Approach to Study pH-Dependent Protein Association Using Constant-pH Molecular Dynamics: Application to the...

Area of Science:

• Biophysics
• Computational Biology
• Protein Chemistry

Background:

• Protein-protein interactions are crucial for biological functions.
• Electrostatic interactions and pH significantly influence protein association.
• The impact of association on protein protonation states is often overlooked.

Purpose of the Study:

• To develop and apply a constant-pH molecular dynamics (MD) approach for studying pH-dependent protein-protein association.
• To investigate the dimerization of beta-lactoglobulin (BLG) across a pH range of 3-8.
• To elucidate the relationship between protonation states, electrostatic interactions, and dimerization dynamics.

Main Methods:

• Constant-pH molecular dynamics (MD) simulations of monomeric and dimeric bovine beta-lactoglobulin (BLG).
• Estimation of dimerization free energies using Wyman-Tanford linkage theory and thermodynamically based splines.
• Analysis of protonation state correlations, ionic density, and principal component analysis (PCA) of dimerization modes.

Main Results:

• Identified significant correlations between protonation sites, particularly at acidic pH, influencing dimerization free energy.
• Observed electrostatic complementarity at the BLG dimer interface, most pronounced at the isoionic point.
• Characterized two distinct pH-dependent dimerization states: a 'relaxed state' (pH 4-8) and a 'compact state' (pH 3-4).

Conclusions:

• Constant-pH MD simulations provide a powerful method for detailed analysis of pH-dependent protein associations.
• The study reveals key residues and electrostatic factors governing BLG dimerization.
• The identified dimerization states highlight significant conformational changes driven by pH.