1
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Pieri E, Weingart O, Huix-Rotllant M, Ledentu V, Garavelli M, Ferré N. Modeling pH-Dependent Biomolecular Photochemistry. J Chem Theory Comput 2024; 20:842-855. [PMID: 38198619 DOI: 10.1021/acs.jctc.3c00980] [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: 01/12/2024]
Abstract
The tuning mechanism of pH can be extremely challenging to model computationally in complex biological systems, especially with respect to the photochemical properties. This article reports a protocol aimed at modeling pH-dependent photodynamics using a combination of constant-pH molecular dynamics and semiclassical nonadiabatic molecular dynamics simulations. With retinal photoisomerization in Anabaena sensory rhodopsin (ASR) as a testbed, we show that our protocol produces pH-dependent photochemical properties, such as the isomerization quantum yield or decay rates. We decompose our results into single-titrated residue contributions, identifying some key tuning amino acids. Additionally, we assess the validity of the single protonation state picture to represent the system at a given pH and propose the most populated protein charge state as a compromise between cost and accuracy.
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Affiliation(s)
- Elisa Pieri
- Aix-Marseille Univ, CNRS, Institut de Chimie Radicalaire, 13013 Marseille, France
| | - Oliver Weingart
- Faculty of Mathematics and Natural Sciences, Institute for Theoretical and Computational Chemistry, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Miquel Huix-Rotllant
- Aix-Marseille Univ, CNRS, Institut de Chimie Radicalaire, 13013 Marseille, France
| | - Vincent Ledentu
- Aix-Marseille Univ, CNRS, Institut de Chimie Radicalaire, 13013 Marseille, France
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari", Università degli Studi di Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Nicolas Ferré
- Aix-Marseille Univ, CNRS, Institut de Chimie Radicalaire, 13013 Marseille, France
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2
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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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3
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Cárdenas G, Ledentu V, Huix-Rotllant M, Olivucci M, Ferré N. Automatic Rhodopsin Modeling with Multiple Protonation Microstates. J Phys Chem A 2023; 127:9365-9380. [PMID: 37877699 DOI: 10.1021/acs.jpca.3c05413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Automatic Rhodopsin Modeling (ARM) is a simulation protocol providing QM/MM models of rhodopsins capable of reproducing experimental electronic absorption and emission trends. Currently, ARM is restricted to a single protonation microstate for each rhodopsin model. Herein, we incorporate an extension of the minimal electrostatic model (MEM) into the ARM protocol to account for all relevant protonation microstates at a given pH. The new ARM+MEM protocol determines the most important microstates contributing to the description of the absorption spectrum. As a test case, we have applied this methodology to simulate the pH-dependent absorption spectrum of a toy model, showing that the single-microstate picture breaks down at certain pH values. Subsequently, we applied ARM+MEM toAnabaenasensory rhodopsin, confirming an improved description of its absorption spectrum when the titration of several key residues is considered.
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Affiliation(s)
| | | | | | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, 53100 Siena, Italy
| | - Nicolas Ferré
- Aix-Marseille Univ, CNRS, ICR, 13013 Marseille, France
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4
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Chang C, Kuramochi H, Singh M, Abe‐Yoshizumi R, Tsukuda T, Kandori H, Tahara T. A Unified View on Varied Ultrafast Dynamics of the Primary Process in Microbial Rhodopsins. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Chun‐Fu Chang
- Molecular Spectroscopy Laboratory RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
- Department of Chemistry Graduate School of Science The University of Tokyo 7-3-1 Hongo Bunkyo-Ku Tokyo 113-0033 Japan
| | - Hikaru Kuramochi
- Molecular Spectroscopy Laboratory RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
