Accelerated Enveloping Distribution Sampling (AEDS) Allows for Efficient Sampling of Orthogonal Degrees of Freedom

One of the most challenging aspects in the molecular simulation of proteins is the study of slowly relaxing processes, such as loop rearrangements or ligands that adopt different conformations in the binding site. State-of-the-art methods used to calculate binding free energies rely on performing several short simulations (lambda steps), in which the ligand is slowly transformed into the endstates of interest. This makes capturing the slowly relaxing processes even more difficult, as they would need to be observed in all of the lambda steps. One attractive alternative is the use of a reference state capable of sampling all of the endstates of interest in a single simulation. However, the energy barriers between the states can be too high to overcome, thus hindering the sampling of all of the relevant conformations. Accelerated enveloping distribution sampling (AEDS) is a recently developed reference state technique that circumvents the high-energy-barrier challenge by adding a boosting potential that flattens the energy landscape without distorting the energy minima. In the present work, we apply AEDS to the well-studied benchmark system T4 lysozyme L99A. The T4 lysozyme L99A mutant contains a hydrophobic pocket in which there is a valine (valine 111), whose conformation influences the binding efficiencies of the different ligands. Incorrectly sampling the dihedral angle can lead to errors in predicted binding free energies of up to 16 kJ mol. This protein constitutes an ideal scenario to showcase the advantages and challenges when using AEDS in the presence of slow relaxing processes. We show that AEDS is able to successfully sample the relevant degrees of freedom, providing accurate binding free energies, without the need of previous information of the system in the form of collective variables. Additionally, we showcase the capabilities of AEDS to efficiently screen a set of ligands. These results represent a promising first step toward the development of free-energy methods that can respond to more intricate molecular events.