1
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de Grip WJ, Ganapathy S. Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering. Front Chem 2022; 10:879609. [PMID: 35815212 PMCID: PMC9257189 DOI: 10.3389/fchem.2022.879609] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/16/2022] [Indexed: 01/17/2023] Open
Abstract
The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.
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Affiliation(s)
- Willem J. de Grip
- Leiden Institute of Chemistry, Department of Biophysical Organic Chemistry, Leiden University, Leiden, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Srividya Ganapathy
- Department of Imaging Physics, Delft University of Technology, Netherlands
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2
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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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3
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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] [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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4
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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] [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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5
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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] [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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6
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Borin VA, Wiebeler C, Schapiro I. A QM/MM study of the initial excited state dynamics of green-absorbing proteorhodopsin. Faraday Discuss 2019; 207:137-152. [PMID: 29393940 DOI: 10.1039/c7fd00198c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The primary photochemical reaction of the green-absorbing proteorhodopsin is studied by means of a hybrid quantum mechanics/molecular mechanics (QM/MM) approach. The simulations are based on a homology model derived from the blue-absorbing proteorhodopsin crystal structure. The geometry of retinal and the surrounding sidechains in the protein binding pocket were optimized using the QM/MM method. Starting from this geometry the isomerization was studied with a relaxed scan along the C13[double bond, length as m-dash]C14 dihedral. It revealed an "aborted bicycle pedal" mechanism of isomerization that was originally proposed by Warshel for bovine rhodopsin and bacteriorhodopsin. However, the isomerization involved the concerted rotation about C13[double bond, length as m-dash]C14 and C15[double bond, length as m-dash]N, with the latter being highly twisted but not isomerized. Further, the simulation showed an increased steric interaction between the hydrogen at the C14 of the isomerizing bond and the hydroxyl group at the neighbouring tyrosine 200. In addition, we have simulated a nonadiabatic trajectory which showed the timing of the isomerization. In the first 20 fs upon excitation the order of the conjugated double and single bonds is inverted, consecutively the C13[double bond, length as m-dash]C14 rotation is activated for 200 fs until the S1-S0 transition is detected. However, the isomerization is reverted due to the specific interaction with the tyrosine as observed along the relaxed scan calculation. Our simulations indicate that the retinal - tyrosine 200 interaction plays an important role in the outcome of the photoisomerization.
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Affiliation(s)
- Veniamin A Borin
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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7
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Fujisawa T, Abe M, Tamogami J, Kikukawa T, Kamo N, Unno M. Low-temperature Raman spectroscopy reveals small chromophore distortion in primary photointermediate of proteorhodopsin. FEBS Lett 2018; 592:3054-3061. [PMID: 30098005 DOI: 10.1002/1873-3468.13219] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/29/2018] [Accepted: 08/03/2018] [Indexed: 11/07/2022]
Abstract
Proteorhodopsin (PR) is a microbial rhodopsin functioning as a light-driven proton pump in aquatic bacteria. We performed low-temperature Raman measurements of PR to obtain the structure of the primary photoproduct, the K intermediate (PRK ). PRK showed the hydrogen-out-of-plane modes that are much less intense than those of bacteriorhodopsin as the prototypical light-driven proton pump from haloarchaea. The present results reveal the significantly relaxed chromophore structure in PRK , which can be coupled to the slow kinetics of the K intermediate. This structure suggests that PR transports protons using the small energy storage within the chromophore at the start of its photocycle.
