1
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Malakar P, Gholami S, Aarabi M, Rivalta I, Sheves M, Garavelli M, Ruhman S. Retinal photoisomerization versus counterion protonation in light and dark-adapted bacteriorhodopsin and its primary photoproduct. Nat Commun 2024; 15:2136. [PMID: 38459010 PMCID: PMC10923925 DOI: 10.1038/s41467-024-46061-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/08/2024] [Indexed: 03/10/2024] Open
Abstract
Discovered over 50 years ago, bacteriorhodopsin is the first recognized and most widely studied microbial retinal protein. Serving as a light-activated proton pump, it represents the archetypal ion-pumping system. Here we compare the photochemical dynamics of bacteriorhodopsin light and dark-adapted forms with that of the first metastable photocycle intermediate known as "K". We observe that following thermal double isomerization of retinal in the dark from bio-active all-trans 15-anti to 13-cis, 15-syn, photochemistry proceeds even faster than the ~0.5 ps decay of the former, exhibiting ballistic wave packet curve crossing to the ground state. In contrast, photoexcitation of K containing a 13-cis, 15-anti chromophore leads to markedly multi-exponential excited state decay including much slower stages. QM/MM calculations, aimed to interpret these results, highlight the crucial role of protonation, showing that the classic quadrupole counterion model poorly reproduces spectral data and dynamics. Single protonation of ASP212 rectifies discrepancies and predicts triple ground state structural heterogeneity aligning with experimental observations. These findings prompt a reevaluation of counter ion protonation in bacteriorhodopsin and contribute to the broader understanding of its photochemical dynamics.
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Affiliation(s)
- Partha Malakar
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Samira Gholami
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy
| | - Mohammad Aarabi
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy
| | - Ivan Rivalta
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy
- ENSL, CNRS, Laboratoire de Chimie UMR 5182, 46 allée d'Italie, 69364, Lyon, France
| | - Mordechai Sheves
- Department of Molecular Chemistry and Materials Science, The Weizmann Institute of Science, Rehovot, 7610001, Israel.
| | - Marco Garavelli
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy.
| | - Sanford Ruhman
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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Li Z, Mizuno M, Ejiri T, Hayashi S, Kandori H, Mizutani Y. Unique Vibrational Characteristics and Structures of the Photoexcited Retinal Chromophore in Ion-Pumping Rhodopsins. J Phys Chem B 2023; 127:9873-9886. [PMID: 37940604 DOI: 10.1021/acs.jpcb.3c02146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Photoisomerization of an all-trans-retinal chromophore triggers ion transport in microbial ion-pumping rhodopsins. Understanding chromophore structures in the electronically excited (S1) state provides insights into the structural evolution on the potential energy surface of the photoexcited state. In this study, we examined the structure of the S1-state chromophore in Natronomonas pharaonis halorhodopsin (NpHR), a chloride ion-pumping rhodopsin, using time-resolved resonance Raman spectroscopy. The spectral patterns of the S1-state chromophore were completely different from those of the ground-state chromophore, resulting from unique vibrational characteristics and the structure of the S1 state. Mode assignments were based on a combination of deuteration shifts of the Raman bands and hybrid quantum mechanics-molecular mechanics calculations. The present observations suggest a weakened bond alternation in the π conjugation system. A strong hydrogen-out-of-plane bending band was observed in the Raman spectra of the S1-state chromophore in NpHR, indicating a twisted polyene structure. Similar frequency shifts for the C═N/C═C and C-C stretching modes of the S1-state chromophore in NpHR were observed in the Raman spectra of sodium ion-pumping and proton-pumping rhodopsins, suggesting that these unique features are common to the S1 states of ion-pumping rhodopsins.
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Affiliation(s)
- Zixuan Li
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Osaka, Toyonaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Osaka, Toyonaka 560-0043, Japan
| | - Tomo Ejiri
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Osaka, Toyonaka 560-0043, Japan
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5
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Asido M, Wachtveitl J. Photochemistry of the Light-Driven Sodium Pump Krokinobacter eikastus Rhodopsin 2 and Its Implications on Microbial Rhodopsin Research: Retrospective and Perspective. J Phys Chem B 2023; 127:3766-3773. [PMID: 36919947 DOI: 10.1021/acs.jpcb.2c08933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
The discovery of the light-driven sodium pump Krokinobacter eikastus rhodopsin 2 (KR2) in 2013 has changed the paradigm that cation transport in microbial rhodopsins is restricted to the translocation of protons. Even though this finding is already remarkable by itself, it also reignited more general discussions about the functional mechanism of ion transport. The unique composition of the retinal binding pocket in KR2 with a tight interaction between the retinal Schiff base and its respective counterion D116 also has interesting implications on the photochemical pathway of the chromophore. Here, we discuss the most recent advances in our understanding of the KR2 functionality from the primary event of photon absorption by all-trans retinal up to the actual protein response in the later phases of the photocycle, mainly from the point of view of optical spectroscopy. In this context, we furthermore highlight some of the ongoing debates on the photochemistry of microbial rhodopsins and give some perspectives for promising future directions in this field of research.
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Affiliation(s)
- Marvin Asido
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany
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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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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 2021; 61:e202111930. [PMID: 34670002 DOI: 10.1002/anie.202111930] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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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8
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Kusochek PA, Scherbinin AV, Bochenkova AV. Insights into the Early-Time Excited-State Dynamics of Structurally Inhomogeneous Rhodopsin KR2. J Phys Chem Lett 2021; 12:8664-8671. [PMID: 34472871 DOI: 10.1021/acs.jpclett.1c02312] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The light-driven sodium-pump rhodopsin KR2 exhibits ultrafast photoisomerization dynamics of its all-trans protonated Schiff-base retinal (PSBR). However, the excited-state decay of KR2 also shows slow picosecond time constants, which are attributed to nonreactive states. The mechanism that produces long-lived states is unclear. Here, by using molecular dynamics simulations and large-scale XMCQDPT2-based QM/MM modeling, we explore the origin of reactive and nonreactive states in KR2. By calculating the S0-S1 vibronic band shapes, we gain insight into the early-time excited-state dynamics of PSBR and show that the protein environment can significantly alter vibrational modes that are active upon photoexcitation, thus facilitating photoisomerization from all-trans to 13-cis PSBR. Importantly, we reveal structural heterogeneity of the retinal-binding pocket of KR2, characterized by three distinct conformations, and conclude that the formation of a strong hydrogen bond between the retinal Schiff base and its counterion is essential for the ultrafast reaction dynamics.
