Determination of a Transition State at Atomic Resolution from Protein Engineering Data

We present a method for determining the structure of the transition state ensemble (TSE) of a protein by using φ values derived from protein engineering experiments as restraints in molecular dynamics simulations employing a realistic all-atom molecular mechanics energy function. The method uses a biasing potential to select an ensemble of structures having φ values in agreement with the experimental data set. An application to acylphosphatase (AcP), a protein for which φ values have been measured for 24 out of 98 residues, illustrates the approach. The properties of the TSE determined in this way are compared with those of a coarse-grained model obtained using a Monte Carlo (MC) sampling method based on a Cα representation of the structure. The two TSEs determined at different structural resolution are consistent and complementary. While the Cα model allows better sampling of the conformation space occupied by the transition state, the all-atom model offers a more detailed description of the structural and energetic properties of the conformations included in the TSE. The combination of low-resolution Cα results with all-atom molecular dynamics simulations provides a powerful and general method for determining the nature of TSEs from protein engineering data.