1
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Salvadori G, Mazzeo P, Accomasso D, Cupellini L, Mennucci B. Deciphering Photoreceptors Through Atomistic Modeling from Light Absorption to Conformational Response. J Mol Biol 2024; 436:168358. [PMID: 37944793 DOI: 10.1016/j.jmb.2023.168358] [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: 09/13/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
In this review, we discuss the successes and challenges of the atomistic modeling of photoreceptors. Throughout our presentation, we integrate explanations of the primary methodological approaches, ranging from quantum mechanical descriptions to classical enhanced sampling methods, all while providing illustrative examples of their practical application to specific systems. To enhance the effectiveness of our analysis, our primary focus has been directed towards the examination of applications across three distinct photoreceptors. These include an example of Blue Light-Using Flavin (BLUF) domains, a bacteriophytochrome, and the orange carotenoid protein (OCP) employed by cyanobacteria for photoprotection. Particular emphasis will be placed on the pivotal role played by the protein matrix in fine-tuning the initial photochemical event within the embedded chromophore. Furthermore, we will investigate how this localized perturbation initiates a cascade of events propagating from the binding pocket throughout the entire protein structure, thanks to the intricate network of interactions between the chromophore and the protein.
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Affiliation(s)
- Giacomo Salvadori
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Patrizia Mazzeo
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Davide Accomasso
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
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2
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Noji T, Tamura H, Ishikita H, Saito K. Difference in the Charge-Separation Energetics between Distinct Conformers in the PixD Photoreceptor. J Phys Chem B 2023; 127:10351-10359. [PMID: 38014591 DOI: 10.1021/acs.jpcb.3c06483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Blue light using flavin (BLUF) domain proteins are photoreceptors in various organisms. The PixD BLUF domain can adopt two conformations, W91out and W91in, with Trp91 either proximal or distal to flavin (FMN). Using a quantum mechanical/molecular mechanical/polarizable continuum model approach, the energetics of charge-separated and biradical states in the two conformations were investigated. In the W91out conformation, the charge-separated state (FMN•-) is more stable than the photoexcited state (FMN*), whereas it is less stable due to an electrostatic repulsive interaction with the Ser28 side chain in the W91in conformation. This leads to a lower activation energy for the charge separation in the W91out conformation, resulting in a faster charge separation compared to that in the W91in conformation. In the W91out conformation, the radical state (FMNH•) is more stable than FMN•- and forms from FMN•-, leading to reorientation of the Gln50 side chain adjacent to FMN and formation of a hydrogen bond between Gln50 and FMN. Subsequently, a signaling state forms through charge recombination. In contrast, in the W91in conformation, FMN•- cannot proceed further, returning to the dark-adapted state, as FMNH• is less stable. Thus, formation of the signaling state exclusively occurs in the W91out conformation.
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Affiliation(s)
- Tomoyasu Noji
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroyuki Tamura
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroshi Ishikita
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Keisuke Saito
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
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3
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Hashem S, Macaluso V, Nottoli M, Lipparini F, Cupellini L, Mennucci B. From crystallographic data to the solution structure of photoreceptors: the case of the AppA BLUF domain. Chem Sci 2021; 12:13331-13342. [PMID: 34777752 PMCID: PMC8528011 DOI: 10.1039/d1sc03000k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/01/2021] [Indexed: 12/28/2022] Open
Abstract
Photoreceptor proteins bind a chromophore, which, upon light absorption, modifies its geometry or its interactions with the protein, finally inducing the structural change needed to switch the protein from an inactive to an active or signaling state. In the Blue Light-Using Flavin (BLUF) family of photoreceptors, the chromophore is a flavin and the changes have been connected with a rearrangement of the hydrogen bond network around it on the basis of spectroscopic changes measured for the dark-to-light conversion. However, the exact conformational change triggered by the photoexcitation is still elusive mainly because a clear consensus on the identity not only of the light activated state but also of the dark one has not been achieved. Here, we present an integrated investigation that combines microsecond MD simulations starting from the two conflicting crystal structures available for the AppA BLUF domain with calculations of NMR, IR and UV-Vis spectra using a polarizable QM/MM approach. Thanks to such a combined analysis of the three different spectroscopic responses, a robust characterization of the structure of the dark state in solution is given together with the uncovering of important flaws of the most popular molecular mechanisms present in the literature for the dark-to-light activation.
