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Li G, Meng J, Yu S, Bai X, Dai J, Song Y, Peng X, Zhao Q. Excited-State Dynamics of a CRABPII-Based Microbial Rhodopsin Mimic. J Phys Chem B 2024; 128:7712-7721. [PMID: 38940335 DOI: 10.1021/acs.jpcb.4c01296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Microbial rhodopsin, a pivotal photoreceptor protein, has garnered widespread application in diverse fields such as optogenetics, biotechnology, biodevices, etc. However, current microbial rhodopsins are all transmembrane proteins, which both complicates the investigation on the photoreaction mechanism and limits their further applications. Therefore, a specific mimic for microbial rhodopsin can not only provide a better model for understanding the mechanism but also can extend the applications. The human protein CRABPII turns out to be a good template for design mimics on rhodopsin due to the convenience in synthesis and the stability after mutations. Recently, Geiger et al. designed a new CRABPII-based mimic M1-L121E on microbial rhodopsin with the 13-cis, syn (13C) isomerization after irradiation. However, it still remains a question as to how similar it is compared with the natural microbial rhodopsin, in particular, in the aspect of the photoreaction dynamics. In this article, we investigate the excited-state dynamics of this mimic by measuring its transient absorption spectra. Our results reveal that there are two components in the solution of mimic M1-L121E at pH 8, known as protonated Schiff base (PSB) and unprotonated Schiff base (USB) states. In both states, the photoreaction process from 13-cis, syn(13C) to all-trans,anti (AT) is faster than that from the inverse direction. In addition, the photoreaction process in the PSB state is faster than that in the USB state. We compared the isomerization time of the PSB state to that of microbial rhodopsin. Our findings indicate that M1-L121E exhibits behaviors similar to those of microbial rhodopsins in the general pattern of PSB isomerization, where the isomerization from 13C to AT is much faster than its inverse direction. However, our results also reveal significant differences in the excited-state dynamics of the mimic relative to the native microbial rhodopsin, including the slower PSB isomerization rates as well as the unusual USB photoreaction dynamics at pH = 8. By elucidating the distinctive characteristics of mimics M1-L121E, this study enhances our understanding of microbial rhodopsin mimics and their potential applications.
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Affiliation(s)
- Gaoshang Li
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Jiajia Meng
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Shuang Yu
- MIIT Key Laboratory of Complex-field Intelligent Exploration, School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
| | - Xiaolu Bai
- MIIT Key Laboratory of Complex-field Intelligent Exploration, School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
| | - Jin Dai
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Yin Song
- MIIT Key Laboratory of Complex-field Intelligent Exploration, School of Optics and Photonics, Beijing Institute of Technology, Beijing 100081, China
| | - Xubiao Peng
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
- Beijing Academy of Quantum Information Sciences, Beijing 100081, China
| | - Qing Zhao
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
- Beijing Academy of Quantum Information Sciences, Beijing 100081, China
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2
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Palombo R, Barneschi L, Pedraza-González L, Yang X, Olivucci M. Picosecond quantum-classical dynamics reveals that the coexistence of light-induced microbial and animal chromophore rotary motion modulates the isomerization quantum yield of heliorhodopsin. Phys Chem Chem Phys 2024; 26:10343-10356. [PMID: 38501246 DOI: 10.1039/d4cp00193a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Rhodopsins are light-responsive proteins forming two vast and evolutionary distinct superfamilies whose functions are invariably triggered by the photoisomerization of a single retinal chromophore. In 2018 a third widespread superfamily of rhodopsins called heliorhodopsins was discovered using functional metagenomics. Heliorhodopsins, with their markedly different structural features with respect to the animal and microbial superfamilies, offer an opportunity to study how evolution has manipulated the chromophore photoisomerization to achieve adaptation. One question is related to the mechanism of such a reaction and how it differs from that of animal and microbial rhodopsins. To address this question, we use hundreds of quantum-classical trajectories to simulate the spectroscopically documented picosecond light-induced dynamics of a heliorhodopsin from the archaea thermoplasmatales archaeon (TaHeR). We show that, consistently with the observations, the trajectories reveal two excited state decay channels. However, inconsistently with previous hypotheses, only one channel is associated with the -C13C14- rotation of microbial rhodopsins while the second channel is characterized by the -C11C12- rotation typical of animal rhodopsins. The fact that such -C11C12- rotation is aborted upon decay and ground state relaxation, explains why illumination of TaHeR only produces the 13-cis isomer with a low quantum efficiency. We argue that the documented lack of regioselectivity in double-bond excited state twisting motion is the result of an "adaptation" that could be completely lost via specific residue substitutions modulating the steric hindrance experienced along the isomerization motion.
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Affiliation(s)
- Riccardo Palombo
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Siena, Italy.
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, USA.
| | - Leonardo Barneschi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Siena, Italy.
| | - Laura Pedraza-González
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi, 13, I-56124 Pisa, Italy
| | - Xuchun Yang
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, USA.
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Siena, Italy.
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, USA.
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3
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Nikolaev DM, Shtyrov AA, Vyazmin SY, Vasin AV, Panov MS, Ryazantsev MN. Fluorescence of the Retinal Chromophore in Microbial and Animal Rhodopsins. Int J Mol Sci 2023; 24:17269. [PMID: 38139098 PMCID: PMC10743670 DOI: 10.3390/ijms242417269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 11/30/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Fluorescence of the vast majority of natural opsin-based photoactive proteins is extremely low, in accordance with their functions that depend on efficient transduction of absorbed light energy. However, several recently proposed classes of engineered rhodopsins with enhanced fluorescence, along with the discovery of a new natural highly fluorescent rhodopsin, NeoR, opened a way to exploit these transmembrane proteins as fluorescent sensors and draw more attention to studies on this untypical rhodopsin property. Here, we review the available data on the fluorescence of the retinal chromophore in microbial and animal rhodopsins and their photocycle intermediates, as well as different isomers of the protonated retinal Schiff base in various solvents and the gas phase.
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Affiliation(s)
- Dmitrii M. Nikolaev
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, 198504 St. Petersburg, Russia
| | - Andrey A. Shtyrov
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, 198504 St. Petersburg, Russia
| | - Sergey Yu. Vyazmin
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, 8/3 Khlopina Street, 194021 St. Petersburg, Russia
| | - Andrey V. Vasin
- Institute of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, 29 Polytechnicheskaya Str., 195251 St. Petersburg, Russia
| | - Maxim S. Panov
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, 198504 St. Petersburg, Russia
- Center for Biophysical Studies, St. Petersburg State Chemical Pharmaceutical University, Professor Popov str. 14, lit. A, 197022 St. Petersburg, Russia
| | - Mikhail N. Ryazantsev
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, 198504 St. Petersburg, Russia
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Ostrovsky MA, Smitienko OA, Bochenkova AV, Feldman TB. Similarities and Differences in Photochemistry of Type I and Type II Rhodopsins. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1528-1543. [PMID: 38105022 DOI: 10.1134/s0006297923100097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/20/2023] [Accepted: 08/12/2023] [Indexed: 12/19/2023]
Abstract
The diversity of the retinal-containing proteins (rhodopsins) in nature is extremely large. Fundamental similarity of the structure and photochemical properties unites them into one family. However, there is still a debate about the origin of retinal-containing proteins: divergent or convergent evolution? In this review, based on the results of our own and literature data, a comparative analysis of the similarities and differences in the photoconversion of the rhodopsin of types I and II is carried out. The results of experimental studies of the forward and reverse photoreactions of the bacteriorhodopsin (type I) and visual rhodopsin (type II) rhodopsins in the femto- and picosecond time scale, photo-reversible reaction of the octopus rhodopsin (type II), photovoltaic reactions, as well as quantum chemical calculations of the forward photoreactions of bacteriorhodopsin and visual rhodopsin are presented. The issue of probable convergent evolution of type I and type II rhodopsins is discussed.
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Affiliation(s)
- Mikhail A Ostrovsky
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Emanuel Institute of Biochemical Physics, Moscow, 119334, Russia
| | - Olga A Smitienko
- Emanuel Institute of Biochemical Physics, Moscow, 119334, Russia
| | | | - Tatiana B Feldman
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
- Emanuel Institute of Biochemical Physics, Moscow, 119334, Russia
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Spectroscopic Determination of the Synergistic Effect of Natural Antioxidants in Bio-Transformer Oils. RESULTS IN CHEMISTRY 2023. [DOI: 10.1016/j.rechem.2023.100852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
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6
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Kojima K, Sudo Y. Convergent evolution of animal and microbial rhodopsins. RSC Adv 2023; 13:5367-5381. [PMID: 36793294 PMCID: PMC9923458 DOI: 10.1039/d2ra07073a] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/05/2023] [Indexed: 02/15/2023] Open
Abstract
Rhodopsins, a family of photoreceptive membrane proteins, contain retinal as a chromophore and were firstly identified as reddish pigments from frog retina in 1876. Since then, rhodopsin-like proteins have been identified mainly from animal eyes. In 1971, a rhodopsin-like pigment was discovered from the archaeon Halobacterium salinarum and named bacteriorhodopsin. While it was believed that rhodopsin- and bacteriorhodopsin-like proteins were expressed only in animal eyes and archaea, respectively, before the 1990s, a variety of rhodopsin-like proteins (called animal rhodopsins or opsins) and bacteriorhodopsin-like proteins (called microbial rhodopsins) have been progressively identified from various tissues of animals and microorganisms, respectively. Here, we comprehensively introduce the research conducted on animal and microbial rhodopsins. Recent analysis has revealed that the two rhodopsin families have common molecular properties, such as the protein structure (i.e., 7-transmembrane structure), retinal structure (i.e., binding ability to cis- and trans-retinal), color sensitivity (i.e., UV- and visible-light sensitivities), and photoreaction (i.e., triggering structural changes by light and heat), more than what was expected at the early stages of rhodopsin research. Contrastingly, their molecular functions are distinctively different (e.g., G protein-coupled receptors and photoisomerases for animal rhodopsins and ion transporters and phototaxis sensors for microbial rhodopsins). Therefore, based on their similarities and dissimilarities, we propose that animal and microbial rhodopsins have convergently evolved from their distinctive origins as multi-colored retinal-binding membrane proteins whose activities are regulated by light and heat but independently evolved for different molecular and physiological functions in the cognate organism.
