1
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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: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [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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2
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Filiba O, Borin VA, Schapiro I. The involvement of triplet states in the isomerization of retinaloids. Phys Chem Chem Phys 2022; 24:26223-26231. [PMID: 36278932 DOI: 10.1039/d2cp03791b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Rhodopsins form a family of photoreceptor proteins which utilize the retinal chromophore for light energy conversion. Upon light absorption the retinal chromophore undergoes a photoisomerization. This reaction involves a non-radiative relaxation through a conical intersection between the singlet excited state and the ground state. In this work we studied the possible involvement of triplet states in the photoisomerization of retinaloids using the extended multistate (XMS) version of CASPT2. To this end, truncated models of three retinaloids were considered: protonated Schiff base, deprotonated Schiff base and the aldehyde form. The optimized geometries of the reactant, the product and the conical intersection were connected by a linear interpolation of internal coordinates to describe the isomerization. The energetic position of the low-lying singlet and triplet states as well as their spin-orbit coupling matrix elements (SOCME) were calculated along the isomerization profile. The SOCME values peaked in vicinity of the conical intersection for all the retinaloids. Furthermore, the magnitude of SOCME is invariant to the number of double bonds in the model. The SOCME for the protonated Schiff base is negligible (1.5 cm-1) which renders the involvement of the triplet state as improbable. However, the largest SOCME value of 30 cm-1 was found for the aldehyde form, followed by 15 cm-1 for the deprotonated Schiff base.
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Affiliation(s)
- Ofer Filiba
- Fritz Haber Research Center for Molecular Dynamics and Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel.
| | - Veniamin A Borin
- Fritz Haber Research Center for Molecular Dynamics and Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel.
| | - Igor Schapiro
- Fritz Haber Research Center for Molecular Dynamics and Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel.
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3
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Abstract
Microbial rhodopsins represent the most abundant phototrophic systems known today. A similar molecular architecture with seven transmembrane helices and a retinal cofactor linked to a lysine in helix 7 enables a wide range of functions including ion pumping, light-controlled ion channel gating, or sensing. Deciphering their molecular mechanisms therefore requires a combined consideration of structural, functional, and spectroscopic data in order to identify key factors determining their function. Important insight can be gained by solid-state NMR spectroscopy by which the large homo-oligomeric rhodopsin complexes can be studied directly within lipid bilayers. This chapter describes the methodological background and the necessary sample preparation requirements for the study of photointermediates, for the analysis of protonation states, H-bonding and chromophore conformations, for 3D structure determination, and for probing oligomer interfaces of microbial rhodopsins. The use of data extracted from these NMR experiments is discussed in the context of complementary biophysical methods.
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Affiliation(s)
- Clara Nassrin Kriebel
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Johanna Becker-Baldus
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Clemens Glaubitz
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
- Centre for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany.
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4
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Weissbecker J, Boumrifak C, Breyer M, Wießalla T, Shevchenko V, Mager T, Slavov C, Alekseev A, Kovalev K, Gordeliy V, Bamberg E, Wachtveitl J. Die spannungsabhängige Richtung der Reprotonierung der Schiff'schen Base bestimmt das Einwärtspumpen von Xenorhodopsin. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Juliane Weissbecker
- Abteilung Biophysikalische Chemie Max-Planck-Institut für Biophysik Max-von-Laue-Straße 3 60438 Frankfurt am Main Deutschland
| | - Chokri Boumrifak
- Institut für Physikalische and Theoretische Chemie Goethe Universität Max-von-Laue-Straße 7 60438 Frankfurt am Main Deutschland
| | - Maximilian Breyer
- Abteilung Biophysikalische Chemie Max-Planck-Institut für Biophysik Max-von-Laue-Straße 3 60438 Frankfurt am Main Deutschland
| | - Tristan Wießalla
- Abteilung Biophysikalische Chemie Max-Planck-Institut für Biophysik Max-von-Laue-Straße 3 60438 Frankfurt am Main Deutschland
| | - Vitaly Shevchenko
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) Forschungszentrum Jülich GmbH Wilhelm-Johnen-Straße 52425 Jülich Deutschland
| | - Thomas Mager
- Abteilung Biophysikalische Chemie Max-Planck-Institut für Biophysik Max-von-Laue-Straße 3 60438 Frankfurt am Main Deutschland
| | - Chavdar Slavov