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Affiliation(s)
- Shaima Hashem
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Veronica Macaluso
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
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4
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Macaluso V, Hashem S, Nottoli M, Lipparini F, Cupellini L, Mennucci B. Ultrafast Transient Infrared Spectroscopy of Photoreceptors with Polarizable QM/MM Dynamics. J Phys Chem B 2021; 125:10282-10292. [PMID: 34476939 PMCID: PMC8450903 DOI: 10.1021/acs.jpcb.1c05753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/04/2021] [Indexed: 01/02/2023]
Abstract
Ultrafast transient infrared (TRIR) spectroscopy is widely used to measure the excitation-induced structural changes of protein-bound chromophores. Here, we design a novel and general strategy to compute TRIR spectra of photoreceptors by combining μs-long MM molecular dynamics with ps-long QM/AMOEBA Born-Oppenheimer molecular dynamics (BOMD) trajectories for both ground and excited electronic states. As a proof of concept, the strategy is here applied to AppA, a blue-light-utilizing flavin (BLUF) protein, found in bacteria. We first analyzed the short-time evolution of the embedded flavin upon excitation revealing that its dynamic Stokes shift is ultrafast and mainly driven by the internal reorganization of the chromophore. A different normal-mode representation was needed to describe ground- and excited-state IR spectra. In this way, we could assign all of the bands observed in the measured transient spectrum. In particular, we could characterize the flavin isoalloxazine-ring region of the spectrum, for which a full and clear description was missing.
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Affiliation(s)
| | | | - Michele Nottoli
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
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5
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Hoffmann JF, Roos AH, Schmitt FJ, Hinderberger D, Binder WH. Fluorescent and Water Dispersible Single-Chain Nanoparticles: Core-Shell Structured Compartmentation. Angew Chem Int Ed Engl 2021; 60:7820-7827. [PMID: 33373475 PMCID: PMC8048794 DOI: 10.1002/anie.202015179] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/13/2020] [Indexed: 12/20/2022]
Abstract
Single-chain nanoparticles (SCNPs) are highly versatile structures resembling proteins, able to function as catalysts or biomedical delivery systems. Based on their synthesis by single-chain collapse into nanoparticular systems, their internal structure is complex, resulting in nanosized domains preformed during the crosslinking process. In this study we present proof of such nanocompartments within SCNPs via a combination of electron paramagnetic resonance (EPR) and fluorescence spectroscopy. A novel strategy to encapsulate labels within these water dispersible SCNPs with hydrodynamic radii of ≈5 nm is presented, based on amphiphilic polymers with additional covalently bound labels, attached via the copper catalyzed azide/alkyne "click" reaction (CuAAC). A detailed profile of the interior of the SCNPs and the labels' microenvironment was obtained via electron paramagnetic resonance (EPR) experiments, followed by an assessment of their photophysical properties.
