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Submillisecond Conformational Changes in Proteins Resolved by Photothermal Beam Deflection

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Modeling pH-Dependent Biomolecular Photochemistry.

Elisa Pieri¹, Oliver Weingart², Miquel Huix-Rotllant¹

¹Aix-Marseille Univ, CNRS, Institut de Chimie Radicalaire, 13013 Marseille, France.

Journal of Chemical Theory and Computation

|January 10, 2024

Summary

This study introduces a computational protocol to model pH effects on photochemical properties in biological systems. The method accurately predicts pH-dependent photodynamics and identifies key amino acids influencing these changes.

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Area of Science:

Biophysics
Computational Chemistry
Photochemistry

Background:

Modeling pH-dependent photochemical properties in biological systems is computationally challenging.
Understanding these mechanisms is crucial for various biological processes.

Purpose of the Study:

To develop and validate a computational protocol for modeling pH-dependent photodynamics.
To investigate the role of specific amino acids in tuning photochemical properties.

Main Methods:

Combined constant-pH molecular dynamics and semiclassical nonadiabatic molecular dynamics simulations.
Utilized retinal photoisomerization in Anabaena sensory rhodopsin (ASR) as a model system.

Main Results:

The protocol successfully reproduced pH-dependent photochemical properties, including isomerization quantum yield and decay rates.
Identified key amino acid residues responsible for pH-dependent tuning.
Evaluated the accuracy of single protonation state approximations.

Conclusions:

The developed protocol provides an accurate approach for modeling pH-dependent photodynamics.
The study highlights the importance of specific residues in modulating photochemical behavior.
The most populated protein charge state offers a balance between computational cost and accuracy.