1
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Li Z, Mizuno M, Ejiri T, Hayashi S, Kandori H, Mizutani Y. Unique Vibrational Characteristics and Structures of the Photoexcited Retinal Chromophore in Ion-Pumping Rhodopsins. J Phys Chem B 2023; 127:9873-9886. [PMID: 37940604 DOI: 10.1021/acs.jpcb.3c02146] [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: 11/10/2023]
Abstract
Photoisomerization of an all-trans-retinal chromophore triggers ion transport in microbial ion-pumping rhodopsins. Understanding chromophore structures in the electronically excited (S1) state provides insights into the structural evolution on the potential energy surface of the photoexcited state. In this study, we examined the structure of the S1-state chromophore in Natronomonas pharaonis halorhodopsin (NpHR), a chloride ion-pumping rhodopsin, using time-resolved resonance Raman spectroscopy. The spectral patterns of the S1-state chromophore were completely different from those of the ground-state chromophore, resulting from unique vibrational characteristics and the structure of the S1 state. Mode assignments were based on a combination of deuteration shifts of the Raman bands and hybrid quantum mechanics-molecular mechanics calculations. The present observations suggest a weakened bond alternation in the π conjugation system. A strong hydrogen-out-of-plane bending band was observed in the Raman spectra of the S1-state chromophore in NpHR, indicating a twisted polyene structure. Similar frequency shifts for the C═N/C═C and C-C stretching modes of the S1-state chromophore in NpHR were observed in the Raman spectra of sodium ion-pumping and proton-pumping rhodopsins, suggesting that these unique features are common to the S1 states of ion-pumping rhodopsins.
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Affiliation(s)
- Zixuan Li
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Osaka, Toyonaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Osaka, Toyonaka 560-0043, Japan
| | - Tomo Ejiri
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Osaka, Toyonaka 560-0043, Japan
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2
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Tsujimura M, Saito K, Ishikita H. Stretching vibrational frequencies and pK a differences in H-bond networks of protein environments. Biophys J 2023; 122:4336-4347. [PMID: 37838831 PMCID: PMC10722396 DOI: 10.1016/j.bpj.2023.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 08/22/2023] [Accepted: 10/12/2023] [Indexed: 10/16/2023] Open
Abstract
The experimentally measured stretching vibrational frequencies of O-D [νO-D(donor)] and C=O [νC=O(donor)] H-bond donor groups can provide valuable information about the H-bonds in proteins. Here, using a quantum mechanical/molecular mechanical approach, the relationship between these vibrational frequencies and the difference in pKa values between H-bond donor and acceptor groups [ΔpKa(donor … acceptor)] in bacteriorhodopsin and photoactive yellow protein environments was investigated. The results show that νO-D(donor) is correlated with ΔpKa(donor … acceptor), regardless of the specific protein environment. νC=O(donor) is also correlated with ΔpKa(donor … acceptor), although the correlation is weak because the C=O bond does not have a proton. Importantly, the shifts in νO-D(donor) and νC=O(donor) are not caused by changes in pKa(donor) alone, but rather by changes in ΔpKa(donor … acceptor). Specifically, a decrease in ΔpKa(donor … acceptor) can lead to proton release from the H-bond donor group toward the acceptor group, resulting in shifts in the vibrational frequencies of the protein environment. These findings suggest that changes in the stretching vibrational frequencies, in particular νO-D(donor), can be used to monitor proton transfer in protein environments.
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Affiliation(s)
- Masaki Tsujimura
- Department of Advanced Interdisciplinary Studies, The University of Tokyo, Meguro-ku, Tokyo, Japan.
| | - Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo, Japan.