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Affiliation(s)
- Justus F Hoffmann
- Macromolecular Chemistry, Institute of Chemistry, Faculty of Natural Science II (Chemistry, Physics and Mathematics), Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 4, 06120, Halle, Germany
| | - Andreas H Roos
- Physical Chemistry, Institute of Chemistry, Faculty of Natural Science II (Chemistry, Physics and Mathematics), Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 4, 06120, Halle, Germany
| | - Franz-Josef Schmitt
- Institute of Physics, Faculty of Natural Science II (Chemistry, Physics and Mathematics), Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 3, 06120, Halle, Germany
| | - Dariush Hinderberger
- Physical Chemistry, Institute of Chemistry, Faculty of Natural Science II (Chemistry, Physics and Mathematics), Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 4, 06120, Halle, Germany
| | - Wolfgang H Binder
- Macromolecular Chemistry, Institute of Chemistry, Faculty of Natural Science II (Chemistry, Physics and Mathematics), Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 4, 06120, Halle, Germany
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6
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Hoffmann JF, Roos AH, Schmitt F, Hinderberger D, Binder WH. Fluorescent and Water Dispersible Single‐Chain Nanoparticles: Core–Shell Structured Compartmentation. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Justus F. Hoffmann
- Macromolecular Chemistry Institute of Chemistry, Faculty of Natural Science II (Chemistry, Physics and Mathematics) Martin Luther University Halle-Wittenberg von-Danckelmann-Platz 4 06120 Halle Germany
| | - Andreas H. Roos
- Physical Chemistry Institute of Chemistry Faculty of Natural Science II (Chemistry, Physics and Mathematics) Martin Luther University Halle-Wittenberg von-Danckelmann-Platz 4 06120 Halle Germany
| | - Franz‐Josef Schmitt
- Institute of Physics, Faculty of Natural Science II (Chemistry, Physics and Mathematics) Martin Luther University Halle-Wittenberg von-Danckelmann-Platz 3 06120 Halle Germany
| | - Dariush Hinderberger
- Physical Chemistry Institute of Chemistry Faculty of Natural Science II (Chemistry, Physics and Mathematics) Martin Luther University Halle-Wittenberg von-Danckelmann-Platz 4 06120 Halle Germany
| | - Wolfgang H. Binder
- Macromolecular Chemistry Institute of Chemistry, Faculty of Natural Science II (Chemistry, Physics and Mathematics) Martin Luther University Halle-Wittenberg von-Danckelmann-Platz 4 06120 Halle Germany
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7
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Karadi K, Kapetanaki SM, Raics K, Pecsi I, Kapronczai R, Fekete Z, Iuliano JN, Collado JT, Gil AA, Orban J, Nyitrai M, Greetham GM, Vos MH, Tonge PJ, Meech SR, Lukacs A. Functional dynamics of a single tryptophan residue in a BLUF protein revealed by fluorescence spectroscopy. Sci Rep 2020; 10:2061. [PMID: 32029866 PMCID: PMC7005313 DOI: 10.1038/s41598-020-59073-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/23/2020] [Indexed: 11/17/2022] Open
Abstract
Blue Light Using Flavin (BLUF) domains are increasingly being adopted for use in optogenetic constructs. Despite this, much remains to be resolved on the mechanism of their activation. The advent of unnatural amino acid mutagenesis opens up a new toolbox for the study of protein structural dynamics. The tryptophan analogue, 7-aza-Trp (7AW) was incorporated in the BLUF domain of the Activation of Photopigment and pucA (AppA) photoreceptor in order to investigate the functional dynamics of the crucial W104 residue during photoactivation of the protein. The 7-aza modification to Trp makes selective excitation possible using 310 nm excitation and 380 nm emission, separating the signals of interest from other Trp and Tyr residues. We used Förster energy transfer (FRET) between 7AW and the flavin to estimate the distance between Trp and flavin in both the light- and dark-adapted states in solution. Nanosecond fluorescence anisotropy decay and picosecond fluorescence lifetime measurements for the flavin revealed a rather dynamic picture for the tryptophan residue. In the dark-adapted state, the major population of W104 is pointing away from the flavin and can move freely, in contrast to previous results reported in the literature. Upon blue-light excitation, the dominant tryptophan population is reorganized, moves closer to the flavin occupying a rigidly bound state participating in the hydrogen-bond network around the flavin molecule.
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Affiliation(s)
- Kristof Karadi
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary.,Szentagothai Research Center, University of Pécs, 7624, Pécs, Hungary
| | - Sofia M Kapetanaki
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary.,Szentagothai Research Center, University of Pécs, 7624, Pécs, Hungary
| | - Katalin Raics
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - Ildiko Pecsi
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - Robert Kapronczai
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - Zsuzsanna Fekete
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - James N Iuliano
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794-3400, USA
| | | | - Agnieszka A Gil
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794-3400, USA
| | - Jozsef Orban
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - Miklos Nyitrai
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary.,Szentagothai Research Center, University of Pécs, 7624, Pécs, Hungary
| | - Greg M Greetham
- Central Laser Facility, Harwell Science and Innovation Campus, Didcot, Oxfordshire, UK
| | - Marten H Vos
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, Cedex, France
| | - Peter J Tonge
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794-3400, USA
| | - Stephen R Meech
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Andras Lukacs
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary. .,Szentagothai Research Center, University of Pécs, 7624, Pécs, Hungary.
