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Pedraza-González L, Barneschi L, Padula D, De Vico L, Olivucci M. Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol. Top Curr Chem (Cham) 2022; 380:21. [PMID: 35291019 PMCID: PMC8924150 DOI: 10.1007/s41061-022-00374-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/29/2022] [Indexed: 10/27/2022]
Abstract
In recent years, photoactive proteins such as rhodopsins have become a common target for cutting-edge research in the field of optogenetics. Alongside wet-lab research, computational methods are also developing rapidly to provide the necessary tools to analyze and rationalize experimental results and, most of all, drive the design of novel systems. The Automatic Rhodopsin Modeling (ARM) protocol is focused on providing exactly the necessary computational tools to study rhodopsins, those being either natural or resulting from mutations. The code has evolved along the years to finally provide results that are reproducible by any user, accurate and reliable so as to replicate experimental trends. Furthermore, the code is efficient in terms of necessary computing resources and time, and scalable in terms of both number of concurrent calculations as well as features. In this review, we will show how the code underlying ARM achieved each of these properties.
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Affiliation(s)
- Laura Pedraza-González
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy. .,Department of Chemistry and Industrial Chemistry, University of Pisa, Via Moruzzi 13, 56124, Pisa, Italy.
| | - Leonardo Barneschi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Daniele Padula
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Luca De Vico
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy.
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy. .,Department of Chemistry, Bowling Green State University, Bowling Green, OH, 43403, USA.
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Chen JL, Lin YC, Fu HY, Yang CS. The Blue-Green Sensory Rhodopsin SRM from Haloarcula marismortui Attenuates Both Phototactic Responses Mediated by Sensory Rhodopsin I and II in Halobacterium salinarum. Sci Rep 2019; 9:5672. [PMID: 30952934 PMCID: PMC6450946 DOI: 10.1038/s41598-019-42193-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/25/2019] [Indexed: 11/10/2022] Open
Abstract
Haloarchaea utilize various microbial rhodopsins to harvest light energy or to mediate phototaxis in search of optimal environmental niches. To date, only the red light-sensing sensory rhodopsin I (SRI) and the blue light-sensing sensory rhodopsin II (SRII) have been shown to mediate positive and negative phototaxis, respectively. In this work, we demonstrated that a blue-green light-sensing (504 nm) sensory rhodopsin from Haloarcula marismortui, SRM, attenuated both positive and negative phototaxis through its sensing region. The H. marismortui genome encodes three sensory rhodopsins: SRI, SRII and SRM. Using spectroscopic assays, we first demonstrated the interaction between SRM and its cognate transducer, HtrM. We then transformed an SRM-HtrM fusion protein into Halobacterium salinarum, which contains only SRI and SRII, and observed that SRM-HtrM fusion protein decreased both positive and negative phototaxis of H. salinarum. Together, our results suggested a novel phototaxis signalling system in H. marismortui comprised of three sensory rhodopsins in which the phototactic response of SRI and SRII were attenuated by SRM.
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Affiliation(s)
- Jheng-Liang Chen
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10616, Taiwan
| | - Yu-Cheng Lin
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10616, Taiwan
| | - Hsu-Yuan Fu
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10616, Taiwan
| | - Chii-Shen Yang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10616, Taiwan.
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Naito A, Makino Y, Shigeta A, Kawamura I. Photoreaction pathways and photointermediates of retinal-binding photoreceptor proteins as revealed by in situ photoirradiation solid-state NMR spectroscopy. Biophys Rev 2019; 11:167-181. [PMID: 30811009 DOI: 10.1007/s12551-019-00501-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 01/28/2019] [Indexed: 12/20/2022] Open
Abstract
Photoirradiation solid-state NMR spectroscopy is a powerful means to study photoreceptor retinal-binding proteins by the detection of short-lived photointermediates to elucidate the photoreaction cycle and photoactivated structural changes. An in situ photoirradiation solid-state NMR apparatus has been developed for the irradiation of samples with extremely high efficiency to enable observation of photointermediates which are stationary trapped states. Such observation enables elucidation of the photoreaction processes of photoreceptor membrane proteins. Therefore, in situ photoirradiation is particularly useful study the photocycle of retinal-binding proteins such as sensory rhodopsin I (SRI) and sensory rhodopsin II (SRII) because functional photointermediates have relatively longer half-lives than other photointermediates. As a result, several photointermediates have been trapped as stationary state and their detailed structures and photoreaction cycles have been revealed using photoirradiation solid-state NMR spectroscopy at low temperature. Photoreaction intermediates of bacteriorhodopsin, which functions to provide light-driven proton pump activity, were difficult to trap because the half-lives of the photointermediates were shorter than those of sensory rhodopsin. Therefore, these photointermediates are trapped in a freeze-trapped state at a very low temperature and the NMR signals were observed using a combination of photoirradiation and dynamic nuclear polarization (DNP) experiments.