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Affiliation(s)
- Pavel A Kusochek
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Andrei V Scherbinin
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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9
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Yun JH, Li X, Yue J, Park JH, Jin Z, Li C, Hu H, Shi Y, Pandey S, Carbajo S, Boutet S, Hunter MS, Liang M, Sierra RG, Lane TJ, Zhou L, Weierstall U, Zatsepin NA, Ohki M, Tame JRH, Park SY, Spence JCH, Zhang W, Schmidt M, Lee W, Liu H. Early-stage dynamics of chloride ion-pumping rhodopsin revealed by a femtosecond X-ray laser. Proc Natl Acad Sci U S A 2021; 118:e2020486118. [PMID: 33753488 DOI: 10.1073/pnas.2020486118] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Light-driven rhodopsin proteins pump ions across cell membranes. They have applications in optogenetics and can potentially be used to develop solar energy–harvesting devices. A detailed understanding of rhodopsin dynamics and functions may therefore assist research in medicine, health, and clean energy. This time-resolved crystallography study carried out with X-ray free-electron lasers reveals detailed dynamics of chloride ion–pumping rhodopsin (ClR) within 100 ps of light activation. It shows the dissociation of Cl− from the Schiff base binding site upon light-triggered retinal isomerization. This Cl− dissociation is followed by diffusion toward the intracellular direction. The results hint at a common ion-pumping mechanism across rhodopsin families. Chloride ion–pumping rhodopsin (ClR) in some marine bacteria utilizes light energy to actively transport Cl− into cells. How the ClR initiates the transport is elusive. Here, we show the dynamics of ion transport observed with time-resolved serial femtosecond (fs) crystallography using the Linac Coherent Light Source. X-ray pulses captured structural changes in ClR upon flash illumination with a 550 nm fs-pumping laser. High-resolution structures for five time points (dark to 100 ps after flashing) reveal complex and coordinated dynamics comprising retinal isomerization, water molecule rearrangement, and conformational changes of various residues. Combining data from time-resolved spectroscopy experiments and molecular dynamics simulations, this study reveals that the chloride ion close to the Schiff base undergoes a dissociation–diffusion process upon light-triggered retinal isomerization.
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10
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Smitienko OA, Feldman TB, Petrovskaya LE, Nekrasova OV, Yakovleva MA, Shelaev IV, Gostev FE, Cherepanov DA, Kolchugina IB, Dolgikh DA, Nadtochenko VA, Kirpichnikov MP, Ostrovsky MA. Comparative Femtosecond Spectroscopy of Primary Photoreactions of Exiguobacterium sibiricum Rhodopsin and Halobacterium salinarum Bacteriorhodopsin. J Phys Chem B 2021; 125:995-1008. [PMID: 33475375 DOI: 10.1021/acs.jpcb.0c07763] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The primary stages of the Exiguobacterium sibiricum rhodopsin (ESR) photocycle were investigated by femtosecond absorption laser spectroscopy in the spectral range of 400-900 nm with a time resolution of 25 fs. The dynamics of the ESR photoreaction were compared with the reactions of bacteriorhodopsin (bR) in purple membranes (bRPM) and in recombinant form (bRrec). The primary intermediates of the ESR photocycle were similar to intermediates I, J, and K in bacteriorhodopsin photoconversion. The CONTIN program was applied to analyze the characteristic times of the observed processes and to clarify the reaction scheme. A similar photoreaction pattern was observed for all studied retinal proteins, including two consecutive dynamic Stokes shift phases lasting ∼0.05 and ∼0.15 ps. The excited state decays through a femtosecond reactive pathway, leading to retinal isomerization and formation of product J, and a picosecond nonreactive pathway that leads only to the initial state. Retinal photoisomerization in ESR takes 0.69 ps, compared with 0.48 ps in bRPM and 0.74 ps in bRrec. The nonreactive excited state decay takes 5 ps in ESR and ∼3 ps in bR. We discuss the similarity of the primary reactions of ESR and other retinal proteins.
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Affiliation(s)
| | - Tatiana B Feldman
- Emanuel Institute of Biochemical Physics, Moscow 119334, Russia.,Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Lada E Petrovskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Oksana V Nekrasova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | | | - Ivan V Shelaev
- Semenov Federal Research Center of Chemical Physics, Moscow 119991, Russia
| | - Fedor E Gostev
- Semenov Federal Research Center of Chemical Physics, Moscow 119991, Russia
| | | | - Irina B Kolchugina
- Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Dmitry A Dolgikh
- Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Victor A Nadtochenko
- Semenov Federal Research Center of Chemical Physics, Moscow 119991, Russia.,Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Mikhail P Kirpichnikov
- Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Mikhail A Ostrovsky
- Emanuel Institute of Biochemical Physics, Moscow 119334, Russia.,Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
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11
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Chang CF, Kuramochi H, Singh M, Abe-Yoshizumi R, Tsukuda T, Kandori H, Tahara T. Acid-base equilibrium of the chromophore counterion results in distinct photoisomerization reactivity in the primary event of proteorhodopsin. Phys Chem Chem Phys 2019; 21:25728-25734. [PMID: 31720623 DOI: 10.1039/c9cp04991f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proteorhodopsin (PR) is a proton-pumping rhodopsin, and it is known to exhibit a multi-phasic decay of the excited-state population in the primary process. So far, this complex excited-state decay has been attributed to the branching of the relaxation pathway on the excited-state potential energy surface. However, a recent ultrafast spectroscopic study on a sodium-pumping rhodopsin suggested that such a complex decay may originate from the heterogeneity in the ground state due to the acid-base equilibrium of the counterion of the protonated retinal Schiff base (PRSB). In this study, we studied the excited-state dynamics of PR at pH 11 and 4, in which the counterion of the PRSB, Asp97, is completely deprotonated and protonated, respectively. The obtained time-resolved absorption data revealed that the excited-state lifetime is decisively governed by the protonation state of Asp97, and the photoisomerization of the PRSB chromophore proceeds faster and more efficiently when Asp97 is deprotonated. This conclusion was further supported by high similarity of the excited-state dynamics between PR at pH 4 and the D97N mutant in which Asp97 is replaced with neutral Asn. The results of this study suggest that the protonation state of the PRSB counterion plays a decisive role in determining the excited-state dynamics and the photoisomerization reactivity of rhodopsins in general, by making a significant influence on the exited-state potential energy surface of the PRSB chromophore.
