pK(a) calculations along a bacteriorhodopsin molecular dynamics trajectory

Area of Science:

• Biophysics
• Computational Chemistry
• Structural Biology

Background:

• Bacteriorhodopsin is a crucial membrane protein involved in light-driven proton pumping.
• Understanding the protonation states of amino acid residues is key to elucidating its mechanism.
• Electrostatic calculations offer a computational approach to study these protonation states.

Purpose of the Study:

• To calculate pK(a) values for bacteriorhodopsin using electrostatic methods along a molecular dynamics trajectory.
• To investigate the sensitivity of pK(a) calculations to structural and electrostatic modeling parameters.
• To determine the influence of internal water molecules and trajectory averaging on protonation states.

Main Methods:

• Molecular dynamics (MD) simulations of bacteriorhodopsin over 400 ps.
• Electrostatic calculations to determine pK(a) values.
• Analysis of the impact of internal dielectric constant (2-4) and inclusion of water molecules.
• Averaging over equilibrium MD trajectory portions (approx. 100 ps).

Main Results:

• Calculated pK(a) values are highly sensitive to the internal dielectric constant of the protein.
• Inclusion of internal water molecules is necessary for correct protonation of key residues (Schiff base, Arg 82, Asp 85, Asp 212).
• A relationship between Arg 82, Asp 85, and Glu 204 protonation states was identified, with Glu 204's pK(a) decreasing upon chromophore isomerization.

Conclusions:

• Accurate electrostatic modeling of bacteriorhodopsin requires careful consideration of the internal dielectric constant and explicit water molecules.
• Averaging over MD trajectories is vital for obtaining correct protonation states, especially at non-neutral pH.
• The protonation dynamics of Glu 204 are linked to the chromophore's photoisomerization state.