- Ultrafast Spectroscopy Research Team RIKEN Center for Advanced Photonics (RAP), RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
- PRESTO (Japan) Science and Technology Agency 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
- Present address: Research Center of Integrative Molecular Systems Institute for Molecular Science 38 Nishigo-Naka Myodaiji Okazaki 444-8585 Japan
| | - Manish Singh
- Department of Life Science and Applied Chemistry Nagoya Institute of Technology, Showa-Ku Nagoya Aichi 466-8555 Japan
| | - Rei Abe‐Yoshizumi
- Department of Life Science and Applied Chemistry Nagoya Institute of Technology, Showa-Ku Nagoya Aichi 466-8555 Japan
| | - Tatsuya Tsukuda
- Department of Chemistry Graduate School of Science The University of Tokyo 7-3-1 Hongo Bunkyo-Ku Tokyo 113-0033 Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry Nagoya Institute of Technology, Showa-Ku Nagoya Aichi 466-8555 Japan
- OptoBioTechnology Research Center Nagoya Institute of Technology Showa-Ku, Nagoya Aichi 466-8555 Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
- Ultrafast Spectroscopy Research Team RIKEN Center for Advanced Photonics (RAP), RIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
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5
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Chang CF, Kuramochi H, Singh M, Abe-Yoshizumi R, Tsukuda T, Kandori H, Tahara T. A Unified View on Varied Ultrafast Dynamics of the Primary Process in Microbial Rhodopsins. Angew Chem Int Ed Engl 2022; 61:e202111930. [PMID: 34670002 DOI: 10.1002/anie.202111930] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Indexed: 11/08/2022]
Abstract
All-trans to 13-cis photoisomerization of the protonated retinal Schiff base (PRSB) chromophore is the primary step that triggers various biological functions of microbial rhodopsins. While this ultrafast primary process has been extensively studied, it has been recognized that the relevant excited-state relaxation dynamics differ significantly from one rhodopsin to another. To elucidate the origin of the complicated ultrafast dynamics of the primary process in microbial rhodopsins, we studied the excited-state dynamics of proteorhodopsin, its D97N mutant, and bacteriorhodopsin by femtosecond time-resolved absorption (TA) spectroscopy in a wide pH range. The TA data showed that their excited-state relaxation dynamics drastically change when pH approaches the pKa of the counterion residue of the PRSB chromophore in the ground state. This result reveals that the varied excited-state relaxation dynamics in different rhodopsins mainly originate from the difference of the ground-state heterogeneity (i.e., protonation/deprotonation of the PRSB counterion).
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Affiliation(s)
- Chun-Fu Chang
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Hikaru Kuramochi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- PRESTO (Japan) Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama, 332-0012, Japan
- Present address: Research Center of Integrative Molecular Systems, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki, 444-8585, Japan
| | - Manish Singh
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya, Aichi, 466-8555, Japan
| | - Rei Abe-Yoshizumi
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya, Aichi, 466-8555, Japan
| | - Tatsuya Tsukuda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya, Aichi, 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-Ku, Nagoya, Aichi, 466-8555, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
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6
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Mroginski MA, Adam S, Amoyal GS, Barnoy A, Bondar AN, Borin VA, Church JR, Domratcheva T, Ensing B, Fanelli F, Ferré N, Filiba O, Pedraza-González L, González R, González-Espinoza CE, Kar RK, Kemmler L, Kim SS, Kongsted J, Krylov AI, Lahav Y, Lazaratos M, NasserEddin Q, Navizet I, Nemukhin A, Olivucci M, Olsen JMH, Pérez de Alba Ortíz A, Pieri E, Rao AG, Rhee YM, Ricardi N, Sen S, Solov'yov IA, De Vico L, Wesolowski TA, Wiebeler C, Yang X, Schapiro I. Frontiers in Multiscale Modeling of Photoreceptor Proteins. Photochem Photobiol 2021; 97:243-269. [PMID: 33369749 DOI: 10.1111/php.13372] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/01/2020] [Indexed: 02/06/2023]
Abstract
This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments.