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3
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Tomida S, Wada A, Furutani Y. Protonation of Asp116 and distortion of the all-trans retinal chromophore in Krokinobacter eikastus rhodopsin 2 causes a redshift in absorption maximum upon dehydration. Photochem Photobiol Sci 2023; 22:2499-2517. [PMID: 37498510 DOI: 10.1007/s43630-023-00464-8] [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: 04/20/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023]
Abstract
Water is usually indispensable for protein function. For ion-pumping rhodopsins, water molecules inside the proteins play an important role in ion transportation. In addition to amino acid residues, water molecules regulate the colors of retinal proteins. It was reported that a sodium-pumping rhodopsin, Krokinobacter eikastus rhodopsin 2 (KR2), showed a color change from red to purple upon dehydration under crystalline conditions. Here, we applied comprehensive visible and IR absorption spectroscopy and resonance Raman spectroscopy to KR2 in liposomes under hydration-controlled conditions. A large increase in the hydrogen-out-of-plane (HOOP) vibration at 947 (H-C11=C12-H Au mode) and moderate increases at 893 (C7-H and C10-H) and 808 (C14-H) cm-1 were observed under dehydrated conditions, which were assigned by using systematically deuterated retinal. Moreover, the Asn variant at Asp116, which functions as a counter ion for the protonated retinal Schiff base (PRSB), caused a large redshift in the absorption maximum and constitutive increase in the HOOP modes under hydrated and dehydrated conditions. The protonation of a counter ion at Asp116 clearly causes a redshift in the absorption maximum as the all-trans retinal chromophore twists upon dehydration. Namely, the results strongly suggested that water molecules are important for maintaining the hydrogen-bonding network at the PRSB and deprotonation state of Asp116 in KR2.
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Affiliation(s)
- Sahoko Tomida
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
| | - Akimori Wada
- Laboratory of Organic Chemistry for Life Science, Kobe Pharmaceutical University, Higashinada-ku, Kobe, 658-8558, Japan
| | - Yuji Furutani
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan.
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan.
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4
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Suzuki R, Nagashima T, Kojima K, Hironishi R, Hirohata M, Ueta T, Murata T, Yamazaki T, Sudo Y, Takahashi H. Nuclear Magnetic Resonance Detection of Hydrogen Bond Network in a Proton Pump Rhodopsin RxR and Its Alteration during the Cyclic Photoreaction. J Am Chem Soc 2023. [PMID: 37410967 DOI: 10.1021/jacs.3c02833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Hydrogen bond formation and deformation are crucial for the structural construction and functional expression of biomolecules. However, direct observation of exchangeable hydrogens, especially for oxygen-bound hydrogens, relevant to hydrogen bonds is challenging for current structural analysis approaches. Using solution-state NMR spectroscopy, this study detected the functionally important exchangeable hydrogens (i.e., Y49-ηOH and Y178-ηOH) involved in the pentagonal hydrogen bond network in the active site of R. xylanophilus rhodopsin (RxR), which functions as a light-driven proton pump. Moreover, utilization of the original light-irradiation NMR approach allowed us to detect and characterize the late photointermediate state (i.e., O-state) of RxR and revealed that hydrogen bonds relevant to Y49 and Y178 are still maintained during the photointermediate state. In contrast, the hydrogen bond between W75-εNH and D205-γCOO- is strengthened and stabilizes the O-state.
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Affiliation(s)
- Rika Suzuki
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Toshio Nagashima
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan
| | - Keiichi Kojima
- Faculty of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Reika Hironishi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Masafumi Hirohata
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Tetsuya Ueta
- Faculty of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Takeshi Murata
- Graduate School of Science, Chiba University, Inage, Chiba 263-8522, Japan
| | - Toshio Yamazaki
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan
| | - Yuki Sudo
- Faculty of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Hideo Takahashi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
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5
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Hanai S, Nagata T, Katayama K, Inukai S, Koyanagi M, Inoue K, Terakita A, Kandori H. Difference FTIR Spectroscopy of Jumping Spider Rhodopsin-1 at 77 K. Biochemistry 2023; 62:1347-1359. [PMID: 37001008 DOI: 10.1021/acs.biochem.3c00022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Animal visual rhodopsins can be classified into monostable and bistable rhodopsins, which are typically found in vertebrates and invertebrates, respectively. The former example is bovine rhodopsin (BovRh), whose structures and functions have been extensively studied. On the other hand, those of bistable rhodopsins are less known, despite their importance in optogenetics. Here, low-temperature Fourier-transform infrared (FTIR) spectroscopy was applied to jumping spider rhodopsin-1 (SpiRh1) at 77 K, and the obtained light-induced spectral changes were compared with those of squid rhodopsin (SquRh) and BovRh. Although chromophore distortion of the resting state monitored by HOOP vibrations is not distinctive between invertebrate and vertebrate rhodopsins, distortion of the all-trans chromophore after photoisomerization is unique for BovRh, and the distortion was localized at the center of the chromophore in SpiRh1 and SquRh. Highly conserved aspartate (D83 in BovRh) does not change the hydrogen-bonding environment in invertebrate rhodopsins. Thus, present FTIR analysis provides specific structural changes, leading to activation of invertebrate and vertebrate rhodopsins. On the other hand, the analysis of O-D stretching vibrations in D2O revealed unique features of protein-bound water molecules. Numbers of water bands in SpiRh1 and SquRh were less and more than those in BovRh. The X-ray crystal structure of SpiRh1 observed a bridged water molecule between the protonated Schiff base and its counterion (E194), but strongly hydrogen-bonded water molecules were never detected in SpiRh1, as well as SquRh and BovRh. Thus, absence of strongly hydrogen-bonded water molecules is substantial for animal rhodopsins, which is distinctive from microbial rhodopsins.
