Cargando…

Retinal Vibrations in Bacteriorhodopsin are Mechanically Harmonic but Electrically Anharmonic: Evidence From Overtone and Combination Bands

Fundamental vibrations of the chromophore in the membrane protein bacteriorhodopsin (BR), a protonated Schiff base retinal, have been studied for decades, both by resonance Raman and by infrared (IR) difference spectroscopy. Such studies started comparing vibrational changes between the initial BR s...

Descripción completa

Detalles Bibliográficos
Autores principales: Lorenz-Fonfria, Victor A., Yagi, Kiyoshi, Ito, Shota, Kandori, Hideki
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8718751/
https://www.ncbi.nlm.nih.gov/pubmed/34977154
http://dx.doi.org/10.3389/fmolb.2021.749261
_version_ 1784624797773201408
author Lorenz-Fonfria, Victor A.
Yagi, Kiyoshi
Ito, Shota
Kandori, Hideki
author_facet Lorenz-Fonfria, Victor A.
Yagi, Kiyoshi
Ito, Shota
Kandori, Hideki
author_sort Lorenz-Fonfria, Victor A.
collection PubMed
description Fundamental vibrations of the chromophore in the membrane protein bacteriorhodopsin (BR), a protonated Schiff base retinal, have been studied for decades, both by resonance Raman and by infrared (IR) difference spectroscopy. Such studies started comparing vibrational changes between the initial BR state (all-trans retinal) and the K intermediate (13-cis retinal), being later extended to the rest of intermediates. They contributed to our understanding of the proton-pumping mechanism of BR by exploiting the sensitivity of fundamental vibrational transitions of the retinal to its conformation. Here, we report on new bands in the 2,500 to 1,800 cm(−1) region of the K-BR difference FT-IR spectrum. We show that the bands between 2,500 and 2,300 cm(−1) originate from overtone and combination transitions from C-C stretches of the retinal. We assigned bands below 2,300 cm(−1) to the combination of retinal C-C stretches with methyl rocks and with hydrogen-out-of-plane vibrations. Remarkably, experimental C-C overtone bands appeared at roughly twice the wavenumber of their fundamentals, with anharmonic mechanical constants ≤3.5 cm(−1), and in some cases of ∼1 cm(−1). Comparison of combination and fundamental bands indicates that most of the mechanical coupling constants are also very small. Despite the mechanical quasi-harmonicity of the C-C stretches, the area of their overtone bands was only ∼50 to ∼100 times smaller than of their fundamental bands. We concluded that electrical anharmonicity, the second mechanism giving intensity to overtone bands, must be particularly high for the retinal C-C stretches. We corroborated the assignments of negative bands in the K-BR difference FT-IR spectrum by ab initio anharmonic vibrational calculations of all-trans retinal in BR using a quantum-mechanics/molecular mechanics approach, reproducing reasonably well the small experimental anharmonic and coupling mechanical constants. Yet, and in spite accounting for both mechanical and electrical anharmonicities, the intensity of overtone C-C transitions was underestimated by a factor of 4–20, indicating room for improvement in state-of-the-art anharmonic vibrational calculations. The relatively intense overtone and combination bands of the retinal might open the possibility to detect retinal conformational changes too subtle to significantly affect fundamental transitions but leaving a footprint in overtone and combination transitions.
format Online
Article
Text
id pubmed-8718751
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-87187512022-01-01 Retinal Vibrations in Bacteriorhodopsin are Mechanically Harmonic but Electrically Anharmonic: Evidence From Overtone and Combination Bands Lorenz-Fonfria, Victor A. Yagi, Kiyoshi Ito, Shota Kandori, Hideki Front Mol Biosci Molecular Biosciences Fundamental vibrations of the chromophore in the membrane protein bacteriorhodopsin (BR), a protonated Schiff base retinal, have been studied for decades, both by resonance Raman and by infrared (IR) difference spectroscopy. Such studies started comparing vibrational changes between the initial BR state (all-trans retinal) and the K intermediate (13-cis retinal), being later extended