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Affiliation(s)
- Keiichi Kojima
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University Japan
| | - Yuki Sudo
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University Japan
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Chuang C, Brumer P. Steady State Photoisomerization Quantum Yield of Model Rhodopsin: Insights from Wavepacket Dynamics? J Phys Chem Lett 2022; 13:4963-4970. [PMID: 35639452 DOI: 10.1021/acs.jpclett.2c01200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We simulate the nonequilibrium steady state cis-trans photoisomerization of retinal chromophore in rhodopsin on the basis of a two-state, two-mode model coupled to a thermal environment. By analyzing the systematic trends within an inhomogeneously broadened ensemble of systems, we find that the steady state reaction quantum yield (QY) correlates strongly with the excess energy above the crossing point of the system, in agreement with the prediction of the short-time dynamical wavepacket picture. However, the nontrivial dependence of the QY on the system-environment interaction indicates that a pure dynamical picture is insufficient and that environment-induced partial internal energy redistribution takes place before the reaction concludes. These results imply that a proper treatment of the photoisomerization reaction, particularly its high QY, must account for the redistribution and dissipation of energy beyond the dynamical wavepacket motion that is typically employed in the literature and that is appropriate only in the transient regime.
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Affiliation(s)
- Chern Chuang
- Chemical Physics Theory Group, Department of Chemistry, and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Paul Brumer
- Chemical Physics Theory Group, Department of Chemistry, and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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8
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Ostrovsky MA, Nadtochenko VA. Femtochemistry of Rhodopsins. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2021. [DOI: 10.1134/s1990793121020226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
The review considers the spectral kinetic data obtained by us by femtosecond absorption laser spectroscopy for the photochromic reaction of retinal isomerization in animal rhodopsin (type II), namely, bovine visual rhodopsin and microbial rhodopsins (type I), such as Exiguobacterium sibiricum rhodopsin and Halobacterium salinarum bacteriorhodopsin. It is shown that the elementary act of the photoreaction of retinal isomerization in type I and type II rhodopsins can be interpreted as a transition through a conical intersection with retention of the coherence of the vibrational wave packets generated during excitation. The coherent nature of the reaction is most pronounced in visual rhodopsin as a result of the barrier-free movement along the excited surface of potential energy, which also leads to an extremely high rate of retinal isomerization compared to microbial rhodopsins. Differences in the dynamics of photochemical reactions of type I and type II rhodopsins can be related to both differences in the initial isomeric forms of their chromophores (all-trans and 11-cis retinal, respectively), as well as with the effect of the protein environment on the chromophore. Despite the practically identical values of the quantum yields of the direct photoreaction of visual rhodopsin and bacteriorhodopsin, the reverse photoreaction of visual rhodopsin is much less effective (φ = 0.15) than in the case of bacteriorhodopsin (φ = 0.81). It can be assumed that the photobiological mechanism for converting light into an information process in the evolutionarily younger visual rhodopsins (type II rhodopsins) should be more reliable than the mechanism for converting light into a photoenergetic process in the evolutionarily more ancient microbial rhodopsins (type I rhodopsins). The low value of the quantum yield of the reverse reaction of visual rhodopsin can be considered as an increase in the reliability of the forward reaction, which triggers the process of phototransduction.
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9
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How does the skin sense sun light? An integrative view of light sensing molecules. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2021. [DOI: 10.1016/j.jphotochemrev.2021.100403] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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10
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Chuang C, Brumer P. Extreme Parametric Sensitivity in the Steady-State Photoisomerization of Two-Dimensional Model Rhodopsin. J Phys Chem Lett 2021; 12:3618-3624. [PMID: 33825472 DOI: 10.1021/acs.jpclett.1c00577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We computationally studied the photoisomerization reaction of the retinal chromophore in rhodopsin using a two-state two-mode model coupled to thermal baths. Reaction quantum yields at the steady state (10 ps and beyond) were found to be considerably different than their transient values, suggesting a weak correlation between transient and steady-state dynamics in these systems. Significantly, the steady-state quantum yield was highly sensitive to minute changes in system parameters, while transient dynamics was nearly unaffected. Correlation of such sensitivity with standard level spacing statistics of the nonadiabatic vibronic system suggests a possible origin in quantum chaos. The significance of this observation of quantum yield parametric sensitivity in biological models of vision has profound conceptual and fundamental implications.
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Affiliation(s)
- Chern Chuang
- Chemical Physics Theory Group, Department of Chemistry, and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Paul Brumer
- Chemical Physics Theory Group, Department of Chemistry, and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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11
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El‐Tahawy MMT, Conti I, Bonfanti M, Nenov A, Garavelli M. Tailoring Spectral and Photochemical Properties of Bioinspired Retinal Mimics by in Silico Engineering. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mohsen M. T. El‐Tahawy
- Dipartimento di Chimica industriale “Toso Montanari” Università di Bologna Viale del Risorigmento 4 40136 Bologna Italy
- Chemistry Department Faculty of Science Damanhour University Damanhour 22511 Egypt
| | - Irene Conti
- Dipartimento di Chimica industriale “Toso Montanari” Università di Bologna Viale del Risorigmento 4 40136 Bologna Italy
| | - Matteo Bonfanti
- Dipartimento di Chimica industriale “Toso Montanari” Università di Bologna Viale del Risorigmento 4 40136 Bologna Italy
| | - Artur Nenov
- Dipartimento di Chimica industriale “Toso Montanari” Università di Bologna Viale del Risorigmento 4 40136 Bologna Italy
| | - Marco Garavelli
- Dipartimento di Chimica industriale “Toso Montanari” Università di Bologna Viale del Risorigmento 4 40136 Bologna Italy
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12
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Jenkins AJ, Gottlieb SM, Chang CW, Kim PW, Hayer RJ, Hanke SJ, Martin SS, Lagarias JC, Larsen DS. Conservation and Diversity in the Primary Reverse Photodynamics of the Canonical Red/Green Cyanobacteriochrome Family. Biochemistry 2020; 59:4015-4028. [PMID: 33021375 DOI: 10.1021/acs.biochem.0c00454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this report, we compare the femtosecond to nanosecond primary reverse photodynamics (15EPg → 15ZPr) of eight tetrapyrrole binding photoswitching cyanobacteriochromes in the canonical red/green family from the cyanobacterium Nostoc punctiforme. Three characteristic classes were identified on the basis of the diversity of excited-state and ground-state properties, including the lifetime, photocycle initiation quantum yield, photointermediate stability, spectra, and temporal properties. We observed a correlation between the excited-state lifetime and peak wavelength of the electronic absorption spectrum with higher-energy-absorbing representatives exhibiting both faster excited-state decay times and higher photoisomerization quantum yields. The latter was attributed to both an increased number of structural restraints and differences in H-bonding networks that facilitate photoisomerization. All three classes exhibited primary Lumi-Go intermediates, with class II and III representatives evolving to a secondary Meta-G photointermediate. Class II Meta-GR intermediates were orange absorbing, whereas class III Meta-G had structurally relaxed, red-absorbing chromophores that resemble their dark-adapted 15ZPr states. Differences in the reverse and forward reaction mechanisms are discussed within the context of structural constraints.
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Affiliation(s)
- Adam J Jenkins
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Sean Marc Gottlieb
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Che-Wei Chang
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Peter W Kim
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Randeep J Hayer
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Samuel J Hanke
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Shelley S Martin
- Department of Molecular and Cellular Biology, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - J Clark Lagarias
- Department of Molecular and Cellular Biology, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Delmar S Larsen
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
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Hernández-Rodríguez EW, Escorcia AM, van der Kamp MW, Montero-Alejo AL, Caballero J. Multi-scale simulation reveals that an amino acid substitution increases photosensitizing reaction inputs in Rhodopsins. J Comput Chem 2020; 41:2278-2295. [PMID: 32757375 DOI: 10.1002/jcc.26392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 06/27/2020] [Accepted: 07/04/2020] [Indexed: 11/11/2022]
Abstract
Evaluating the availability of molecular oxygen (O2 ) and energy of excited states in the retinal binding site of rhodopsin is a crucial challenging first step to understand photosensitizing reactions in wild-type (WT) and mutant rhodopsins by absorbing visible light. In the present work, energies of the ground and excited states related to 11-cis-retinal and the O2 accessibility to the β-ionone ring are evaluated inside WT and human M207R mutant rhodopsins. Putative O2 pathways within rhodopsins are identified by using molecular dynamics simulations, Voronoi-diagram analysis, and implicit ligand sampling while retinal energetic properties are investigated through density functional theory, and quantum mechanical/molecular mechanical methods. Here, the predictions reveal that an amino acid substitution can lead to enough energy and O2 accessibility in the core hosting retinal of mutant rhodopsins to favor the photosensitized singlet oxygen generation, which can be useful in understanding retinal degeneration mechanisms and in designing blue-lighting-absorbing proteic photosensitizers.