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Affiliation(s)
- Chun-Fu Chang
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.
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12
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Feroz H, Ferlez B, Lefoulon C, Ren T, Baker CS, Gajewski JP, Lugar DJ, Gaudana SB, Butler PJ, Hühn J, Lamping M, Parak WJ, Hibberd JM, Kerfeld CA, Smirnoff N, Blatt MR, Golbeck JH, Kumar M. Light-Driven Chloride Transport Kinetics of Halorhodopsin. Biophys J 2019; 115:353-360. [PMID: 30021110 DOI: 10.1016/j.bpj.2018.06.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 05/19/2018] [Accepted: 06/05/2018] [Indexed: 01/25/2023] Open
Abstract
Despite growing interest in light-driven ion pumps for use in optogenetics, current estimates of their transport rates span two orders of magnitude due to challenges in measuring slow transport processes and determining protein concentration and/or orientation in membranes in vitro. In this study, we report, to our knowledge, the first direct quantitative measurement of light-driven Cl- transport rates of the anion pump halorohodopsin from Natronomonas pharaonis (NpHR). We used light-interfaced voltage clamp measurements on NpHR-expressing oocytes to obtain a transport rate of 219 (± 98) Cl-/protein/s for a photon flux of 630 photons/protein/s. The measurement is consistent with the literature-reported quantum efficiency of ∼30% for NpHR, i.e., 0.3 isomerizations per photon absorbed. To reconcile our measurements with an earlier-reported 20 ms rate-limiting step, or 35 turnovers/protein/s, we conducted, to our knowledge, novel consecutive single-turnover flash experiments that demonstrate that under continuous illumination, NpHR bypasses this step in the photocycle.
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Affiliation(s)
- Hasin Feroz
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania
| | - Bryan Ferlez
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania
| | - Cecile Lefoulon
- Laboratory of Plant Physiology and Biophysics, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
| | - Tingwei Ren
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania
| | - Carol S Baker
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania
| | - John P Gajewski
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania
| | - Daniel J Lugar
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania
| | - Sandeep B Gaudana
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | - Peter J Butler
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania
| | - Jonas Hühn
- Department of Physics and Chemistry, Philipps University of Marburg, Marburg, Germany
| | - Matthias Lamping
- Department of Physics and Chemistry, Philipps University of Marburg, Marburg, Germany
| | - Wolfgang J Parak
- Department of Physics and Chemistry, Philipps University of Marburg, Marburg, Germany
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California
| | | | - Michael R Blatt
- Laboratory of Plant Physiology and Biophysics, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
| | - John H Golbeck
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania; Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania
| | - Manish Kumar
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania.
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13
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Penzkofer A, Silapetere A, Hegemann P. Absorption and Emission Spectroscopic Investigation of the Thermal Dynamics of the Archaerhodopsin 3 Based Fluorescent Voltage Sensor QuasAr1. Int J Mol Sci 2019; 20:E4086. [PMID: 31438573 PMCID: PMC6747118 DOI: 10.3390/ijms20174086] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 08/15/2019] [Accepted: 08/16/2019] [Indexed: 12/13/2022] Open
Abstract
QuasAr1 is a fluorescent voltage sensor derived from Archaerhodopsin 3 (Arch) of Halorubrum sodomense by directed evolution. Here we report absorption and emission spectroscopic studies of QuasAr1 in Tris buffer at pH 8. Absorption cross-section spectra, fluorescence quantum distributions, fluorescence quantum yields, and fluorescence excitation spectra were determined. The thermal stability of QuasAr1 was studied by long-time attenuation coefficient measurements at room temperature (23 ± 2 °C) and at 2.5 ± 0.5 °C. The apparent melting temperature was determined by stepwise sample heating up and cooling down (obtained apparent melting temperature: 65 ± 3 °C). In the protein melting process the originally present protonated retinal Schiff base (PRSB) with absorption maximum at 580 nm converted to de-protonated retinal Schiff base (RSB) with absorption maximum at 380 nm. Long-time storage of QuasAr1 at temperatures around 2.5 °C and around 23 °C caused gradual protonated retinal Schiff base isomer changes to other isomer conformations, de-protonation to retinal Schiff base isomers, and apoprotein structure changes showing up in ultraviolet absorption increase. Reaction coordinate schemes are presented for the thermal protonated retinal Schiff base isomerizations and deprotonations in parallel with the dynamic apoprotein restructurings.
