1
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Nikolaev D, Mironov VN, Metelkina EM, Shtyrov AA, Mereshchenko AS, Demidov NA, Vyazmin SY, Tennikova TB, Moskalenko SE, Bondarev SA, Zhouravleva GA, Vasin AV, Panov MS, Ryazantsev MN. Rational Design of Far-Red Archaerhodopsin-3-Based Fluorescent Genetically Encoded Voltage Indicators: from Elucidation of the Fluorescence Mechanism in Archers to Novel Red-Shifted Variants. ACS PHYSICAL CHEMISTRY AU 2024; 4:347-362. [PMID: 39069984 PMCID: PMC11274289 DOI: 10.1021/acsphyschemau.3c00073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 04/07/2024] [Accepted: 04/08/2024] [Indexed: 07/30/2024]
Abstract
Genetically encoded voltage indicators (GEVIs) have found wide applications as molecular tools for visualization of changes in cell membrane potential. Among others, several classes of archaerhodopsin-3-based GEVIs have been developed and have proved themselves promising in various molecular imaging studies. To expand the application range for this type of GEVIs, new variants with absorption band maxima shifted toward the first biological window and enhanced fluorescence signal are required. Here, we integrate computational and experimental strategies to reveal structural factors that distinguish far-red bright archaerhodopsin-3-based GEVIs, Archers, obtained by directed evolution in a previous study (McIsaac et al., PNAS, 2014) and the wild-type archaerhodopsin-3 with an extremely dim fluorescence signal, aiming to use the obtained information in subsequent rational design. We found that the fluorescence can be enhanced by stabilization of a certain conformation of the protein, which, in turn, can be achieved by tuning the pK a value of two titratable residues. These findings were supported further by introducing mutations into wild-type archeorhodopsin-3 and detecting the enhancement of the fluorescence signal. Finally, we came up with a rational design and proposed previously unknown Archers variants with red-shifted absorption bands (λmax up to 640 nm) and potential-dependent bright fluorescence (quantum yield up to 0.97%).
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Affiliation(s)
- Dmitrii
M. Nikolaev
- Institute
of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, St. Petersburg 198504, Russia
- Institute
of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, 29 Polytechnicheskaya Str., St. Petersburg 195251, Russia
| | - Vladimir N. Mironov
- Saint
Petersburg Academic University, 8/3 Khlopina Street, St.
Petersburg 194021, Russia
| | - Ekaterina M. Metelkina
- Institute
of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, St. Petersburg 198504, Russia
| | - Andrey A. Shtyrov
- Institute
of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, St. Petersburg 198504, Russia
| | - Andrey S. Mereshchenko
- Institute
of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, St. Petersburg 198504, Russia
| | - Nikita A. Demidov
- Saint
Petersburg Academic University, 8/3 Khlopina Street, St.
Petersburg 194021, Russia
| | - Sergey Yu. Vyazmin
- Saint
Petersburg Academic University, 8/3 Khlopina Street, St.
Petersburg 194021, Russia
| | - Tatiana B. Tennikova
- Institute
of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, St. Petersburg 198504, Russia
| | - Svetlana E. Moskalenko
- Department
of Genetics and Biotechnology, Saint Petersburg
State University, 7/9
Universitetskaya emb, St. Petersburg 199034, Russia
- Vavilov
Institute of General Genetics, St. Petersburg
Branch, Russian Academy of Sciences, St. Petersburg 199034, Russia
| | - Stanislav A. Bondarev
- Department
of Genetics and Biotechnology, Saint Petersburg
State University, 7/9
Universitetskaya emb, St. Petersburg 199034, Russia
- Laboratory
of Amyloid Biology, Saint Petersburg State
University, St. Petersburg 199034, Russia
| | - Galina A. Zhouravleva
- Department
of Genetics and Biotechnology, Saint Petersburg
State University, 7/9
Universitetskaya emb, St. Petersburg 199034, Russia
- Laboratory
of Amyloid Biology, Saint Petersburg State
University, St. Petersburg 199034, Russia
| | - Andrey V. Vasin
- Institute
of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, 29 Polytechnicheskaya Str., St. Petersburg 195251, Russia
| | - Maxim S. Panov
- Institute
of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, St. Petersburg 198504, Russia
- St.
