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Dey P, Santra S, Ghosh D. Effect of the protein environment on the excited state phenomena in a bacteriophytochrome. Phys Chem Chem Phys 2024; 26:20875-20882. [PMID: 39044617 DOI: 10.1039/d4cp02112f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
The excited state processes of a bacteriophytochrome are studied using high-level multireference methods. The various non-radiative channels of deactivation are identified for the chromophore. The effects of the protein environment and substituents are elucidated for these excited state processes. It is observed that while the excited states are completely delocalized in the Franck-Condon (FC) region, they acquire significant charge transfer character near the conical intersections. Earlier studies have emphasized the delocalized nature of the excited states in the FC region, which leads to absorption spectra with minimal Stokes shift [Rumyantsev et al., Sci. Rep., 2015, 5, 18348]. The effect of the protein environment on the vertical excitation energies was minimal, while that on the conical intersection (CI) energetics was significant. This may lead one to believe that it is charge transfer driven. However, energy decomposition analysis shows that it is the effect of the dispersion of nearby residues and the steric effect on the rings and substituents that lead to the large effect of proteins on the energetics of the CIs.
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Affiliation(s)
- Pradipta Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India.
| | - Supriyo Santra
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India.
| | - Debashree Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India.
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2
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Do TN, Menendez D, Bizhga D, Stojković EA, Kennis JTM. Two-photon Absorption and Photoionization of a Bacterial Phytochrome. J Mol Biol 2024; 436:168357. [PMID: 37944794 DOI: 10.1016/j.jmb.2023.168357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/19/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
Phytochromes constitute a family of photosensory proteins that are utilized by various organisms to regulate several physiological processes. Phytochromes bind a bilin pigment that switches its isomeric state upon absorption of red or far-red photons, resulting in protein conformational changes that are sensed by the organism. Previously, the ultrafast dynamics in bacterial phytochrome was resolved to atomic resolution by time-resolved serial femtosecond X-ray diffraction (TR-SFX), showing extensive changes in its molecular conformation at 1 picosecond delay time. However, the large excitation fluence of mJ/mm2 used in TR-SFX questions the validity of the observed dynamics. In this work, we present an excitation-dependent ultrafast transient absorption study to test the response of a related bacterial phytochrome to excitation fluence. We observe excitation power-dependent sub-picosecond dynamics, assigned to the population of high-lying excited state Sn through resonantly enhanced two-photon absorption, followed by rapid internal conversion to the low-lying S1 state. Inspection of the long-lived spectrum under high fluence shows that in addition to the primary intermediate Lumi-R, spectroscopic signatures of solvated electrons and ionized chromophore radicals are observed. Supported by numerical modelling, we propose that under excitation fluences of tens of μJ/mm2 and higher, bacterial phytochrome partly undergoes photoionization from the Sn state in competition with internal conversion to the S1 state in 300 fs. We suggest that the extensive structural changes of related, shorter bacterial phytochrome, lacking the PHY domain, resolved from TR-SFX may have been affected by the ionized species. We propose approaches to minimize the two-photon absorption process by tuning the excitation spectrum away from the S1 absorption or using phytochromes exhibiting minimized or shifted S1 absorption.
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Affiliation(s)
- Thanh Nhut Do
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - David Menendez
- Department of Biology, Northeastern Illinois University, 5500 N. St. Louis Ave., Chicago, IL 60625, USA
| | - Dorina Bizhga
- Department of Biology, Northeastern Illinois University, 5500 N. St. Louis Ave., Chicago, IL 60625, USA
| | - Emina A Stojković
- Department of Biology, Northeastern Illinois University, 5500 N. St. Louis Ave., Chicago, IL 60625, USA
| | - John T M Kennis
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.
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3
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Kannan P, Oh J, Yeon YJ, Park YI, Seo MH, Park K. Computational identification of key residues regulating fluorescence emission in a red/green cyanobacteriochrome. Proteins 2024; 92:106-116. [PMID: 37646483 DOI: 10.1002/prot.26586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/03/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023]
Abstract
Cyanobacteriochromes (CBCRs) are linear tetrapyrrole bilin-binding photoreceptors of cyanobacteria that exhibit high spectral diversity, gaining attention in optogenetics and bioimaging applications. Several engineering studies on CBCRs were attempted, especially for designing near-infrared (NIR) fluorescent proteins with longer fluorescence wavelengths. However, despite continuous efforts, a key component regulating fluorescence emission property in CBCRs is still poorly understood. As a model system, we focused on red/green CBCR Slr1393g3, from the unicellular cyanobacterium Synechocystis sp. PCC 6803 to engineer Pr to get far-red light-emitting property. Energy profiling and pairwise structural comparison of Slr1393g3 variants effectively reveal the mutations that are critical to the fluorescence changes. H497 seems to play a key role in stabilizing the chromophore environment, especially the α3 helix, while H495, T499, and Q502 are potential key residues determining fluorescence emission peak wavelength. We also found that mutations of α2 and α4 helical regions are closely related to the chromophore binding stability and likely affect fluorescence properties. Taken together, our computational analysis suggests that the fluorescence of Slr1393g3 is mainly controlled by the stabilization of the chromophore binding pocket. The predicted key residues potentially regulating the fluorescence emission property of a red/green CBCR will be advantageous for designing improved NIR fluorescent protein when combined with in vitro molecular evolution approaches.
