Using a charging coordinate in studies of ionization induced partial unfolding

Area of Science:

• Biophysics
• Computational Chemistry
• Protein Science

Background:

• Protein ionization can induce structural changes like unfolding or water penetration.
• Standard nanosecond free energy perturbation (FEP) simulations often fail to capture these changes due to activation barriers.
• This limitation is evident in mutation studies and challenges in predicting pKa values.

Purpose of the Study:

• To develop a novel computational approach for accurately simulating protein ionization and associated structural rearrangements.
• To overcome the limitations of existing FEP methods in handling large-scale conformational changes driven by ionization.
• To provide a more reliable method for calculating pKa values of ionizable residues within proteins.

Main Methods:

• Developed a new
• overcharging
• approach.
• This method artificially increases the charge of the ionized group to overcome activation barriers for protein structural changes.
• Applied the method to calculate the pKa of the Val66Glu mutant in staphylococcal nuclease.

Main Results:

• Standard FEP simulations yielded inaccurate pKa predictions for the Val66Glu mutant.
• The novel
• overcharging
• approach provided significantly more realistic pKa results.
• Demonstrated the method's effectiveness in cases where standard FEP fails.

Conclusions:

• The
• overcharging
• approach represents a breakthrough for FEP studies of ionizable protein residues.
• This method accurately captures ionization-induced structural changes and pKa shifts.
• The strategy is expected to be valuable for various challenging problems, including hydrogen exchange simulations.