In silico concurrent multisite pH titration in proteins.

Area of Science:

• Biochemistry
• Computational Biology
• Chemical Physics

Background:

• Concurrent proton binding at multiple sites in macromolecules is a significant challenge in biochemistry.
• Understanding these processes is crucial for deciphering pH-dependent biomolecular mechanisms.

Purpose of the Study:

• To develop an efficient generalized Hamiltonian approach for simulating concurrent multisite proton titration.
• To accurately determine free energy differences between protonation states and construct the grand canonical partition function.

Main Methods:

• Developed an effective potential energy combining contributions from all relevant protonation states.
• Utilized generalized-ensemble methods for efficient sampling of phase regions.
• Reduced the need for intermediate states in alchemical free energy simulations.

Main Results:

• Successfully simulated the pKa of specific residues (Glu49, Asp50) and the C-terminus of bovine pancreatic trypsin inhibitor.
• Demonstrated good agreement with existing experimental data.
• Provided a detailed atomistic view of protonation state population changes during pH titration.

Conclusions:

• The generalized Hamiltonian approach offers a powerful tool for simulating complex proton titration processes in proteins.
• This method provides unprecedented insights into the molecular mechanisms of pH-dependent biomolecular functions.
• The approach is highly valuable for atomistic descriptions of biological systems influenced by pH.