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Affiliation(s)
- Priyadharshini Kannan
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung, Republic of Korea
- Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Jisung Oh
- Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung, Republic of Korea
- Natural Product Research Center, Korea Institute of Science and Technology, Gangneung, Republic of Korea
| | - Young Joo Yeon
- Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Moon-Hyeong Seo
- Natural Product Research Center, Korea Institute of Science and Technology, Gangneung, Republic of Korea
- Department of Convergence Medicine, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
- Department of YM-KIST Bio-Health Convergence, Yonsei University, Wonju, Republic of Korea
| | - Keunwan Park
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung, Republic of Korea
- Department of YM-KIST Bio-Health Convergence, Yonsei University, Wonju, Republic of Korea
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4
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Fischer T, Köhler L, Engel PD, Song C, Gärtner W, Wachtveitl J, Slavov C. Conserved tyrosine in phytochromes controls the photodynamics through steric demand and hydrogen bonding capabilities. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148996. [PMID: 37437858 DOI: 10.1016/j.bbabio.2023.148996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/02/2023] [Accepted: 07/06/2023] [Indexed: 07/14/2023]
Abstract
Using ultrafast spectroscopy and site-specific mutagenesis, we demonstrate the central role of a conserved tyrosine within the chromophore binding pocket in the forward (Pr → Pfr) photoconversion of phytochromes. Taking GAF1 of the knotless phytochrome All2699g1 from Nostoc as representative member of phytochromes, it was found that the mutations have no influence on the early (<30 ps) dynamics associated with conformational changes of the chromophore in the excited state. Conversely, they drastically impact the extended protein-controlled excited state decay (>100 ps). Thus, the steric demand, position and H-bonding capabilities of the identified tyrosine control the chromophore photoisomerization while leaving the excited state chromophore dynamics unaffected. In effect, this residue operates as an isomerization-steric-gate that tunes the excited state lifetime and the photoreaction efficiency by modulating the available space of the chromophore and by stabilizing the primary intermediate Lumi-R. Understanding the role of such a conserved structural element sheds light on a key aspect of phytochrome functionality and provides a basis for rational design of optimized photoreceptors for biotechnological applications.
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Affiliation(s)
- Tobias Fischer
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt, Germany.
| | - Lisa Köhler
- Institute for Analytical Chemistry, University of Leipzig, Linnéstraße 3, 04103 Leipzig, Germany.
| | - Philipp D Engel
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt, Germany.
| | - Chen Song
- Institute for Analytical Chemistry, University of Leipzig, Linnéstraße 3, 04103 Leipzig, Germany.
| | - Wolfgang Gärtner
- Institute for Analytical Chemistry, University of Leipzig, Linnéstraße 3, 04103 Leipzig, Germany.
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt, Germany.
| | - Chavdar Slavov
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt, Germany; Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, 33620 Tampa, United States of America.
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5
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Janis MK, Zou W, Zastrow ML. A Single-Site Mutation Tunes Fluorescence and Chromophorylation of an Orange Fluorescent Cyanobacteriochrome. Chembiochem 2023; 24:e202300358. [PMID: 37423892 PMCID: PMC10653908 DOI: 10.1002/cbic.202300358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/11/2023]
Abstract
Cyanobacteriochrome (CBCR) cGMP-specific phosphodiesterase, adenylyl cyclase, and FhlA (GAF) domains bind bilin cofactors to confer sensory wavelengths important for various cyanobacterial photosensory processes. Many isolated GAF domains autocatalytically bind bilins, including the third GAF domain of CBCR Slr1393 from Synechocystis sp. PCC6803, which binds phycoerythrobilin (PEB) to yield a bright orange fluorescent protein. Compared to green fluorescent proteins, the smaller size and lack of an oxygen requirement for fluorescence make Slr1393g3 a promising platform for new genetically encoded fluorescent tools. Slr1393g3, however, shows low PEB binding efficiency (chromophorylation) at ~3 % compared to total Slr1393g3 expressed in E. coli. Here we used site-directed mutagenesis and plasmid redesign methods to improve Slr1393g3-PEB binding and demonstrate its utility as a fluorescent marker in live cells. Mutation at a single site, Trp496, tuned the emission over ~30 nm, likely by shifting autoisomerization of PEB to phycourobilin (PUB). Plasmid modifications for tuning relative expression of Slr1393g3 and PEB synthesis enzymes also improved chromophorylation and moving from a dual to single plasmid system facilitated exploration of a range of mutants via site saturation mutagenesis and sequence truncation. Collectively, the PEB/PUB chromophorylation was raised up to a total of 23 % with combined sequence truncation and W496H mutation.
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Affiliation(s)
- Makena K Janis
- Department of Chemistry, University of Houston, 3585 Cullen Blvd, Houston, TX, 77204, USA
| | - Wenping Zou
- Department of Chemistry, University of Houston, 3585 Cullen Blvd, Houston, TX, 77204, USA
| | - Melissa L Zastrow
- Department of Chemistry, University of Houston, 3585 Cullen Blvd, Houston, TX, 77204, USA
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6
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Thwaites O, Christianson BM, Cowan AJ, Jäckel F, Liu LN, Gardner AM. Unravelling the Roles of Integral Polypeptides in Excitation Energy Transfer of Photosynthetic RC-LH1 Supercomplexes. J Phys Chem B 2023; 127:7283-7290. [PMID: 37556839 PMCID: PMC10461223 DOI: 10.1021/acs.jpcb.3c04466] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/24/2023] [Indexed: 08/11/2023]
Abstract
Elucidating the photosynthetic processes that occur within the reaction center-light-harvesting 1 (RC-LH1) supercomplexes from purple bacteria is crucial for uncovering the assembly and functional mechanisms of natural photosynthetic systems and underpinning the development of artificial photosynthesis. Here, we examined excitation energy transfer of various RC-LH1 supercomplexes of Rhodobacter sphaeroides using transient absorption spectroscopy, coupled with lifetime density analysis, and studied the roles of the integral transmembrane polypeptides, PufX and PufY, in energy transfer within the RC-LH1 core complex. Our results show that the absence of PufX increases both the LH1 → RC excitation energy transfer lifetime and distribution due to the role of PufX in defining the interaction and orientation of the RC within the LH1 ring. While the absence of PufY leads to the conformational shift of several LH1 subunits toward the RC, it does not result in a marked change in the excitation energy transfer lifetime.