- Institut für Physikalische and Theoretische Chemie Goethe Universität Max-von-Laue-Straße 7 60438 Frankfurt am Main Deutschland
| | - Alexey Alekseev
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) Forschungszentrum Jülich GmbH Wilhelm-Johnen-Straße 52425 Jülich Deutschland
| | - Kirill Kovalev
- European Molecular Biology Laboratory Notkestraße 85 22607 Hamburg Deutschland
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases Moscow Institute of Physics and Technology Dolgoprudny Russland
| | - Valentin Gordeliy
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) Forschungszentrum Jülich GmbH Wilhelm-Johnen-Straße 52425 Jülich Deutschland
| | - Ernst Bamberg
- Abteilung Biophysikalische Chemie Max-Planck-Institut für Biophysik Max-von-Laue-Straße 3 60438 Frankfurt am Main Deutschland
| | - Josef Wachtveitl
- Institut für Physikalische and Theoretische Chemie Goethe Universität Max-von-Laue-Straße 7 60438 Frankfurt am Main Deutschland
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5
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Wachtveitl J, Weissbecker J, Boumrifak C, Breyer M, Wießalla T, Shevchenko V, Mager T, Slavov C, Alekseev A, Kovalev K, Gordeliy V, Bamberg E. The voltage dependent sidedness of the reprotonation of the retinal Schiff base determines the unique inward pumping of Xenorhodopsin. Angew Chem Int Ed Engl 2021; 60:23010-23017. [PMID: 34339559 PMCID: PMC8518763 DOI: 10.1002/anie.202103882] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Indexed: 11/07/2022]
Abstract
The new class of microbial rhodopsins, called xenorhodopsins (XeRs) (1), extends the versatility of this family by inward H + pumps (2-4). These pumps are an alternative optogenetic tool to the light-gated ion channels (e.g. ChR1,2), because the activation of electrically excitable cells by XeRs is independent from the surrounding physiological conditions. In this work we functionally and spectroscopically characterized XeR from Nanosalina ( Ns XeR) (1). The photodynamic behavior of Ns XeR was investigated on the ps to s time scale elucidating the formation of the J and K and a previously unknown long-lived intermediate. The pH dependent kinetics reveal that alkalization of the surrounding medium accelerates the photocycle and the pump turnover. In patch-clamp experiments the blue-light illumination of Ns XeR in the M state shows a potential-dependent vectoriality of the photocurrent transients, suggesting a variable accessibility of reprotonation of the retinal Schiff base. Insights on the kinetically independent switching mechanism could furthermore be obtained by mutational studies on the putative intracellular H + acceptor D220.
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Affiliation(s)
- Josef Wachtveitl
- Goethe-Universität Frankfurt am Main, Physical and Theoretical Chemistry, Max von Laue-Straße 7, 60438, Frankfurt am Main, GERMANY
| | | | - Chokri Boumrifak
- Goethe-Universitat Frankfurt am Main, Biochemistry, Chemistry and Pharmacy, GERMANY
| | | | - Tristan Wießalla
- Max-Planck-Institut fur Biophysik, Biophysical Chemistry, GERMANY
| | - Vitaly Shevchenko
- Forschungszentrum Julich ICG: Forschungszentrum Julich GmbH, Biological Information Processing, GERMANY
| | - Thomas Mager
- Max Planck Institute of Biophysics: Max-Planck-Institut fur Biophysik, Biophysical Chemistry, GERMANY
| | - Chavdar Slavov
- Goethe-Universitat Frankfurt am Main, Chemistry, GERMANY
| | - Alexey Alekseev
- Forschungszentrum Jülich: Forschungszentrum Julich GmbH, Biological Information Processing, GERMANY
| | - Kirill Kovalev
- Forschungszentrum Jülich: Forschungszentrum Julich GmbH, Biological Information Processing, GERMANY
| | - Valentin Gordeliy
- Forschungszentrum Jülich: Forschungszentrum Julich GmbH, Biological Information Processing, GERMANY
| | - Ernst Bamberg
- Max-Planck-Institut fur Biophysik, Biophysical Chemistry, GERMANY
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6
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Asido M, Kar RK, Kriebel CN, Braun M, Glaubitz C, Schapiro I, Wachtveitl J. Transient Near-UV Absorption of the Light-Driven Sodium Pump Krokinobacter eikastus Rhodopsin 2: A Spectroscopic Marker for Retinal Configuration. J Phys Chem Lett 2021; 12:6284-6291. [PMID: 34213348 DOI: 10.1021/acs.jpclett.1c01436] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We report a transient signature in the near-UV absorption of Krokinobacter eikastus rhodopsin 2 (KR2), which spans from the femtosecond up to the millisecond time scale. The signature rises with the all-trans to 13-cis isomerization of retinal and decays with the reisomerization to all-trans in the late photocycle, making it a promising marker band for retinal configuration. Hybrid quantum mechanics/molecular mechanics simulations show that the near-UV absorption signal corresponds to an S0 → S3 and/or an S0 → S5 transition, which is present in all photointermediates. These transitions exhibit a negligible spectral shift by the altering protein environment, in contrast to the main absorption band. This is rationalized by the extension of the transition densities that omits the Schiff base nitrogen. Further characterization and first steps into possible optogenetic applications were performed with near-UV quenching experiments of an induced photostationary state, yielding an ultrafast regeneration of the parent state of KR2.
