Exploring the Effect of Enhanced Sampling on Protein Stability Prediction

Changes in protein stability due to side-chain mutations are evaluated by alchemical free-energy calculations based on classical molecular dynamics (MD) simulations in explicit solvent using the GROMOS forcefield. Three proteins of different complexity with a total number of 93 single-point mutations are analyzed, and the relative free-energy differences are discussed with respect to configurational sampling and (dis)agreement with experimental data. For the smallest protein studied, a 34-residue WW domain, the startingstructure dependence of the alchemical free-energy changes, is discussed indetail. Deviations from previous simulations for the two other proteins are shown to result from insufficient sampling in the earlier studies. Hamiltonian replica exchange in combination with multiple starting structures and sufficient sampling time of more than 100 ns per intermediate alchemical state is required in some cases to reach convergence

Automated summary

The impact of side-chain mutations on protein stability is analyzed using alchemical free-energy calculations based on molecular dynamics simulations. Different proteins with a total of 93 mutations are studied, and the relative free-energy differences are compared with experimental data. Insufficient sampling in previous studies is identified as a cause for deviations from previous simulations in some cases.