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Affiliation(s)
- Owen Thwaites
- Stephenson
Institute of Renewable Energy, University
of Liverpool, Liverpool L69 7ZF, U.K.
- Department
of Physics, University of Liverpool, Liverpool L69 7ZE, U.K.
| | - Bern M. Christianson
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K.
| | - Alexander J. Cowan
- Stephenson
Institute of Renewable Energy, University
of Liverpool, Liverpool L69 7ZF, U.K.
- Department
of Chemistry, University of Liverpool, Liverpool L69 7ZD, U.K.
| | - Frank Jäckel
- Stephenson
Institute of Renewable Energy, University
of Liverpool, Liverpool L69 7ZF, U.K.
- Department
of Physics, University of Liverpool, Liverpool L69 7ZE, U.K.
| | - Lu-Ning Liu
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K.
- College
of Marine Life Sciences, and Frontiers Science Center for Deep Ocean
Multispheres and Earth System, Ocean University
of China, Qingdao 266003, China
| | - Adrian M. Gardner
- Stephenson
Institute of Renewable Energy, University
of Liverpool, Liverpool L69 7ZF, U.K.
- Department
of Chemistry, University of Liverpool, Liverpool L69 7ZD, U.K.
- Early Career
Laser Laboratory, University of Liverpool, Liverpool L69 3BX, U.K.
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7
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Janis MK, Zou W, Zastrow ML. A Single Site Mutation Tunes Fluorescence and Chromophorylation of an Orange Fluorescent Cyanobacteriochrome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540396. [PMID: 37214816 PMCID: PMC10197653 DOI: 10.1101/2023.05.11.540396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cyanobacteriochrome (CBCR) GAF domains bind bilin cofactors to confer sensory wavelengths important for various cyanobacterial photosensory processes. Many isolated GAF domains autocatalytically bind bilins, becoming fluorescent. The third GAF domain of CBCR Slr1393 from Synechocystis sp. PCC6803 binds phycocyanobilin (PCB) natively, yielding red/green photoswitching properties but also binds phycoerythrobilin (PEB). GAF3-PCB has low quantum yields but non-photoswitching GAF3-PEB is brighter, making it a promising platform for new genetically encoded fluorescent tools. GAF3, however, shows low PEB binding efficiency (chromophorylation) at ∼3% compared to total protein expressed in E. coli . Here we explored site-directed mutagenesis and plasmid-based methods to improve GAF3-PEB binding and demonstrate its utility as a fluorescent marker in live cells. We found that a single mutation improved chromophorylation while tuning the emission over ∼30 nm, likely by shifting autoisomerization of PEB to phycourobilin (PUB). Plasmid modifications also improved chromophorylation and moving from a dual to single plasmid system facilitated exploration of a range of mutants via site saturation mutagenesis and sequence truncation. Collectively, the PEB/PUB chromophorylation was raised by ∼7-fold. Moreover, we show that protein-chromophore interactions can tune autoisomerization of PEB to PUB in a GAF domain, which will facilitate future engineering of similar GAF domain-derived fluorescent proteins.
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Affiliation(s)
- Makena K Janis
- Department of Chemistry, University of Houston, 3585 Cullen Blvd, Houston, TX, 77204 (USA)
| | - Wenping Zou
- Department of Chemistry, University of Houston, 3585 Cullen Blvd, Houston, TX, 77204 (USA)
| | - Melissa L Zastrow
- Department of Chemistry, University of Houston, 3585 Cullen Blvd, Houston, TX, 77204 (USA)
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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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Capone M, Sirohiwal A, Aschi M, Pantazis DA, Daidone I. Alternative Fast and Slow Primary Charge-Separation Pathways in Photosystem II. Angew Chem Int Ed Engl 2023; 62:e202216276. [PMID: 36791234 DOI: 10.1002/anie.202216276] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/23/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023]
Abstract
Photosystem-II (PSII) is a multi-subunit protein complex that harvests sunlight to perform oxygenic photosynthesis. Initial light-activated charge separation takes place at a reaction centre consisting of four chlorophylls and two pheophytins. Understanding the processes following light excitation remains elusive due to spectral congestion, the ultrafast nature, and multi-component behaviour of the charge-separation process. Here, using advanced computational multiscale approaches which take into account the large-scale configurational flexibility of the system, we identify two possible primary pathways to radical-pair formation that differ by three orders of magnitude in their kinetics. The fast (short-range) pathway is dominant, but the existence of an alternative slow (long-range) charge-separation pathway hints at the evolution of redundancy that may serve other purposes, adaptive or protective, related to formation of the unique oxidative species that drives water oxidation in PSII.