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Affiliation(s)
- Erix W Hernández-Rodríguez
- Laboratorio de Bioinformática y Química Computacional, Escuela de Química y Farmacia, Facultad de Medicina, Universidad Católica del Maule, Talca, Chile
| | - Andrés M Escorcia
- School of Biochemistry, University of Bristol, University Walk, Bristol, UK
| | | | - Ana L Montero-Alejo
- Departamento de Física, Facultad de Ciencias Naturales, Matemática y del Medio Ambiente (FCNMM), Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Julio Caballero
- Departamento de Bioinformática, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Talca, Chile
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14
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El‐Tahawy MMT, Conti I, Bonfanti M, Nenov A, Garavelli M. Tailoring Spectral and Photochemical Properties of Bioinspired Retinal Mimics by in Silico Engineering. Angew Chem Int Ed Engl 2020; 59:20619-20627. [DOI: 10.1002/anie.202008644] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Indexed: 11/08/2022]
Affiliation(s)
- Mohsen M. T. El‐Tahawy
- Dipartimento di Chimica industriale “Toso Montanari” Università di Bologna Viale del Risorigmento 4 40136 Bologna Italy
- Chemistry Department Faculty of Science Damanhour University Damanhour 22511 Egypt
| | - Irene Conti
- Dipartimento di Chimica industriale “Toso Montanari” Università di Bologna Viale del Risorigmento 4 40136 Bologna Italy
| | - Matteo Bonfanti
- Dipartimento di Chimica industriale “Toso Montanari” Università di Bologna Viale del Risorigmento 4 40136 Bologna Italy
| | - Artur Nenov
- Dipartimento di Chimica industriale “Toso Montanari” Università di Bologna Viale del Risorigmento 4 40136 Bologna Italy
| | - Marco Garavelli
- Dipartimento di Chimica industriale “Toso Montanari” Università di Bologna Viale del Risorigmento 4 40136 Bologna Italy
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15
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Guntner AS, Doppler C, Wechselberger C, Bernhard D, Buchberger W. HPLC-MS/MS Shows That the Cellular Uptake of All- Trans-Retinoic Acid under Hypoxia Is Downregulated by the Novel Active Agent 5-Methoxyleoligin. Cells 2020; 9:cells9092048. [PMID: 32911794 PMCID: PMC7563598 DOI: 10.3390/cells9092048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/28/2020] [Accepted: 09/07/2020] [Indexed: 11/16/2022] Open
Abstract
All-trans-retinoic acid (atRA) is the essential derivative of vitamin A and is of interest due to its various biological key functions. As shown in the recent literature, atRA also plays a role in the failing heart during myocardial infarction, the leading cause of death globally. To date insufficient mechanistic information has been available on related hypoxia-induced cell damage and reperfusion injuries. However, it has been demonstrated that a reduction in cellular atRA uptake abrogates hypoxia-mediated cell and tissue damage, which may offer a new route for intervention. Consequently, in this study, the effect of the novel cardio-protective compound 5-methoxyleoligin (5ML) on cellular atRA uptake was tested in human umbilical-vein endothelial cells (HUVECs). For this purpose, a high-performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS) method was developed to assess intra-cellular levels of the active substance and corresponding levels of vitamin A and its derivatives, including potential cis/trans isomers. This work also focused on light-induced isomerization and the stability of biological sample material to ensure sample integrity and avoid biased conclusions. This study provides evidence of the inhibitory effect of 5ML on cellular atRA uptake, a promising step toward a novel therapy for myocardial infarction.
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Affiliation(s)
- Armin Sebastian Guntner
- Institute of Analytical Chemistry, Johannes Kepler University Linz, 4040 Linz, Austria;
- Correspondence: ; Tel.: +43-732-2468-9700
| | - Christian Doppler
- Division of Pathophysiology, Institute of Physiology and Pathophysiology, Medical Faculty, Johannes Kepler University Linz, 4020 Linz, Austria; (C.D.); (C.W.); (D.B.)
| | - Christian Wechselberger
- Division of Pathophysiology, Institute of Physiology and Pathophysiology, Medical Faculty, Johannes Kepler University Linz, 4020 Linz, Austria; (C.D.); (C.W.); (D.B.)
| | - David Bernhard
- Division of Pathophysiology, Institute of Physiology and Pathophysiology, Medical Faculty, Johannes Kepler University Linz, 4020 Linz, Austria; (C.D.); (C.W.); (D.B.)
| | - Wolfgang Buchberger
- Institute of Analytical Chemistry, Johannes Kepler University Linz, 4040 Linz, Austria;
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16
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Feldman T, Yakovleva M, Viljanen M, Lindström M, Donner K, Ostrovsky M. Dark-adaptation in the eyes of a lake and a sea population of opossum shrimp (Mysis relicta): retinoid isomer dynamics, rhodopsin regeneration, and recovery of light sensitivity. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2020; 206:871-889. [PMID: 32880702 PMCID: PMC7603447 DOI: 10.1007/s00359-020-01444-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/22/2020] [Accepted: 08/25/2020] [Indexed: 11/30/2022]
Abstract
We have studied dark-adaptation at three levels in the eyes of the crustacean Mysis relicta over 2-3 weeks after exposing initially dark-adapted animals to strong white light: regeneration of 11-cis retinal through the retinoid cycle (by HPLC), restoration of native rhodopsin in photoreceptor membranes (by MSP), and recovery of eye photosensitivity (by ERG). We compare two model populations ("Sea", Sp, and "Lake", Lp) inhabiting, respectively, a low light and an extremely dark environment. 11-cis retinal reached 60-70% of the pre-exposure levels after 2 weeks in darkness in both populations. The only significant Lp/Sp difference in the retinoid cycle was that Lp had much higher levels of retinol, both basal and light-released. In Sp, rhodopsin restoration and eye photoresponse recovery parallelled 11-cis retinal regeneration. In Lp, however, even after 3 weeks only ca. 25% of the rhabdoms studied had incorporated new rhodopsin, and eye photosensitivity showed only incipient recovery from severe depression. The absorbance spectra of the majority of the Lp rhabdoms stayed constant around 490-500 nm, consistent with metarhodopsin II dominance. We conclude that sensitivity recovery of Sp eyes was rate-limited by the regeneration of 11-cis retinal, whilst that of Lp eyes was limited by inertia in photoreceptor membrane turnover.
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Affiliation(s)
- Tatiana Feldman
- Department of Molecular Physiology, Biological Faculty, Lomonosov Moscow State University, Leninskie Gory 1, Moscow, Russia, 119991.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin st. 4, Moscow, Russia, 119334
| | - Marina Yakovleva
- Department of Molecular Physiology, Biological Faculty, Lomonosov Moscow State University, Leninskie Gory 1, Moscow, Russia, 119991
| | - Martta Viljanen
- Molecular and Integrative Biosciences Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Magnus Lindström
- Tvärminne Zoological Station, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Kristian Donner
- Molecular and Integrative Biosciences Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
| | - Mikhail Ostrovsky
- Department of Molecular Physiology, Biological Faculty, Lomonosov Moscow State University, Leninskie Gory 1, Moscow, Russia, 119991.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin st. 4, Moscow, Russia, 119334
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17
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Manathunga M, Jenkins AJ, Orozco-Gonzalez Y, Ghanbarpour A, Borhan B, Geiger JH, Larsen DS, Olivucci M. Computational and Spectroscopic Characterization of the Photocycle of an Artificial Rhodopsin. J Phys Chem Lett 2020; 11:4245-4252. [PMID: 32374610 PMCID: PMC9272672 DOI: 10.1021/acs.jpclett.0c00751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The photocycle of a reversible photoisomerizing rhodopsin mimic (M2) is investigated. This system, based on the cellular retinoic acid binding protein, is structurally different from natural rhodopsin systems, but exhibits a similar isomerization upon light irradiation. More specifically, M2 displays a 15-cis to all-trans conversion of retinal protonated Schiff base (rPSB) and all-trans to 15-cis isomerization of unprotonated Schiff base (rUSB). Here we use hybrid quantum mechanics/molecular mechanics (QM/MM) tools coupled with transient absorption and cryokinetic UV-vis spectroscopies to investigate these isomerization processes. The results suggest that primary rPSB photoisomerization of M2 occurs around the C13═C14 double bond within 2 ps following an aborted-bicycle pedal (ABP) isomerization mechanism similar to natural microbial rhodopsins. The rUSB isomerization is much slower and occurs within 48 ps around the C15═N double bond. Our findings reveal the possibility to engineer naturally occurring mechanistic features into artificial rhodopsins and also constitute a step toward understanding the photoisomerization of UV pigments. We conclude by reinforcing the idea that the presence of the retinal chromophore inside a tight protein cavity is not mandatory to exhibit ABP mechanism.