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6
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Noji T, Ishikita H. Mechanism of Absorption Wavelength Shift of Bacteriorhodopsin During Photocycle. J Phys Chem B 2022; 126:9945-9955. [PMID: 36413506 DOI: 10.1021/acs.jpcb.2c04359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Bacteriorhodopsin, a light-driven proton pump, alters the absorption wavelengths in the range of 410-617 nm during the photocycle. Here, we report the absorption wavelengths, calculated using 12 bacteriorhodopsin crystal structures (including the BR, BR13-cis, J, K0, KE, KL, L, M, N, and O state structures) and a combined quantum mechanical/molecular mechanical/polarizable continuum model (QM/MM/PCM) approach. The QM/MM/PCM calculations reproduced the experimentally measured absorption wavelengths with a standard deviation of 4 nm. The shifts in the absorption wavelengths can be explained mainly by the following four factors: (i) retinal Schiff base deformation/twist induced by the protein environment, leading to a decrease in the electrostatic interaction between the protein environment and the retinal Schiff base; (ii) changes in the protonation state of the protein environment, directly altering the electrostatic interaction between the protein environment and the retinal Schiff base; (iii) changes in the protonation state; or (iv) isomerization of the retinal Schiff base, where the absorption wavelengths of the isomers originally differ.
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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, Tokyo153-8904, Japan
| | - Hiroshi Ishikita
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo153-8904, Japan.,Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo113-8654, Japan
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7
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Ohmine I, Saito S. Dynamical Behavior of Water; Fluctuation, Reactions and Phase Transitions. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Iwao Ohmine
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
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8
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Yagi K, Sugita Y. Anharmonic Vibrational Calculations Based on Group-Localized Coordinates: Applications to Internal Water Molecules in Bacteriorhodopsin. J Chem Theory Comput 2021; 17:5007-5020. [PMID: 34296615 PMCID: PMC10986902 DOI: 10.1021/acs.jctc.1c00060] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
An efficient anharmonic vibrational method is developed exploiting the locality of molecular vibration. Vibrational coordinates localized to a group of atoms are employed to divide the potential energy surface (PES) of a system into intra- and inter-group contributions. Then, the vibrational Schrödinger equation is solved based on a PES, in which the inter-group coupling is truncated at the harmonic level while accounting for the intra-group anharmonicity. The method is applied to a pentagonal hydrogen bond network (HBN) composed of internal water molecules and charged residues in a membrane protein, bacteriorhodopsin. The PES is calculated by the quantum mechanics/molecular mechanics (QM/MM) calculation at the level of B3LYP-D3/aug-cc-pVDZ. The infrared (IR) spectrum is computed using a set of coordinates localized to each water molecule and amino acid residue by second-order vibrational quasi-degenerate perturbation theory (VQDPT2). Benchmark calculations show that the proposed method yields the N-D/O-D stretching frequencies with an error of 7 cm-1 at the cost reduced by more than five times. In contrast, the harmonic approximation results in a severe error of 150 cm-1. Furthermore, the size of QM regions is carefully assessed to find that the QM regions should include not only the pentagonal HBN itself but also its HB partners. VQDPT2 calculations starting from transient structures obtained by molecular dynamics simulations have shown that the structural sampling has a significant impact on the calculated IR spectrum. The incorporation of anharmonicity, sufficiently large QM regions, and structural samplings are of essential importance to reproduce the experimental IR spectrum. The computational spectrum paves the way for decoding the IR signal of strong HBNs and helps elucidate their functional roles in biomolecules.
