Dynamic and Thermodynamic Signatures of Native and Non-Native Protein States with Application to the Improvement of Protein Structures.

Abstract

Accurate knowledge of the 3D structural ensemble of proteins is important for understanding of their biological function. We report here the application of microsecond all-atom molecular dynamics (MD) simulations in explicit solvent for the improvement of the quality of low-resolution structures obtained by protein structure prediction (decoys). Seventy MD simulations of ∼1 μs average duration were performed on 13 different protein systems starting from X-ray crystal structures and decoys. Their behavior can be divided into three groups: 22 trajectories converged toward the native state, 27 trajectories displayed a quasi-equilibrium by populating mainly a single non-native free energy basin, and 21 trajectories drifted away from their initial decoy structure transiently visiting multiple free energy minima. To determine whether the native structure can be identified among non-native ensembles, the free energy was determined for each basin by the MM/GBSA method together with the von Mises entropy estimator in dihedral angle space. For the proteins studied here, it is found that the ensembles belonging to free energy basins with the lowest free energies and the longest residence times are most native-like. The results demonstrate that explicit solvent microsecond MD simulations using the latest generation of protein force fields and free energy metrics are sufficiently accurate to permit positive identification of native state ensembles against low-resolution structural models and decoys. The approach can be applied to the direct refinement of predicted or experimental low-resolution protein structures.