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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
| | - Rajiv K Kar
- Fritz Haber Center for Molecular Dynamics Research at the Institute of Chemistry, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Clara Nassrin Kriebel
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue Straße 9, 60438 Frankfurt am Main, Germany
| | - Markus Braun
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue Straße 9, 60438 Frankfurt am Main, Germany
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research at the Institute of Chemistry, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - 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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7
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Kataoka C, Sugimoto T, Shigemura S, Katayama K, Tsunoda SP, Inoue K, Béjà O, Kandori H. TAT Rhodopsin Is an Ultraviolet-Dependent Environmental pH Sensor. Biochemistry 2021; 60:899-907. [PMID: 33721993 DOI: 10.1021/acs.biochem.0c00951] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In many rhodopsins, the retinal Schiff base pKa remains very high, ensuring Schiff base protonation captures visible light. Nevertheless, recently we found that TAT rhodopsin contains protonated and unprotonated forms at physiological pH. The protonated form displays a unique photochemical behavior in which the primary K intermediate returns to the original state within 10-5 s, and the lack of photocycle completion poses questions about the functional role of TAT rhodopsin. Here we studied the molecular properties of the protonated and unprotonated forms of the Schiff base in TAT rhodopsin. We confirmed no photointermediate formation at >10-5 s for the protonated form of TAT rhodopsin in microenvironments such as detergents, nanodiscs, and liposomes. In contrast, the unprotonated form features a very long photocycle with a time constant of 15 s. A low-temperature study revealed that the primary reaction of the unprotonated form is all-trans to 13-cis photoisomerization, which is usual, but with a proton transfer reaction occurring at 77 K, which is unusual. The active intermediate contains the unprotonated Schiff base as well as the resting state. Electrophysiological measurements excluded ion-transport activity for TAT rhodopsin, while transient outward proton movement only at an alkaline extracellular pH indicates that TAT rhodopsin senses the extracellular pH. On the basis of the findings presented here, we propose that TAT rhodopsin is an ultraviolet (UV)-dependent environmental pH sensor in marine bacteria. At acidic pH, absorbed visible light energy is quickly dissipated into heat without any function. In contrast, when the environmental pH becomes high, absorption of UV/blue light yields formation of the long-lived intermediates, possibly driving the signal transduction cascade in marine bacteria.
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Affiliation(s)
- Chihiro Kataoka
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Teppei Sugimoto
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Shunta Shigemura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Kota Katayama
- 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
| | - Satoshi P Tsunoda
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Keiichi Inoue
- 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
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Oded Béjà
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - 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
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8
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Hontani Y, Broser M, Luck M, Weißenborn J, Kloz M, Hegemann P, Kennis JTM. Dual Photoisomerization on Distinct Potential Energy Surfaces in a UV-Absorbing Rhodopsin. J Am Chem Soc 2020; 142:11464-11473. [PMID: 32475117 PMCID: PMC7315636 DOI: 10.1021/jacs.0c03229] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
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UV-absorbing rhodopsins are essential
for UV vision and sensing
in all kingdoms of life. Unlike the well-known visible-absorbing rhodopsins,
which bind a protonated retinal Schiff base for light absorption,
UV-absorbing rhodopsins bind an unprotonated retinal Schiff base.
Thus far, the photoreaction dynamics and mechanisms of UV-absorbing
rhodopsins have remained essentially unknown. Here, we report the
complete excited- and ground-state dynamics of the UV form of histidine
kinase rhodopsin 1 (HKR1) from eukaryotic algae, using femtosecond
stimulated Raman spectroscopy (FSRS) and transient absorption spectroscopy,
covering time scales from femtoseconds to milliseconds. We found that
energy-level ordering is inverted with respect to visible-absorbing
rhodopsins, with an optically forbidden low-lying S1 excited
state that has Ag– symmetry and a higher-lying UV-absorbing
S2 state of Bu+ symmetry. UV-photoexcitation
to the S2 state elicits a unique dual-isomerization reaction:
first, C13=C14 cis–trans isomerization occurs during S2–S1 evolution
in <100 fs. This very fast reaction features the remarkable property
that the newly formed isomer appears in the excited state rather than
in the ground state. Second, C15=N16 anti–syn isomerization occurs on the S1–S0 evolution to the ground state in 4.8 ps. We detected two
ground-state unprotonated retinal photoproducts, 13-trans/15-anti (all-trans) and 13-cis/15-syn, after relaxation to the ground
state. These isomers become protonated in 58 μs and 3.2 ms,
respectively, resulting in formation of the blue-absorbing form of
HKR1. Our results constitute a benchmark of UV-induced photochemistry
of animal and microbial rhodopsins.