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Affiliation(s)
- Akira Naito
- Graduate School of Engineering, Yokohama National University, Yokohama, 240-8501, Japan.
| | - Yoshiteru Makino
- Graduate School of Engineering, Yokohama National University, Yokohama, 240-8501, Japan
| | - Arisu Shigeta
- Graduate School of Engineering, Yokohama National University, Yokohama, 240-8501, Japan
| | - Izuru Kawamura
- Graduate School of Engineering, Yokohama National University, Yokohama, 240-8501, Japan
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Kaneko A, Inoue K, Kojima K, Kandori H, Sudo Y. Conversion of microbial rhodopsins: insights into functionally essential elements and rational protein engineering. Biophys Rev 2017; 9:861-876. [PMID: 29178082 DOI: 10.1007/s12551-017-0335-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 11/07/2017] [Indexed: 01/16/2023] Open
Abstract
Technological progress has enabled the successful application of functional conversion to a variety of biological molecules, such as nucleotides and proteins. Such studies have revealed the functionally essential elements of these engineered molecules, which are difficult to characterize at the level of an individual molecule. The functional conversion of biological molecules has also provided a strategy for their rational and atomistic design. The engineered molecules can be used in studies to improve our understanding of their biological functions and to develop protein-based tools. In this review, we introduce the functional conversion of membrane-embedded photoreceptive retinylidene proteins (also called rhodopsins) and discuss these proteins mainly on the basis of results obtained from our own studies. This information provides insights into the molecular mechanism of light-induced protein functions and their use in optogenetics, a technology which involves the use of light to control biological activities.
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Affiliation(s)
- Akimasa Kaneko
- Faculty of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama, 332-0012, Japan
| | - Keiichi Kojima
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
| | - Yuki Sudo
- Faculty of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan.
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Yomoda H, Makino Y, Tomonaga Y, Hidaka T, Kawamura I, Okitsu T, Wada A, Sudo Y, Naito A. Color-Discriminating Retinal Configurations of Sensory Rhodopsin I by Photo-Irradiation Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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6
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Yomoda H, Makino Y, Tomonaga Y, Hidaka T, Kawamura I, Okitsu T, Wada A, Sudo Y, Naito A. Color-discriminating retinal configurations of sensory rhodopsin I by photo-irradiation solid-state NMR spectroscopy. Angew Chem Int Ed Engl 2014; 53:6960-4. [PMID: 24846351 DOI: 10.1002/anie.201309258] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 02/17/2014] [Indexed: 12/20/2022]
Abstract
SRI (sensory rhodopsin I) can discriminate multiple colors for the attractant and repellent phototaxis. Studies aimed at revealing the color-dependent mechanism show that SRI is a challenging system not only in photobiology but also in photochemistry. During the photoreaction of SRI, an M-intermediate (attractant) transforms into a P-intermediate (repellent) by absorbing blue light. Consequently, SRI then cycles back to the G-state. The photoreactions were monitored with the (13)C NMR signals of [20-(13)C]retnal-SrSRI using in situ photo-irradiation solid-state NMR spectroscopy. The M-intermediate was trapped at -40 °C by illumination at 520 nm. It was transformed into the P-intermediate by subsequent illumination at 365 nm. These results reveal that the G-state could be directly transformed to the P-intermediate by illumination at 365 nm. Thus, the stationary trapped M- and P-intermediates are responsible for positive and negative phototaxis, respectively.
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Affiliation(s)
- Hiroki Yomoda
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501 (Japan)
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Inoue K, Sudo Y, Homma M, Kandori H. Spectrally Silent Intermediates during the Photochemical Reactions of Salinibacter Sensory Rhodopsin I. J Phys Chem B 2011; 115:4500-8. [DOI: 10.1021/jp2000706] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Yuki Sudo
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama, 332-0012, Japan
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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Sineshchekov OA, Sasaki J, Wang J, Spudich JL. Attractant and repellent signaling conformers of sensory rhodopsin-transducer complexes. Biochemistry 2010; 49:6696-704. [PMID: 20590098 PMCID: PMC2914491 DOI: 10.1021/bi100798w] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Attractant and repellent signaling conformers of the dual-signaling phototaxis receptor sensory rhodopsin I and its transducer subunit (SRI−HtrI) have recently been distinguished experimentally by the opposite connection of their retinylidene protonated Schiff bases to the outwardly located periplasmic side and inwardly located cytoplasmic side. Here we show that the pKa of the outwardly located Asp76 counterion in the outwardly connected conformer is lowered by ∼1.5 units from that of the inwardly connected conformer. The pKa difference enables quantitative determination of the relative amounts of the two conformers in wild-type cells and behavioral mutants prior to photoexcitation, comparison of their absorption spectra, and determination of their relative signaling efficiency. We have shown that the one-photon excitation of the SRI−HtrI attractant conformer causes a Schiff base connectivity switch from inwardly connected to outwardly connected states in the attractant signaling photoreaction. Conversely, a second near-UV photon drives the complex back to the inwardly connected conformer in the repellent signaling photoreaction. The results suggest a model of the color-discriminating dual-signaling mechanism in which phototaxis responses (his-kinase modulation) result from the photointerconversion of the two oppositely connected SRI−HtrI conformers by one-photon and two-photon activation. Furthermore, we find that the related repellent phototaxis SRII−HtrII receptor complex has an outwardly connected retinylidene Schiff base like the repellent signaling forms of the SRI−HtrI complex, indicating the general applicability of macro conformational changes, which can be detected by the connectivity switch, to phototaxis signaling by sensory rhodopsin−transducer complexes.
