Applying Absolute Free Energy Perturbation Molecular Dynamics to Diffusively Binding Ligands

Area of Science:

• Computational Chemistry
• Structural Biology
• Biophysics

Background:

• Ligands that bind diffusively to proteins pose challenges for traditional free energy perturbation (FEP) simulations.
• Understanding these binding mechanisms is crucial for drug discovery and molecular biology.

Purpose of the Study:

• To develop and validate an advanced FEP protocol for calculating binding free energy and mechanism of diffusively binding ligands.
• To investigate the binding of a minNLS peptide to importin-α, a system with no well-defined binding poses.

Main Methods:

• Developed an absolute free energy perturbation (FEP) protocol integrating all-atom molecular dynamics, replica exchange with solute tempering (REST) enhanced sampling, and spherical harmonic restraints.
• Applied the FEP/REST protocol to simulate the binding of the minNLS peptide (KKPK) to importin-α.
• Analyzed simulation data to determine binding free energy, binding mechanism, and structural ensemble of the bound ligand.

Main Results:

• The FEP/REST protocol successfully computed a converged binding free energy estimate for minNLS.
• Demonstrated that minNLS binds to importin-α with moderate affinity via a unique, purely entropic mechanism.
• Identified the release of water from charged amino acid solvation shells as the primary driver of favorable binding entropy.
• Characterized the distribution of bound structures, interactions, and binding sites on importin-α.

Conclusions:

• The developed FEP/REST protocol is effective for simulating diffusively binding ligands.
• The binding of minNLS to importin-α is primarily driven by favorable entropic contributions, particularly water release.
• This study provides insights into unusual binding mechanisms and offers a robust computational approach for challenging ligand-protein systems.