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8
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Xu Y, Bao P, Song K, Shi Q. Theoretical study of proton coupled electron transfer reaction in the light state of the AppA BLUF photoreceptor. J Comput Chem 2018; 40:1005-1014. [PMID: 30341953 DOI: 10.1002/jcc.25561] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 07/01/2018] [Accepted: 07/24/2018] [Indexed: 11/10/2022]
Abstract
The BLUF (blue light sensor using flavin adenine dinucleotide) domain is widely studied as a prototype for proton coupled electron transfer (PCET) reactions in biological systems. In this work, the photo-induced concerted PCET reaction from the light state of the AppA BLUF domain is investigated. To model the simultaneous transfer of two protons in the reaction, two-dimensional potential energy surfaces for the double proton transfer are first calculated for the locally excited and charge transfer states, which are then used to obtain the vibrational wave function overlaps and the vibrational energy levels. Contributions to the PCET rate constant from each pair of vibronic states are then analyzed using the theory based on the Fermi's golden rule. We show that, the recently proposed light state structure of the BLUF domain with a tautomerized Gln63 residue is consistent with the concerted transfer of one electron and two protons. It is also found that, thermal fluctuations of the protein structure, especially the proton donor-acceptor distances, play an important role in determining the PCET reaction rate. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Yang Xu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Peng Bao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Kai Song
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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9
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Iwata T, Nagai T, Ito S, Osoegawa S, Iseki M, Watanabe M, Unno M, Kitagawa S, Kandori H. Hydrogen Bonding Environments in the Photocycle Process around the Flavin Chromophore of the AppA-BLUF domain. J Am Chem Soc 2018; 140:11982-11991. [DOI: 10.1021/jacs.8b05123] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tatsuya Iwata
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- Department of Pharmaceutical Sciences, Toho University, Funabashi, Chiba 274-8510, Japan
| | - Takashi Nagai
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Shota Ito
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Shinsuke Osoegawa
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Mineo Iseki
- Department of Pharmaceutical Sciences, Toho University, Funabashi, Chiba 274-8510, Japan
| | - Masakatsu Watanabe
- The Graduate School for the Creation of New Photonics Industries, Nishi-ku, Hamamatsu 431-1202, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Shinya Kitagawa
- Department of Life Science and Applied Chemistry, 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
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10
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Collette F, Renger T, Müh F, Schmidt am Busch M. Red/Green Color Tuning of Visual Rhodopsins: Electrostatic Theory Provides a Quantitative Explanation. J Phys Chem B 2018; 122:4828-4837. [DOI: 10.1021/acs.jpcb.8b02702] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Florimond Collette
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
| | - Frank Müh
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
| | - Marcel Schmidt am Busch
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
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11
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Molecular mechanism of photoactivation of a light-regulated adenylate cyclase. Proc Natl Acad Sci U S A 2017; 114:8562-8567. [PMID: 28739908 DOI: 10.1073/pnas.1704391114] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The photoactivated adenylate cyclase (PAC) from the photosynthetic cyanobacterium Oscillatoria acuminata (OaPAC) detects light through a flavin chromophore within the N-terminal BLUF domain. BLUF domains have been found in a number of different light-activated proteins, but with different relative orientations. The two BLUF domains of OaPAC are found in close contact with each other, forming a coiled coil at their interface. Crystallization does not impede the activity switching of the enzyme, but flash cooling the crystals to cryogenic temperatures prevents the signature spectral changes that occur on photoactivation/deactivation. High-resolution crystallographic analysis of OaPAC in the fully activated state has been achieved by cryocooling the crystals immediately after light exposure. Comparison of the isomorphous light- and dark-state structures shows that the active site undergoes minimal changes, yet enzyme activity may increase up to 50-fold, depending on conditions. The OaPAC models will assist the development of simple, direct means to raise the cyclic AMP levels of living cells by light, and other tools for optogenetics.