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Affiliation(s)
- Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Japan
| | - Masahiro Abe
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Japan
| | - Jun Tamogami
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime, Japan
| | - Takashi Kikukawa
- Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan.,Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Naoki Kamo
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Japan
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8
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Yi A, Li H, Mamaeva N, Fernandez De Cordoba RE, Lugtenburg J, DeGrip WJ, Spudich JL, Rothschild KJ. Structural Changes in an Anion Channelrhodopsin: Formation of the K and L Intermediates at 80 K. Biochemistry 2017; 56:2197-2208. [PMID: 28350445 DOI: 10.1021/acs.biochem.7b00002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A recently discovered natural family of light-gated anion channelrhodopsins (ACRs) from cryptophyte algae provides an effective means of optogenetically silencing neurons. The most extensively studied ACR is from Guillardia theta (GtACR1). Earlier studies of GtACR1 have established a correlation between formation of a blue-shifted L-like intermediate and the anion channel "open" state. To study structural changes of GtACR1 in the K and L intermediates of the photocycle, a combination of low-temperature Fourier transform infrared (FTIR) and ultraviolet-visible absorption difference spectroscopy was used along with stable-isotope retinal labeling and site-directed mutagenesis. In contrast to bacteriorhodopsin (BR) and other microbial rhodopsins, which form only a stable red-shifted K intermediate at 80 K, GtACR1 forms both stable K and L-like intermediates. Evidence includes the appearance of positive ethylenic and fingerprint vibrational bands characteristic of the L intermediate as well as a positive visible absorption band near 485 nm. FTIR difference bands in the carboxylic acid C═O stretching region indicate that several Asp/Glu residues undergo hydrogen bonding changes at 80 K. The Glu68 → Gln and Ser97 → Glu substitutions, residues located close to the retinylidene Schiff base, altered the K:L ratio and several of the FTIR bands in the carboxylic acid region. In the case of the Ser97 → Glu substitution, a significant red-shift of the absorption wavelength of the K and L intermediates occurs. Sequence comparisons suggest that L formation in GtACR1 at 80 K is due in part to the substitution of the highly conserved Leu or Ile at position 93 in helix 3 (BR sequence) with the homologous Met105 in GtACR1.
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Affiliation(s)
- Adrian Yi
- Molecular Biophysics Laboratory, Photonics Center, and Department of Physics, Boston University , Boston, Massachusetts 02215, United States
| | - Hai Li
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, McGovern Medical School , Houston, Texas 77030, United States
| | - Natalia Mamaeva
- Molecular Biophysics Laboratory, Photonics Center, and Department of Physics, Boston University , Boston, Massachusetts 02215, United States
| | - Roberto E Fernandez De Cordoba
- Molecular Biophysics Laboratory, Photonics Center, and Department of Physics, Boston University , Boston, Massachusetts 02215, United States
| | - Johan Lugtenburg
- Department of Biophysical Organic Chemistry, Leiden Institute of Chemistry, Leiden University , 2300 AR Leiden, The Netherlands
| | - Willem J DeGrip
- Department of Biophysical Organic Chemistry, Leiden Institute of Chemistry, Leiden University , 2300 AR Leiden, The Netherlands
| | - John L Spudich
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, McGovern Medical School , Houston, Texas 77030, United States
| | - Kenneth J Rothschild
- Molecular Biophysics Laboratory, Photonics Center, and Department of Physics, Boston University , Boston, Massachusetts 02215, United States
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9
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Eckert CE, Kaur J, Glaubitz C, Wachtveitl J. Ultrafast Photoinduced Deactivation Dynamics of Proteorhodopsin. J Phys Chem Lett 2017; 8:512-517. [PMID: 28072545 DOI: 10.1021/acs.jpclett.6b02975] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We report femtosecond time-resolved absorption change measurements of the photoinduced deactivation dynamics of a microbial rhodopsin in the ultraviolet-visible and mid-infrared range. The blue light quenching process is recorded in green proteorhodopsin's (GPR) primary proton donor mutant E108Q from the deprotonated 13-cis photointermediate. The return of GPR to the dark state occurs in two steps, starting with the photoinduced 13-cis to all-trans reisomerization of the retinal. The subsequent Schiff base reprotonation via the primary proton acceptor (D97) occurs on a nanosecond time scale. This step is two orders of magnitude faster than that in bacteriorhodopsin, potentially because of the very high pKA of the GPR primary proton acceptor.
