Relative Binding Enthalpies from Molecular Dynamics Simulations Using a Direct Method

Area of Science:

• Computational chemistry
• Biophysics
• Molecular modeling

Background:

• Accurate prediction of binding enthalpies is crucial for drug discovery.
• Molecular dynamics (MD) simulations offer a potential route for calculating these values.
• The Src SH2 domain is a key protein in cellular signaling pathways.

Purpose of the Study:

• To evaluate the reliability of a direct molecular dynamics method for predicting relative binding enthalpies (ΔΔE).
• To assess the accuracy and uncertainties associated with this computational approach.
• To investigate the binding of phosphotyrosyl peptides to the Src SH2 domain.

Main Methods:

• Utilized equilibrium molecular dynamics simulations in explicit water.
• Calculated binding enthalpies from potential energy differences between bound and unbound states.
• Employed a bootstrap method to determine statistical uncertainties from multiple independent simulations.
• Initiated simulations with varied starting coordinates and velocities.

Main Results:

• Achieved statistical uncertainties of 2-3 kcal/mol for ΔΔE in the Src SH2-peptide system.
• Observed significantly larger uncertainties in component energy contributions (solute-solute, solute-solvent, solvent-solvent).
• Analysis indicated trajectories sampled the same conformational basin, with variations attributed to local sampling differences.

Conclusions:

• The direct estimation of relative binding enthalpies via MD is a reasonable approach for well-ordered systems with ΔΔE > ~3 kcal/mol.
• The method's accuracy is dependent on adequate sampling of conformational space.
• Future work should focus on optimizing starting point distribution for enhanced sampling efficiency.