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12
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Song K, Shi Q. Theoretical study of photoinduced proton coupled electron transfer reaction using the non-perturbative hierarchical equations of motion method. J Chem Phys 2017. [DOI: 10.1063/1.4982928] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Kai Song
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
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13
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Park SY, Tame JRH. Seeing the light with BLUF proteins. Biophys Rev 2017; 9:169-176. [PMID: 28510088 DOI: 10.1007/s12551-017-0258-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/05/2017] [Indexed: 10/19/2022] Open
Abstract
First described about 15 years ago, BLUF (Blue Light Using Flavin) domains are light-triggered switches that control enzyme activity or gene expression in response to blue light, remaining activated for seconds or even minutes after stimulation. The conserved, ferredoxin-like fold holds a flavin chromophore that captures the light and somehow triggers downstream events. BLUF proteins are found in both prokaryotes and eukaryotes and have a variety of architectures and oligomeric forms, but the BLUF domain itself seems to have a well-preserved structure and mechanism that have been the focus of intense study for a number of years. Crystallographic and NMR structures of BLUF domains have been solved, but the conflicting models have led to considerable debate about the atomic details of photo-activation. Advanced spectroscopic and computational methods have been used to analyse the early events after photon absorption, but these too have led to widely differing conclusions. New structural models are improving our understanding of the details of the mechanism and may lead to novel tailor-made tools for optogenetics.
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Affiliation(s)
- Sam-Yong Park
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama, 230-0045, Japan
| | - Jeremy R H Tame
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama, 230-0045, Japan.
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14
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Udvarhelyi A, Olivucci M, Domratcheva T. Role of the Molecular Environment in Flavoprotein Color and Redox Tuning: QM Cluster versus QM/MM Modeling. J Chem Theory Comput 2016; 11:3878-94. [PMID: 26574469 DOI: 10.1021/acs.jctc.5b00197] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigate the origin of the excitation energy shifts induced by the apoprotein in the active site of the bacterial photoreceptor BLUF (Blue Light sensor Using Flavin adenine dinucleotide). In order to compute the vertical excitation energies of three low-lying electronic states, including two π-π* states of flavin (S1 and S2) and a π-π* tyrosine-flavin electron-transfer state (ET), with respect to the energy of the closed-shell ground state (S0), we prepared alternative quantum mechanical (QM) cluster and quantum mechanics/molecular mechanics (QM/MM) models. We found that the excitation energies computed with both types of models correlate with the magnitude of the charge transfer character of the excitation. Accordingly, we conclude that the small charge transfer character of the light absorbing S0-S1 transition and the substantial charge transfer character of the nonabsorbing but redox active S0-ET transition explain the small color changes but substantial redox tuning in BLUF and also in other flavoproteins. Further analysis showed that redox tuning is governed by the electrostatic interaction in the QM/MM model and transfer of charge between the active site and its environment in the QM cluster. Moreover, the wave function polarization of the QM subsystem by the MM subsystem influences the magnitude of the charge transfer, resulting in the QM/MM and QM excitation energies that are not entirely consistent.