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Affiliation(s)
- C Elias Eckert
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt am Main , Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Jagdeep Kaur
- Institute of Biophysical Chemistry, Goethe-University Frankfurt am Main , Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Clemens Glaubitz
- Institute of Biophysical Chemistry, Goethe-University Frankfurt am Main , Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt am Main , Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
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10
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Neumann-Verhoefen MK, Neumann K, Bamann C, Radu I, Heberle J, Bamberg E, Wachtveitl J. Ultrafast Infrared Spectroscopy on Channelrhodopsin-2 Reveals Efficient Energy Transfer from the Retinal Chromophore to the Protein. J Am Chem Soc 2013; 135:6968-76. [DOI: 10.1021/ja400554y] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Mirka-Kristin Neumann-Verhoefen
- Institute of Physical and Theoretical
Chemistry, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Karsten Neumann
- Institute of Physical and Theoretical
Chemistry, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Christian Bamann
- Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt
am Main, Germany
| | - Ionela Radu
- Department
of Physics, Molecular
Biospectroscopy, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Joachim Heberle
- Department of Physics, Experimental
Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt
am Main, Germany
| | - Josef Wachtveitl
- 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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11
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Wand A, Loevsky B, Friedman N, Sheves M, Ruhman S. Probing Ultrafast Photochemistry of Retinal Proteins in the Near-IR: Bacteriorhodopsin and Anabaena Sensory Rhodopsin vs Retinal Protonated Schiff Base in Solution. J Phys Chem B 2012; 117:4670-9. [DOI: 10.1021/jp309189y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amir Wand
- Institute of Chemistry
and the Farkas Center for Light-Induced Processes, The Hebrew University of Jerusalem, Edmond J. Safra
Campus, Givat Ram, Jerusalem 91904, Israel
| | - Boris Loevsky
- Institute of Chemistry
and the Farkas Center for Light-Induced Processes, The Hebrew University of Jerusalem, Edmond J. Safra
Campus, Givat Ram, Jerusalem 91904, Israel
| | - Noga Friedman
- Department of Organic
Chemistry, The Weizmann Institute of Science, Rehovot 76100, 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, Edmond J. Safra
Campus, Givat Ram, Jerusalem 91904, Israel
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12
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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] [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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13
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Low temperature FTIR spectroscopy provides new insights in the pH-dependent proton pathway of proteorhodopsin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1583-90. [DOI: 10.1016/j.bbabio.2011.09.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 08/25/2011] [Accepted: 09/05/2011] [Indexed: 11/15/2022]
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14
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Evidence from Chlamydomonas on the photoactivation of rhodopsins without isomerization of their chromophore. ACTA ACUST UNITED AC 2011; 18:733-42. [PMID: 21700209 DOI: 10.1016/j.chembiol.2011.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 03/12/2011] [Accepted: 04/04/2011] [Indexed: 12/16/2022]
Abstract
Attachment of retinal to opsin forms the chromophore N-retinylidene, which isomerizes during photoactivation of rhodopsins. To test whether isomerization is crucial, custom-tailored chromophores lacking the β-ionone ring and any isomerizable bonds were incorporated in vivo into the opsin of a blind mutant of the eukaryote Chlamydomonas reinhardtii. The analogs restored phototaxis with the anticipated action spectra, ruling out the need for isomerization in photoactivation. To further elucidate photoactivation, responses to chromophores formed from naphthalene aldehydes were studied. The resulting action spectral shifts suggest that charge separation within the excited chromophore leads to electric field-induced polarization of nearby amino acid residues and altered hydrogen bonding. This redistribution of charge facilitates the reported multiple bond rotations and protein rearrangements of rhodopsin activation. These results provide insight into the activation of rhodopsins and related GPCRs.