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Affiliation(s)
- Matteo Capone
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), 67010, L'Aquila, Italy
| | - Abhishek Sirohiwal
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany.,Present Address: Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, 10691, Stockholm, Sweden
| | - Massimiliano Aschi
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), 67010, L'Aquila, Italy
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), 67010, L'Aquila, Italy
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10
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Rao AG, Schapiro I. Photoisomerization of phytochrome chromophore models: an XMS-CASPT2 study. Phys Chem Chem Phys 2022; 24:29393-29405. [PMID: 36468544 DOI: 10.1039/d2cp04249e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Phytochromes are a superfamily of photoreceptors that harbor linear tetrapyrroles as chromophores. Upon light illumination, the linear tetrapyrrole chromophore undergoes a double bond isomerization which starts a photocycle. In this work, we studied the photoisomerization of chromophore models designed based on the C- and D-rings of the phycocyanobilin (PCB) chromophore. In total, five different models with varying substitutions were investigated. Firstly, the vertical excitation energies were benchmarked using different computational methods to establish the relative order of the excited states. Based on these calculations, we computed the photoisomerization profiles using the extended multi-state (XMS) version of the CASPT2 method. The profiles were obtained for both the clockwise and counterclockwise rotations of the C15C16 bond in the Z and E isomers using a linear interpolation of internal coordinates between the Franck-Condon and MECI geometries. In the minimal chromophore model that lacks the substitutions at the pyrrole rings, the isomerization involves both C14-C15 and C15C16 bonds of the methine bridge between the C- and D-rings, resembling the hula-twist motion. The MECIs are characterized by a partial charge transfer between the two pyrrole rings pointing towards a twisted intramolecular charge transfer. Systematic introduction of substituents leads to an increase in the steric repulsion between the two pyrrole rings causing a pretwist of the dihedral around the C15C16 bond, which creates a preference for the counterclockwise isomerization. An introduction of the carbonyl group at the D-ring increases the extent of charge transfer which changes the isomerization mechanism from hula-twist to one-bond flip.
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Affiliation(s)
- Aditya G Rao
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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11
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Fang Y, Huang H, Lin K, Xu C, Gu FL, Lan Z. The impact of different geometrical restrictions on the nonadiabatic photoisomerization of biliverdin chromophores. Phys Chem Chem Phys 2022; 24:26190-26199. [PMID: 36278817 DOI: 10.1039/d2cp02941c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The photoisomerization mechanism of the chromophore of bacterial biliverdin (BV) phytochromes is explored via nonadiabatic dynamics simulation by using the on-the-fly trajectory surface-hopping method at the semi-empirical OM2/MRCI level. Particularly, the current study focuses on the influence of geometrical constrains on the nonadiabatic photoisomerization dynamics of the BV chromophore. Here a rather simplified approach is employed in the nonadiabatic dynamics to capture the features of geometrical constrains, which adds mechanical restrictions to the specific moieties of the BV chromophore. This simplified method provides a rather quick approach to examine the influence of geometrical restrictions on photoisomerization. As expected, different constrains bring distinctive influences on the photoisomerization mechanism of the BV chromophore, giving either strong or minor modification of both involved reaction channels and excited-state lifetimes after the constrains are added in different ring moieties. These observations not only contribute to the primary understanding of the role of the spatial restriction caused by biological environments in photoinduced dynamics of the BV chromophore, but also provide useful ideas for the artificial regulation of the photoisomerization reaction channels of phytochrome proteins.
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Affiliation(s)
- Yuan Fang
- School of Chemistry, South China Normal University, Guangzhou 510006, China
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, P. R. China.
| | - Haiyi Huang
- School of Chemistry, South China Normal University, Guangzhou 510006, China
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, P. R. China.
| | - Kunni Lin
- School of Chemistry, South China Normal University, Guangzhou 510006, China
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, P. R. China.
| | - Chao Xu
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, P. R. China.
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
| | - Feng Long Gu
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, P. R. China.
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
| | - Zhenggang Lan
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, P. R. China.
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
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12
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Influence of the PHY domain on the ms-photoconversion dynamics of a knotless phytochrome. Photochem Photobiol Sci 2022; 21:1627-1636. [PMID: 35687310 DOI: 10.1007/s43630-022-00245-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/11/2022] [Indexed: 10/18/2022]
Abstract
The ability of some knotless phytochromes to photoconvert without the PHY domain allows evaluation of the distinct effect of the PHY domain on their photodynamics. Here, we compare the ms dynamics of the single GAF domain (g1) and the GAF-PHY (g1g2) construct of the knotless phytochrome All2699 from cyanobacterium Nostoc punctiforme. While the spectral signatures and occurrence of the intermediates are mostly unchanged by the domain composition, the presence of the PHY domain slows down the early forward and reverse dynamics involving chromophore and protein binding pocket relaxation. We assign this effect to a more restricted binding pocket imprinted by the PHY domain. The photoproduct formation is also slowed down by the presence of the PHY domain but to a lesser extent than the early dynamics. This indicates a rate limiting step within the GAF and not the PHY domain. We further identify a pH dependence of the biphasic photoproduct formation hinting towards a pKa dependent tuning mechanism. Our findings add to the understanding of the role of the individual domains in the photocycle dynamics and provide a basis for engineering of phytochromes towards biotechnological applications.