Petersburg State Chemical Pharmaceutical University, Professor Popov str., 14, lit. A, St. Petersburg 197022, Russia
| | - Mikhail N. Ryazantsev
- Institute
of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, St. Petersburg 198504, Russia
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2
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Singh M, Hashimoto M, Katayama K, Furutani Y, Kandori H. Internal Proton Transfer in the Activation of Heliorhodopsin. J Mol Biol 2024; 436:168273. [PMID: 37709010 DOI: 10.1016/j.jmb.2023.168273] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 09/16/2023]
Abstract
Heliorhodopsin (HeR), a recently discovered new rhodopsin family, contains a single counterion of the protonated Schiff base, E108 in HeR from Thermoplasmatales archaeon SG8-52-1 (TaHeR). Upon light absorption, the M and O intermediates form in HeRs, as well as type-1 microbial rhodopsins, indicating that the proton transfer from the Schiff base leads to the activation of HeRs. The present flash photolysis study of TaHeR in the presence of a pH-sensitive dye showed that TaHeR contains a proton-accepting group (PAG) inside protein. Comprehensive mutation study of TaHeR found the E108D mutant abolishing the M formation, which is not only at pH 8, but also at pH 9 and 10. The lack of M observation does not originate from the short lifetime of the M intermediate in E108D, as FTIR spectroscopy revealed that a red-shifted K-like intermediate is long lived in E108D. It is likely that the K-like intermediate returns to the unphotolyzed state without internal proton transfer in E108D. E108 and D108 are the Schiff base counterions of the wild-type and E108D mutant TaHeR, respectively, whereas small difference in length of side chains determine internal proton transfer reaction from the Schiff base. Based on the present finding, we propose that the internal water cluster (four water molecules) constitutes PAG in the M intermediate of TaHeR. In the wild type TaHeR, a protonated water cluster is stabilized by forming a salt bridge with E108. In contrast, slightly shortened counterion (D108) cannot stabilize the protonated water cluster in E108D, and thus impairs internal proton transfer from the Schiff base.
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Affiliation(s)
- Manish Singh
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Masanori Hashimoto
- 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; PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Yuji Furutani
- 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
| | - 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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3
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Asido M, Boumrifak C, Weissbecker J, Bamberg E, Wachtveitl J. Vibrational Study of the Inward Proton Pump Xenorhodopsin NsXeR: Switch Order Determines Vectoriality. J Mol Biol 2024; 436:168447. [PMID: 38244766 DOI: 10.1016/j.jmb.2024.168447] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/12/2024] [Accepted: 01/12/2024] [Indexed: 01/22/2024]
Abstract
Common proton pumps, e.g. HsBR and PR, transport protons out of the cell. Xenorhodopsins (XeR) were the first discovered microbial rhodopsins which come as natural inward proton pumps. In this work we combine steady-state (cryo-)FTIR and Raman spectroscopy with time-resolved IR and UV/Vis measurements to roadmap the inward proton transport of NsXeR and pinpoint the most important mechanistic features. Through the assignment of characteristic bands of the protein backbone, the retinal chromophore, the retinal Schiff base and D220, we could follow the switching processes for proton accessibility in accordance with the isomerization / switch / transfer model. The corresponding transient IR signatures suggest that the initial assignment of D220 as the proton acceptor needs to be questioned due to the temporal mismatch of the Schiff base and D220 protonation steps. The switching events in the K-L and MCP-MEC transitions are finely tuned by changes of the protein backbone and rearrangements of the Schiff base. This finely tuned mechanism is disrupted at cryogenic temperatures, being reflected in the replacement of the previously reported long-lived intermediate GS* by an actual redshifted (O-like) intermediate.