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Affiliation(s)
| | - Suliman Adam
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gil S Amoyal
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Avishai Barnoy
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Veniamin A Borin
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jonathan R Church
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tatiana Domratcheva
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Department Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Bernd Ensing
- Van 't Hoff Institute for Molecular Science and Amsterdam Center for Multiscale Modeling, University of Amsterdam, Amsterdam, The Netherlands
| | - Francesca Fanelli
- Department of Life Sciences, Center for Neuroscience and Neurotechnology, Università degli Studi di Modena e Reggio Emilia, Modena, Italy
| | | | - Ofer Filiba
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Laura Pedraza-González
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Siena, Italy
| | - Ronald González
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | | | - Rajiv K Kar
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lukas Kemmler
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Seung Soo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Yigal Lahav
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.,MIGAL - Galilee Research Institute, S. Industrial Zone, Kiryat Shmona, Israel
| | - Michalis Lazaratos
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Qays NasserEddin
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isabelle Navizet
- MSME, Univ Gustave Eiffel, CNRS UMR 8208, Univ Paris Est Creteil, Marne-la-Vallée, France
| | - Alexander Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Siena, Italy.,Chemistry Department, Bowling Green State University, Bowling Green, OH, USA
| | - Jógvan Magnus Haugaard Olsen
- Department of Chemistry, Aarhus University, Aarhus, Denmark.,Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Alberto Pérez de Alba Ortíz
- Van 't Hoff Institute for Molecular Science and Amsterdam Center for Multiscale Modeling, University of Amsterdam, Amsterdam, The Netherlands
| | - Elisa Pieri
- Aix-Marseille Univ, CNRS, ICR, Marseille, France
| | - Aditya G Rao
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Young Min Rhee
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Niccolò Ricardi
- Département de Chimie Physique, Université de Genève, Genève, Switzerland
| | - Saumik Sen
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ilia A Solov'yov
- Department of Physics, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Luca De Vico
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Siena, Italy
| | | | - Christian Wiebeler
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Xuchun Yang
- Chemistry Department, Bowling Green State University, Bowling Green, OH, USA
| | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
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7
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Lokiarchaeota archaeon schizorhodopsin-2 (LaSzR2) is an inward proton pump displaying a characteristic feature of acid-induced spectral blue-shift. Sci Rep 2020; 10:20857. [PMID: 33257762 PMCID: PMC7704677 DOI: 10.1038/s41598-020-77936-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 10/29/2020] [Indexed: 11/25/2022] Open
Abstract
The photoreactive protein rhodopsin is widespread in microorganisms and has a variety of photobiological functions. Recently, a novel phylogenetically distinctive group named ‘schizorhodopsin (SzR)’ has been identified as an inward proton pump. We performed functional and spectroscopic studies on an uncharacterised schizorhodopsin from the phylum Lokiarchaeota archaeon. The protein, LaSzR2, having an all-trans-retinal chromophore, showed inward proton pump activity with an absorption maximum at 549 nm. The pH titration experiments revealed that the protonated Schiff base of the retinal chromophore (Lys188, pKa = 12.3) is stabilised by the deprotonated counterion (presumably Asp184, pKa = 3.7). The flash-photolysis experiments revealed the presence of two photointermediates, K and M. A proton was released and uptaken from bulk solution upon the formation and decay of the M intermediate. During the M-decay, the Schiff base was reprotonated by the proton from a proton donating residue (presumably Asp172). These properties were compared with other inward (SzRs and xenorhodopsins, XeRs) and outward proton pumps. Notably, LaSzR2 showed acid-induced spectral ‘blue-shift’ due to the protonation of the counterion, whereas outward proton pumps showed opposite shifts (red-shifts). Thus, we can distinguish between inward and outward proton pumps by the direction of the acid-induced spectral shift.
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8
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Harris A, Lazaratos M, Siemers M, Watt E, Hoang A, Tomida S, Schubert L, Saita M, Heberle J, Furutani Y, Kandori H, Bondar AN, Brown LS. Mechanism of Inward Proton Transport in an Antarctic Microbial Rhodopsin. J Phys Chem B 2020; 124:4851-4872. [DOI: 10.1021/acs.jpcb.0c02767] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Andrew Harris
- Department of Physics, University of Guelph, 50 Stone Rd. E., Guelph, Ontario N1G 2W1, Canada
| | - Michalis Lazaratos
- Theoretical Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Malte Siemers
- Theoretical Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Ethan Watt
- Department of Physics, University of Guelph, 50 Stone Rd. E., Guelph, Ontario N1G 2W1, Canada
| | - Anh Hoang
- Department of Physics, University of Guelph, 50 Stone Rd. E., Guelph, Ontario N1G 2W1, Canada
| | - Sahoko Tomida
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Luiz Schubert
- Experimental Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Mattia Saita
- Experimental Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Joachim Heberle
- Experimental Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Yuji Furutani
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Ana-Nicoleta Bondar
- Theoretical Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Leonid S. Brown
- Department of Physics, University of Guelph, 50 Stone Rd. E., Guelph, Ontario N1G 2W1, Canada
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9
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Pieri E, Ledentu V, Sahlin M, Dehez F, Olivucci M, Ferré N. CpHMD-Then-QM/MM Identification of the Amino Acids Responsible for the Anabaena Sensory Rhodopsin pH-Dependent Electronic Absorption Spectrum. J Chem Theory Comput 2019; 15:4535-4546. [PMID: 31264415 DOI: 10.1021/acs.jctc.9b00221] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Anabaena Sensory Rhodopsin (ASR), a microbial photoactive protein featuring the retinal chromophore in two different conformations, exhibits a pH-dependent electronic absorption spectrum. Using the recently developed CpHMD-then-QM/MM multiscale protocol applied to ASR embedded in a membrane model, the pH-induced changes in its maximum absorption wavelength have been reproduced and analyzed. While the acidic tiny red-shift is essentially correlated with the deprotonation of an aspartic acid located on the ASR extracellular side, the larger blue-shift experimentally reported at pH values larger than 5 involves a cluster of titrating residues sitting on the cytoplasmic side. The ASR pH-dependent spectrum is the consequence of the competitive stabilization of retinal ground and excited states by the protein electrostatic potential.
