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Channel Rhodopsins

Channel Rhodopsins

Most organisms use photoreceptors to sense and respond to light. Examples of photoreceptors include bacteriorhodopsins and bacteriophytochromes in some bacteria, phytochromes in plants, and rhodopsins in the photoreceptor cells of the vertebral retina. The light-sensitive property of these receptors is because of the bound chromophores, such as bilin in the phytochromes and retinal in the rhodopsins.
Rhodopsins belong to the family of cell surface proteins called G-protein coupled receptors,...

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Automatic Rhodopsin Modeling with Multiple Protonation Microstates.

Gustavo Cárdenas¹, Vincent Ledentu¹, Miquel Huix-Rotllant¹

¹Aix-Marseille Univ, CNRS, ICR, 13013 Marseille, France.

The Journal of Physical Chemistry. A

|October 25, 2023

Summary

This summary is machine-generated.

The enhanced Automatic Rhodopsin Modeling (ARM) protocol now includes the minimal electrostatic model (MEM) to simulate multiple protonation states, improving rhodopsin absorption spectrum accuracy across different pH levels.

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Area of Science:

Biophysics
Computational Chemistry
Spectroscopy

Background:

The Automatic Rhodopsin Modeling (ARM) protocol uses QM/MM models to simulate rhodopsin electronic absorption and emission.
Current ARM limitations include modeling only a single protonation microstate per rhodopsin model.

Purpose of the Study:

To extend the ARM protocol to incorporate multiple protonation microstates using the minimal electrostatic model (MEM).
To improve the accuracy of simulated rhodopsin absorption spectra across varying pH conditions.

Main Methods:

Integration of the minimal electrostatic model (MEM) into the existing Automatic Rhodopsin Modeling (ARM) protocol.
Simulation of pH-dependent absorption spectra for a toy model and *Anabaena* sensory rhodopsin.

Main Results:

The new ARM+MEM protocol successfully accounts for relevant protonation microstates at a given pH.
Simulations demonstrated that single-microstate models are inadequate at certain pH values.
ARM+MEM provided an improved description of the *Anabaena* sensory rhodopsin absorption spectrum by considering key residue titrations.

Conclusions:

The ARM+MEM protocol offers a more comprehensive approach to modeling rhodopsin spectral properties.
Accounting for protonation microstates is crucial for accurately predicting pH-dependent spectroscopic behavior in rhodopsins.