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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
| | - Chokri Boumrifak
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany
| | - Juliane Weissbecker
- Department of Biophysical Chemistry, Max-Planck-Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Ernst Bamberg
- Department of Biophysical Chemistry, Max-Planck-Institute of Biophysics, Max-von-Laue-Straße 3, 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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4
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Leonarski F, Nan J, Matej Z, Bertrand Q, Furrer A, Gorgisyan I, Bjelčić M, Kepa M, Glover H, Hinger V, Eriksson T, Cehovin A, Eguiraun M, Gasparotto P, Mozzanica A, Weinert T, Gonzalez A, Standfuss J, Wang M, Ursby T, Dworkowski F. Kilohertz serial crystallography with the JUNGFRAU detector at a fourth-generation synchrotron source. IUCRJ 2023; 10:729-737. [PMID: 37830774 PMCID: PMC10619449 DOI: 10.1107/s2052252523008618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023]
Abstract
Serial and time-resolved macromolecular crystallography are on the rise. However, beam time at X-ray free-electron lasers is limited and most third-generation synchrotron-based macromolecular crystallography beamlines do not offer the necessary infrastructure yet. Here, a new setup is demonstrated, based on the JUNGFRAU detector and Jungfraujoch data-acquisition system, that enables collection of kilohertz serial crystallography data at fourth-generation synchrotrons. More importantly, it is shown that this setup is capable of collecting multiple-time-point time-resolved protein dynamics at kilohertz rates, allowing the probing of microsecond to second dynamics at synchrotrons in a fraction of the time needed previously. A high-quality complete X-ray dataset was obtained within 1 min from lysozyme microcrystals, and the dynamics of the light-driven sodium-pump membrane protein KR2 with a time resolution of 1 ms could be demonstrated. To make the setup more accessible for researchers, downstream data handling and analysis will be automated to allow on-the-fly spot finding and indexing, as well as data processing.
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Affiliation(s)
- Filip Leonarski
- Photon Science Division, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Jie Nan
- MAX IV Laboratory, Lund University, POB. 118, SE-22100 Lund, Sweden
| | - Zdenek Matej
- MAX IV Laboratory, Lund University, POB. 118, SE-22100 Lund, Sweden
| | - Quentin Bertrand
- Division of Biology and Chemistry, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Antonia Furrer
- Division of Biology and Chemistry, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | | | - Monika Bjelčić
- MAX IV Laboratory, Lund University, POB. 118, SE-22100 Lund, Sweden
| | - Michal Kepa
- Division of Biology and Chemistry, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Hannah Glover
- Division of Biology and Chemistry, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Viktoria Hinger
- Photon Science Division, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Thomas Eriksson
- MAX IV Laboratory, Lund University, POB. 118, SE-22100 Lund, Sweden
| | | | - Mikel Eguiraun
- MAX IV Laboratory, Lund University, POB. 118, SE-22100 Lund, Sweden
| | - Piero Gasparotto
- Scientific Computing, Theory and Data, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Aldo Mozzanica
- Photon Science Division, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Tobias Weinert
- Division of Biology and Chemistry, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Ana Gonzalez
- MAX IV Laboratory, Lund University, POB. 118, SE-22100 Lund, Sweden
| | - Jörg Standfuss
- Division of Biology and Chemistry, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Meitian Wang
- Photon Science Division, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Thomas Ursby
- MAX IV Laboratory, Lund University, POB. 118, SE-22100 Lund, Sweden
| | - Florian Dworkowski
- Photon Science Division, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
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5
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Yang Q, Chen D. Na + Binding and Transport: Insights from Light-Driven Na +-Pumping Rhodopsin. Molecules 2023; 28:7135. [PMID: 37894614 PMCID: PMC10608830 DOI: 10.3390/molecules28207135] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/07/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Na+ plays a vital role in numerous physiological processes across humans and animals, necessitating a comprehensive understanding of Na+ transmembrane transport. Among the various Na+ pumps and channels, light-driven Na+-pumping rhodopsin (NaR) has emerged as a noteworthy model in this field. This review offers a concise overview of the structural and functional studies conducted on NaR, encompassing ground/intermediate-state structures and photocycle kinetics. The primary focus lies in addressing key inquiries: (1) unraveling the translocation pathway of Na+; (2) examining the role of structural changes within the photocycle, particularly in the O state, in facilitating Na+ transport; and (3) investigating the timing of Na+ uptake/release. By delving into these unresolved issues and existing debates, this review aims to shed light on the future direction of Na+ pump research.