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Affiliation(s)
- Elisa Pieri
- Aix-Marseille Univ , CNRS, ICR , 13013 Marseille , France
| | | | - Michael Sahlin
- Aix-Marseille Univ , CNRS, ICR , 13013 Marseille , France
| | - François Dehez
- Laboratoire de Physique et Chimie Théorique , UMR 7019, Faculté des Sciences et Technique , Campus Aiguillettes , 54506 Vandoeuvre-les-Nancy , France
| | - Massimo Olivucci
- Department of Chemistry , Bowling Green State University , Bowling Green , Ohio 43403 , United States.,Dipartimento di Biotecnologie, Chimica e Farmacia , Università degli Studi di Siena , via A. Moro 2 , 53100 Siena , Italy
| | - Nicolas Ferré
- Aix-Marseille Univ , CNRS, ICR , 13013 Marseille , France
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10
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Agathangelou D, Orozco-Gonzalez Y, Del Carmen Marín M, Roy PP, Brazard J, Kandori H, Jung KH, Léonard J, Buckup T, Ferré N, Olivucci M, Haacke S. Effect of point mutations on the ultrafast photo-isomerization of Anabaena sensory rhodopsin. Faraday Discuss 2019; 207:55-75. [PMID: 29388996 DOI: 10.1039/c7fd00200a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Anabaena sensory rhodopsin (ASR) is a particular microbial retinal protein for which light-adaptation leads to the ability to bind both the all-trans, 15-anti (AT) and the 13-cis, 15-syn (13C) isomers of the protonated Schiff base of retinal (PSBR). In the context of obtaining insight into the mechanisms by which retinal proteins catalyse the PSBR photo-isomerization reaction, ASR is a model system allowing to study, within the same protein, the protein-PSBR interactions for two different PSBR conformers at the same time. A detailed analysis of the vibrational spectra of AT and 13C, and their photo-products in wild-type ASR obtained through femtosecond (pump-) four-wave-mixing is reported for the first time, and compared to bacterio- and channelrhodopsin. As part of an extensive study of ASR mutants with blue-shifted absorption spectra, we present here a detailed computational analysis of the origin of the mutation-induced blue-shift of the absorption spectra, and identify electrostatic interactions as dominating steric effects that would entail a red-shift. The excited state lifetimes and isomerization reaction times (IRT) for the three mutants V112N, W76F, and L83Q are studied experimentally by femtosecond broadband transient absorption spectroscopy. Interestingly, in all three mutants, isomerization is accelerated for AT with respect to wild-type ASR, and this the more, the shorter the wavelength of maximum absorption. On the contrary, the 13C photo-reaction is slightly slowed down, leading to an inversion of the ESLs of AT and 13C, with respect to wt-ASR, in the blue-most absorbing mutant L83Q. Possible mechanisms for these mutation effects, and their steric and electrostatic origins are discussed.
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Affiliation(s)
- D Agathangelou
- University of Strasbourg, CNRS, Inst. de Physique et Chimie des Matériaux de Strasbourg, 67034 Strasbourg, France.
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11
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Inoue S, Yoshizawa S, Nakajima Y, Kojima K, Tsukamoto T, Kikukawa T, Sudo Y. Spectroscopic characteristics ofRubricoccus marinusxenorhodopsin (RmXeR) and a putative model for its inward H+transport mechanism. Phys Chem Chem Phys 2018; 20:3172-3183. [DOI: 10.1039/c7cp05033j] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
On the basis of functional and spectroscopic characterization, we propose a model for the inward proton transport inRmXeR, a newly discovered microbial rhodopsin.
