltonian replica exchange MD (HREMD) setup with 54 unequally spaced replicas
Forward and reverse cumulative averages of ΔGurensbind of both the complex involving wt UBM2 and P692A UBM2 calculated with Bennett’s acceptance ratio (BAR) for systems RS are given in Figure 4
Summary
All biological processes rely on the interaction between macromolecules at some point. In the field of drug design, the computational modeling of macromolecular interactions can give insight into the mode of action of biological therapeutics like antibodies and aid the development thereof. Methods like protein−protein docking attempt to overcome the mismatch between the number of available complex structures and single protein structures by the prediction of binding interfaces. The binding free energy estimates given by the scoring algorithms used in such approaches show only poor correlation with experimentally determined binding free energies.[1] It is noted that thermodynamic properties are intrinsically determined by ensembles of microstates and not from single structures.[2] If a precise binding free energy estimate should be calculated from a complex structure by computational means, molecular dynamics (MD) simulations are the method of choice, given the efficient sampling of macromolecular phase-space. Because of the large phase-space and the possible conformational changes accompanying binding reactions, different approaches to the efficient calculation of protein−protein binding free energies have been proposed
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