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Affiliation(s)
- Qifan Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Deliang Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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6
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Xu J, Yang Q, Ma B, Li L, Kong F, Xiao L, Chen D. K +-Dependent Photocycle and Photocurrent Reveal the Uptake of K + in Light-Driven Sodium Pump. Int J Mol Sci 2023; 24:14414. [PMID: 37833864 PMCID: PMC10572131 DOI: 10.3390/ijms241914414] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 09/16/2023] [Accepted: 09/18/2023] [Indexed: 10/15/2023] Open
Abstract
Engineering light-controlled K+ pumps from Na+-pumping rhodopsins (NaR) greatly expands the scope of optogenetic applications. However, the limited knowledge regarding the kinetic and selective mechanism of K+ uptake has significantly impeded the modification and design of light-controlled K+ pumps, as well as their practical applications in various fields, including neuroscience. In this study, we presented K+-dependent photocycle kinetics and photocurrent of a light-driven Na+ pump called Nonlabens dokdonensis rhodopsin 2 (NdR2). As the concentration of K+ increased, we observed the accelerated decay of M intermediate in the wild type (WT) through flash photolysis. In 100 mM KCl, the lifetime of the M decay was approximately 1.0 s, which shortened to around 0.6 s in 1 M KCl. Additionally, the K+-dependent M decay kinetics were also observed in the G263W/N61P mutant, which transports K+. In 100 mM KCl, the lifetime of the M decay was approximately 2.5 s, which shortened to around 0.2 s in 1 M KCl. According to the competitive model, in high KCl, K+ may be taken up from the cytoplasmic surface, competing with Na+ or H+ during M decay. This was further confirmed by the K+-dependent photocurrent of WT liposome. As the concentration of K+ increased to 500 mM, the amplitude of peak current significantly dropped to approximately ~60%. Titration experiments revealed that the ratio of the rate constant of H+ uptake (kH) to that of K+ uptake (kK) is >108. Compared to the WT, the G263W/N61P mutant exhibited a decrease of approximately 40-fold in kH/kK. Previous studies focused on transforming NaR into K+ pumps have primarily targeted the intracellular ion uptake region of Krokinobacter eikastus rhodopsin 2 (KR2) to enhance K+ uptake. However, our results demonstrate that the naturally occurring WT NdR2 is capable of intracellular K+ uptake without requiring structural modifications on the intracellular region. This discovery provides diverse options for future K+ pump designs. Furthermore, we propose a novel photocurrent-based approach to evaluate K+ uptake, which can serve as a reference for similar studies on other ion pumps. In conclusion, our research not only provides new insights into the mechanism of K+ uptake but also offers a valuable point of reference for the development of optogenetic tools and other applications in this field.
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Affiliation(s)
- Jikang Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
| | - Qifan Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Baofu Ma
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
| | - Longjie Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
| | - Fei Kong
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
| | - Lan Xiao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
| | - Deliang Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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7
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Kriebel CN, Asido M, Kaur J, Orth J, Braun P, Becker-Baldus J, Wachtveitl J, Glaubitz C. Structural and functional consequences of the H180A mutation of the light-driven sodium pump KR2. Biophys J 2023; 122:1003-1017. [PMID: 36528791 PMCID: PMC10111219 DOI: 10.1016/j.bpj.2022.12.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 12/04/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Krokinobacter eikastus rhodopsin 2 (KR2) is a light-driven pentameric sodium pump. Its ability to translocate cations other than protons and to create an electrochemical potential makes it an attractive optogenetic tool. Tailoring its ion-pumping characteristics by mutations is therefore of great interest. In addition, understanding the functional and structural consequences of certain mutations helps to derive a functional mechanism of ion selectivity and transfer of KR2. Based on solid-state NMR spectroscopy, we report an extensive chemical shift resonance assignment of KR2 within lipid bilayers. This data set was then used to probe site-resolved allosteric effects of sodium binding, which revealed multiple responsive sites including the Schiff base nitrogen and the NDQ motif. Based on this data set, the consequences of the H180A mutation are probed. The mutant is silenced in the presence of sodium while in its absence proton pumping is observed. Our data reveal specific long-range effects along the sodium transfer pathway. These experiments are complemented by time-resolved optical spectroscopy. Our data suggest a model in which sodium uptake by the mutant can still take place, while sodium release and backflow control are disturbed.