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Affiliation(s)
- Alfons Penzkofer
- Fakultät für Physik, Universität Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany.
| | - Arita Silapetere
- Experimentelle Biophysik, Institut für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany
| | - Peter Hegemann
- Experimentelle Biophysik, Institut für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany
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14
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Affiliation(s)
- C. Punwong
- Department of Physics, Faculty of Science, Prince of Songkla University, Songkhla 90112 Thailand
| | - S. Hannongbua
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - T. J. Martínez
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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15
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Roy PP, Abe-Yoshizumi R, Kandori H, Buckup T. Point Mutation of Anabaena Sensory Rhodopsin Enhances Ground-State Hydrogen Out-of-Plane Wag Raman Activity. J Phys Chem Lett 2019; 10:1012-1017. [PMID: 30742765 DOI: 10.1021/acs.jpclett.8b03805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The interaction between the retinal protonated Schiff base (RPSB) and surrounding protein residues inside the retinal pocket is believed to play a major role in the ultrafast isomerization of the former. Coherent time-resolved vibrational spectroscopic techniques are applied to reveal the effect of changes in the protein architecture by point mutations (V112N and L83Q) close to the RPSB in Anabaena sensory rhodopsin (ASR). Our study reveals that such point mutations have a minor effect on the low-frequency (<400 cm-1) torsional modes but dramatically influence the ground-state vibrational Raman activity of the C14-H out-of-plane (HOOP) wag mode (800-820 cm-1). In mutated ASR, the increase of HOOP Raman activity in the ground state is experimentally observed for the all- trans RPSB, which has shorter excited-state lifetime than in wild-type ASR. This indicates that predistortion of the RPSB inside the mutated retinal pocket is a major factor in the acceleration of the isomerization rate.
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Affiliation(s)
- Partha Pratim Roy
- Physikalisch-Chemisches Institut , Ruprecht-Karls Universität Heidelberg , D-69120 Heidelberg , Germany
| | - Rei Abe-Yoshizumi
- 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
- OptoBioTechnology Research Center , Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555 , Japan
| | - Tiago Buckup
- Physikalisch-Chemisches Institut , Ruprecht-Karls Universität Heidelberg , D-69120 Heidelberg , Germany
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16
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Chattopadhyay A, Saini P, Hakim R, Komainda A, Köppel H. A computational investigation on the photo-isomerization of 2,4,6-octatriene and its UV–visible spectrum. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2017.12.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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17
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Tahara S, Takeuchi S, Abe-Yoshizumi R, Inoue K, Ohtani H, Kandori H, Tahara T. Origin of the Reactive and Nonreactive Excited States in the Primary Reaction of Rhodopsins: pH Dependence of Femtosecond Absorption of Light-Driven Sodium Ion Pump Rhodopsin KR2. J Phys Chem B 2018; 122:4784-4792. [DOI: 10.1021/acs.jpcb.8b01934] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | | | | | - Keiichi Inoue
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Hiroyuki Ohtani
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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18
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Niho A, Yoshizawa S, Tsukamoto T, Kurihara M, Tahara S, Nakajima Y, Mizuno M, Kuramochi H, Tahara T, Mizutani Y, Sudo Y. Demonstration of a Light-Driven SO42– Transporter and Its Spectroscopic Characteristics. J Am Chem Soc 2017; 139:4376-4389. [DOI: 10.1021/jacs.6b12139] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Akiko Niho
- Faculty
of Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Susumu Yoshizawa
- Atmosphere
and Ocean Research Institute, The University of Tokyo, Chiba 277-8564, Japan
| | - Takashi Tsukamoto
- Faculty
of Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
- Graduate
School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Marie Kurihara
- Graduate
School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Shinya Tahara
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Yu Nakajima
- Atmosphere
and Ocean Research Institute, The University of Tokyo, Chiba 277-8564, Japan
| | - Misao Mizuno
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hikaru Kuramochi
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast
Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
| | - Tahei Tahara
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast
Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
| | - Yasuhisa Mizutani
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yuki Sudo
- Faculty
of Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
- Graduate
School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
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19
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Gdor I, Mani-Hazan M, Friedman N, Sheves M, Ruhman S. Membrane Independence of Ultrafast Photochemistry in Pharaonis Halorhodopsin: Testing the Role of Bacterioruberin. J Phys Chem B 2017; 121:2319-2325. [PMID: 28230358 DOI: 10.1021/acs.jpcb.6b12698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ultrafast photochemistry of pharaonis halorhodopsin (p-HR) in the intact membrane of Natronomonas pharaonis has been studied by photoselective femtosecond pump-hyperspectral probe spectroscopy with high time resolution. Two variants of this sample were studied, one with wild-type retinal prosthetic groups and another after shifting the retinal absorption deep into the blue range by reducing the Schiff base linkage, and the results were compared to a previous study on detergent-solubilized p-HR. This comparison shows that retinal photoisomerization dynamics is identical in the membrane and in the solubilized sample. Selective photoexcitation of bacterioruberin, which is associated with the protein in the native membrane, in wild-type and reduced samples, demonstrates conclusively that unlike the carotenoids associated with some bacterial retinal proteins the carrotenoid in p-HR does not act as a light-harvesting antenna.
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Affiliation(s)
- Itay Gdor
- Institute of Chemistry, the Hebrew University , Jerusalem 91904, Israel
| | - Maya Mani-Hazan
- Department of Organic Chemistry, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Noga Friedman
- Department of Organic Chemistry, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Mordechai Sheves
- Department of Organic Chemistry, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Sanford Ruhman
- Institute of Chemistry, the Hebrew University , Jerusalem 91904, Israel
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20
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Iyer ESS, Misra R, Maity A, Liubashevski O, Sudo Y, Sheves M, Ruhman S. Temperature Independence of Ultrafast Photoisomerization in Thermophilic Rhodopsin: Assessment versus Other Microbial Proton Pumps. J Am Chem Soc 2016; 138:12401-7. [DOI: 10.1021/jacs.6b05002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Ramprasad Misra
- Department
of Organic Chemistry, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Arnab Maity
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Oleg Liubashevski
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Yuki Sudo
- Division
of Pharmaceutical sciences, Okayama University, Kita-Ku, Okayama 700-0082, Japan
| | - Mordechai Sheves
- Department
of Organic Chemistry, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sanford Ruhman
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
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21
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Abstract
The first photo-excited singlet state of all-trans donor (amine), acceptor (cyano)-substituted hexatriene forms donor side-twisted minima and its passage towards the cis–trans–trans isomer is characterized by an S0/S1 conical intersection.