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Rupenyan A, van Stokkum IHM, Arents JC, van Grondelle R, Hellingwerf KJ, Groot ML. Reaction pathways of photoexcited retinal in proteorhodopsin studied by pump-dump-probe spectroscopy. J Phys Chem B 2010; 113:16251-6. [PMID: 19928893 DOI: 10.1021/jp9065289] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteorhodopsin (pR) is a membrane-embedded proton pump from the microbial rhodopsin family. Light absorption by its retinal chromophore initiates a photocycle, driven by trans/cis isomerization on the femtosecond to picosecond time scales. Here, we report a study on the photoisomerization dynamics of the retinal chromophore of pR, using dispersed ultrafast pump-dump-probe spectroscopy. The application of a pump pulse initiates the photocycle, and with an appropriately tuned dump pulse applied at a time delay after the dump, the molecules in the initial stages of the photochemical process can be de-excited and driven back to the ground state. In this way, we were able to resolve an intermediate on the electronic ground state that represents chromophores that are unsuccessful in isomerization. In particular, the fractions of molecules that undergo slow isomerization (20 ps) have a high probability to enter this state rather than the isomerized K-state. On the ground state reaction surface, return to the stable ground state conformation via a structural or vibrational relaxation occurs in 2-3 ps. Inclusion of this intermediate in the kinetic scheme led to more consistent spectra of the retinal-excited state, and to a more accurate estimation of the quantum yield of isomerization (Phi = 0.4 at pH 6).
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Affiliation(s)
- Alisa Rupenyan
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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16
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Gross R, Wolf MMN, Schumann C, Friedman N, Sheves M, Li L, Engelhard M, Trentmann O, Neuhaus HE, Diller R. Primary photoinduced protein response in bacteriorhodopsin and sensory rhodopsin II. J Am Chem Soc 2010; 131:14868-78. [PMID: 19778046 DOI: 10.1021/ja904218n] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Essential for the biological function of the light-driven proton pump, bacteriorhodopsin (BR), and the light sensor, sensory rhodopsin II (SRII), is the coupling of the activated retinal chromophore to the hosting protein moiety. In order to explore the dynamics of this process we have performed ultrafast transient mid-infrared spectroscopy on isotopically labeled BR and SRII samples. These include SRII in D(2)O buffer, BR in H(2)(18)O medium, SRII with (15)N-labeled protein, and BR with (13)C(14)(13)C(15)-labeled retinal chromophore. Via observed shifts of infrared difference bands after photoexcitation and their kinetics we provide evidence for nonchromophore bands in the amide I and the amide II region of BR and SRII. A band around 1550 cm(-1) is very likely due to an amide II vibration. In the amide I region, contributions of modes involving exchangeable protons and modes not involving exchangeable protons can be discerned. Observed bands in the amide I region of BR are not due to bending vibrations of protein-bound water molecules. The observed protein bands appear in the amide I region within the system response of ca. 0.3 ps and in the amide II region within 3 ps, and decay partially in both regions on a slower time scale of 9-18 ps. Similar observations have been presented earlier for BR5.12, containing a nonisomerizable chromophore (R. Gross et al. J. Phys. Chem. B 2009, 113, 7851-7860). Thus, the results suggest a common mechanism for ultrafast protein response in the artificial and the native system besides isomerization, which could be induced by initial chromophore polarization.
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Affiliation(s)
- Ruth Gross
- University of Kaiserslautern, Department of Physics, Erwin-Schrodinger-Strasse, 67663 Kaiserslautern, Germany
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17
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Gross R, Schumann C, Wolf MMN, Herbst J, Diller R, Friedman N, Sheves M. Ultrafast Protein Conformational Alterations in Bacteriorhodopsin and Its Locked Analogue BR5.12. J Phys Chem B 2009; 113:7851-60. [PMID: 19422251 DOI: 10.1021/jp810042f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ruth Gross
- Department of Physics, University of Kaiserslautern, D-67663 Kaiserslautern, Germany, and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Christian Schumann
- Department of Physics, University of Kaiserslautern, D-67663 Kaiserslautern, Germany, and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Matthias M. N. Wolf
- Department of Physics, University of Kaiserslautern, D-67663 Kaiserslautern, Germany, and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Johannes Herbst
- Department of Physics, University of Kaiserslautern, D-67663 Kaiserslautern, Germany, and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Rolf Diller
