Deciphering Infrared Difference Spectra of Bovine Rhodopsin in the Amide I Region by Localized Anharmonic Vibrational...

Area of Science:

• Biophysics
• Computational Chemistry
• Spectroscopy

Background:

• Bovine rhodopsin's amide bands change significantly upon photoactivation.
• Understanding these spectral shifts requires advanced computational methods.
• Previous methods struggled to accurately model anharmonicity in large biomolecular systems.

Purpose of the Study:

• To develop and apply a novel computational approach for analyzing vibrational spectra of large biomolecules.
• To investigate the amide bands of bovine rhodopsin in its inactive and active states.
• To interpret the microscopic origins of spectral changes upon photoactivation.

Main Methods:

• Combining vibrational quasi-degenerate perturbation theory (VQDPT2) with quantum mechanics/molecular mechanics (QM/MM).
• Developing a novel subsystem-based localization scheme for amide groups.
• Calculating and summing local amide spectra to construct the total spectrum.

Main Results:

• The method accurately reproduced the experimental IR difference spectrum of bovine rhodopsin.
• Amide I band shifts were found to originate from both helical and loop regions.
• Specific residues like Thr118 and Trp265 showed significant frequency shifts linked to structural changes.

Conclusions:

• The developed subsystem-based anharmonic vibrational approach is effective for large biomolecular systems.
• Accounting for anharmonicity is crucial for accurate spectral interpretation.
• This method provides a powerful tool for microscopic interpretation of vibrational spectra.