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Affiliation(s)
- Anjan Chattopadhyay
- Department of Chemistry
- Birla Institute of Technology and Science (BITS)
- Pilani – K.K. Birla Goa Campus
- India
| | - Praveen Saini
- Department of Chemistry
- Birla Institute of Technology and Science (BITS)
- Pilani – K.K. Birla Goa Campus
- India
| | - Riddhish Pandharkar
- Department of Chemistry
- Birla Institute of Technology and Science (BITS)
- Pilani – K.K. Birla Goa Campus
- India
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22
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Punwong C, Martínez T, Hannongbua S. Direct QM/MM simulation of photoexcitation dynamics in bacteriorhodopsin and halorhodopsin. Chem Phys Lett 2014; 610-611:213-8. [DOI: 10.1016/j.cplett.2014.07.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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23
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Saini P, Chattopadhyay A. Spectroscopic features of the low-lying singlet states of some N-alkyl retinylnitrone model systems and their involvement in oxaziridine formation. RSC Adv 2014. [DOI: 10.1039/c3ra47186a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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25
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Schapiro I, Ruhman S. Ultrafast photochemistry of anabaena sensory rhodopsin: experiment and theory. Biochim Biophys Acta 2014; 1837:589-97. [PMID: 24099700 DOI: 10.1016/j.bbabio.2013.09.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 09/28/2013] [Accepted: 09/29/2013] [Indexed: 11/20/2022]
Abstract
Light induced isomerization of the retinal chromophore activates biological function in all retinal protein (RP) driving processes such as ion-pumping, vertebrate vision and phototaxis in organisms as primitive as archea, or as complex as mammals. This process and its consecutive reactions have been the focus of experimental and theoretical research for decades. The aim of this review is to demonstrate how the experimental and theoretical research efforts can now be combined to reach a more comprehensive understanding of the excited state process on the molecular level. Using the Anabaena Sensory Rhodopsin as an example we will show how contemporary time-resolved spectroscopy and recently implemented excited state QM/MM methods consistently describe photochemistry in retinal proteins. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
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26
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Affiliation(s)
- Amir Wand
- Institute of Chemistry and the Farkas Center for Light-Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel;
| | - Itay Gdor
- Institute of Chemistry and the Farkas Center for Light-Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel;
| | - Jingyi Zhu
- Institute of Chemistry and the Farkas Center for Light-Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel;
| | - Mordechai Sheves
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sanford Ruhman
- Institute of Chemistry and the Farkas Center for Light-Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel;
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27
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Chattopadhyay A. Comparative study of spectroscopic properties of the low-lying electronic states of 2,4-pentadien-1-iminium cation and its N-substituted analogues. J CHEM SCI 2012; 124:985-94. [DOI: 10.1007/s12039-012-0311-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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28
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Wand A, Rozin R, Eliash T, Jung KH, Sheves M, Ruhman S. Asymmetric Toggling of a Natural Photoswitch: Ultrafast Spectroscopy of Anabaena Sensory Rhodopsin. J Am Chem Soc 2011; 133:20922-32. [DOI: 10.1021/ja208371g] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amir Wand
- Institute of Chemistry and Farkash Center for Light-Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Rinat Rozin
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tamar Eliash
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Shinsu-Dong 1, Mapo-Gu, Seoul 121-742, South Korea
| | - Mordechai Sheves
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sanford Ruhman
- Institute of Chemistry and Farkash Center for Light-Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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29
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Verhoefen MK, Bamann C, Blöcher R, Förster U, Bamberg E, Wachtveitl J. The photocycle of channelrhodopsin-2: ultrafast reaction dynamics and subsequent reaction steps. Chemphyschem 2011; 11:3113-22. [PMID: 20730849 DOI: 10.1002/cphc.201000181] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The photocycle of channelrhodopsin-2 is investigated in a comprehensive study by ultrafast absorption and fluorescence spectroscopy as well as flash photolysis in the visible spectral range. The ultrafast techniques reveal an excited-state decay mechanism analogous to that of the archaeal bacteriorhodopsin and sensory rhodopsin II from Natronomonas pharaonis. After a fast vibrational relaxation of the excited-state population with 150 fs its decay with mainly 400 fs is observed. Hereby, both the initial all-trans retinal ground state and the 13-cis-retinal K photoproduct are populated. The reaction proceeds with a 2.7 ps component assigned to cooling processes. Small spectral shifts are observed on a 200 ps timescale. They are attributed to conformational rearrangements in the retinal binding pocket. The subsequent dynamics progresses with the formation of an M-like intermediate (7 and 120 μs), which decays into red-shifted states within 3 ms. Ground-state recovery including channel closing and reisomerization of the retinal chromophore occurs in a triexponential manner (6 ms, 33 ms, 3.4 s). To learn more about the energy barriers between the different photocycle intermediates, temperature-dependent flash photolysis measurements are performed between 10 and 30°C. The first five time constants decrease with increasing temperature. The calculated thermodynamic parameters indicate that the closing mechanism is controlled by large negative entropy changes. The last time constant is temperature independent, which demonstrates that the photocycle is most likely completed by a series of individual steps recovering the initial structure.