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Affiliation(s)
- Clara Nassrin Kriebel
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marvin Asido
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jagdeep Kaur
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jennifer Orth
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Philipp Braun
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Johanna Becker-Baldus
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Josef Wachtveitl
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany.
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8
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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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9
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Deniz E, Löffler JG, Kondratiev A, Thun AR, Shen Y, Wille G, Bredenbeck J. High-precision background correction and artifact suppression for ultrafast spectroscopy by quasi-simultaneous measurements in a split-sample cell. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:033001. [PMID: 35364971 DOI: 10.1063/5.0079958] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Alternating acquisition of background and sample spectra is often employed in conventional Fourier-transform infrared spectroscopy or ultraviolet-visible spectroscopy for accurate background subtraction. For example, for solvent background correction, typically a spectrum of a cuvette with solvent is measured and subtracted from a spectrum of a cuvette with solvent and solute. Ultrafast spectroscopies, though, come with many peculiarities that make the collection of well-matched, subtractable background and sample spectra challenging. Here, we present a demountable split-sample cell in combination with a modified Lissajous scanner to overcome these challenges. It allows for quasi-simultaneous measurements of background and sample spectra, mitigating the effects of drifts of the setup and maintaining the beam and sample geometry when swapping between background and sample measurements. The cell is moving between subsequent laser shots to refresh the excited sample volume. With less than 45 μl of solution for 150 μm optical thickness, sample usage is economical. Cell assembly is a key step and covered in an illustrated protocol.
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Affiliation(s)
- E Deniz
- Institute of Biophysics, Goethe University Frankfurt am Main, Frankfurt am Main 60438, Germany
| | - J G Löffler
- Institute of Biophysics, Goethe University Frankfurt am Main, Frankfurt am Main 60438, Germany
| | - A Kondratiev
- Institute of Biophysics, Goethe University Frankfurt am Main, Frankfurt am Main 60438, Germany
| | - A R Thun
- Institute of Biophysics, Goethe University Frankfurt am Main, Frankfurt am Main 60438, Germany
| | - Y Shen
- Institute of Biophysics, Goethe University Frankfurt am Main, Frankfurt am Main 60438, Germany
| | - G Wille
- Institute of Biophysics, Goethe University Frankfurt am Main, Frankfurt am Main 60438, Germany
| | - J Bredenbeck
- Institute of Biophysics, Goethe University Frankfurt am Main, Frankfurt am Main 60438, Germany
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10
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Monteiro DCF, Amoah E, Rogers C, Pearson AR. Using photocaging for fast time-resolved structural biology studies. Acta Crystallogr D Struct Biol 2021; 77:1218-1232. [PMID: 34605426 PMCID: PMC8489231 DOI: 10.1107/s2059798321008809] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/23/2021] [Indexed: 12/02/2022] Open
Abstract
Careful selection of photocaging approaches is critical to achieve fast and well synchronized reaction initiation and perform successful time-resolved structural biology experiments. This review summarizes the best characterized and most relevant photocaging groups previously described in the literature. It also provides a walkthrough of the essential factors to consider in designing a suitable photocaged molecule to address specific biological questions, focusing on photocaging groups with well characterized spectroscopic properties. The relationships between decay rates (k in s-1), quantum yields (ϕ) and molar extinction coefficients (ϵmax in M-1 cm-1) are highlighted for different groups. The effects of the nature of the photocaged group on these properties is also discussed. Four main photocaging scaffolds are presented in detail, o-nitrobenzyls, p-hydroxyphenyls, coumarinyls and nitrodibenzofuranyls, along with three examples of the use of this technology. Furthermore, a subset of specialty photocages are highlighted: photoacids, molecular photoswitches and metal-containing photocages. These extend the range of photocaging approaches by, for example, controlling pH or generating conformationally locked molecules.