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Affiliation(s)
- Kiyoshi Yagi
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yuji Sugita
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, 1-6-5 Minatojima-Minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
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9
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Tomida S, Kitagawa S, Kandori H, Furutani Y. Inverse Hydrogen-Bonding Change Between the Protonated Retinal Schiff Base and Water Molecules upon Photoisomerization in Heliorhodopsin 48C12. J Phys Chem B 2021; 125:8331-8341. [PMID: 34292728 DOI: 10.1021/acs.jpcb.1c01907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Heliorhodopsin (HeR) is a new class of the rhodopsin family discovered in 2018 through functional metagenomic analysis (named 48C12). Similar to typical microbial rhodopsins, HeR possesses seven transmembrane (TM) α-helices and an all-trans-retinal covalently bonded to the lysine residue on TM7 via a protonated Schiff base. Remarkably, the HeR membrane topology is inverted compared with that of typical microbial rhodopsins. The X-ray crystal structure of HeR 48C12 was elucidated after the first report on a HeR variant from Thermoplasmatales archaeon SG8-52-1, which revealed the water-mediated hydrogen-bonding network connected to the Schiff base region in the cytoplasmic side. Herein, low-temperature light-induced FTIR spectroscopic analyses of HeR 48C12 and 15N isotopically labeled proteins were used to elucidate the structural changes during retinal photoisomerization. N-D stretching vibrations of the protonated retinal Schiff base (PRSB) at 2286 and 2302 cm-1 in the dark state, and 2239 and 2252 cm-1 in the K intermediate were observed. The frequency changes indicated that the hydrogen bond of PRSB strengthens upon photoisomerization in HeR. Moreover, O-D stretching vibration frequencies of the internal water molecules indicate that the hydrogen-bonding strength decreases concomitantly. Therefore, the PRSB hydrogen bond responds to photoisomerization in an opposite way to the hydrogen-bonding network involving water molecules. No frequency changes of the indole N-H or N-D stretching vibrations of tryptophan residues were observed upon photoisomerization, suggesting that all tryptophan residues in the HeR 48C12 maintained the hydrogen-bonding strengths in the K intermediate. These results provide insights into the molecular mechanism of the energy storage and propagation upon retinal photoisomerization in HeR.
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Affiliation(s)
- Sahoko Tomida
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, 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.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Yuji Furutani
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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10
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Tanaka T, Singh M, Shihoya W, Yamashita K, Kandori H, Nureki O. Structural basis for unique color tuning mechanism in heliorhodopsin. Biochem Biophys Res Commun 2020; 533:262-267. [PMID: 32951839 DOI: 10.1016/j.bbrc.2020.06.124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 06/24/2020] [Indexed: 10/23/2022]
Abstract
Microbial rhodopsins comprise an opsin protein with seven transmembrane helices and a retinal as the chromophore. An all-trans retinal is covalently bonded to a lysine residue through the retinal Schiff base (RSB) and stabilized by a negatively charged counterion. The distance between the RSB and counterion is closely related to the light energy absorption. However, in heliorhodopsin-48C12 (HeR-48C12), while E107 acts as the counterion, E107D mutation exhibits an identical absorption spectrum to the wild-type, suggesting that the distance does not affect its absorption spectra. Here we present the 2.6 Å resolution crystal structure of the Thermoplasmatales archaeon HeR E108D mutant, which also has an identical absorption spectrum to the wild-type. The structure revealed that D108 does not form a hydrogen bond with the RSB, and its counterion interaction becomes weaker. Alternatively, the serine cluster, S78, S112, and S238 form a distinct interaction network around the RSB. The absorption spectra of the E to D and S to A double mutants suggested that S112 influences the spectral shift by compensating for the weaker counterion interaction. Our structural and spectral studies have revealed the unique spectral shift mechanism of HeR and clarified the physicochemical properties of HeRs.
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Affiliation(s)
- Tatsuki Tanaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Manish Singh
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa, Nagoya, 466-8555, Japan
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.
| | - Keitaro Yamashita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa, Nagoya, 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa, Nagoya, 466-8555, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.
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11
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Kandori H. Structure/Function Study of Photoreceptive Proteins by FTIR Spectroscopy. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20200109] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Hideki Kandori
- Department of Life Science and Applied Chemistry & OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
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12
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Tomida S, Ito S, Mato T, Furutani Y, Inoue K, Kandori H. Infrared spectroscopic analysis on structural changes around the protonated Schiff base upon retinal isomerization in light-driven sodium pump KR2. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148190. [DOI: 10.1016/j.bbabio.2020.148190] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 01/30/2020] [Accepted: 03/13/2020] [Indexed: 10/24/2022]
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13
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Abstract
Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.
