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Buhrke D, Lahav Y, Rao A, Ruf J, Schapiro I, Hamm P. Transient 2D IR Spectroscopy and Multiscale Simulations Reveal Vibrational Couplings in the Cyanobacteriochrome Slr1393-g3. J Am Chem Soc 2023. [PMID: 37450891 DOI: 10.1021/jacs.3c00896] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Cyanobacteriochromes are bistable photoreceptor proteins with desirable photochemical properties for biotechnological applications, such as optogenetics or fluorescence microscopy. Here, we investigate Slr1393-g3, a cyanobacteriochrome that reversibly photoswitches between a red-absorbing (Pr) and green-absorbing (Pg) form. We applied advanced IR spectroscopic methods to track the sequence of intermediates during the photocycle over many orders of magnitude in time. In the conversion from Pg to Pr, we have revealed a new intermediate with distinct spectroscopic features in the IR, which precedes Pr formation using transient IR spectroscopy. In addition, stationary and transient 2D IR experiments measured the vibrational couplings between different groups of the chromophore and the protein in these intermediate states, as well as their structural disorder. Anharmonic QM/MM calculations predict spectra in good agreement with experimental 2D IR spectra of the initial and final states of the photocycle. They facilitate the assignment of the IR spectra that serve as a basis for the interpretation of the spectroscopic results and suggest structural changes of the intermediates along the photocycle.
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Affiliation(s)
- David Buhrke
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
- Institute of Biology, Humboldt University Berlin, 10115 Berlin, Germany
| | - Yigal Lahav
- Fritz Haber Center for Molecular Dynamics, Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
- MIGAL - Galilee Research Institute, 1101602 Kiryat Shmona, Israel
| | - Aditya Rao
- Fritz Haber Center for Molecular Dynamics, Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Jeannette Ruf
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics, Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Peter Hamm
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
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Ruf J, Hamm P, Buhrke D. Needles in a haystack: H-bonding in an optogenetic protein observed with isotope labeling and 2D-IR spectroscopy. Phys Chem Chem Phys 2021; 23:10267-10273. [PMID: 33899887 PMCID: PMC8099029 DOI: 10.1039/d1cp00996f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/09/2021] [Indexed: 11/29/2022]
Abstract
Recently, re-purposing of cyanobacterial photoreceptors as optogentic actuators enabled light-regulated protein expression in different host systems. These new bi-stable optogenetic tools enable interesting new applications, but their light-driven working mechanism remains largely elusive on a molecular level. Here, we study the optogenetic cyanobacteriochrome Am1-c0023g2 with isotope labeling and two dimensional infrared (2D-IR) spectroscopy. Isotope labeling allows us to isolate two site-specific carbonyl marker modes from the overwhelming mid-IR signal of the peptide backbone vibrations. Unlike conventional difference-FTIR spectroscopy, 2D-IR is sensitive to homogeneous and inhomogeneous broadening mechanisms of these two vibrational probes in the different photostates of the protein. We analyse the 2D-IR line shapes in the context of available structural models and find that they reflect the hydrogen-bonding environment of these two marker groups.
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Affiliation(s)
- Jeannette Ruf
- Department of Chemistry, University of Zürich, Zürich, Switzerland.
| | - Peter Hamm
- Department of Chemistry, University of Zürich, Zürich, Switzerland.
| | - David Buhrke
- Department of Chemistry, University of Zürich, Zürich, Switzerland.
