Protocols utilizing constant pH molecular dynamics to compute pH-dependent binding free energies.

Area of Science:

• Biochemistry
• Computational Chemistry
• Molecular Dynamics

Background:

• Protein-ligand binding can alter electrostatic environments, leading to protonation changes.
• Ligand binding can be pH-dependent if proton uptake or release occurs.
• Standard free energy calculations often neglect protonation state changes.

Purpose of the Study:

• To develop a computational methodology for calculating pH-dependent binding free energies.
• To account for protonation changes during molecular binding events.
• To apply the method to cucurbit[7]uril (CB[7]) host-guest systems.

Main Methods:

• Utilized Wyman's binding polynomial formalism.
• Employed constant pH molecular dynamics simulations.
• Integrated experimental or thermodynamic integration data for reference binding free energy.

Main Results:

• Accurately captured significant pKa shifts upon CB[7]:guest association.
• Reproduced experimental binding free energies across various pH levels.
• Demonstrated that fixed protonation states can introduce >2 kcal/mol errors.

Conclusions:

• The presented computational protocol effectively determines proton-linked binding free energies.
• This method improves accuracy in host-guest systems and is applicable to protein-ligand complexes.
• Avoids errors associated with assuming fixed protonation states in calculations.