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Affiliation(s)
- Yusaku Hontani
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan, Amsterdam 1081 HV, The Netherlands
| | - Matthias Broser
- Institut für Biologie, Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany
| | - Meike Luck
- Institut für Biologie, Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany
| | - Jörn Weißenborn
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan, Amsterdam 1081 HV, The Netherlands
| | - Miroslav Kloz
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan, Amsterdam 1081 HV, The Netherlands.,ELI-Beamlines, Institute of Physics, Na Slovance 2, 182 21 Praha 8, Czech Republic
| | - Peter Hegemann
- Institut für Biologie, Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany
| | - John T M Kennis
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan, Amsterdam 1081 HV, The Netherlands
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9
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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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10
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Asido M, Eberhardt P, Kriebel CN, Braun M, Glaubitz C, Wachtveitl J. Time-resolved IR spectroscopy reveals mechanistic details of ion transport in the sodium pump Krokinobacter eikastus rhodopsin 2. Phys Chem Chem Phys 2019; 21:4461-4471. [PMID: 30734791 DOI: 10.1039/c8cp07418f] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a comparative study on the structural dynamics of the light-driven sodium pump Krokinobacter eikastus rhodopsin 2 wild type under sodium and proton pumping conditions by means of time-resolved IR spectroscopy. The kinetics of KR2 under sodium pumping conditions exhibits a sequential character, whereas the kinetics of KR2 under proton pumping conditions involves several equilibrium states. The sodium translocation itself is characterized by major conformational changes of the protein backbone, such as distortions of the α-helices and probably of the ECL1 domain, indicated by distinct marker bands in the amide I region. Carbonyl stretch modes of specific amino acid residues helped to elucidate structural changes in the retinal Schiff base moiety, including the protonation and deprotonation of D116, which is crucial for a deeper understanding of the mechanistic features in the photocycle of KR2.
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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.
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11
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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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12
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Mehler M, Eckert CE, Leeder AJ, Kaur J, Fischer T, Kubatova N, Brown LJ, Brown RCD, Becker-Baldus J, Wachtveitl J, Glaubitz C. Chromophore Distortions in Photointermediates of Proteorhodopsin Visualized by Dynamic Nuclear Polarization-Enhanced Solid-State NMR. J Am Chem Soc 2017; 139:16143-16153. [PMID: 29027800 DOI: 10.1021/jacs.7b05061] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Proteorhodopsin (PR) is the most abundant retinal protein on earth and functions as a light-driven proton pump. Despite extensive efforts, structural data for PR photointermediate states have not been obtained. On the basis of dynamic nuclear polarization (DNP)-enhanced solid-state NMR, we were able to analyze the retinal polyene chain between positions C10 and C15 as well as the Schiff base nitrogen in the ground state in comparison to light-induced, cryotrapped K- and M-states. A high M-state population could be achieved by preventing reprotonation of the Schiff base through a mutation of the primary proton donor (E108Q). Our data reveal unexpected large and alternating 13C chemical shift changes in the K-state propagating away from the Schiff base along the polyene chain. Furthermore, two different M-states have been observed reflecting the Schiff base reorientation after the deprotonation step. Our study provides novel insight into the photocycle of PR and also demonstrates the power of DNP-enhanced solid-state NMR to bridge the gap between functional and structural data and models.
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Affiliation(s)
- Michaela Mehler
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Carl Elias Eckert
- Institute for Physical and Theoretical Chemistry, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Alexander J Leeder
- Department of Chemistry, University of Southampton , Southampton SO17 1BJ, United Kingdom
| | - Jagdeep Kaur
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Tobias Fischer
- Institute for Physical and Theoretical Chemistry, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Nina Kubatova
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Lynda J Brown
- Department of Chemistry, University of Southampton , Southampton SO17 1BJ, United Kingdom
| | - Richard C D Brown
- Department of Chemistry, University of Southampton , Southampton SO17 1BJ, United Kingdom
| | - Johanna Becker-Baldus
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Josef Wachtveitl
- Institute for Physical and Theoretical Chemistry, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt , Frankfurt 60438, Germany
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