- Department of Physics, University of Kaiserslautern, D-67663 Kaiserslautern, Germany, and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Noga Friedman
- Department of Physics, University of Kaiserslautern, D-67663 Kaiserslautern, Germany, and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Mordechai Sheves
- Department of Physics, University of Kaiserslautern, D-67663 Kaiserslautern, Germany, and Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
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18
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Functional electric field changes in photoactivated proteins revealed by ultrafast Stark spectroscopy of the Trp residues. Proc Natl Acad Sci U S A 2009; 106:7718-23. [PMID: 19416877 DOI: 10.1073/pnas.0812877106] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ultrafast transient absorption spectroscopy of wild-type bacteriorhodopsin (WT bR) and 2 tryptophan mutants (W86F and W182F) is performed with visible light excitation (pump) and UV probe. The aim is to investigate the photoinduced change in the charge distribution with 50-fs time resolution by probing the effects on the tryptophan absorption bands. A systematic, quantitative comparison of the transient absorption of the 3 samples is carried out. The main result is the absence in the W86F mutant of a transient induced absorption band observed at approximately 300-310 nm in WT bR and W182F. A simple model describing the dipolar interaction of the retinal moiety with the 2 tryptophan residues of interest allows us to reproduce the dominant features of the transient signals observed in the 3 samples at ultrashort pump-probe delays. In particular, we show that Trp(86) undergoes a significant Stark shift induced by the transient retinal dipole moment. The corresponding transient signal can be isolated by direct subtraction of experimental data obtained for WT bR and W86F. It shows an instantaneous rise, followed by a decay over approximately 500 fs corresponding to the isomerization time. Interestingly, it does not decay back to zero, thus revealing a change in the local electrostatic environment that remains long after isomerization, in the K intermediate state of the protein cycle. The comparison of WT bR and W86F also leads to a revised interpretation of the overall transient UV absorption of bR.
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Verhoefen MK, Neumann K, Weber I, Glaubitz C, Wachtveitl J. Primary Reaction Dynamics of Proteorhodopsin Mutant D97N Observed by Femtosecond Infrared and Visible Spectroscopy. Photochem Photobiol 2009; 85:540-6. [DOI: 10.1111/j.1751-1097.2008.00513.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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van Thor JJ. Photoreactions and dynamics of the green fluorescent protein. Chem Soc Rev 2009; 38:2935-50. [DOI: 10.1039/b820275n] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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21
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Amsden JJ, Kralj JM, Bergo VB, Spudich EN, Spudich JL, Rothschild KJ. Different structural changes occur in blue- and green-proteorhodopsins during the primary photoreaction. Biochemistry 2008; 47:11490-8. [PMID: 18842006 DOI: 10.1021/bi800945t] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We examine the structural changes during the primary photoreaction in blue-absorbing proteorhodopsin (BPR), a light-driven retinylidene proton pump, using low-temperature FTIR difference spectroscopy. Comparison of the light-induced BPR difference spectrum recorded at 80 K to that of green-absorbing proteorhodopsin (GPR) reveals that there are several differences in the BPR and GPR primary photoreactions despite the similar structure of the retinal chromophore and all-trans --> 13-cis isomerization. Strong bands near 1700 cm(-1) assigned previously to a change in hydrogen bonding of Asn230 in GPR are still present in BPR. However, additional bands in the same region are assigned on the basis of site-directed mutagenesis to changes occurring in Gln105. In the amide II region, bands are assigned on the basis of total (15)N labeling to structural changes of the protein backbone, although no such bands were previously observed for GPR. A band at 3642 cm(-1) in BPR, assigned to the OH stretching mode of a water molecule on the basis of H2(18)O substitution, appears at a different frequency than a band at 3626 cm(-1) previously assigned to a water molecule in GPR. However, the substitution of Gln105 for Leu105 in BPR leads to the appearance of both bands at 3642 and 3626 cm(-1), indicating the waters assigned in BPR and GPR exist in separate distinct locations and can coexist in the GPR-like Q105L mutant of BPR. These results indicate that there exist significant differences in the conformational changes occurring in these two types proteorhodopsin during the initial photoreaction despite their similar chromophore structures, which might reflect a different arrangement of water in the active site as well as substitution of a hydrophilic for hydrophobic residue at residue 105.