to the rest of intermediates. They contributed to our understanding of the proton-pumping mechanism of BR by exploiting the sensitivity of fundamental vibrational transitions of the retinal to its conformation. Here, we report on new bands in the 2,500 to 1,800 cm(−1) region of the K-BR difference FT-IR spectrum. We show that the bands between 2,500 and 2,300 cm(−1) originate from overtone and combination transitions from C-C stretches of the retinal. We assigned bands below 2,300 cm(−1) to the combination of retinal C-C stretches with methyl rocks and with hydrogen-out-of-plane vibrations. Remarkably, experimental C-C overtone bands appeared at roughly twice the wavenumber of their fundamentals, with anharmonic mechanical constants ≤3.5 cm(−1), and in some cases of ∼1 cm(−1). Comparison of combination and fundamental bands indicates that most of the mechanical coupling constants are also very small. Despite the mechanical quasi-harmonicity of the C-C stretches, the area of their overtone bands was only ∼50 to ∼100 times smaller than of their fundamental bands. We concluded that electrical anharmonicity, the second mechanism giving intensity to overtone bands, must be particularly high for the retinal C-C stretches. We corroborated the assignments of negative bands in the K-BR difference FT-IR spectrum by ab initio anharmonic vibrational calculations of all-trans retinal in BR using a quantum-mechanics/molecular mechanics approach, reproducing reasonably well the small experimental anharmonic and coupling mechanical constants. Yet, and in spite accounting for both mechanical and electrical anharmonicities, the intensity of overtone C-C transitions was underestimated by a factor of 4–20, indicating room for improvement in state-of-the-art anharmonic vibrational calculations. The relatively intense overtone and combination bands of the retinal might open the possibility to detect retinal conformational changes too subtle to significantly affect fundamental transitions but leaving a footprint in overtone and combination transitions. Frontiers Media S.A. 2021-12-17 /pmc/articles/PMC8718751/ /pubmed/34977154 http://dx.doi.org/10.3389/fmolb.2021.749261 Text en Copyright © 2021 Lorenz-Fonfria, Yagi, Ito and Kandori. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Molecular Biosciences
Lorenz-Fonfria, Victor A.
Yagi, Kiyoshi
Ito, Shota
Kandori, Hideki
Retinal Vibrations in Bacteriorhodopsin are Mechanically Harmonic but Electrically Anharmonic: Evidence From Overtone and Combination Bands
title Retinal Vibrations in Bacteriorhodopsin are Mechanically Harmonic but Electrically Anharmonic: Evidence From Overtone and Combination Bands
title_full Retinal Vibrations in Bacteriorhodopsin are Mechanically Harmonic but Electrically Anharmonic: Evidence From Overtone and Combination Bands
title_fullStr Retinal Vibrations in Bacteriorhodopsin are Mechanically Harmonic but Electrically Anharmonic: Evidence From Overtone and Combination Bands
title_full_unstemmed Retinal Vibrations in Bacteriorhodopsin are Mechanically Harmonic but Electrically Anharmonic: Evidence From Overtone and Combination Bands
title_short Retinal Vibrations in Bacteriorhodopsin are Mechanically Harmonic but Electrically Anharmonic: Evidence From Overtone and Combination Bands
title_sort retinal vibrations in bacteriorhodopsin are mechanically harmonic but electrically anharmonic: evidence from overtone and combination bands
topic Molecular Biosciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8718751/
https://www.ncbi.nlm.nih.gov/pubmed/34977154
http://dx.doi.org/10.3389/fmolb.2021.749261
work_keys_str_mv AT lorenzfonfriavictora retinalvibrationsinbacteriorhodopsinaremechanicallyharmonicbutelectricallyanharmonicevidencefromovertoneandcombinationbands
AT yagikiyoshi retinalvibrationsinbacteriorhodopsinaremechanicallyharmonicbutelectricallyanharmonicevidencefromovertoneandcombinationbands
AT itoshota retinalvibrationsinbacteriorhodopsinaremechanicallyharmonicbutelectricallyanharmonicevidencefromovertoneandcombinationbands
AT kandorihideki retinalvibrationsinbacteriorhodopsinaremechanicallyharmonicbutelectricallyanharmonicevidencefromovertoneandcombinationbands