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Affiliation(s)
- Madushanka Manathunga
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Adam J Jenkins
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Yoelvis Orozco-Gonzalez
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Alireza Ghanbarpour
- Department of Chemistry, Michigan State University, Lansing, Michigan 48824, United States
| | - Babak Borhan
- Department of Chemistry, Michigan State University, Lansing, Michigan 48824, United States
| | - James H Geiger
- Department of Chemistry, Michigan State University, Lansing, Michigan 48824, United States
| | - Delmar S Larsen
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
- Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 Université de Strasbourg-CNRS, F-67034 Strasbourg, France
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18
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Li W. Residue-Residue Mutual Work Analysis of Retinal-Opsin Interaction in Rhodopsin: Implications for Protein-Ligand Binding. J Chem Theory Comput 2020; 16:1834-1842. [PMID: 31972074 DOI: 10.1021/acs.jctc.9b01035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Energetic contributions at the single-residue level for retinal-opsin interactions in rhodopsin were studied by combining molecular dynamics simulations, transition path sampling, and a newly developed energy decomposition approach. The virtual work at an infinitesimal time interval was decomposed into the work components on one residue due to its interaction with another residue, which were then averaged over the transition path ensemble along a proposed reaction coordinate. Such residue-residue mutual work analysis on 62 residues within the active center of rhodopsin resulted in a very sparse interaction matrix, which is generally not symmetric but antisymmetric to some extent. Fourteen residues were identified to be major players in retinal relaxation along a plausible pathway from bathorhodopsin to the blue-shifted intermediate, which is in good agreement with an existing NMR study. Based on the matrix of mutual work, a comprehensive network was constructed to provide detailed insights into the chromophore-protein interaction from a viewpoint of energy flow.
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Affiliation(s)
- Wenjin Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
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19
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Bull JN, West CW, Anstöter CS, da Silva G, Bieske EJ, Verlet JRR. Ultrafast photoisomerisation of an isolated retinoid. Phys Chem Chem Phys 2019; 21:10567-10579. [PMID: 31073587 DOI: 10.1039/c9cp01624d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The photoinduced excited state dynamics of gas-phase trans-retinoate (deprotonated trans-retinoic acid, trans-RA-) are studied using tandem ion mobility spectrometry coupled with laser spectroscopy, and frequency-, angle- and time-resolved photoelectron imaging. Photoexcitation of the bright S3(ππ*) ← S0 transition leads to internal conversion to the S1(ππ*) state on a ≈80 fs timescale followed by recovery of S0 and concomitant isomerisation to give the 13-cis (major) and 9-cis (minor) photoisomers on a ≈180 fs timescale. The sub-200 fs stereoselective photoisomerisation parallels that for the retinal protonated Schiff base chromophore in bacteriorhodopsin. Measurements on trans-RA- in methanol using the solution photoisomerisation action spectroscopy technique show that 13-cis-RA- is also the principal photoisomer, although the 13-cis and 9-cis photoisomers are formed with an inverted branching ratio with photon energy in methanol when compared with the gas phase, presumably due to solvent-induced modification of potential energy surfaces and inhibition of electron detachment processes. Comparison of the gas-phase time-resolved data with transient absorption spectroscopy measurements on retinoic acid in methanol suggest that photoisomerisation is roughly six times slower in solution. This work provides clear evidence that solvation significantly affects the photoisomerisation dynamics of retinoid molecules.
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Affiliation(s)
- James N Bull
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, UK.
| | - Christopher W West
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Cate S Anstöter
- Department of Chemistry, Durham University, Durham DH1 3LE, UK
| | - Gabriel da Silva
- Department of Chemical Engineering, University of Melbourne, Parkville, VIC 3010, Australia
| | - Evan J Bieske
- School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jan R R Verlet
- Department of Chemistry, Durham University, Durham DH1 3LE, UK
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20
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Dodin A, Brumer P. Light-induced processes in nature: Coherences in the establishment of the nonequilibrium steady state in model retinal isomerization. J Chem Phys 2019; 150:184304. [DOI: 10.1063/1.5092981] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Amro Dodin
- Chemical Physics Theory Group, Department of Chemistry, and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Paul Brumer
- Chemical Physics Theory Group, Department of Chemistry, and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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21
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Valentini A, Nucci M, Frutos LM, Marazzi M. Photosensitized Retinal Isomerization in Rhodopsin Mediated by a Triplet State. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Alessio Valentini
- Departamento de Química Analítica, Química Física e Ingeniería Química, Unidad de Química FísicaUniversidad de Alcalá Ctra. Madrid-Barcelona Km. 33,600 E-28871 Alcalá de Henares, Madrid Spain
- Department of Biotechnology, Chemistry and PharmacyUniversity of Siena via A. Moro 2 53100 Siena Italy
- Theoretical Physical Chemistry, Research Unit MolSysUniversité de Liège Allée du 6 Aôut, 11 4000 Liège Belgium
| | - Martina Nucci
- Departamento de Química Analítica, Química Física e Ingeniería Química, Unidad de Química FísicaUniversidad de Alcalá Ctra. Madrid-Barcelona Km. 33,600 E-28871 Alcalá de Henares, Madrid Spain
| | - Luis Manuel Frutos
- Departamento de Química Analítica, Química Física e Ingeniería Química, Unidad de Química FísicaUniversidad de Alcalá Ctra. Madrid-Barcelona Km. 33,600 E-28871 Alcalá de Henares, Madrid Spain
- Instituto de Investigación Química “Andrés M. del Río” (IQAR)Universidad de Alcalá E-28871 Alcalá de Henares, Madrid Spain
| | - Marco Marazzi
- Departamento de Química Analítica, Química Física e Ingeniería Química, Unidad de Química FísicaUniversidad de Alcalá Ctra. Madrid-Barcelona Km. 33,600 E-28871 Alcalá de Henares, Madrid Spain
- Instituto de Investigación Química “Andrés M. del Río” (IQAR)Universidad de Alcalá E-28871 Alcalá de Henares, Madrid Spain
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22
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Abstract
One of the important features of polymethine (cyanine) dyes is isomerization about one of C–C bonds of the polymethine chain. In this review, spectral properties of the isomers, photoisomer-ization and thermal back isomerization of carbocyanine dyes, mostly meso-substituted carbocy-anine dyes, are considered. meso-Alkyl-substituted thiacarbocyanine dyes are present in polar solvents mainly as cis isomers and, hence, exhibit no photoisomerization, whereas in nonpolar solvents, in which the dyes are in the trans form, photoisomerization takes place. In contrast, the meso-substituted dyes 3,3′-dimethyl-9-phenylthiacarbocyanine and 3,3′-diethyl-9-(2-hydroxy-4-methoxyphenyl)thiacarbocyanine occur as trans isomers and exhibit photoisomerization in both polar and nonpolar solvents. The behavior of these dyes may be ex-plained by the fact that the phenyl ring of the substituent in their molecules can be twisted at some angle, removing the substituent from the plane of the molecule and reducing its steric ef-fect on the conformation of the trans isomer. In some cases, photoisomerization of cis isomers of meso-substituted carbocyanine dyes is also observed (for some meso-alkyl-substituted dyes com-plexed with DNA and chondroitin-4-sulfate; for 3,3′-diethyl-9-methoxythiacarbocyanine in moderate polarity solvents). The cycle photoisomerization–thermal back isomerization of cya-nine dyes can be used in various systems of information storage and deserves further investiga-tion using modern research methods.
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23
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Katayama K, Gulati S, Ortega JT, Alexander NS, Sun W, Shenouda MM, Palczewski K, Jastrzebska B. Specificity of the chromophore-binding site in human cone opsins. J Biol Chem 2019; 294:6082-6093. [PMID: 30770468 DOI: 10.1074/jbc.ra119.007587] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/13/2019] [Indexed: 01/21/2023] Open
Abstract
The variable composition of the chromophore-binding pocket in visual receptors is essential for vision. The visual phototransduction starts with the cis-trans isomerization of the retinal chromophore upon absorption of photons. Despite sharing the common 11-cis-retinal chromophore, rod and cone photoreceptors possess distinct photochemical properties. Thus, a detailed molecular characterization of the chromophore-binding pocket of these receptors is critical to understanding the differences in the photochemistry of vision between rods and cones. Unlike for rhodopsin (Rh), the crystal structures of cone opsins remain to be determined. To obtain insights into the specific chromophore-protein interactions that govern spectral tuning in human visual pigments, here we harnessed the unique binding properties of 11-cis-6-membered-ring-retinal (11-cis-6mr-retinal) with human blue, green, and red cone opsins. To unravel the specificity of the chromophore-binding pocket of cone opsins, we applied 11-cis-6mr-retinal analog-binding analyses to human blue, green, and red cone opsins. Our results revealed that among the three cone opsins, only blue cone opsin can accommodate the 11-cis-6mr-retinal in its chromophore-binding pocket, resulting in the formation of a synthetic blue pigment (B6mr) that absorbs visible light. A combination of primary sequence alignment, molecular modeling, and mutagenesis experiments revealed the specific amino acid residue 6.48 (Tyr-262 in blue cone opsins and Trp-281 in green and red cone opsins) as a selectivity filter in human cone opsins. Altogether, the results of our study uncover the molecular basis underlying the binding selectivity of 11-cis-6mr-retinal to the cone opsins.