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Affiliation(s)
- Anikó Udvarhelyi
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, via A. Moro 2, Universitá di Siena , I-53100 Siena, Italy.,Chemistry Department, Overman Hall, Bowling Green State University , Bowling Green, Ohio 67200, United States.,Institut de Physique et de Chimie des Materiaux de Strasbourg, Université de Strasbourg , Batiment 69, 23 Rue du Loess, 67200 Strasbourg, France
| | - Tatiana Domratcheva
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg, Germany
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15
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Gil A, Haigney A, Laptenok SP, Brust R, Lukacs A, Iuliano J, Jeng J, Melief E, Zhao RK, Yoon E, Clark I, Towrie M, Greetham GM, Ng A, Truglio J, French J, Meech SR, Tonge PJ. Mechanism of the AppABLUF Photocycle Probed by Site-Specific Incorporation of Fluorotyrosine Residues: Effect of the Y21 pKa on the Forward and Reverse Ground-State Reactions. J Am Chem Soc 2016; 138:926-935. [PMID: 26708408 PMCID: PMC4830125 DOI: 10.1021/jacs.5b11115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The transcriptional antirepressor AppA is a blue light using flavin (BLUF) photoreceptor that releases the transcriptional repressor PpsR upon photoexcitation. Light activation of AppA involves changes in a hydrogen-bonding network that surrounds the flavin chromophore on the nanosecond time scale, while the dark state of AppA is then recovered in a light-independent reaction with a dramatically longer half-life of 15 min. Residue Y21, a component of the hydrogen-bonding network, is known to be essential for photoactivity. Here, we directly explore the effect of the Y21 pKa on dark state recovery by replacing Y21 with fluorotyrosine analogues that increase the acidity of Y21 by 3.5 pH units. Ultrafast transient infrared measurements confirm that the structure of AppA is unperturbed by fluorotyrosine substitution, and that there is a small (3-fold) change in the photokinetics of the forward reaction over the fluorotyrosine series. However, reduction of 3.5 pH units in the pKa of Y21 increases the rate of dark state recovery by 4000-fold with a Brønsted coefficient of ∼ 1, indicating that the Y21 proton is completely transferred in the transition state leading from light to dark adapted AppA. A large solvent isotope effect of ∼ 6-8 is also observed on the rate of dark state recovery. These data establish that the acidity of Y21 is a crucial factor for stabilizing the light activated form of the protein, and have been used to propose a model for dark state recovery that will ultimately prove useful for tuning the properties of BLUF photosensors for optogenetic applications.
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Affiliation(s)
- Agnieszka Gil
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA
| | - Allison Haigney
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA
| | - Sergey P. Laptenok
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Richard Brust
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA
| | - Andras Lukacs
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - James Iuliano
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA
| | - Jessica Jeng
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA
| | - Eduard Melief
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA
| | - Rui-Kun Zhao
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - EunBin Yoon
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA
| | - Ian Clark
- Central Laser Facility, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, UK
| | - Michael Towrie
- Central Laser Facility, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, UK
| | - Gregory M. Greetham
- Central Laser Facility, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, UK
| | - Annabelle Ng
- William A. Shine Great Neck South High School, 341 Lakeville Rd, Great Neck, NY 11020, USA
| | - James Truglio
- William A. Shine Great Neck South High School, 341 Lakeville Rd, Great Neck, NY 11020, USA
| | - Jarrod French
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA
- Biochemistry & Cell Biology, Stony Brook University, Stony Brook, New York 11794-3400, USA
| | - Stephen R. Meech
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Peter J. Tonge
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA
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16
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Farrán MÁ, Listorti A, Roiati V, Accorsi G, Gigli G, Clarkson GJ, Claramunt RM. Photoinduced processes in macrocyclic isoalloxazine–anthracene systems. J Photochem Photobiol A Chem 2016. [DOI: 10.1016/j.jphotochem.2015.08.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Mathes T, Götze JP. A proposal for a dipole-generated BLUF domain mechanism. Front Mol Biosci 2015; 2:62. [PMID: 26579529 PMCID: PMC4630285 DOI: 10.3389/fmolb.2015.00062] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 10/12/2015] [Indexed: 11/25/2022] Open
Abstract
The resting and signaling structures of the blue-light sensing using flavin (BLUF) photoreceptor domains are still controversially debated due to differences in the molecular models obtained by crystal and NMR structures. Photocycles for the given preferred structural framework have been established, but a unifying picture combining experiment and theory remains elusive. We summarize present work on the AppA BLUF domain from both experiment and theory. We focus on IR and UV/vis spectra, and to what extent theory was able to reproduce experimental data and predict the structural changes upon formation of the signaling state. We find that the experimental observables can be theoretically reproduced employing any structural model, as long as the orientation of the signaling essential Gln63 and its tautomer state are a choice of the modeler. We also observe that few approaches are comparative, e.g., by considering all structures in the same context. Based on recent experimental findings and a few basic calculations, we suggest the possibility for a BLUF activation mechanism that only relies on electron transfer and its effect on the local electrostatics, not requiring an associated proton transfer. In this regard, we investigate the impact of dispersion correction on the interaction energies arising from weakly bound amino acids.