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13
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Nagano S, Sadeghi M, Balke J, Fleck M, Heckmann N, Psakis G, Alexiev U. Improved fluorescent phytochromes for in situ imaging. Sci Rep 2022; 12:5587. [PMID: 35379835 PMCID: PMC8980088 DOI: 10.1038/s41598-022-09169-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 03/14/2022] [Indexed: 12/18/2022] Open
Abstract
AbstractModern biology investigations on phytochromes as near-infrared fluorescent pigments pave the way for the development of new biosensors, as well as for optogenetics and in vivo imaging tools. Recently, near-infrared fluorescent proteins (NIR-FPs) engineered from biliverdin-binding bacteriophytochromes and cyanobacteriochromes, and from phycocyanobilin-binding cyanobacterial phytochromes have become promising probes for fluorescence microscopy and in vivo imaging. However, current NIR-FPs typically suffer from low fluorescence quantum yields and short fluorescence lifetimes. Here, we applied the rational approach of combining mutations known to enhance fluorescence in the cyanobacterial phytochrome Cph1 to derive a series of highly fluorescent variants with fluorescence quantum yield exceeding 15%. These variants were characterised by biochemical and spectroscopic methods, including time-resolved fluorescence spectroscopy. We show that these new NIR-FPs exhibit high fluorescence quantum yields and long fluorescence lifetimes, contributing to their bright fluorescence, and provide fluorescence lifetime imaging measurements in E.coli cells.
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14
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Light- and pH-dependent structural changes in cyanobacteriochrome AnPixJg2. Photochem Photobiol Sci 2022; 21:447-469. [PMID: 35394641 DOI: 10.1007/s43630-022-00204-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/03/2022] [Indexed: 10/18/2022]
Abstract
Cyanobacteriochromes (CBCRs) are phytochrome-related photosensory proteins that play an essential role in regulating phototaxis, chromatic acclimation, and cell aggregation in cyanobacteria. Here, we apply solid-state NMR spectroscopy to the red/green GAF2 domain of the CBCR AnPixJ assembled in vitro with a uniformly 13C- and 15N-labeled bilin chromophore, tracking changes in electronic structure, geometry, and structural heterogeneity of the chromophore as well as intimate contacts between the chromophore and protein residues in the photocycle. Our data confirm that the bilin ring D is strongly twisted with respect to the B-C plane in both dark and photoproduct states. We also identify a greater structural heterogeneity of the bilin chromophore in the photoproduct than in the dark state. In addition, the binding pocket is more hydrated in the photoproduct. Observation of interfacial 1H contacts of the photoproduct chromophore, together with quantum mechanics/molecular mechanics (QM/MM)-based structural models for this photoproduct, clearly suggests the presence of a biprotonated (cationic) imidazolium side-chain for a conserved histidine residue (322) at a distance of ~2.7 Å, generalizing the recent theoretical findings that explicitly link the structural heterogeneity of the dark-state chromophore to the protonation of this specific residue. Moreover, we examine pH effects on this in vitro assembled holoprotein, showing a substantially altered electronic structure and protonation of the photoproduct chromophore even with a small pH drop from 7.8 to 7.2. Our studies provide further information regarding the light- and pH-induced changes of the chromophore and the rearrangements of the hydrogen-bonding and electrostatic interaction network around it. Possible correlations between structural heterogeneity of the chromophore, protonation of the histidine residue nearby, and hydration of the pocket in both photostates are discussed.
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15
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Rockwell NC, Moreno MV, Martin SS, Lagarias JC. Protein-chromophore interactions controlling photoisomerization in red/green cyanobacteriochromes. Photochem Photobiol Sci 2022; 21:471-491. [PMID: 35411484 PMCID: PMC9609751 DOI: 10.1007/s43630-022-00213-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/21/2022] [Indexed: 10/18/2022]
Abstract
Photoreceptors in the phytochrome superfamily use 15,16-photoisomerization of a linear tetrapyrrole (bilin) chromophore to photoconvert between two states with distinct spectral and biochemical properties. Canonical phytochromes include master regulators of plant growth and development in which light signals trigger interconversion between a red-absorbing 15Z dark-adapted state and a metastable, far-red-absorbing 15E photoproduct state. Distantly related cyanobacteriochromes (CBCRs) carry out a diverse range of photoregulatory functions in cyanobacteria and exhibit considerable spectral diversity. One widespread CBCR subfamily typically exhibits a red-absorbing 15Z dark-adapted state similar to that of phytochrome that gives rise to a distinct green-absorbing 15E photoproduct. This red/green CBCR subfamily also includes red-inactive examples that fail to undergo photoconversion, providing an opportunity to study protein-chromophore interactions that either promote photoisomerization or block it. In this work, we identified a conserved lineage of red-inactive CBCRs. This enabled us to identify three substitutions sufficient to block photoisomerization in photoactive red/green CBCRs. The resulting red-inactive variants faithfully replicated the fluorescence and circular dichroism properties of naturally occurring examples. Converse substitutions restored photoconversion in naturally red-inactive CBCRs. This work thus identifies protein-chromophore interactions that control the fate of the excited-state population in red/green cyanobacteriochromes.
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Affiliation(s)
- Nathan C Rockwell
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, CA, 95616, USA.
| | - Marcus V Moreno
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, CA, 95616, USA
| | - Shelley S Martin
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, CA, 95616, USA
| | - J Clark Lagarias
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, CA, 95616, USA.
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16
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Thumser S, Köttner L, Hoffmann N, Mayer P, Dube H. All-Red-Light Photoswitching of Indirubin Controlled by Supramolecular Interactions. J Am Chem Soc 2021; 143:18251-18260. [PMID: 34665961 PMCID: PMC8867725 DOI: 10.1021/jacs.1c08206] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Red-light responsiveness
of photoswitches is a highly desired property
for many important application areas such as biology or material sciences.
The main approach to elicit this property uses strategic substitution
of long-known photoswitch motives such as azobenzenes or diarylethenes.