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Affiliation(s)
- Oleg A Sineshchekov
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, Texas 77030, USA
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Sudo Y, Okada A, Suzuki D, Inoue K, Irieda H, Sakai M, Fujii M, Furutani Y, Kandori H, Homma M. Characterization of a Signaling Complex Composed of Sensory Rhodopsin I and Its Cognate Transducer Protein from the Eubacterium Salinibacter ruber. Biochemistry 2009; 48:10136-45. [DOI: 10.1021/bi901338d] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yuki Sudo
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Akiko Okada
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Daisuke Suzuki
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Keiichi Inoue
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Hiroki Irieda
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Makoto Sakai
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Masaaki Fujii
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Yuji Furutani
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
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Sasaki J, Phillips BJ, Chen X, Van Eps N, Tsai AL, Hubbell WL, Spudich JL. Different dark conformations function in color-sensitive photosignaling by the sensory rhodopsin I-HtrI complex. Biophys J 2007; 92:4045-53. [PMID: 17351006 PMCID: PMC1868990 DOI: 10.1529/biophysj.106.101121] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The haloarchaeal phototaxis receptor sensory rhodopsin I (SRI) in complex with its transducer HtrI delivers an attractant signal from excitation with an orange photon and a repellent signal from a second near-UV photon excitation. Using a proteoliposome system with purified SRI in complex with its transducer HtrI, we identified by site-directed fluorescence labeling a site (Ser(155)) on SRI that is conformationally active in signal relay to HtrI. Using site-directed spin labeling of Ser(155)Cys with a nitroxide side chain, we detected a change in conformation following one-photon excitation such that the spin probe exhibits a splitting of the outer hyperfine extrema (2A'(zz)) significantly smaller than that of the electron paramagnetic resonance spectrum in the dark state. The dark conformations of five mutant complexes that do not discriminate between orange and near-UV excitation show shifts to lower or higher 2A'(zz) values correlated with the alterations in their motility behavior to one- and two-photon stimuli. These data are interpreted in terms of a model in which the dark complex is populated by two conformers in the wild type, one that inhibits the CheA kinase (A) and the other that activates it (R), shifted in the dark by mutations and shifted in the wild-type SRI-HtrI complex in opposite directions by one-photon and two-photon reactions.
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Affiliation(s)
- Jun Sasaki
- Center for Membrane Biology, Department of Biochemistry & Molecular Biology, University of Texas Medical School, Houston, Texas 77030, USA
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Coureux PD, Genick UK. Triggering and Monitoring Light‐Sensing Reactions in Protein Crystals. Methods Enzymol 2007; 422:305-37. [PMID: 17628146 DOI: 10.1016/s0076-6879(06)22015-9] [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: 05/16/2023]
Abstract
Many bacterial photoreceptors signal via histidine kinases. The light-activated nature of these proteins provides unique experimental opportunities to study their molecular mechanisms of signal transduction. One of these opportunities is the combined application of X-ray crystallography and optical spectroscopy in protein crystals. By combining these two methods it is possible to correlate protein structure to protein function in a way that is exceedingly difficult or impossible to achieve in most other experimental systems. This chapter is divided into two parts. The first part provides a brief overview of light-regulated histidine kinases and the most important techniques for studying the structure of photocycle intermediates by crystallography. The second part of the chapter is dedicated to practical advice on how to select, mount, activate, and monitor the structural and spectroscopic responses of photoreceptor crystals. This chapter is intended for readers who want to start using these experimental tools themselves or who wish to understand enough about the techniques to critically evaluate the work of others.
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Metzler DE, Metzler CM, Sauke DJ. Light and Life. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50026-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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