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Buhrke D, Oppelt KT, Heckmeier PJ, Fernández-Terán R, Hamm P. Nanosecond protein dynamics in a red/green cyanobacteriochrome revealed by transient IR spectroscopy. J Chem Phys 2020; 153:245101. [DOI: 10.1063/5.0033107] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- David Buhrke
- Department of Chemistry, University of Zürich, Zürich, Switzerland
| | | | | | | | - Peter Hamm
- Department of Chemistry, University of Zürich, Zürich, Switzerland
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Jenkins AJ, Gottlieb SM, Chang CW, Kim PW, Hayer RJ, Hanke SJ, Martin SS, Lagarias JC, Larsen DS. Conservation and Diversity in the Primary Reverse Photodynamics of the Canonical Red/Green Cyanobacteriochrome Family. Biochemistry 2020; 59:4015-4028. [PMID: 33021375 DOI: 10.1021/acs.biochem.0c00454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this report, we compare the femtosecond to nanosecond primary reverse photodynamics (15EPg → 15ZPr) of eight tetrapyrrole binding photoswitching cyanobacteriochromes in the canonical red/green family from the cyanobacterium Nostoc punctiforme. Three characteristic classes were identified on the basis of the diversity of excited-state and ground-state properties, including the lifetime, photocycle initiation quantum yield, photointermediate stability, spectra, and temporal properties. We observed a correlation between the excited-state lifetime and peak wavelength of the electronic absorption spectrum with higher-energy-absorbing representatives exhibiting both faster excited-state decay times and higher photoisomerization quantum yields. The latter was attributed to both an increased number of structural restraints and differences in H-bonding networks that facilitate photoisomerization. All three classes exhibited primary Lumi-Go intermediates, with class II and III representatives evolving to a secondary Meta-G photointermediate. Class II Meta-GR intermediates were orange absorbing, whereas class III Meta-G had structurally relaxed, red-absorbing chromophores that resemble their dark-adapted 15ZPr states. Differences in the reverse and forward reaction mechanisms are discussed within the context of structural constraints.
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Affiliation(s)
- Adam J Jenkins
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Sean Marc Gottlieb
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Che-Wei Chang
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Peter W Kim
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Randeep J Hayer
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Samuel J Hanke
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Shelley S Martin
- Department of Molecular and Cellular Biology, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - J Clark Lagarias
- Department of Molecular and Cellular Biology, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Delmar S Larsen
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
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Kirpich JS, Gottlieb SM, Chang CW, Kim PW, Martin SS, Lagarias JC, Larsen DS. Forward Photodynamics of the Noncanonical Red/Green NpR3784 Cyanobacteriochrome from Nostoc punctiforme. Biochemistry 2019; 58:2297-2306. [PMID: 30973006 DOI: 10.1021/acs.biochem.8b01274] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyanobacteriochromes (CBCRs) make up a diverse family of cyanobacterial photoreceptors distantly related to the phytochrome photoreceptors of land plants. At least two lineages of CBCRs have reacquired red-absorbing dark states similar to the phytochrome Pr resting state but are coupled to green-absorbing light-adapted states rather than the canonical far-red-absorbing light-adapted state. One such lineage includes the canonical red/green (R/G) CBCRs that includes AnPixJg2 (UniProtKB Q8YXY7 ) and NpR6012g4 (UniProtKB B2IU14 ) that have been extensively characterized. Here we examine the forward Pr photodynamics of NpR3784 (UniProtKB B2J457 ), a representative member of the second R/G CBCR subfamily. Using broadband transient absorption pump-probe spectroscopy, we characterize both primary (100 fs to 10 ns) and secondary (10 ns to 1 ms) forward (Pr → Pg) photodynamics and compare the results to temperature-jump cryokinetics measurements. Our studies show that primary isomerization dynamics occur on an ∼10 ps timescale, yet remarkably, the red-shifted primary Lumi-Rf photoproduct found in all photoactive canonical R/G CBCRs examined to date is extremely short-lived in NpR3784. These results demonstrate that differences in reaction pathways reflect the evolutionary history of R/G CBCRs despite the convergent evolution of their photocycle end products.
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Affiliation(s)
- Julia S Kirpich
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Sean M Gottlieb
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Che-Wei Chang
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Peter W Kim
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Shelley S Martin
- Department of Molecular and Cell Biology , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - J Clark Lagarias
- Department of Molecular and Cell Biology , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Delmar S Larsen
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
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