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14
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Ghanbarpour A, Nairat M, Nosrati M, Santos EM, Vasileiou C, Dantus M, Borhan B, Geiger JH. Mimicking Microbial Rhodopsin Isomerization in a Single Crystal. J Am Chem Soc 2019; 141:1735-1741. [PMID: 30580520 DOI: 10.1021/jacs.8b12493] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacteriorhodopsin represents the simplest, and possibly most abundant, phototropic system requiring only a retinal-bound transmembrane protein to convert photons of light to an energy-generating proton gradient. The creation and interrogation of a microbial rhodopsin mimic, based on an orthogonal protein system, would illuminate the design elements required to generate new photoactive proteins with novel function. We describe a microbial rhodopsin mimic, created using a small soluble protein as a template, that specifically photoisomerizes all- trans to 13- cis retinal followed by thermal relaxation to the all- trans isomer, mimicking the bacteriorhodopsin photocycle, in a single crystal. The key element for selective isomerization is a tuned steric interaction between the chromophore and protein, similar to that seen in the microbial rhodopsins. It is further demonstrated that a single mutation converts the system to a protein photoswitch without chromophore photoisomerization or conformational change.
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Affiliation(s)
- Alireza Ghanbarpour
- Michigan State University , Department of Chemistry , East Lansing , Michigan 48824 , United States
| | - Muath Nairat
- Michigan State University , Department of Chemistry , East Lansing , Michigan 48824 , United States
| | - Meisam Nosrati
- Michigan State University , Department of Chemistry , East Lansing , Michigan 48824 , United States
| | - Elizabeth M Santos
- Michigan State University , Department of Chemistry , East Lansing , Michigan 48824 , United States
| | - Chrysoula Vasileiou
- Michigan State University , Department of Chemistry , East Lansing , Michigan 48824 , United States
| | - Marcos Dantus
- Michigan State University , Department of Chemistry , East Lansing , Michigan 48824 , United States
| | - Babak Borhan
- Michigan State University , Department of Chemistry , East Lansing , Michigan 48824 , United States
| | - James H Geiger
- Michigan State University , Department of Chemistry , East Lansing , Michigan 48824 , United States
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15
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Watari M, Ikuta T, Yamada D, Shihoya W, Yoshida K, Tsunoda SP, Nureki O, Kandori H. Spectroscopic study of the transmembrane domain of a rhodopsin-phosphodiesterase fusion protein from a unicellular eukaryote. J Biol Chem 2019; 294:3432-3443. [PMID: 30622140 DOI: 10.1074/jbc.ra118.006277] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/31/2018] [Indexed: 02/02/2023] Open
Abstract
The choanoflagellate Salpingoeca rosetta contains a chimeric rhodopsin protein composed of an N-terminal rhodopsin (Rh) domain and a C-terminal cyclic nucleotide phosphodiesterase (PDE) domain. The Rh-PDE enzyme light-dependently decreases the concentrations of cyclic nucleotides such as cGMP and cAMP. Photoexcitation of purified full-length Rh-PDE yields an "M" intermediate with a deprotonated Schiff base, and its recovery is much faster than that of the enzyme domain. To gain structural and mechanistic insights into the Rh domain, here we expressed and purified the transmembrane domain of Rh-PDE, Rh-PDE(TMD), and analyzed it with transient absorption, light-induced difference UV-visible, and FTIR spectroscopy methods. These analyses revealed that the "K" intermediate forms within 0.005 ms and converts into the M intermediate with a time constant of 4 ms, with the latter returning to the original state within 4 s. FTIR spectroscopy revealed that all-trans to 13-cis photoisomerization occurs as the primary event during which chromophore distortion is located at the middle of the polyene chain, allowing the Schiff base to form a stronger hydrogen bond. We also noted that the peptide backbone of the α-helix becomes deformed upon M intermediate formation. Results from site-directed mutagenesis suggested that Glu-164 is protonated and that Asp-292 acts as the only Schiff base counterion in Rh-PDE. A strong reduction of enzymatic activity in a D292N variant, but not in an E164Q variant, indicated an important catalytic role of the negative charge at Asp-292. Our findings provide further mechanistic insights into rhodopsin-mediated, light-dependent regulation of second-messenger levels in eukaryotic microbes.