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Affiliation(s)
- Kota Katayama
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106; Department of Life Science and Applied Chemistry, Showa-ku, Nagoya 466-8555, Japan; OptoBio Technology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Sahil Gulati
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697
| | - Joseph T Ortega
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Nathan S Alexander
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Wenyu Sun
- Polgenix Inc., Cleveland, Ohio 44106
| | - Marina M Shenouda
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697; Polgenix Inc., Cleveland, Ohio 44106.
| | - Beata Jastrzebska
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106.
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24
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Roy PP, Kato Y, Abe-Yoshizumi R, Pieri E, Ferré N, Kandori H, Buckup T. Mapping the ultrafast vibrational dynamics of all-trans and 13-cis retinal isomerization in Anabaena Sensory Rhodopsin. Phys Chem Chem Phys 2018; 20:30159-30173. [PMID: 30484447 DOI: 10.1039/c8cp05469j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Discrepancies in the isomerization dynamics and quantum yields of the trans and cis retinal protonated Schiff base is a well-known issue in the context of retinal photochemistry. Anabaena Sensory Rhodopsin (ASR) is a microbial retinal protein that comprises a retinal chromophore in two ground state (GS) conformations: all-trans, 15-anti (AT) and 13-cis, 15-syn (13C). In this study, we applied impulsive vibrational spectroscopic techniques (DFWM, pump-DFWM and pump-IVS) to ASR to shed more light on how the structural changes take place in the excited state within the same protein environment. Our findings point to distinct features in the ground state structural conformations as well as to drastically different evolutions in the excited state manifold. The ground state vibrational spectra show stronger Raman activity of the C14-H out-of-plane wag (at about 805 cm-1) for the 13C isomer than that for the AT isomer, which hints at a pre-distortion of 13C in the ground state. Evolution of the Raman frequency after interaction with the actinic pulse shows a blue-shift for the C[double bond, length as m-dash]C stretching and CH3 rocking mode for both isomers. For AT, however, the blue-shift is not instantaneous as observed for the 13C isomer, rather it takes more than 200 fs to reach the maximum frequency shift. This frequency blue-shift is rationalized by a decrease in the effective conjugation length during the isomerization reaction, which further confirms a slower formation of the twisted state for the AT isomer and corroborates the presence of a barrier in the excited state trajectory previously predicted by quantum chemical calculations.
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Affiliation(s)
- Partha Pratim Roy
- Physikalisch-Chemisches Institut, Ruprecht-Karls Universität Heidelberg, D-69210, Heidelberg, Germany.
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25
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Abstract
One of the important features of polymethine (cyanine) dyes is isomerization around one of C–C bonds of the polymethine chain. In this review, spectral properties of the isomers, photoisomerization and thermal back isomerization of carbocyanine dyes, mostly meso-substituted carbocyanine dyes, are considered. meso-Alkyl-substituted thiacarbocyanine dyes are present in polar solvents mainly as cis isomers and, hence, exhibit no photoisomerization, whereas in nonpolar solvents, in which the dyes are in the trans form, photoisomerization takes place. In contrast, the meso-substituted dyes 3,3′-dimethyl-9-phenylthiacarbocyanine and 3,3′-diethyl-9-(2-hydroxy-4-methoxyphenyl)thiacarbocyanine occur as trans isomers and exhibit photoisomerization in both polar and nonpolar solvents. The behavior of these dyes may be explained by the fact that the phenyl ring of the substituent in their molecules can be twisted at some angle, removing the substituent from the plane of the molecule and reducing its steric effect on the conformation of the trans isomer. In some cases, photoisomerization of cis isomers of meso-substituted carbocyanine dyes is also observed (for some meso-alkyl-substituted dyes complexed with DNA and chondroitin-4-sulfate; for 3,3′-diethyl-9-methoxythiacarbocyanine in moderate polarity solvents). The cycle photoisomerization–thermal back isomerization of cyanine dyes can be used in various systems of information storage and deserves further investigation using modern research methods.
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26
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Sala M, Egorova D. Quantum dynamics of multi-dimensional rhodopsin photoisomerization models: Approximate versus accurate treatment of the secondary modes. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.07.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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27
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Grabarek D, Andruniów T. Initial excited-state relaxation of locked retinal protonated schiff base chromophore. An insight from coupled cluster and multireference perturbation theory calculations. J Comput Chem 2018; 39:1720-1727. [PMID: 29727036 DOI: 10.1002/jcc.25346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/06/2018] [Accepted: 04/12/2018] [Indexed: 11/07/2022]
Abstract
The initial S1 excited-state relaxation of retinal protonated Schiff base (RPSB) analog with central C11C12 double bond locked by eight-membered ring (locked-11.8) was investigated by means of multireference perturbation theory methods (XMCQDPT2, XMS-CASPT2, MS-CASPT2) as well as single-reference coupled-cluster CC2 method. The analysis of XMCQDPT2-based geometries reveals rather weak coupling between in-plane and out-of-plane structural evolution and minor energetical relaxation of three locked-11.8 conformers. Therefore, a strong coupling between bonds length inversion and backbone out-of-plane deformation resulting in a very steep S1 energy profile predicted by CASSCF/CASPT2 calculations is in clear contradiction with the reference XMCQDPT2 results. Even though CC2 method predicts good quality ground-state structures, the excited-state structures display more advanced torsional deformation leading to ca. 0.2 eV exaggerated energy relaxation and significantly red shifted (0.4-0.7 eV) emission maxima. According to our findings, the initial photoisomerization process in locked-11.8, and possibly in other RPSB analogs, studied fully (both geometries and energies) by multireference perturbation theory may be somewhat slower than predicted by CASSCF/CASPT2 or CC2 methods. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Dawid Grabarek
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
| | - Tadeusz Andruniów
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
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28
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Abstract
Photoreceptor chromophore, 11-cis retinal (11CR) and the photoproduct, all-trans retinal (ATR), are present in the retina at higher concentrations and interact with the visual cells. Non-visual cells in the body are also exposed to retinal that enters the circulation. Although the cornea and the lens of the eye are transparent to the blue light region where retinal can absorb and undergo excitation, the reported phototoxicity in the eye has been assigned to lipophilic non-degradable materials known as lipofuscins, which also includes retinal condensation products. The possibility of blue light excited retinal interacting with cells; intercepting signaling in the presence or absence of light has not been explored. Using live cell imaging and optogenetic signaling control, we uncovered that blue light-excited ATR and 11CR irreversibly change/distort plasma membrane (PM) bound phospholipid; phosphatidylinositol 4,5 bisphosphate (PIP2) and disrupt its function. This distortion in PIP2 was independent of visual or non-visual G-protein coupled receptor activation. The change in PIP2 was followed by an increase in the cytosolic calcium, excessive cell shape change, and cell death. Blue light alone or retinal alone did not perturb PIP2 or elicit cytosolic calcium increase. Our data also suggest that photoexcited retinal-induced PIP2 distortion and subsequent oxidative damage incur in the core of the PM. These findings suggest that retinal exerts light sensitivity to both photoreceptor and non-photoreceptor cells, and intercepts crucial signaling events, altering the cellular fate.
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29
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Opn5L1 is a retinal receptor that behaves as a reverse and self-regenerating photoreceptor. Nat Commun 2018; 9:1255. [PMID: 29593298 PMCID: PMC5871776 DOI: 10.1038/s41467-018-03603-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 02/25/2018] [Indexed: 11/09/2022] Open
Abstract
Most opsins are G protein-coupled receptors that utilize retinal both as a ligand and as a chromophore. Opsins' main established mechanism is light-triggered activation through retinal 11-cis-to-all-trans photoisomerization. Here we report a vertebrate non-visual opsin that functions as a Gi-coupled retinal receptor that is deactivated by light and can thermally self-regenerate. This opsin, Opn5L1, binds exclusively to all-trans-retinal. More interestingly, the light-induced deactivation through retinal trans-to-cis isomerization is followed by formation of a covalent adduct between retinal and a nearby cysteine, which breaks the retinal-conjugated double bond system, probably at the C11 position, resulting in thermal re-isomerization to all-trans-retinal. Thus, Opn5L1 acts as a reverse photoreceptor. We conclude that, like vertebrate rhodopsin, Opn5L1 is a unidirectional optical switch optimized from an ancestral bidirectional optical switch, such as invertebrate rhodopsin, to increase the S/N ratio of the signal transduction, although the direction of optimization is opposite to that of vertebrate rhodopsin.
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Barata-Morgado R, Sánchez ML, Muñoz-Losa A, Martín ME, Olivares Del Valle FJ, Aguilar MA. How Methylation Modifies the Photophysics of the Native All- trans-Retinal Protonated Schiff Base: A CASPT2/MD Study in Gas Phase and in Methanol. J Phys Chem A 2018; 122:3096-3106. [PMID: 29489369 DOI: 10.1021/acs.jpca.8b00773] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A comparison between the free-energy surfaces of the all- trans-retinal protonated Schiff base (RPSB) and its 10-methylated derivative in gas phase and methanol solution is performed at CASSCF//CASSCF and CASPT2//CASSCF levels. Solvent effects were included using the average solvent electrostatic potential from molecular dynamics method. This is a QM/MM (quantum mechanics/molecular mechanics) method that makes use of the mean field approximation. It is found that the methyl group bonded to C10 produces noticeable changes in the solution free-energy profile of the S1 excited state, mainly in the relative stability of the minimum energy conical intersections (MECIs) with respect to the Franck-Condon (FC) point. The conical intersections yielding the 9- cis and 11- cis isomers are stabilized while that yielding the 13- cis isomer is destabilized; in fact, it becomes inaccessible by excitation to S1. Furthermore, the planar S1 minimum is not present in the methylated compound. The solvent notably stabilizes the S2 excited state at the FC geometry. Therefore, if the S2 state has an effect on the photoisomerization dynamics, it must be because it permits the RPSB population to branch around the FC point. All these changes combine to speed up the photoisomerization in the 10-methylated compound with respect to the native compound.
