Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins

Area of Science:

• Computational Biology
• Biophysics
• Protein Chemistry

Background:

• Protein stability and function depend on the correct ionization states of amino acid residues at physiological pH.
• In situ residue pK(a) values serve as sensitive indicators of the local protein microenvironment.

Purpose of the Study:

• To develop and validate a computational method for simultaneously calculating side chain ionization and conformation.
• To assess the accuracy of predicted residue pK(a) values across diverse protein structures.

Main Methods:

• Utilized Multiconformation Continuum Electrostatics (MCCE), integrating continuum electrostatics and molecular mechanics force fields.
• Employed Monte Carlo sampling to simultaneously determine side chain ionization states and conformations.
• Incorporated protein response to charges via a protein dielectric constant and explicit conformational changes.

Main Results:

• Calculated pK(a) for 166 residues across 12 proteins with a root mean square error of 0.83 pH units.
• Achieved high accuracy, with over 90% of predictions having errors less than 1 pH unit.
• Demonstrated method robustness, showing similar results with crystal and solution structures, and insensitivity to protein dielectric constant variations (4-20).

Conclusions:

• MCCE accurately predicts residue pK(a) values, with explicit conformational sampling reducing sensitivity to initial structure.
• Demonstrated coupling between conformational flexibility and ionization state changes, impacting side chain positioning and molecular interactions.
• The method provides insights into pH-dependent protein behavior, including ligand binding and structural rearrangements.