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Affiliation(s)
- Tilo Mathes
- Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit Amsterdam, Netherlands ; Institut für Biologie/Experimentelle Biophysik, Humboldt Universität zu Berlin Berlin, Germany
| | - Jan P Götze
- School of Chemistry, University of St Andrews St Andrews, UK
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18
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The quest for energy traps in the CP43 antenna of photosystem II. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 152:286-300. [DOI: 10.1016/j.jphotobiol.2015.05.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Revised: 05/13/2015] [Accepted: 05/28/2015] [Indexed: 01/08/2023]
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19
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Khrenova MG, Nemukhin AV, Domratcheva T. Theoretical Characterization of the Flavin-Based Fluorescent Protein iLOV and its Q489K Mutant. J Phys Chem B 2015; 119:5176-83. [DOI: 10.1021/acs.jpcb.5b01299] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria G. Khrenova
- Chemistry
Department, M.V. Lomonosov Moscow State University, Leninskie
Gory 1/3, Moscow, 119991, Russian Federation
| | - Alexander V. Nemukhin
- Chemistry
Department, M.V. Lomonosov Moscow State University, Leninskie
Gory 1/3, Moscow, 119991, Russian Federation
- N.M.
Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow, 119334, Russian Federation
| | - Tatiana Domratcheva
- Department
of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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Laptenok SP, Lukacs A, Brust R, Haigney A, Gil A, Towrie M, Greetham GM, Tonge PJ, Meech SR. Electron transfer quenching in light adapted and mutant forms of the AppA BLUF domain. Faraday Discuss 2015; 177:293-311. [DOI: 10.1039/c4fd00189c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Blue Light Using Flavin (BLUF) domain proteins are an important family of photoreceptors controlling a range of responses in a wide variety of organisms. The details of the primary photochemical mechanism, by which light absorption in the isoalloxazine ring of the flavin is converted into a structure change to form the signalling state of the protein, is unresolved. In this work we apply ultrafast time resolved infra-red (TRIR) spectroscopy to investigate the primary photophysics of the BLUF domain of the protein AppA (AppABLUF) a light activated antirepressor. Here a number of mutations at Y21 and W104 in AppABLUF are investigated. The Y21 mutants are known to be photoinactive, while W104 mutants show the characteristic spectral red-shift associated with BLUF domain activity. Using TRIR we observed separately the decay of the excited state and the recovery of the ground state. In both cases the kinetics are found to be non-single exponential for all the proteins studied, suggesting a range of ground state structures. In the Y21 mutants an intermediate state was also observed, assigned to formation of the radical of the isoalloxazine (flavin) ring. The electron donor is the W104 residue. In contrast, no radical intermediates were detected in the studies of the photoactive dark adapted proteins, dAppABLUF and the dW104 mutants, suggesting a structure change in the Y21 mutants which favours W104 to isoalloxazine electron transfer. In contrast, in the light adapted form of the proteins (lAppABLUF, lW104) a radical intermediate was detected and the kinetics were greatly accelerated. In this case the electron donor was Y21 and major structural changes are associated with the enhanced quenching. In AppABLUF and the seven mutants studied radical intermediates are readily observed by TRIR spectroscopy, but there is no correlation with photoactivity. This suggests that if a charge separated state has a role in the BLUF photocycle it is only as a very short lived intermediate.
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Affiliation(s)
| | - Andras Lukacs
- School of Chemistry
- University of East Anglia
- Norwich NR4 7TJ
- UK
- Department of Biophysics
| | - Richard Brust
- Department of Chemistry
- Stony Brook University
- Stony Brook
- USA
| | | | - Agnieszka Gil
- Department of Chemistry
- Stony Brook University
- Stony Brook
- USA
| | - Michael Towrie
- Central Laser Facility
- Research Complex at Harwell
- Harwell Science and Innovation Campus
- Didcot
- UK
| | - Gregory M. Greetham
- Central Laser Facility
- Research Complex at Harwell
- Harwell Science and Innovation Campus
- Didcot
- UK
| | - Peter J. Tonge
- Department of Chemistry
- Stony Brook University
- Stony Brook
- USA
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