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Affiliation(s)
- Rute Barata-Morgado
- Área de Química Física , University of Extremadura , Avda. Elvas s/n , Edif. José Ma Viguera Lobo 3a, planta, Badajoz 06006 , Spain
| | - M Luz Sánchez
- Área de Química Física , University of Extremadura , Avda. Elvas s/n , Edif. José Ma Viguera Lobo 3a, planta, Badajoz 06006 , Spain
| | - Aurora Muñoz-Losa
- Dpto. Didáctica de las Ciencias Experimentales y Matemáticas, Facultad de Formación del Profesorado , University of Extremadura , Avda. Universidad s/n , Cáceres 10003 , Spain
| | - M Elena Martín
- Área de Química Física , University of Extremadura , Avda. Elvas s/n , Edif. José Ma Viguera Lobo 3a, planta, Badajoz 06006 , Spain
| | - Francisco J Olivares Del Valle
- Área de Química Física , University of Extremadura , Avda. Elvas s/n , Edif. José Ma Viguera Lobo 3a, planta, Badajoz 06006 , Spain
| | - Manuel A Aguilar
- Área de Química Física , University of Extremadura , Avda. Elvas s/n , Edif. José Ma Viguera Lobo 3a, planta, Badajoz 06006 , Spain
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31
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Evidence for a vibrational phase-dependent isotope effect on the photochemistry of vision. Nat Chem 2018; 10:449-455. [DOI: 10.1038/s41557-018-0014-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 01/23/2018] [Indexed: 01/05/2023]
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32
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Mix LT, Carroll EC, Morozov D, Pan J, Gordon WR, Philip A, Fuzell J, Kumauchi M, van Stokkum I, Groenhof G, Hoff WD, Larsen DS. Excitation-Wavelength-Dependent Photocycle Initiation Dynamics Resolve Heterogeneity in the Photoactive Yellow Protein from Halorhodospira halophila. Biochemistry 2018; 57:1733-1747. [PMID: 29465990 DOI: 10.1021/acs.biochem.7b01114] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photoactive yellow proteins (PYPs) make up a diverse class of blue-light-absorbing bacterial photoreceptors. Electronic excitation of the p-coumaric acid chromophore covalently bound within PYP results in triphasic quenching kinetics; however, the molecular basis of this behavior remains unresolved. Here we explore this question by examining the excitation-wavelength dependence of the photodynamics of the PYP from Halorhodospira halophila via a combined experimental and computational approach. The fluorescence quantum yield, steady-state fluorescence emission maximum, and cryotrapping spectra are demonstrated to depend on excitation wavelength. We also compare the femtosecond photodynamics in PYP at two excitation wavelengths (435 and 475 nm) with a dual-excitation-wavelength-interleaved pump-probe technique. Multicompartment global analysis of these data demonstrates that the excited-state photochemistry of PYP depends subtly, but convincingly, on excitation wavelength with similar kinetics with distinctly different spectral features, including a shifted ground-state beach and altered stimulated emission oscillator strengths and peak positions. Three models involving multiple excited states, vibrationally enhanced barrier crossing, and inhomogeneity are proposed to interpret the observed excitation-wavelength dependence of the data. Conformational heterogeneity was identified as the most probable model, which was supported with molecular mechanics simulations that identified two levels of inhomogeneity involving the orientation of the R52 residue and different hydrogen bonding networks with the p-coumaric acid chromophore. Quantum calculations were used to confirm that these inhomogeneities track to altered spectral properties consistent with the experimental results.
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Affiliation(s)
- L Tyler Mix
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Elizabeth C Carroll
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Dmitry Morozov
- Department of Chemistry and NanoScience Center , University of Jyväskylä , P.O. Box 35, 40014 Jyväskylä , Finland
| | - Jie Pan
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | | | | | - Jack Fuzell
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Masato Kumauchi
- Department of Microbiology and Molecular Genetics , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Ivo van Stokkum
- Faculty of Sciences , Vrije Universiteit Amsterdam , De Boelelaan 1081 , 1081 HV Amsterdam , The Netherlands
| | - Gerrit Groenhof
- Department of Chemistry and NanoScience Center , University of Jyväskylä , P.O. Box 35, 40014 Jyväskylä , Finland
| | - Wouter D Hoff
- Department of Microbiology and Molecular Genetics , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Delmar S Larsen
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
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Scarbath-Evers LK, Jähnigen S, Elgabarty H, Song C, Narikawa R, Matysik J, Sebastiani D. Structural heterogeneity in a parent ground-state structure of AnPixJg2 revealed by theory and spectroscopy. Phys Chem Chem Phys 2018; 19:13882-13894. [PMID: 28513754 DOI: 10.1039/c7cp01218g] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We investigated the red absorbing, dark stable state (Pr state) of the second GAF domain of the cyanobacteriochrome AnPixJ (AnPixJg2) by a molecular dynamics simulation of 1 μs duration. Our results reveal two distinct conformational isoforms of the chromophore, from which only one was known from crystallographic experiments. The interconversion between both isoforms is accompanied by alterations in the hydrogen bond pattern between the chromophore and the protein and the solvation structure of the chromophore binding pocket. The existence of sub-states in the Pr form of AnPixJg2 is supported by the results from experimental 13C MAS NMR spectroscopy. Our finding is consistent with the observation of structural heterogeneity in other cyanobacteriochromes and phytochromes.
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Affiliation(s)
- Laura Katharina Scarbath-Evers
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany.
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34
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Donati G, Wildman A, Caprasecca S, Lingerfelt DB, Lipparini F, Mennucci B, Li X. Coupling Real-Time Time-Dependent Density Functional Theory with Polarizable Force Field. J Phys Chem Lett 2017; 8:5283-5289. [PMID: 28994290 DOI: 10.1021/acs.jpclett.7b02320] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Real-time time-dependent density functional theory (RT-TDDFT) is a powerful tool for obtaining spectroscopic observables and understanding complex, time-dependent properties. Currently, performing RT-TDDFT calculations on large, fully quantum mechanical systems is not computationally feasible. Previously, polarizable mixed quantum mechanical and molecular mechanical (QM/MMPol) models have been successful in providing accurate, yet efficient, approximations to a fully quantum mechanical system. Here we develop a coupling scheme between induced dipole based QM/MMPol and RT-TDDFT. Our approach is validated by comparing calculated spectra with both real-time and linear-response TDDFT calculations. The model developed within provides an accurate method for performing RT-TDDFT calculations on extended systems while accounting for mutual polarization between the quantum mechanical and molecular mechanical regions.
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Affiliation(s)
- Greta Donati
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Andrew Wildman
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Stefano Caprasecca
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa , Via G. Moruzzi 13, 56124 Pisa, Italy
| | - David B Lingerfelt
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa , Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa , Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Xiaosong Li
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
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El Hage K, Brickel S, Hermelin S, Gaulier G, Schmidt C, Bonacina L, van Keulen SC, Bhattacharyya S, Chergui M, Hamm P, Rothlisberger U, Wolf JP, Meuwly M. Implications of short time scale dynamics on long time processes. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:061507. [PMID: 29308419 PMCID: PMC5741438 DOI: 10.1063/1.4996448] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/15/2017] [Indexed: 05/02/2023]
Abstract
This review provides a comprehensive overview of the structural dynamics in topical gas- and condensed-phase systems on multiple length and time scales. Starting from vibrationally induced dissociation of small molecules in the gas phase, the question of vibrational and internal energy redistribution through conformational dynamics is further developed by considering coupled electron/proton transfer in a model peptide over many orders of magnitude. The influence of the surrounding solvent is probed for electron transfer to the solvent in hydrated I-. Next, the dynamics of a modified PDZ domain over many time scales is analyzed following activation of a photoswitch. The hydration dynamics around halogenated amino acid side chains and their structural dynamics in proteins are relevant for iodinated TyrB26 insulin. Binding of nitric oxide to myoglobin is a process for which experimental and computational analyses have converged to a common view which connects rebinding time scales and the underlying dynamics. Finally, rhodopsin is a paradigmatic system for multiple length- and time-scale processes for which experimental and computational methods provide valuable insights into the functional dynamics. The systems discussed here highlight that for a comprehensive understanding of how structure, flexibility, energetics, and dynamics contribute to functional dynamics, experimental studies in multiple wavelength regions and computational studies including quantum, classical, and more coarse grained levels are required.