Only very few photoswitches possess inherent red-light absorption
of their core chromophore structures. Here, we present a strategy
to convert the long-known purple indirubin dye into a prolific red-light-responsive
photoswitch. In a supramolecular approach, its photochromism can be
changed from a negative to a positive one, while at the same time,
significantly higher yields of the metastable E-isomer
are obtained upon irradiation. E- to Z-photoisomerization can then also be induced by red light of longer
wavelengths. Indirubin therefore represents a unique example of reversible
photoswitching using entirely red light for both switching directions.
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Affiliation(s)
- Stefan Thumser
- Friedrich-Alexander Universität Erlangen-Nürnberg, Department of Chemistry and Pharmacy, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Laura Köttner
- Friedrich-Alexander Universität Erlangen-Nürnberg, Department of Chemistry and Pharmacy, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Nadine Hoffmann
- Ludwig-Maximilians Universität München, Department of Chemistry and Center for Integrated Protein Science CIPSM, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Peter Mayer
- Ludwig-Maximilians Universität München, Department of Chemistry and Center for Integrated Protein Science CIPSM, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Henry Dube
- Friedrich-Alexander Universität Erlangen-Nürnberg, Department of Chemistry and Pharmacy, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
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17
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Fischer T, van Wilderen LJGW, Gnau P, Bredenbeck J, Essen LO, Wachtveitl J, Slavov C. Ultrafast Photoconversion Dynamics of the Knotless Phytochrome SynCph2. Int J Mol Sci 2021; 22:ijms221910690. [PMID: 34639031 PMCID: PMC8508867 DOI: 10.3390/ijms221910690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/24/2021] [Accepted: 09/28/2021] [Indexed: 12/03/2022] Open
Abstract
The family of phytochrome photoreceptors contains proteins with different domain architectures and spectral properties. Knotless phytochromes are one of the three main subgroups classified by their distinct lack of the PAS domain in their photosensory core module, which is in contrast to the canonical PAS-GAF-PHY array. Despite intensive research on the ultrafast photodynamics of phytochromes, little is known about the primary kinetics in knotless phytochromes. Here, we present the ultrafast Pr ⇆ Pfr photodynamics of SynCph2, the best-known knotless phytochrome. Our results show that the excited state lifetime of Pr* (~200 ps) is similar to bacteriophytochromes, but much longer than in most canonical phytochromes. We assign the slow Pr* kinetics to relaxation processes of the chromophore-binding pocket that controls the bilin chromophore’s isomerization step. The Pfr photoconversion dynamics starts with a faster excited state relaxation than in canonical phytochromes, but, despite the differences in the respective domain architectures, proceeds via similar ground state intermediate steps up to Meta-F. Based on our observations, we propose that the kinetic features and overall dynamics of the ultrafast photoreaction are determined to a great extent by the geometrical context (i.e., available space and flexibility) within the binding pocket, while the general reaction steps following the photoexcitation are most likely conserved among the red/far-red phytochromes.
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Affiliation(s)
- Tobias Fischer
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue Straße 7, 60438 Frankfurt, Germany;
| | - Luuk J. G. W. van Wilderen
- Institute of Biophysics, Goethe University Frankfurt am Main, Max-von-Laue Straße 1, 60438 Frankfurt, Germany; (L.J.G.W.v.W.); (J.B.)
| | - Petra Gnau
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany; (P.G.); (L.-O.E.)
| | - Jens Bredenbeck
- Institute of Biophysics, Goethe University Frankfurt am Main, Max-von-Laue Straße 1, 60438 Frankfurt, Germany; (L.J.G.W.v.W.); (J.B.)
| | - Lars-Oliver Essen
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany; (P.G.); (L.-O.E.)
- Center for Synthetic Microbiology, Philipps-Universität Marburg, Hans-Meerwein-Straße 6, 35032 Marburg, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue Straße 7, 60438 Frankfurt, Germany;
- Correspondence: (J.W.); (C.S.)
| | - Chavdar Slavov
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue Straße 7, 60438 Frankfurt, Germany;
- Correspondence: (J.W.); (C.S.)
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18
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Liu X, Zhang T, Fang Q, Fang W, González L, Cui G. Hydrogen‐Bond Network Determines the Early Photoisomerization Processes of Cph1 and AnPixJ Phytochromes. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xiang‐Yang Liu
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education College of Chemistry Beijing Normal University Beijing 100875 China
- College of Chemistry and Material Science Sichuan Normal University Chengdu 610068 China
| | - Teng‐Shuo Zhang
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education College of Chemistry Beijing Normal University Beijing 100875 China
| | - Qiu Fang
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education College of Chemistry Beijing Normal University Beijing 100875 China
| | - Wei‐Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education College of Chemistry Beijing Normal University Beijing 100875 China
| | - Leticia González
- Institute of Theoretical Chemistry Faculty of Chemistry University of Vienna Währinger Straße 17 1090 Vienna Austria
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education College of Chemistry Beijing Normal University Beijing 100875 China
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19
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Liu XY, Zhang TS, Fang Q, Fang WH, González L, Cui G. Hydrogen-Bond Network Determines the Early Photoisomerization Processes of Cph1 and AnPixJ Phytochromes. Angew Chem Int Ed Engl 2021; 60:18688-18693. [PMID: 34097335 PMCID: PMC8456922 DOI: 10.1002/anie.202104853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/24/2021] [Indexed: 11/14/2022]
Abstract
Phytochrome proteins are light receptors that play a pivotal role in regulating the life cycles of plants and microorganisms. Intriguingly, while cyanobacterial phytochrome Cph1 and cyanobacteriochrome AnPixJ use the same phycocyanobilin (PCB) chromophore to absorb light, their excited‐state behavior is very different. We employ multiscale calculations to rationalize the different early photoisomerization mechanisms of PCB in Cph1 and AnPixJ. We found that their electronic S1, T1, and S0 potential minima exhibit distinct geometric and electronic structures due to different hydrogen bond networks with the protein environment. These specific interactions influence the S1 electronic structures along the photoisomerization paths, ultimately leading to internal conversion in Cph1 but intersystem crossing in AnPixJ. This explains why the excited‐state relaxation in AnPixJ is much slower (ca. 100 ns) than in Cph1 (ca. 30 ps). Further, we predict that efficient internal conversion in AnPixJ can be achieved upon protonating the carboxylic group that interacts with PCB.
