De Novo Hydration of Cryo-EM Reconstructions through Molecular Dynamics Simulations of the Excess Chemical Potential

Abstract

Predicting the precise positions of water molecules at the protein interface remains a formidable challenge, fueling active research in this field. Here, we present a novel approach based on molecular dynamics simulations that utilizes statistical thermodynamic signatures of water at protein interfaces to improve the accuracy of water placement in cryo-EM maps, with apoferritin as a model benchmark system. The interaction energy of solvent with the protein is insufficient to distinguish between high- and lower-consensus water positions, consistent with reports of earlier work. Instead, we employ a detailed statistical thermodynamic analysis based on the excess chemical potential (WT) - a measure of the thermodynamic balance between the interaction energy of an interfacial water molecule with the protein and its free energy of interaction with all of the other solvent molecules. WT is proportional to the log ratio of the local density of water molecules at the protein interface to the bulk density. 85% of the top 100 water locations with the most favorable excess chemical potential values are observed in one or more high resolution Cryo-EM maps deposited in the PDB, and 70% of the top 200 water locations indexed by excess chemical potential are observed in the cryo-EM maps. This work paves the way for the development of a cryo-EM refinement tool that integrates molecular dynamics simulations with cryo-EM data for high-resolution modeling of water networks.