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Affiliation(s)
- Saki Inoue
- Graduate School of Medicine
- Dentistry and Pharmaceutical Sciences
- Okayama University
- Okayama 700-8530
- Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute
- The University of Tokyo
- Chiba 277-8564
- Japan
| | - Yu Nakajima
- Atmosphere and Ocean Research Institute
- The University of Tokyo
- Chiba 277-8564
- Japan
| | - Keiichi Kojima
- Graduate School of Medicine
- Dentistry and Pharmaceutical Sciences
- Okayama University
- Okayama 700-8530
- Japan
| | - Takashi Tsukamoto
- Graduate School of Medicine
- Dentistry and Pharmaceutical Sciences
- Okayama University
- Okayama 700-8530
- Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science
- Hokkaido University
- Sapporo 060-0810
- Japan
- Global Station for Soft Matter
| | - Yuki Sudo
- Graduate School of Medicine
- Dentistry and Pharmaceutical Sciences
- Okayama University
- Okayama 700-8530
- Japan
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12
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Kowalewski M, Fingerhut BP, Dorfman KE, Bennett K, Mukamel S. Simulating Coherent Multidimensional Spectroscopy of Nonadiabatic Molecular Processes: From the Infrared to the X-ray Regime. Chem Rev 2017; 117:12165-12226. [DOI: 10.1021/acs.chemrev.7b00081] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Markus Kowalewski
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
| | - Benjamin P. Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Konstantin E. Dorfman
- State
Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China
| | - Kochise Bennett
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
| | - Shaul Mukamel
- Department
of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697-2025, United States
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13
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Ito S, Sugita S, Inoue K, Kandori H. FTIR Analysis of a Light-driven Inward Proton-pumping Rhodopsin at 77 K. Photochem Photobiol 2017; 93:1381-1387. [DOI: 10.1111/php.12771] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/22/2017] [Indexed: 01/27/2023]
Affiliation(s)
- Shota Ito
- Department of Life Science and Applied Chemistry; Nagoya Institute of Technology; Showa-ku Nagoya Japan
| | - Shinya Sugita
- Department of Life Science and Applied Chemistry; Nagoya Institute of Technology; Showa-ku Nagoya Japan
| | - Keiichi Inoue
- Department of Life Science and Applied Chemistry; Nagoya Institute of Technology; Showa-ku Nagoya Japan
- OptoBioTechnology Research Center; Nagoya Institute of Technology; Showa-ku Nagoya Japan
- PRESTO; Japan Science and Technology Agency; Kawaguchi Saitama Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry; Nagoya Institute of Technology; Showa-ku Nagoya Japan
- OptoBioTechnology Research Center; Nagoya Institute of Technology; Showa-ku Nagoya Japan
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14
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Tamogami J, Kikukawa T, Nara T, Demura M, Kimura-Someya T, Shirouzu M, Yokoyama S, Miyauchi S, Shimono K, Kamo N. Existence of two O-like intermediates in the photocycle of Acetabularia rhodopsin II, a light-driven proton pump from a marine alga. Biophys Physicobiol 2017; 14:49-55. [PMID: 28560129 PMCID: PMC5437830 DOI: 10.2142/biophysico.14.0_49] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/02/2017] [Indexed: 12/01/2022] Open
Abstract
A spectrally silent change is often observed in the photocycle of microbial rhodopsins. Here, we suggest the presence of two O intermediates in the photocycle of Acetabularia rhodopsin II (ARII or also called Ace2), a light-driven algal proton pump from Acetabularia acetabulum. ARII exhibits a photocycle including a quasi-equilibrium state of M, N, and O (M⇄N⇄O→) at near neutral and above pH values. However, acidification of the medium below pH ~5.5 causes no accumulation of N, resulting in that the photocycle of ARII can be described as an irreversible scheme (M→O→). This may facilitate the investigation of the latter part of the photocycle, especially the rise and decay of O, during which molecular events have not been sufficiently understood. Thus we analyzed the photocycle under acidic conditions (pH ≤ 5.5). Analysis of the absorbance change at 610 nm, which mainly monitors the fractional concentration changes of K and O, was performed and revealed a photocycle scheme containing two sequential O-states with the different molar extinction coefficients. These photoproducts, termed O1 and O2, may be even produced at physiological pH, although they are not clearly observed under this condition due to the existence of a long M-N-O equilibrium.