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Affiliation(s)
- Mirka-Kristin Verhoefen
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe University Frankfurt, Max von Laue-Straße 7, 60438 Frankfurt am Main, Germany
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30
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Bismuth O, Komm P, Friedman N, Eliash T, Sheves M, Ruhman S. Deciphering Excited State Evolution in Halorhodopsin with Stimulated Emission Pumping. J Phys Chem B 2010; 114:3046-51. [DOI: 10.1021/jp910853n] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Oshrat Bismuth
- Institute of Chemistry and the Farkas Center for Light Induced Processes, The Hebrew University, Jerusalem 91904, Israel, and Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Pavel Komm
- Institute of Chemistry and the Farkas Center for Light Induced Processes, The Hebrew University, Jerusalem 91904, Israel, and Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Noga Friedman
- Institute of Chemistry and the Farkas Center for Light Induced Processes, The Hebrew University, Jerusalem 91904, Israel, and Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tamar Eliash
- Institute of Chemistry and the Farkas Center for Light Induced Processes, The Hebrew University, Jerusalem 91904, Israel, and Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Mordechai Sheves
- Institute of Chemistry and the Farkas Center for Light Induced Processes, The Hebrew University, Jerusalem 91904, Israel, and Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sanford Ruhman
- Institute of Chemistry and the Farkas Center for Light Induced Processes, The Hebrew University, Jerusalem 91904, Israel, and Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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31
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Verhoefen MK, Lenz MO, Amarie S, Klare JP, Tittor J, Oesterhelt D, Engelhard M, Wachtveitl J. Primary Reaction of Sensory Rhodopsin II Mutant D75N and the Influence of Azide. Biochemistry 2009; 48:9677-83. [DOI: 10.1021/bi901197c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mirka-Kristin Verhoefen
- Institute of Physical and Theoretical Chemistry, Institute of Biophysics, Johann Wolfgang Goethe-University Frankfurt, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Martin O. Lenz
- Institute of Physical and Theoretical Chemistry, Institute of Biophysics, Johann Wolfgang Goethe-University Frankfurt, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Sergiu Amarie
- Institute of Physical and Theoretical Chemistry, Institute of Biophysics, Johann Wolfgang Goethe-University Frankfurt, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Johann P. Klare
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44139 Dortmund, Germany
| | - Jörg Tittor
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Dieter Oesterhelt
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Martin Engelhard
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44139 Dortmund, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Institute of Biophysics, Johann Wolfgang Goethe-University Frankfurt, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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Zhu J, Bismuth O, Gdor I, Wand A, Friedman N, Sheves M, Ruhman S. Comparing photochemistry of n- and tert-butylamine all-trans retinal protonated Schiff-base: Effects of C N configurational inhomogeneity. Chem Phys Lett 2009; 479:229-33. [DOI: 10.1016/j.cplett.2009.08.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Sobotta C, Braun M, Tittor J, Oesterhelt D, Zinth W. Influence of the charge at D85 on the initial steps in the photocycle of bacteriorhodopsin. Biophys J 2009; 97:267-76. [PMID: 19580764 DOI: 10.1016/j.bpj.2009.04.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Revised: 03/25/2009] [Accepted: 04/06/2009] [Indexed: 10/20/2022] Open
Abstract
Studies have shown that trans-cis isomerization of retinal is the primary photoreaction in the photocycle of the light-driven proton pump bacteriorhodopsin (BR) from Halobacterium salinarum, as well as in the photocycle of the chloride pump halorhodopsin (HR). The transmembrane proteins HR and BR show extensive structural similarities, but differ in the electrostatic surroundings of the retinal chromophore near the protonated Schiff base. Point mutation of BR of the negatively charged aspartate D85 to a threonine T (D85T) in combination with variation of the pH value and anion concentration is used to study the ultrafast photoisomerization of BR and HR for well-defined electrostatic surroundings of the retinal chromophore. Variations of the pH value and salt concentration allow a switch in the isomerization dynamics of the BR mutant D85T between BR-like and HR-like behaviors. At low salt concentrations or a high pH value (pH 8), the mutant D85T shows a biexponential initial reaction similar to that of HR. The combination of high salt concentration and a low pH value (pH 6) leads to a subpopulation of 25% of the mutant D85T whose stationary and dynamic absorption properties are similar to those of native BR. In this sample, the combination of low pH and high salt concentration reestablishes the electrostatic surroundings originally present in native BR, but only a minor fraction of the D85T molecules have the charge located exactly at the position required for the BR-like fast isomerization reaction. The results suggest that the electrostatics in the native BR protein is optimized by evolution. The accurate location of the fixed charge at the aspartate D85 near the Schiff base in BR is essential for the high efficiency of the primary reaction.
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Affiliation(s)
- Constanze Sobotta
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik, Ludwig-Maximilians-Universität München, Munich, Germany
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Nakamura T, Takeuchi S, Shibata M, Demura M, Kandori H, Tahara T. Ultrafast Pump−Probe Study of the Primary Photoreaction Process in pharaonis Halorhodopsin: Halide Ion Dependence and Isomerization Dynamics. J Phys Chem B 2008; 112:12795-800. [DOI: 10.1021/jp803282s] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Takumi Nakamura
- Molecular Spectroscopy Laboratory, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako 351-0198, Japan, Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, and Division of Biological Science, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Satoshi Takeuchi
- Molecular Spectroscopy Laboratory, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako 351-0198, Japan, Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, and Division of Biological Science, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Mikihiro Shibata
- Molecular Spectroscopy Laboratory, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako 351-0198, Japan, Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, and Division of Biological Science, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Makoto Demura
- Molecular Spectroscopy Laboratory, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako 351-0198, Japan, Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, and Division of Biological Science, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Hideki Kandori
- Molecular Spectroscopy Laboratory, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako 351-0198, Japan, Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, and Division of Biological Science, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako 351-0198, Japan, Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, and Division of Biological Science, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
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35
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Neumann K, Verhoefen MK, Weber I, Glaubitz C, Wachtveitl J. Initial reaction dynamics of proteorhodopsin observed by femtosecond infrared and visible spectroscopy. Biophys J 2008; 94:4796-807. [PMID: 18326639 DOI: 10.1529/biophysj.107.125484] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a comparative study using femtosecond pump/probe spectroscopy in the visible and infrared of the early photodynamics of solubilized proteorhodopsin (green absorbing variant) in D(2)O with deprotonated (pD 9.2) and protonated (pD 6.4) primary proton acceptor Asp-97. The vis-pump/vis-probe experiments show a kinetic isotope effect that is more pronounced for alkaline conditions, thus decreasing the previously reported pH-dependence of the primary reaction of proteorhodopsin in H(2)O. This points to a pH dependent H-bonding network in the binding pocket of proteorhodopsin, that directly influences the primary photo-induced dynamics. The vis-pump/IR-probe experiments were carried out in two different spectral regions and allowed to monitor the retinal C=C (1500 cm(-1)-1580 cm(-1)) and C=N stretching vibration as well as the amide I mode of the protein (1590 cm(-1)-1680 cm(-1)). Like the FTIR spectra of the K intermediate (PR(K)-PR difference spectra) in this spectral range, the kinetic parameters and also the quantum efficiency of photo-intermediate formation are found to be virtually independent of the pD value.
