Rhodopsin charge diffusion computations disclose contrasting color-tuning mechanisms

Area of Science:

• Biophysics
• Computational Biology
• Spectroscopy

Background:

• Understanding spectral tuning in light-absorbing proteins is crucial but limited.
• Rhodopsins exhibit complex electrostatic potential patterns due to chromophore counterion and polar residue interactions.
• The precise effect of these interactions on spectral properties remains unclear.

Purpose of the Study:

• To model the effect of counterion charge diffusion on excitation energies and chromophore geometry in the Arch-3 protein.
• To elucidate the rules governing spectral tuning in microbial rhodopsins.
• To investigate the relationship between spectral shifts and chromophore isomerization.

Main Methods:

• Computational modeling of the Arch-3 optogenetic reporter.
• Optimization of counterion charge diffusion for varying excitation wavelengths (λmax).
• Analysis of compact and extended charge diffusion pathways.
• Validation against experimental data from Arch-3, NeoR variants, and other microbial rhodopsins.

Main Results:

• Two distinct pathways, 'compact' and 'extended' charge diffusion, were identified for red-shifted spectral tuning (increasing λmax).
• These pathways correlate with specific changes in chromophore geometry.
• The model successfully replicates experimentally observed relationships between λmax and chromophore isomerization across diverse microbial rhodopsins.

Conclusions:

• Counterion charge diffusion is a key determinant of spectral tuning in Arch-3 and related microbial rhodopsins.
• The identified 'compact' and 'extended' diffusion pathways provide a framework for understanding spectral shifts.
• This work advances the understanding of structure-function relationships in light-absorbing proteins.