Article, 2024

Color Tuning in Bovine Rhodopsin through Polarizable Embedding

The Journal of Physical Chemistry B, ISSN 1520-5207, 1520-6106, Volume 128, 12, Pages 2864-2873, 10.1021/acs.jpcb.3c07891

Contributors

Di Prima, Duccio [1] Reinholdt, Peter 0000-0003-2406-700X [1] Kongsted, Jacob 0000-0002-7725-2164 (Corresponding author) [1]

Affiliations

  1. [1] University of Southern Denmark
    2. [NORA names: SDU University of Southern Denmark; University; Denmark; Europe, EU; Nordic; OECD]

Abstract

Bovine rhodopsin is among the most studied proteins in the rhodopsin family. Its primary activation mechanism is the photoisomerization of 11-cis retinal, triggered by the absorption of a UV-visible photon. Different mutants of the same rhodopsin show different absorption wavelengths due to the influence of the specific amino acid residues forming the cavity in which the retinal chromophore is embedded, and rhodopsins activated at different wavelengths are, for example, exploited in the field of optogenetics. In this letter, we present a procedure for systematically investigating color tuning in models of bovine rhodopsin and a set of its mutants embedded in a membrane bilayer. Vertical excitation energy calculations were carried out with the polarizable embedding potential for describing the environment surrounding the chromophore. We show that polarizable embedding outperformed regular electrostatic embedding in determining both the vertical excitation energies and associated oscillator strengths of the systems studied.

Keywords

UV-visible photons, absorption, absorption wavelength, acid residues, activation mechanism, amino acid residues, bilayer, bovine rhodopsin, calculations, cavity, chromophore, color, color tuning, electrostatic embedding, embedding, embedding potential, energy, energy calculations, environment, excitation energy, excitation energy calculations, family, field, field of optogenetics, influence, letter, mechanism, membrane, membrane bilayer, model, mutants, optogenetics, oscillations, oscillator strengths, photoisomerization, photons, polarizability, polarizable embedding, potential, primary activation mechanisms, procedure, protein, residues, retinal chromophore, rhodopsin, rhodopsin family, specific amino acid residues, strength, system, systematically, tuning, vertical excitation energies, vertical excitation energy calculations, wavelength

Funders

  • Danish Agency for Science and Higher Education

Data Provider: Digital Science

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