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Affiliation(s)
- Xiang-Yang Liu
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China.,College of Chemistry and Material Science, Sichuan Normal University, Chengdu, 610068, China
| | - Teng-Shuo Zhang
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Qiu Fang
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090, Vienna, Austria
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
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20
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Rao AG, Wiebeler C, Sen S, Cerutti DS, Schapiro I. Histidine protonation controls structural heterogeneity in the cyanobacteriochrome AnPixJg2. Phys Chem Chem Phys 2021; 23:7359-7367. [PMID: 33876095 DOI: 10.1039/d0cp05314g] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Cyanobacteriochromes are compact and spectrally diverse photoreceptor proteins that bind a linear tetrapyrrole as a chromophore. They show photochromicity by having two stable states that can be interconverted by the photoisomerization of the chromophore. These photochemical properties make them an attractive target for biotechnological applications. However, their application is impeded by structural heterogeneity that reduces the yield of the photoconversion. The heterogeneity can originate either from the chromophore structure or the protein environment. Here, we study the origin of the heterogeneity in AnPixJg2, a representative member of the red/green cyanobacteriochrome family, that has a red absorbing parental state and a green absorbing photoproduct state. Using molecular dynamics simulations and umbrella sampling we have identified the protonation state of a conserved histidine residue as a trigger for structural heterogeneity. When the histidine is in a neutral form, the chromophore structure is homogenous, while in a positively charged form, the chromophore is heterogeneous with two different conformations. We have identified a correlation between the protonation of the histidine and the structural heterogeneity of the chromophore by detailed characterization of the interactions in the protein binding site. Our findings reconcile seemingly contradicting spectroscopic studies that attribute the heterogeneity to different sources. Furthermore, we predict that circular dichroism can be used as a diagnostic tool to distinguish different substates.
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Affiliation(s)
- Aditya G Rao
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Christian Wiebeler
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Saumik Sen
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - David S Cerutti
- Department of Chemistry and Chemical Biology, Rutgers University, USA
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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21
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Rathnachalam S, Menger MFS, Faraji S. Influence of the Environment on Shaping the Absorption of Monomeric Infrared Fluorescent Proteins. J Phys Chem B 2021; 125:2231-2240. [PMID: 33626280 PMCID: PMC7957859 DOI: 10.1021/acs.jpcb.0c10466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/25/2021] [Indexed: 12/05/2022]
Abstract
Infrared fluorescent proteins (iRFPs) are potential candidates for deep-tissue in vivo imaging. Here, we provide molecular-level insights into the role of the protein environment in the structural stability of the chromophore within the protein binding pocket through the flexible hydrogen-bonding network using molecular dynamics simulation. Furthermore, we present systematic excited-state analysis to characterize the nature of the first two excited states and the role of the environment in shaping the nature of the chromophore's excited states within the hybrid quantum mechanics/molecular mechanics framework. Our results reveal that the environment red-shifts the absorption of the chromophore by about 0.32 eV compared to the isolated counterpart, and besides the structural stability, the protein environment does not alter the nature of the excited state of the chromophore significantly. Our study contributes to the fundamental understanding of the excited-state processes of iRFPs in a complex environment and provides a design principle for developing iRFPs with desired spectral properties.
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Affiliation(s)
- Sivasudhan Rathnachalam
- Theoretical Chemistry
Group,
Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747AG, The Netherlands
| | - Maximilian F. S.
J. Menger
- Theoretical Chemistry
Group,
Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747AG, The Netherlands
| | - Shirin Faraji
- Theoretical Chemistry
Group,
Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747AG, The Netherlands
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22
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Fischer T, Xu Q, Zhao K, Gärtner W, Slavov C, Wachtveitl J. Effect of the PHY Domain on the Photoisomerization Step of the Forward P r →P fr Conversion of a Knotless Phytochrome. Chemistry 2020; 26:17261-17266. [PMID: 32812681 PMCID: PMC7839672 DOI: 10.1002/chem.202003138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/04/2020] [Indexed: 01/26/2023]
Abstract
Phytochrome photoreceptors operate via photoisomerization of a bound bilin chromophore. Their typical architecture consists of GAF, PAS and PHY domains. Knotless phytochromes lack the PAS domain, while retaining photoconversion abilities, with some being able to photoconvert with just the GAF domain. Therefore, we investigated the ultrafast photoisomerization of the Pr state of a knotless phytochrome to reveal the effect of the PHY domain and its "tongue" region on the transduction of the light signal. We show that the PHY domain does not affect the initial conformational dynamics of the chromophore. However, it significantly accelerates the consecutively induced reorganizational dynamics of the protein, necessary for the progression of the photoisomerization. Consequently, the PHY domain keeps the bilin and its binding pocket in a more reactive conformation, which decreases the extent of protein reorganization required for the chromophore isomerization. Thereby, less energy is lost along nonproductive reaction pathways, resulting in increased efficiency.