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Affiliation(s)
- Krystel El Hage
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Sebastian Brickel
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Sylvain Hermelin
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Geoffrey Gaulier
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Cédric Schmidt
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Luigi Bonacina
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Siri C van Keulen
- Institute of Chemical Sciences and Engineering, EPFL, Lausanne, Switzerland
| | | | - Majed Chergui
- Institute of Chemical Sciences and Engineering, EPFL, Lausanne, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | | | - Jean-Pierre Wolf
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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36
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Paul K, Sengupta P, Ark ED, Tu H, Zhao Y, Boppart SA. Coherent control of an opsin in living brain tissue. NATURE PHYSICS 2017; 13:1111-1116. [PMID: 29983725 PMCID: PMC6029863 DOI: 10.1038/nphys4257] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 08/15/2017] [Indexed: 05/20/2023]
Abstract
Retinal-based opsins are light-sensitive proteins. The photoisomerization reaction of these proteins has been studied outside cellular environments using ultrashort tailored light pulses1-5. However, how living cell functions can be modulated via opsins by modifying fundamental nonlinear optical properties of light interacting with the retinal chromophore has remained largely unexplored. We report the use of chirped ultrashort near-infrared pulses to modulate light-evoked ionic current from Channelrhodopsin-2 (ChR2) in brain tissue, and consequently the firing pattern of neurons, by manipulating the phase of the spectral components of the light. These results confirm that quantum coherence of the retinal-based protein system, even in a living neuron, can influence its current output, and open up the possibilities of using designer-tailored pulses for controlling molecular dynamics of opsins in living tissue to selectively enhance or suppress neuronal function for adaptive feedback-loop applications in the future.
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Affiliation(s)
- Kush Paul
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Parijat Sengupta
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Eugene D Ark
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Haohua Tu
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Youbo Zhao
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Stephen A Boppart
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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37
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van Keulen SC, Solano A, Rothlisberger U. How Rhodopsin Tunes the Equilibrium between Protonated and Deprotonated Forms of the Retinal Chromophore. J Chem Theory Comput 2017; 13:4524-4534. [PMID: 28731695 DOI: 10.1021/acs.jctc.7b00229] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Rhodopsin is a photoactive G-protein-coupled receptor (GPCR) that converts dim light into a signal for the brain, leading to eyesight. Full activation of this GPCR is achieved after passing through several steps of the protein's photoactivation pathway. Key events of rhodopsin activation are the initial cis-trans photoisomerization of the covalently bound retinal moiety followed by conformational rearrangements and deprotonation of the chromophore's protonated Schiff base (PSB), which ultimately lead to full activation in the meta II state. PSB deprotonation is crucial for achieving full activation of rhodopsin; however, the specific structural rearrangements that have to take place to induce this pKa shift are not well understood. Classical molecular dynamics (MD) simulations were employed to identify intermediate states after the cis-trans isomerization of rhodopsin's retinal moiety. In order to select the intermediate state in which PSB deprotonation is experimentally known to occur, the validity of the intermediate configurations was checked through an evaluation of the optical properties in comparison with experiment. Subsequently, the selected state was used to investigate the molecular factors that enable PSB deprotonation at body temperature to obtain a better understanding of the difference between the protonated and the deprotonated state of the chromophore. To this end, the deprotonation reaction has been investigated by applying QM/MM MD simulations in combination with thermodynamic integration. The study shows that, compared to the inactive 11-cis-retinal case, trans-retinal rhodopsin is able to undergo PSB deprotonation due to a change in the conformation of the retinal and a consequent alteration in the hydrogen-bond (HB) network in which PSB and the counterion Glu113 are embedded. Besides the retinal moiety and Glu113, also two water molecules as well as Thr94 and Gly90 that are related to congenital night blindness are part of this essential HB network.
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Affiliation(s)
- Siri C van Keulen
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Alicia Solano
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
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38
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Kaylor JJ, Xu T, Ingram NT, Tsan A, Hakobyan H, Fain GL, Travis GH. Blue light regenerates functional visual pigments in mammals through a retinyl-phospholipid intermediate. Nat Commun 2017; 8:16. [PMID: 28473692 PMCID: PMC5432035 DOI: 10.1038/s41467-017-00018-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 02/15/2017] [Indexed: 11/24/2022] Open
Abstract
The light absorbing chromophore in opsin visual pigments is the protonated Schiff base of 11-cis-retinaldehyde (11cRAL). Absorption of a photon isomerizes 11cRAL to all-trans-retinaldehyde (atRAL), briefly activating the pigment before it dissociates. Light sensitivity is restored when apo-opsin combines with another 11cRAL to form a new visual pigment. Conversion of atRAL to 11cRAL is carried out by enzyme pathways in neighboring cells. Here we show that blue (450-nm) light converts atRAL specifically to 11cRAL through a retinyl-phospholipid intermediate in photoreceptor membranes. The quantum efficiency of this photoconversion is similar to rhodopsin. Photoreceptor membranes synthesize 11cRAL chromophore faster under blue light than in darkness. Live mice regenerate rhodopsin more rapidly in blue light. Finally, whole retinas and isolated cone cells show increased photosensitivity following exposure to blue light. These results indicate that light contributes to visual-pigment renewal in mammalian rods and cones through a non-enzymatic process involving retinyl-phospholipids. It is currently thought that visual pigments in vertebrate photoreceptors are regenerated exclusively through enzymatic cycles. Here the authors show that mammalian photoreceptors also regenerate opsin pigments in light through photoisomerization of N-ret-PE (N-retinylidene-phosphatidylethanolamine.
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Affiliation(s)
- Joanna J Kaylor
- Jules Stein Eye Institute, University of California Los Angeles School of Medicine, Los Angeles, California, 90095, USA
| | - Tongzhou Xu
- Jules Stein Eye Institute, University of California Los Angeles School of Medicine, Los Angeles, California, 90095, USA.,Molecular, Cellular and Integrative Physiology Graduate Program, University of California Los Angeles School of Medicine, Los Angeles, California, 90095, USA
| | - Norianne T Ingram
- Jules Stein Eye Institute, University of California Los Angeles School of Medicine, Los Angeles, California, 90095, USA.,Molecular, Cellular and Integrative Physiology Graduate Program, University of California Los Angeles School of Medicine, Los Angeles, California, 90095, USA
| | - Avian Tsan
- Jules Stein Eye Institute, University of California Los Angeles School of Medicine, Los Angeles, California, 90095, USA
| | - Hayk Hakobyan
- Jules Stein Eye Institute, University of California Los Angeles School of Medicine, Los Angeles, California, 90095, USA
| | - Gordon L Fain
- Jules Stein Eye Institute, University of California Los Angeles School of Medicine, Los Angeles, California, 90095, USA.,Department of Integrative Biology and Physiology, University of California Los Angeles School of Medicine, Los Angeles, California, 90095, USA
| | - Gabriel H Travis
- Jules Stein Eye Institute, University of California Los Angeles School of Medicine, Los Angeles, California, 90095, USA. .,Department of Biological Chemistry, University of California Los Angeles School of Medicine, Los Angeles, California, 90095, USA.
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Photocyclic behavior of rhodopsin induced by an atypical isomerization mechanism. Proc Natl Acad Sci U S A 2017; 114:E2608-E2615. [PMID: 28289214 DOI: 10.1073/pnas.1617446114] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Vertebrate rhodopsin (Rh) contains 11-cis-retinal as a chromophore to convert light energy into visual signals. On absorption of light, 11-cis-retinal is isomerized to all-trans-retinal, constituting a one-way reaction that activates transducin (Gt) followed by chromophore release. Here we report that bovine Rh, regenerated instead with a six-carbon-ring retinal chromophore featuring a C11=C12 double bond locked in its cis conformation (Rh6mr), employs an atypical isomerization mechanism by converting 11-cis to an 11,13-dicis configuration for prolonged Gt activation. Time-dependent UV-vis spectroscopy, HPLC, and molecular mechanics analyses revealed an atypical thermal reisomerization of the 11,13-dicis to the 11-cis configuration on a slow timescale, which enables Rh6mr to function in a photocyclic manner similar to that of microbial Rhs. With this photocyclic behavior, Rh6mr repeatedly recruits and activates Gt in response to light stimuli, making it an excellent candidate for optogenetic tools based on retinal analog-bound vertebrate Rhs. Overall, these comprehensive structure-function studies unveil a unique photocyclic mechanism of Rh activation by an 11-cis-to-11,13-dicis isomerization.
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40
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Ishida T, Nanbu S, Nakamura H. Clarification of nonadiabatic chemical dynamics by the Zhu-Nakamura theory of nonadiabatic transition: from tri-atomic systems to reactions in solutions. INT REV PHYS CHEM 2017. [DOI: 10.1080/0144235x.2017.1293399] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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41
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Feldman TB, Smitienko OA, Shelaev IV, Gostev FE, Nekrasova OV, Dolgikh DA, Nadtochenko VA, Kirpichnikov MP, Ostrovsky MA. Femtosecond spectroscopic study of photochromic reactions of bacteriorhodopsin and visual rhodopsin. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2016; 164:296-305. [PMID: 27723489 DOI: 10.1016/j.jphotobiol.2016.09.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/29/2016] [Accepted: 09/30/2016] [Indexed: 11/16/2022]
Abstract
Photochromic ultrafast reactions of bacteriorhodopsin (H. salinarum) and bovine rhodopsin were conducted with a femtosecond two-pump probe pulse setup with the time resolution of 20-25fs. The dynamics of the forward and reverse photochemical reactions for both retinal-containing proteins was compared. It is demonstrated that when retinal-containing proteins are excited by femtosecond pulses, dynamics pattern of the vibrational coherent wave packets in the course of the reaction is different for bacteriorhodopsin and visual rhodopsin. As shown in these studies, the low-frequencies that form a wave packets experimentally observed in the dynamics of primary products formation as a result of retinal photoisomerization have different intensities and are clearer for bovine rhodopsin. Photo-reversible reactions for both retinal proteins were performed from the stage of the relatively stable photointermediates that appear within 3-5ps after the light pulse impact. It is demonstrated that the efficiency of the reverse phototransition K-form→bacteriorhodopsin is almost five-fold higher than that of the Batho-intermediate→visual rhodopsin phototransition. The results obtained indicate that in the course of evolution the intramolecular mechanism of the chromophore-protein interaction in visual rhodopsin becomes more perfect and specific. The decrease in the probability of the reverse chromophore photoisomerization (all-trans→11-cis retinal) in primary photo-induced rhodopsin products causes an increase in the efficiency of the photoreception process.