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Peters F, Herbst J, Tittor J, Oesterhelt D, Diller R. Primary reaction dynamics of halorhodopsin, observed by sub-picosecond IR – vibrational spectroscopy. Chem Phys 2006. [DOI: 10.1016/j.chemphys.2005.08.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
The early steps in the photocycle of the bacterial proton pump proteorhodopsin (PR) were analyzed by ultrafast pump/probe spectroscopy to compare the rate of retinal isomerization at alkaline and acidic pH values. At pH 9, the functionally important primary proton acceptor (Asp97, pK(a) = 7.7) is negatively charged; consequently, a reaction cycle analogous to the archaeal bacteriorhodopsin (BR) is observed. The excited electronic state of PR displays a pronounced biphasic decay with time constants of 400 fs and 8 ps. At pH 6 where Asp97 is protonated a similar biphasic decay is observed, although it is significantly slower (700 fs and 15 ps). The results indicate, in agreement to similar findings in other retinal proteins, that also in PR the charge distribution within the chromophore binding pocket is a major determinant for the rate and the efficiency of the primary reaction.
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Affiliation(s)
- Robert Huber
- Institut für Physikalische und Theoretische Chemie, Marie-Curie-Strasse 11, Johann Wolfgang Goethe-Universität Frankfurt, 60439 Frankfurt am Main, Germany
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Kennis JTM, Larsen DS, Ohta K, Facciotti MT, Glaeser RM, Fleming GR. Ultrafast Protein Dynamics of Bacteriorhodopsin Probed by Photon Echo and Transient Absorption Spectroscopy. J Phys Chem B 2002. [DOI: 10.1021/jp014681b] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- John T. M. Kennis
- Department of Chemistry, Department of Molecular and Cell Biology, Graduate Group in Biophysics, University of California, Physical Biosciences Division, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Delmar S. Larsen
- Department of Chemistry, Department of Molecular and Cell Biology, Graduate Group in Biophysics, University of California, Physical Biosciences Division, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Kaoru Ohta
- Department of Chemistry, Department of Molecular and Cell Biology, Graduate Group in Biophysics, University of California, Physical Biosciences Division, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Marc T. Facciotti
- Department of Chemistry, Department of Molecular and Cell Biology, Graduate Group in Biophysics, University of California, Physical Biosciences Division, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Robert M. Glaeser
- Department of Chemistry, Department of Molecular and Cell Biology, Graduate Group in Biophysics, University of California, Physical Biosciences Division, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Graham R. Fleming
- Department of Chemistry, Department of Molecular and Cell Biology, Graduate Group in Biophysics, University of California, Physical Biosciences Division, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
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Heyne K, Herbst J, Stehlik D, Esteban B, Lamparter T, Hughes J, Diller R. Ultrafast dynamics of phytochrome from the cyanobacterium synechocystis, reconstituted with phycocyanobilin and phycoerythrobilin. Biophys J 2002; 82:1004-16. [PMID: 11806940 PMCID: PMC1301907 DOI: 10.1016/s0006-3495(02)75460-x] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Femtosecond time-resolved transient absorption spectroscopy was employed to characterize for the first time the primary photoisomerization dynamics of a bacterial phytochrome system in the two thermally stable states of the photocycle. The 85-kDa phytochrome Cph1 from the cyanobacterium Synechocystis PCC 6803 expressed in Escherichia coli was reconstituted with phycocyanobilin (Cph1-PCB) and phycoerythrobilin (Cph1-PEB). The red-light-absorbing form Pr of Cph1-PCB shows an approximately 150 fs relaxation in the S(1) state after photoexcitation at 650 nm. The subsequent Z-E isomerization between rings C and D of the linear tetrapyrrole-chromophore is best described by a distribution of rate constants with the first moment at (16 ps)(-1). Excitation at 615 nm leads to a slightly broadened distribution. The reverse E-Z isomerization, starting from the far-red-absorbing form Pfr, is characterized by two shorter time constants of 0.54 and 3.2 ps. In the case of Cph1-PEB, double-bond isomerization does not take place, and the excited-state lifetime extends into the nanosecond regime. Besides a stimulated emission rise time between 40 and 150 fs, no fast relaxation processes are observed. This suggests that the chromophore-protein interaction along rings A, B, and C does not contribute much to the picosecond dynamics observed in Cph1-PCB but rather the region around ring D near the isomerizing C(15) [double bond] C(16) double bond. The primary reaction dynamics of Cph1-PCB at ambient temperature is found to exhibit very similar features as those described for plant type A phytochrome, i.e., a relatively slow Pr, and a fast Pfr, photoreaction. This suggests that the initial reactions were established already before evolution of plant phytochromes began.
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Affiliation(s)
- Karsten Heyne
- Institut für Experimentalphysik, Freie Universität Berlin, Germany
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40
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Hou B, Friedman N, Ruhman S, Sheves M, Ottolenghi M. Ultrafast Spectroscopy of the Protonated Schiff Bases of Free and C13C14 Locked Retinals. J Phys Chem B 2001. [DOI: 10.1021/jp0034980] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- B. Hou
- Department of Physical Chemistry, The Hebrew University, Jerusalem 91904, Israel and The Weizmann Institute of Science, Rehovot 76100, Israel
| | - N. Friedman
- Department of Physical Chemistry, The Hebrew University, Jerusalem 91904, Israel and The Weizmann Institute of Science, Rehovot 76100, Israel
| | - S. Ruhman
- Department of Physical Chemistry, The Hebrew University, Jerusalem 91904, Israel and The Weizmann Institute of Science, Rehovot 76100, Israel
| | - M. Sheves
- Department of Physical Chemistry, The Hebrew University, Jerusalem 91904, Israel and The Weizmann Institute of Science, Rehovot 76100, Israel
| | - M. Ottolenghi
- Department of Physical Chemistry, The Hebrew University, Jerusalem 91904, Israel and The Weizmann Institute of Science, Rehovot 76100, Israel
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41
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Lutz I, Sieg A, Wegener AA, Engelhard M, Boche I, Otsuka M, Oesterhelt D, Wachtveitl J, Zinth W. Primary reactions of sensory rhodopsins. Proc Natl Acad Sci U S A 2001; 98:962-7. [PMID: 11158578 PMCID: PMC14692 DOI: 10.1073/pnas.98.3.962] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The first steps in the photocycles of the archaeal photoreceptor proteins sensory rhodopsin (SR) I and II from Halobacterium salinarum and SRII from Natronobacterium pharaonis have been studied by ultrafast pump/probe spectroscopy and steady-state fluorescence spectroscopy. The data for both species of the blue-light receptor SRII suggests that their primary reactions are nearly analogous with a fast decay of the excited electronic state in 300-400 fs and a transition between two red-shifted product states in 4-5 ps. Thus SRII behaves similarly to bacteriorhodopsin. In contrast for SRI at pH 6.0, which absorbs in the orange part of the spectrum, a strongly increased fluorescence quantum yield and a drastically slower and biexponential decay of the excited electronic state occurring on the picosecond time scale (5 ps and 33 ps) is observed. The results suggest that the primary reactions are controlled by the charge distribution in the vicinity of the Schiff base and demonstrate that there is no direct connection between absorption properties and reaction dynamics for the retinal protein family.