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Affiliation(s)
- Tobias Fischer
- Institute of Physical and Theoretical ChemistryGoethe University Frankfurt am MainMax-von-Laue Straße 760438FrankfurtGermany
| | - Qianzhao Xu
- Institute of Analytical ChemistryUniversity of LeipzigLinnéstr. 304103LeipzigGermany
| | - Kai‐Hong Zhao
- Key State Laboratory of Agriculture MicrobiologyHuazhong Agriculture University WuhanShizishan Street, Hongshan DistrictWuhan430070P. R. China
| | - Wolfgang Gärtner
- Institute of Analytical ChemistryUniversity of LeipzigLinnéstr. 304103LeipzigGermany
| | - Chavdar Slavov
- Institute of Physical and Theoretical ChemistryGoethe University Frankfurt am MainMax-von-Laue Straße 760438FrankfurtGermany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical ChemistryGoethe University Frankfurt am MainMax-von-Laue Straße 760438FrankfurtGermany
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23
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Wang D, Li X, Wang L, Yang X, Zhong D. Elucidating Ultrafast Multiphasic Dynamics in the Photoisomerization of Cyanobacteriochrome. J Phys Chem Lett 2020; 11:8819-8824. [PMID: 32940473 PMCID: PMC8172094 DOI: 10.1021/acs.jpclett.0c02467] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Understanding photoisomerization dynamics in cyanobacteriochromes is important to the development of optical agents in near-infrared biological imaging and optogenetics. Here, by integrating femtosecond spectroscopy and site-directed mutagenesis, we investigate the photoinduced Pr-state isomerization dynamics and mechanism of a unique red/green cyanobacteriochrome from Leptolyngbya sp. JSC-1. We observed multiphasic dynamics in the Pr state, a widespread phenomenon for photoreceptors in the phytochrome superfamily, and revealed their origins; the initial dynamics over a few to tens and hundreds of picoseconds arises from the local active-site relaxations followed by the slow double-bond isomerization in several hundreds of picoseconds. Such continuous active-site evolution results in a unique spectral tuning effect that favors the blue-side emission and suppresses the red-side emission. We also observed the faster dynamics in both relaxation and isomerization with critical mutants at the active site that render a looser active site. These results clearly distinguish the multiphasic dynamics between relaxation and isomerization and reveal a novel molecular mechanism for better biological applications.
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Affiliation(s)
| | | | | | - Xiaojing Yang
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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24
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Kim Y, Xu QZ, Zhao KH, Gärtner W, Matysik J, Song C. Lyophilization Reveals a Multitude of Structural Conformations in the Chromophore of a Cph2-like Phytochrome. J Phys Chem B 2020; 124:7115-7127. [PMID: 32693592 DOI: 10.1021/acs.jpcb.0c03431] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyanobacteria sense and respond to various colors of light employing a large number of bilin-based phytochrome-like photoreceptors. All2699 from Nostoc 7120 has three consecutive GAF domains with GAF1 and GAF3 binding a phycocyanobilin chromophore. GAF1, even when expressed independently, can be photoconverted between red-absorbing Pr and far-red-absorbing Pfr states, while the nonphotosensory GAF2 domain is structurally and functionally homologous to the PHY domains in canonical and Cph2-like phytochromes. Here, we characterize possible bilin chromophore conformers using solid-state NMR spectroscopy on the two lyophilized All2699 samples (GAF1-only and GAF1-PHY constructs). On the basis of complete 1H, 13C, and 15N assignments for the chromophore obtained on the two Pr lyophilizates, multiple static conformations of the chromophore in both cases are identified. Moreover, most atoms of the chromophore in the bidomain sample show only subtle changes in the mean chemical shifts relative to those in frozen solution (FS), indicating an optimized interaction of the GAF2 domain with the GAF1-bound chromophore. Our results confirm the conservation of key chromophore-protein interactions and the photoreversibility in both All2699 lyophilizates, offering the possibility to investigate conformational distributions of the heterogeneous chromophore and its functional consequences in phytochromes and other bilin-dependent photoreceptors intractable by the solid-state NMR technique as FSs.
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Affiliation(s)
- Yunmi Kim
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, 04103 Leipzig, Germany
| | - Qian-Zhao Xu
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, 04103 Leipzig, Germany.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kai-Hong Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wolfgang Gärtner
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, 04103 Leipzig, Germany
| | - Jörg Matysik
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, 04103 Leipzig, Germany
| | - Chen Song
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, 04103 Leipzig, Germany
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25
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Abstract
![]()
Due
to the recent advances in X-ray free electron laser techniques,
bilin-containing cyanobacteriochrome photoreceptors have become prime
targets for the ever-expanding field of time-resolved structural biology.
However, to facilitate these challenging studies, it is essential
that the time scales of any structural changes during the photocycles
of cyanobacteriochromes be established. Here, we have used visible
and infrared transient absorption spectroscopy to probe the photocycle
of a model cyanobacteriochrome system, TePixJ. The kinetics span multiple
orders of magnitude from picoseconds to seconds. Localized changes
in the bilin binding pocket occur in picoseconds to nanoseconds, followed
by more large-scale changes in protein structure, including formation
and breakage of a second thioether linkage, in microseconds to milliseconds.
The characterization of the entire photocycle will provide a vital
frame of reference for future time-resolved structural studies of
this model photoreceptor.
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Affiliation(s)
- Samantha J O Hardman
- Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Derren J Heyes
- Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Igor V Sazanovich
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Harwell Oxford, Didcot OX11 0QX, United Kingdom
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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