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Affiliation(s)
- Jason J Amsden
- Department of Physics, Photonics Center, and Molecular Biophysics Laboratory, Boston University, Boston, Massachusetts 02215, USA
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22
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Kralj JM, Spudich EN, Spudich JL, Rothschild KJ. Raman spectroscopy reveals direct chromophore interactions in the Leu/Gln105 spectral tuning switch of proteorhodopsins. J Phys Chem B 2008; 112:11770-6. [PMID: 18717545 PMCID: PMC3608850 DOI: 10.1021/jp802629e] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteorhodopsins are an extensive family of photoactive membrane proteins found in proteobacteria distributed throughout the world's oceans which are often classified as green- or blue-absorbing (GPR and BPR, respectively) on the basis of their visible absorption maxima. GPR and BPR have significantly different properties including photocycle lifetimes and wavelength dependence on pH. Previous studies revealed that these different properties are correlated with a single residue, Leu105 in GPR and Gln105 in BPR, although the molecular basis for the different properties of GPR and BPR has not yet been elucidated. We have studied the unexcited states of GPR and BPR using resonance Raman spectroscopy which enhances almost exclusively chromophore vibrations. We find that both spectra are remarkably similar, indicating that the retinylidene structure of GPR and BPR are almost identical. However, the frequency of a band assigned to the retinal C13-methyl-rock vibration is shifted from 1006 cm (-1) in GPR to 1012 cm (-1) in BPR. A similar shift is observed in the GPR mutant L105Q indicating Leu and Gln residues interact differently with the retinal C13-methyl group. The environment of the Schiff base of GPR and BPR differ as indicated by differences in the H/D induced down-shift of the Schiff base vibration. Residues located in transmembrane helices (D-G) do not contribute to the observed differences in the protein-chromophore interaction between BPR and GPR based on the Raman spectra of chimeras. These results support a model whereby the substitution of the hydrophilic Gln105 in BPR with the smaller hydrophobic Leu105 in GPR directly alters the environment of both the retinal C13 group and the Schiff base.
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Affiliation(s)
- Joel M. Kralj
- Department of Physics, Molecular Biophysics Laboratory, Photonics Center, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215
| | - Elena N. Spudich
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas 77030
| | - John L. Spudich
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas 77030
| | - Kenneth J. Rothschild
- Department of Physics, Molecular Biophysics Laboratory, Photonics Center, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215
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23
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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] [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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Characterization of the primary photochemistry of proteorhodopsin with femtosecond spectroscopy. Biophys J 2008; 94:4020-30. [PMID: 18234812 DOI: 10.1529/biophysj.107.121376] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proteorhodopsin is an ion-translocating member of the microbial rhodopsin family. Light absorption by its retinal chromophore initiates a photocycle, driven by trans/cis isomerization, leading to transmembrane translocation of a proton toward the extracellular side of the cytoplasmic membrane. Here we report a study on the photoisomerization dynamics of the retinal chromophore of proteorhodopsin, using femtosecond time-resolved spectroscopy, by probing in the visible- and in the midinfrared spectral regions. Experiments were performed both at pH 9.5 (a physiologically relevant pH value in which the primary proton acceptor of the protonated Schiff base, Asp(97), is deprotonated) and at pH 6.5 (with Asp(97) protonated). Simultaneous analysis of the data sets recorded in the two spectral regions and at both pH values reveals a multiexponential excited state decay, with time constants of approximately 0.2 ps, approximately 2 ps, and approximately 20 ps. From the difference spectra associated with these dynamics, we conclude that there are two chromophore-isomerization pathways that lead to the K-state: one with an effective rate of approximately (2 ps)(-1) and the other with a rate of approximately (20 ps)(-1). At high pH, both pathways are equally effective, with an estimated quantum yield for K-formation of approximately 0.7. At pH 6.5, the slower pathway is less productive, which results in an isomerization quantum yield of 0.5. We further observe an ultrafast response of residue Asp(227), which forms part of the counterion complex, corresponding to a strengthening of its hydrogen bond with the Schiff base on K-state formation; and a feature that develops on the 0.2 ps and 2 ps timescale and probably reflects a response of an amide II band in reaction to the isomerization process.
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