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Affiliation(s)
- Diana C. F. Monteiro
- Hauptman–Woodward Medical Research Institute, 700 Ellicot Street, Buffalo, NY 14203, USA
| | - Emmanuel Amoah
- Hauptman–Woodward Medical Research Institute, 700 Ellicot Street, Buffalo, NY 14203, USA
| | - Cromarte Rogers
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Chemistry, Universität Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Arwen R. Pearson
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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11
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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: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [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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12
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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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13
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Kato T, Tsukamoto T, Demura M, Kikukawa T. Real-time identification of two substrate-binding intermediates for the light-driven sodium pump rhodopsin. J Biol Chem 2021; 296:100792. [PMID: 34019877 PMCID: PMC8219890 DOI: 10.1016/j.jbc.2021.100792] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 11/29/2022] Open
Abstract
Membrane transport proteins undergo critical conformational changes during substrate uptake and release, as the substrate-binding site is believed to switch its accessibility from one side of the membrane to the other. Thus, at least two substrate-binding intermediates should appear during the process, that is, after uptake and before the release of the substrate. However, this view has not been verified for most transporters because of the difficulty in detecting short-lived intermediates. Here, we report real-time identification of these intermediates for the light-driven outward current-generating Na+-pump rhodopsin. We triggered the transport cycle of Na+-pump rhodopsin using a short laser pulse, and subsequent formation and decay of various intermediates was detected by time-resolved measurements of absorption changes. We used this method to analyze transport reactions and elucidated the sequential formation of the Na+-binding intermediates O1 and O2. Both intermediates exhibited red-shifted absorption spectra and generated transient equilibria with short-wavelength intermediates. The equilibria commonly shifted toward O1 and O2 with increasing Na+ concentration, indicating that Na+ is bound to these intermediates. However, these equilibria were formed independently; O1 reached equilibrium with preceding intermediates, indicating Na+ uptake on the cytoplasmic side. In contrast, O2 reached equilibrium with subsequent intermediates, indicating Na+ release on the extracellular side. Thus, there is an irreversible switch in “accessibility” during the O1 to O2 transition, which could represent one of the key processes governing unidirectional Na+ transport.
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Affiliation(s)
- Tomoya Kato
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Takashi Tsukamoto
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan; Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Makoto Demura
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan; Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan; Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan.
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14
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Jakdetchai O, Eberhardt P, Asido M, Kaur J, Kriebel CN, Mao J, Leeder AJ, Brown LJ, Brown RCD, Becker-Baldus J, Bamann C, Wachtveitl J, Glaubitz C. Probing the photointermediates of light-driven sodium ion pump KR2 by DNP-enhanced solid-state NMR. SCIENCE ADVANCES 2021; 7:7/11/eabf4213. [PMID: 33712469 PMCID: PMC7954446 DOI: 10.1126/sciadv.abf4213] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/29/2021] [Indexed: 06/10/2023]
Abstract
The functional mechanism of the light-driven sodium pump Krokinobacter eikastus rhodopsin 2 (KR2) raises fundamental questions since the transfer of cations must differ from the better-known principles of rhodopsin-based proton pumps. Addressing these questions must involve a better understanding of its photointermediates. Here, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance spectroscopy on cryo-trapped photointermediates shows that the K-state with 13-cis retinal directly interconverts into the subsequent L-state with distinct retinal carbon chemical shift differences and an increased out-of-plane twist around the C14-C15 bond. The retinal converts back into an all-trans conformation in the O-intermediate, which is the key state for sodium transport. However, retinal carbon and Schiff base nitrogen chemical shifts differ from those observed in the KR2 dark state all-trans conformation, indicating a perturbation through the nearby bound sodium ion. Our findings are supplemented by optical and infrared spectroscopy and are discussed in the context of known three-dimensional structures.
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Affiliation(s)
- Orawan Jakdetchai
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max von Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Peter Eberhardt
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max von Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Marvin Asido
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max von Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Jagdeep Kaur
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max von Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - 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
| | - Jiafei Mao
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max von Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Alexander J Leeder
- Department of Chemistry, University of Southampton, Southampton SO17 1BJ, Great Britain
| | - Lynda J Brown
- Department of Chemistry, University of Southampton, Southampton SO17 1BJ, Great Britain
| | - Richard C D Brown
- Department of Chemistry, University of Southampton, Southampton SO17 1BJ, Great Britain
| | - Johanna Becker-Baldus
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max von Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Christian Bamann
- Max Planck Institute of Biophysics, Max von Laue Strasse 3, 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.
| | - 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.
