Predicting water at the protein interface in cryo-EM structures from MD-excess chemical potential

Area of Science:

• Structural Biology
• Computational Biology
• Biophysics

Background:

• Accurate prediction of water molecule positions at protein interfaces is crucial for understanding protein function and interactions.
• Current methods for water placement in cryogenic electron microscopy (cryo-EM) maps face challenges in accuracy and reliability.

Purpose of the Study:

• To develop a novel computational approach for improving the accuracy of water molecule placement in cryo-EM maps.
• To leverage statistical thermodynamic signatures, specifically excess chemical potential, from molecular dynamics (MD) simulations for enhanced water positioning.

Main Methods:

• Utilized molecular dynamics (MD) simulations to calculate the excess chemical potential (Work to Transfer - WT) for water molecules at protein interfaces.
• Analyzed the thermodynamic balance of water-protein interactions versus water-solvent interactions using WT.
• Applied the method to apoferritin as a benchmark system, comparing predicted water positions with experimentally determined structures in the Protein Data Bank (PDB).

Main Results:

• 85% of the top 100 predicted water locations based on favorable excess chemical potential (WT) were found in experimentally determined cryo-EM structures.
• 70% of the top 200 predicted water locations correlated strongly with positions observed in PDB structures derived from cryo-EM data.
• MD simulations, performed without experimental restraints, showed a strong correlation between favorable WT values and observed water positions in cryo-EM maps.

Conclusions:

• The developed method integrating MD simulations of excess chemical potential with cryo-EM data shows significant promise for accurate water placement.
• This approach can lead to the development of a new tool for water placement and refinement in cryo-EM studies.
• Improved modeling of water networks at protein interfaces will advance the understanding of biological processes.