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Affiliation(s)
- Tatiana B Feldman
- Biological Faculty, Lomonosov Moscow State University, Leninskie Gory 1, Moscow 119991, Russia; Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin st.4, Moscow 119334, Russia.
| | - Olga A Smitienko
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin st.4, Moscow 119334, Russia
| | - Ivan V Shelaev
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, Kosygin st.4, Moscow 119991, Russia
| | - Fedor E Gostev
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, Kosygin st.4, Moscow 119991, Russia
| | - Oksana V Nekrasova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya st. 16/10, Moscow 117997, Russia
| | - Dmitriy A Dolgikh
- Biological Faculty, Lomonosov Moscow State University, Leninskie Gory 1, Moscow 119991, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya st. 16/10, Moscow 117997, Russia
| | - Victor A Nadtochenko
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin st.4, Moscow 119334, Russia; Semenov Institute of Chemical Physics, Russian Academy of Sciences, Kosygin st.4, Moscow 119991, Russia; Institute of Problems of Chemical Physics, Russian Academy of Sciences, Academician Semenov avenue 1, Chernogolovka, Moscow region 142432, Russia
| | - Mikhail P Kirpichnikov
- Biological Faculty, Lomonosov Moscow State University, Leninskie Gory 1, Moscow 119991, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya st. 16/10, Moscow 117997, Russia
| | - Mikhail A Ostrovsky
- Biological Faculty, Lomonosov Moscow State University, Leninskie Gory 1, Moscow 119991, Russia; Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin st.4, Moscow 119334, Russia
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42
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Liebel M, Kukura P. Lack of evidence for phase-only control of retinal photoisomerization in the strict one-photon limit. Nat Chem 2016; 9:45-49. [DOI: 10.1038/nchem.2598] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 07/19/2016] [Indexed: 12/23/2022]
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Grabarek D, Walczak E, Andruniów T. Assessing the Accuracy of Various Ab Initio Methods for Geometries and Excitation Energies of Retinal Chromophore Minimal Model by Comparison with CASPT3 Results. J Chem Theory Comput 2016; 12:2346-56. [DOI: 10.1021/acs.jctc.6b00108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dawid Grabarek
- Advanced Materials Engineering
and Modelling Group, Wroclaw University of Technology, Wyb. Wyspianskiego
27, 50-370 Wroclaw, Poland
| | - Elżbieta Walczak
- Advanced Materials Engineering
and Modelling Group, Wroclaw University of Technology, Wyb. Wyspianskiego
27, 50-370 Wroclaw, Poland
| | - Tadeusz Andruniów
- Advanced Materials Engineering
and Modelling Group, Wroclaw University of Technology, Wyb. Wyspianskiego
27, 50-370 Wroclaw, Poland
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44
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Johnson PJM, Halpin A, Morizumi T, Prokhorenko VI, Ernst OP, Miller RJD. Local vibrational coherences drive the primary photochemistry of vision. Nat Chem 2015; 7:980-6. [DOI: 10.1038/nchem.2398] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 10/15/2015] [Indexed: 01/06/2023]
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45
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46
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Bassolino G, Sovdat T, Soares Duarte A, Lim JM, Schnedermann C, Liebel M, Odell B, Claridge TDW, Fletcher SP, Kukura P. Barrierless Photoisomerization of 11-cis Retinal Protonated Schiff Base in Solution. J Am Chem Soc 2015; 137:12434-7. [DOI: 10.1021/jacs.5b06492] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Giovanni Bassolino
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Tina Sovdat
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Alex Soares Duarte
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Jong Min Lim
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Christoph Schnedermann
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Matz Liebel
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Barbara Odell
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Timothy D. W. Claridge
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Stephen P. Fletcher
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Philipp Kukura
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
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47
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Hofmann L, Palczewski K. Advances in understanding the molecular basis of the first steps in color vision. Prog Retin Eye Res 2015; 49:46-66. [PMID: 26187035 DOI: 10.1016/j.preteyeres.2015.07.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/07/2015] [Accepted: 07/09/2015] [Indexed: 01/05/2023]
Abstract
Serving as one of our primary environmental inputs, vision is the most sophisticated sensory system in humans. Here, we present recent findings derived from energetics, genetics and physiology that provide a more advanced understanding of color perception in mammals. Energetics of cis-trans isomerization of 11-cis-retinal accounts for color perception in the narrow region of the electromagnetic spectrum and how human eyes can absorb light in the near infrared (IR) range. Structural homology models of visual pigments reveal complex interactions of the protein moieties with the light sensitive chromophore 11-cis-retinal and that certain color blinding mutations impair secondary structural elements of these G protein-coupled receptors (GPCRs). Finally, we identify unsolved critical aspects of color tuning that require future investigation.
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Affiliation(s)
- Lukas Hofmann
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
| | - Krzysztof Palczewski
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
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48
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Panneels V, Wu W, Tsai CJ, Nogly P, Rheinberger J, Jaeger K, Cicchetti G, Gati C, Kick LM, Sala L, Capitani G, Milne C, Padeste C, Pedrini B, Li XD, Standfuss J, Abela R, Schertler G. Time-resolved structural studies with serial crystallography: A new light on retinal proteins. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041718. [PMID: 26798817 PMCID: PMC4711639 DOI: 10.1063/1.4922774] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/03/2015] [Indexed: 05/19/2023]
Abstract
Structural information of the different conformational states of the two prototypical light-sensitive membrane proteins, bacteriorhodopsin and rhodopsin, has been obtained in the past by X-ray cryo-crystallography and cryo-electron microscopy. However, these methods do not allow for the structure determination of most intermediate conformations. Recently, the potential of X-Ray Free Electron Lasers (X-FELs) for tracking the dynamics of light-triggered processes by pump-probe serial femtosecond crystallography has been demonstrated using 3D-micron-sized crystals. In addition, X-FELs provide new opportunities for protein 2D-crystal diffraction, which would allow to observe the course of conformational changes of membrane proteins in a close-to-physiological lipid bilayer environment. Here, we describe the strategies towards structural dynamic studies of retinal proteins at room temperature, using injector or fixed-target based serial femtosecond crystallography at X-FELs. Thanks to recent progress especially in sample delivery methods, serial crystallography is now also feasible at synchrotron X-ray sources, thus expanding the possibilities for time-resolved structure determination.
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Affiliation(s)
- Valérie Panneels
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Wenting Wu
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Ching-Ju Tsai
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Przemek Nogly
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Jan Rheinberger
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Kathrin Jaeger
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Gregor Cicchetti
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | | | - Leonhard M Kick
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Leonardo Sala
- Scientific Computing, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Guido Capitani
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Chris Milne
- SwissFEL Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Celestino Padeste
- Lab for Micro- and Nanotechnology, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Bill Pedrini
- SwissFEL Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Xiao-Dan Li
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Jörg Standfuss
- Laboratory of Biomolecular Research, Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
| | - Rafael Abela
- SwissFEL Paul Scherrer Institute , 5232 Villigen PSI, Switzerland
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49
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Brunk E, Rothlisberger U. Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States. Chem Rev 2015; 115:6217-63. [PMID: 25880693 DOI: 10.1021/cr500628b] [Citation(s) in RCA: 301] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Elizabeth Brunk
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,‡Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94618, United States
| | - Ursula Rothlisberger
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,§National Competence Center of Research (NCCR) MARVEL-Materials' Revolution: Computational Design and Discovery of Novel Materials, 1015 Lausanne, Switzerland
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50
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Tscherbul TV, Brumer P. Quantum coherence effects in natural light-induced processes: cis–trans photoisomerization of model retinal under incoherent excitation. Phys Chem Chem Phys 2015; 17:30904-13. [DOI: 10.1039/c5cp01388g] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cis–Trans isomerization of retinal induced by incoherent solar light. Shown are ground and excited-state diabatic potentials; the horizontal lines represent bright eigenstates (red), intermediate eigenstates (blue), and product eigenstates (green). The inset: the photoreaction efficiency vs. time with (red) and without (blue) Fano coherences.
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Affiliation(s)
- Timur V. Tscherbul
- Chemical Physics Theory Group
- Department of Chemistry
- and Center for Quantum Information and Quantum Control
- University of Toronto
- Toronto
| | - Paul Brumer
- Chemical Physics Theory Group
- Department of Chemistry
- and Center for Quantum Information and Quantum Control
- University of Toronto
- Toronto
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