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15
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Eberhardt P, Slavov C, Sörmann J, Bamann C, Braun M, Wachtveitl J. Temperature Dependence of the Krokinobacter rhodopsin 2 Kinetics. Biophys J 2020; 120:568-575. [PMID: 33347887 DOI: 10.1016/j.bpj.2020.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/13/2020] [Accepted: 12/07/2020] [Indexed: 11/16/2022] Open
Abstract
We investigated the temperature-dependent kinetics of the light-driven Na+ pump Krokinobacter rhodopsin 2 (KR2) at Na+-pumping conditions. The recorded microsecond flash photolysis data were subjected to detailed global target analysis, employing Eyring constraints and spectral decomposition. The analysis resulted in the kinetic rates, the composition of the different photocycle equilibria, and the spectra of the involved photointermediates. Our results show that with the temperature increase (from 10 to 40°C), the overall photocycle duration is accelerated by a factor of 6, with the L-to-M transition exhibiting an impressive 40-fold increase. It follows from the analysis that in KR2 the chromophore and the protein scaffold are more kinetically decoupled than in other microbial rhodopsins. We link this effect to the rigidity of the retinal protein environment. This kinetic decoupling should be considered in future studies and could potentially be exploited for fine-tuning biotechnological applications.
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Affiliation(s)
- Peter Eberhardt
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Chavdar Slavov
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Janina Sörmann
- Department of Biophysical Chemistry, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Christian Bamann
- Department of Biophysical Chemistry, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Markus Braun
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
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16
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Klocke JL, Kottke T. A quantum cascade laser setup for studying irreversible photoreactions in H 2O with nanosecond resolution and microlitre consumption. Phys Chem Chem Phys 2020; 22:26459-26467. [PMID: 33185227 DOI: 10.1039/d0cp03164j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Time-resolved infrared spectroscopy on irreversible reactions requires in general an exchange of sample for thousands of acquisitions leading to high sample consumption. Here, we present a setup employing a modern quantum cascade laser (QCL) as a probe light source to record time-resolved difference spectra of irreversible photoreactions in H2O. The combination of the focused QCL with a pressure-tolerant flow cell and a micrometre stage orthogonal to the flow allowed us to drastically reduce the sample consumption. We investigated the irreversible photoreduction of the cofactor flavin mononucleotide (FMN) in H2O, which is a common reaction taking place in biological photoreceptors. A broad time range from 20 nanoseconds to 1 second was accessible, because the approach minimized any signal drift by the flow. Kinetics were recorded at 46 selected wavenumbers consuming 12 microlitres for a complete dataset. The tuning range of 1490-1740 cm-1 included relevant carbonyl vibrations and the region of strong water absorption at around 1650 cm-1. A continuous dataset in the spectral dimension was generated by applying a fit with a sum of Lorentzians. Subsequent global analysis allowed us to resolve reference spectra and kinetics of the photoreaction proceeding from the triplet excited state via the intermediate flavin anion radical to the product, the fully reduced state of FMN. Accordingly, the neutral radical state is not populated in the disproportionation. The approach strongly facilitates the spectroscopic access to irreversible reactions of flavin-containing photoreceptors and photoenzymes with high time resolution and small sample consumption.
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Affiliation(s)
- Jessica L Klocke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
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17
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Tomida S, Ito S, Mato T, Furutani Y, Inoue K, Kandori H. Infrared spectroscopic analysis on structural changes around the protonated Schiff base upon retinal isomerization in light-driven sodium pump KR2. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148190. [DOI: 10.1016/j.bbabio.2020.148190] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 01/30/2020] [Accepted: 03/13/2020] [Indexed: 10/24/2022]
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18
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Femtosecond-to-millisecond structural changes in a light-driven sodium pump. Nature 2020; 583:314-318. [DOI: 10.1038/s41586-020-2307-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/16/2020] [Indexed: 01/03/2023]
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19
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Abstract
Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.
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