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Affiliation(s)
- I Lutz
- Sektion Physik, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, 80538 Munich, Germany
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42
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Nonella M. Electrostatic Protein−Chromophore Interactions Promote the all-trans → 13-cis Isomerization of the Protonated Retinal Schiff Base in Bacteriorhodopsin: An ab Initio CASSCF/MRCI Study. J Phys Chem B 2000. [DOI: 10.1021/jp0019254] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marco Nonella
- Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, D-80538 München, Germany
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43
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Heyne K, Herbst J, Dominguez-Herradon B, Alexiev U, Diller R. Reaction Control in Bacteriorhodopsin: Impact of Arg82 and Asp85 on the Fast Retinal Isomerization, Studied in the Second Site Revertant Arg82Ala/Gly231Cys and Various Purple and Blue Forms of Bacteriorhodopsin. J Phys Chem B 2000. [DOI: 10.1021/jp992877u] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Karsten Heyne
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Johannes Herbst
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | | | - Ulrike Alexiev
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Rolf Diller
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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44
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Abstract
Halorhodopsin, an archaeal rhodopsin ubiquitous in Haloarchaea, uses light energy to pump chloride through biological membranes. Halorhodopsin crystals were grown in a cubic lipidic phase, which allowed the x-ray structure determination of this anion pump at 1.8 angstrom resolution. Halorhodopsin assembles to trimers around a central patch consisting of palmitic acid. Next to the protonated Schiff base between Lys(242) and the isomerizable retinal chromophore, a single chloride ion occupies the transport site. Energetic calculations on chloride binding reveal a combination of ion-ion and ion-dipole interactions for stabilizing the anion 18 angstroms below the membrane surface. Ion dragging across the protonated Schiff base explains why chloride and proton translocation modes are mechanistically equivalent in archaeal rhodopsins.
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Affiliation(s)
- M Kolbe
- Department of Membrane Biochemistry, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18a, D-82152 Martinsried bei München, Germany
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45
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Ye T, Friedman N, Gat Y, Atkinson GH, Sheves M, Ottolenghi M, Ruhman S. On the Nature of the Primary Light-Induced Events in Bacteriorhodopsin: Ultrafast Spectroscopy of Native and C13=C14 Locked Pigments. J Phys Chem B 1999. [DOI: 10.1021/jp9846227] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- T. Ye
- Department of Physical Chemistry, The Hebrew University, Jerusalem 91904, Israel, Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel, and Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721
| | - N. Friedman
- Department of Physical Chemistry, The Hebrew University, Jerusalem 91904, Israel, Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel, and Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721
| | - Y. Gat
- Department of Physical Chemistry, The Hebrew University, Jerusalem 91904, Israel, Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel, and Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721
| | - G. H. Atkinson
- Department of Physical Chemistry, The Hebrew University, Jerusalem 91904, Israel, Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel, and Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721
| | - M. Sheves
- Department of Physical Chemistry, The Hebrew University, Jerusalem 91904, Israel, Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel, and Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721
| | - M. Ottolenghi
- Department of Physical Chemistry, The Hebrew University, Jerusalem 91904, Israel, Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel, and Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721
| | - S. Ruhman
- Department of Physical Chemistry, The Hebrew University, Jerusalem 91904, Israel, Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel, and Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721
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46
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Abstract
Retinal proteins from halophilic archaea provide a unique opportunity to analyze vectorial ion translocation. Studies on its structure, conformational changes, proton conduction and electrogenic steps have helped to elucidate the catalytic cycle of bacteriorhodopsin in increasing detail. Experimental modulation of the vectoriality and ion specificity by altering the substrate availability, point mutations and light conditions for the different retinal proteins allows the proposal of a general model of ion transport for this protein family.
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Affiliation(s)
- D Oesterhelt
- Max-Planck-Institut für Biochemie, Martinsried, Germany.
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47
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Hamm P, Zurek M, Röschinger T, Patzelt H, Oesterhelt D, Zinth W. Subpicosecond infrared spectroscopy on the photoisomerisation of the protonated Schiff base of all-trans retinal. Chem Phys Lett 1997; 268:180-6. [DOI: 10.1016/s0009-2614(97)00142-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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48
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Hamm P, Zurek M, Röschinger T, Patzelt H, Oesterhelt D, Zinth W. Femtosecond spectroscopy of the photoisomerisation of the protonated Schiff base of all-trans retinal. Chem Phys Lett 1996. [DOI: 10.1016/s0009-2614(96)01269-9] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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49
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Dobado JA, Nonella M. MRCI Calculations of the Ground and Excited State Potential Energy Surfaces of the 2,4-Pentadien-1-iminium Cation. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp961639l] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. A. Dobado
- Physikalisch-Chemisches Institut der Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - M. Nonella
- Physikalisch-Chemisches Institut der Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
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