A delocalized proton-binding site within a membrane protein.

Area of Science:

• Biophysics
• Computational Chemistry
• Spectroscopy

Background:

• Protein-bound water molecules are crucial for protein function and catalysis.
• The proton release site in bacteriorhodopsin involves a water cluster and surrounding amino acids.
• Experimental data show broad absorbance indicative of proton delocalization.

Purpose of the Study:

• Investigate proton solvation by protein-bound water molecules.
• Elucidate the contribution of amino acid residues (Glu-194, Glu-204) to proton delocalization.
• Compare simulation results with experimental infrared spectra to validate models.

Main Methods:

• Quantum mechanics/molecular mechanics (QM/MM) simulations using self-consistent charge density functional tight-binding.
• Systematic investigation of quantum box size effects.
• Comparison of calculated and experimental infrared spectra.

Main Results:

• Small quantum boxes (few amino acids/water) reproduce experimental continuum absorbance, indicating proton delocalization.
• Larger quantum boxes including all involved amino acids yield narrow bands, contradicting experiments.
• Proton delocalization on water molecules better matches experimental absorbance than glutamate-shared delocalization.

Conclusions:

• Small quantum boxes capture extreme proton delocalization modes (water-only or Glu-only).
• Discrepancies between simulations and experiments highlight the need for larger quantum boxes and advanced QM/MM methods.
• Further refinement of computational models is necessary for accurate representation of excess proton delocalization in proteins.