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Affiliation(s)
- Jun Tamogami
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan.,Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo 001-0021, Japan
| | - Toshifumi Nara
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan
| | - Makoto Demura
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan.,Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo 001-0021, Japan
| | - Tomomi Kimura-Someya
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan
| | - Mikako Shirouzu
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, Yokohama 230-0045, Japan.,RIKEN Structural Biology Laboratory, Yokohama 230-0045, Japan
| | - Seiji Miyauchi
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan.,Graduate School of Pharmaceutical Sciences, Toho University, Funabashi, Chiba 274-8510, Japan
| | - Kazumi Shimono
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan.,Graduate School of Pharmaceutical Sciences, Toho University, Funabashi, Chiba 274-8510, Japan
| | - Naoki Kamo
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan.,Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
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15
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Stenrup M, Pieri E, Ledentu V, Ferré N. pH-Dependent absorption spectrum of a protein: a minimal electrostatic model of Anabaena sensory rhodopsin. Phys Chem Chem Phys 2017; 19:14073-14084. [DOI: 10.1039/c7cp00991g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A minimal electrostatic model is introduced which aims at reproducing and analyzing the visible-light absorption energy shift of a protein with pH.
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16
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Schnedermann C, Muders V, Ehrenberg D, Schlesinger R, Kukura P, Heberle J. Vibronic Dynamics of the Ultrafast all-trans to 13-cis Photoisomerization of Retinal in Channelrhodopsin-1. J Am Chem Soc 2016; 138:4757-62. [DOI: 10.1021/jacs.5b12251] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christoph Schnedermann
- Physical
and Theoretical Chemistry Laboratory, University of Oxford, South Parks
Road, Oxford OX1 3QZ, United Kingdom
| | | | | | | | - Philipp Kukura
- Physical
and Theoretical Chemistry Laboratory, University of Oxford, South Parks
Road, Oxford OX1 3QZ, United Kingdom
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17
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Dong X, Ramon E, Herrera-Hernández MG, Garriga P. Phospholipid Bicelles Improve the Conformational Stability of Rhodopsin Mutants Associated with Retinitis Pigmentosa. Biochemistry 2015; 54:4795-804. [PMID: 26181234 DOI: 10.1021/acs.biochem.5b00435] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Mutations in the visual photoreceptor rhodopsin are the cause of the retinal degenerative disease retinitis pigmentosa. Some naturally occurring mutations can lead to protein conformational instability. Two such mutations, N55K and G90V, in the first and second transmembrane helices of the receptor, have been associated with sector and classical retinitis pigmentosa, respectively, and showed enhanced thermal sensitivity. We have carefully analyzed the effect of phospholipid bicelles on the stability and ligand binding properties of these two mutants and compared it with those of the detergent-solubilized samples. We have used a phospholipid bilayer consisting of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) and 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC). We find that DMPC/DHPC bicelles dramatically increase the thermal stability of the rhodopsin mutants G90V and N55K. The chromophore stability and regeneration of the mutants were also increased in bicelles when compared to their behavior in a dodecyl maltoside detergent solution. The retinal release process was slowed in bicelles, and chromophore entry, after illumination, was improved for the G90V mutant but not for N55K. Furthermore, fluorescence spectroscopy measurements showed that bicelles allowed more exogenous retinal binding to the photoactivated G90V mutant than in a detergent solution. In contrast, N55K could not reposition any chromophore either in the detergent or in bicelles. The results demonstrate that DMPC/DHPC bicelles can counteract the destabilizing effect of the disease-causing mutations and can modulate the structural changes in the ensuing receptor photoactivation in a distinct specific manner for different retinitis pigmentosa mutant phenotypes.
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Affiliation(s)
- Xiaoyun Dong
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| | - Eva Ramon
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| | - María Guadalupe Herrera-Hernández
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| | - Pere Garriga
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
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18
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Cheminal A, Léonard J, Kim SY, Jung KH, Kandori H, Haacke S. 100 fs photo-isomerization with vibrational coherences but low quantum yield in Anabaena Sensory Rhodopsin. Phys Chem Chem Phys 2015; 17:25429-39. [DOI: 10.1039/c5cp04353k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Counter-intuitive photochemistry: in Anabaena Sensory Rhodopsin, the retinal 13-cis isomer isomerizes much faster than all-trans ASR, but with a 3-times lower quantum yield.
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Affiliation(s)
- Alexandre Cheminal
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE
- Université de Strasbourg – CNRS
- 67034 Strasbourg
- France
| | - Jérémie Léonard
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE
- Université de Strasbourg – CNRS
- 67034 Strasbourg
- France
| | - So-Young Kim
- Department of Life Science and Institute of Biological Interfaces
- Sogang University
- Mapo-Gu
- South Korea
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces
- Sogang University
- Mapo-Gu
- South Korea
| | - Hideki Kandori
- Department of Frontier Materials
- Nagoya Institute of Technology
- Showa-ku
- Japan
| | - Stefan Haacke
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE
- Université de Strasbourg – CNRS
- 67034 Strasbourg
- France
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