PREDICTING PROTEIN MUTANT ENERGETICS BY SELF-CONSISTENT ENSEMBLE OPTIMIZATION

In this paper we present a self-consistent ensemble optimization (SCEO) theory for efficient conformational search, which we have applied to predicting the effects of mutations on protein thermostability. This approach takes advantage of a statistical mechanical self-consistency condition to home in iteratively on the global minimum structure. We employ a fast potential of mean-force approximation to cut computation time to a few minutes for a typical protein mutation, with only linear time-dependence on the size of the prediction problem. Rather than seeking a single, static structure of minimum energy, the new method optimizes an ensemble of many conformations, seeking to predict the most likely ensemble for the native state at a desired temperature. Testing this approach with a simple physical model focusing entirely on steric interactions and side-chain rearrangement, we obtain robustly convergent prediction of core side-chain conformation, and of hydrophobic core mutations' effects on protein stability. Self-consistent ensemble optimization is superior to simulated annealing in its speed and convergence to the global minimum, and insensitive to starting conformation. In calculations on λ repressor protein, structural predictions for an eight-residue molten-zone had side-chain r.m.s. error of 0.49 Å for the wild-type protein. Evaluation of the method's mutant structure predictions should become possible, as structures of these mutant repressors are solved. Predicted energies for a series of nine hydrophobic core mutants correlated with measured free energies of unfolding with a coefficient of 0.82. © 1994 Academic Press Inc.