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Affiliation(s)
- Masahito Watari
- From the Department of Life Science and Applied Chemistry and
| | - Tatsuya Ikuta
- the Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan, and
| | - Daichi Yamada
- From the Department of Life Science and Applied Chemistry and
| | - Wataru Shihoya
- the Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan, and
| | - Kazuho Yoshida
- From the Department of Life Science and Applied Chemistry and
| | - Satoshi P Tsunoda
- From the Department of Life Science and Applied Chemistry and.,the OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.,PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Osamu Nureki
- the Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan, and
| | - Hideki Kandori
- From the Department of Life Science and Applied Chemistry and .,the OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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16
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Nogly P, Weinert T, James D, Carbajo S, Ozerov D, Furrer A, Gashi D, Borin V, Skopintsev P, Jaeger K, Nass K, Båth P, Bosman R, Koglin J, Seaberg M, Lane T, Kekilli D, Brünle S, Tanaka T, Wu W, Milne C, White T, Barty A, Weierstall U, Panneels V, Nango E, Iwata S, Hunter M, Schapiro I, Schertler G, Neutze R, Standfuss J. Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser. Science 2018; 361:science.aat0094. [PMID: 29903883 DOI: 10.1126/science.aat0094] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/29/2018] [Indexed: 12/23/2022]
Abstract
Ultrafast isomerization of retinal is the primary step in photoresponsive biological functions including vision in humans and ion transport across bacterial membranes. We used an x-ray laser to study the subpicosecond structural dynamics of retinal isomerization in the light-driven proton pump bacteriorhodopsin. A series of structural snapshots with near-atomic spatial resolution and temporal resolution in the femtosecond regime show how the excited all-trans retinal samples conformational states within the protein binding pocket before passing through a twisted geometry and emerging in the 13-cis conformation. Our findings suggest ultrafast collective motions of aspartic acid residues and functional water molecules in the proximity of the retinal Schiff base as a key facet of this stereoselective and efficient photochemical reaction.
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Affiliation(s)
- Przemyslaw Nogly
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Tobias Weinert
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland.,Photon Science Division-Swiss Light Source, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Daniel James
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Sergio Carbajo
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Dmitry Ozerov
- Science IT, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Antonia Furrer
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Dardan Gashi
- SwissFEL, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Veniamin Borin
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Petr Skopintsev
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Kathrin Jaeger
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Karol Nass
- SwissFEL, Paul Scherrer Institut, 5232 Villigen, Switzerland.,Photon Science Division-Swiss Light Source, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE- 40530 Gothenburg, Sweden
| | - Robert Bosman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE- 40530 Gothenburg, Sweden
| | - Jason Koglin
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Matthew Seaberg
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Thomas Lane
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Demet Kekilli
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Steffen Brünle
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe- cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Wenting Wu
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | | | - Thomas White
- Center for Free-Electron Laser Science (CFEL), DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science (CFEL), DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Valerie Panneels
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe- cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe- cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Mark Hunter
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Gebhard Schertler
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland.,Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE- 40530 Gothenburg, Sweden
| | - Jörg Standfuss
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland.
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17
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Ito S, Kandori H, Lorenz-Fonfria VA. Potential Second-Harmonic Ghost Bands in Fourier Transform Infrared (FT-IR) Difference Spectroscopy of Proteins. APPLIED SPECTROSCOPY 2018; 72:956-963. [PMID: 29350538 DOI: 10.1177/0003702818757521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Fourier transform infrared (FT-IR) difference absorption spectroscopy is a common method for studying the structural and dynamical aspects behind protein function. In particular, the 2800-1800 cm-1 spectral range has been used to obtain information about internal (deuterated) water molecules, as well as site-specific details about cysteine residues and chemically modified and artificial amino acids. Here, we report on the presence of ghost bands in cryogenic light-induced FT-IR difference spectra of the protein bacteriorhodopsin. The presence of these ghost bands can be particularly problematic in the 2800-1900 cm-1 region, showing intensities similar to O-D vibrations from water molecules. We demonstrate that they arise from second harmonics from genuine chromophore bands located in the 1400-850 cm-1 region, generated by double-modulation artifacts caused from reflections of the IR beam at the sample and at the cryostat windows back to the interferometer (inter-reflections). The second-harmonic ghost bands can be physically removed by placing an optical filter of suitable cutoff in the beam path, but at the cost of losing part of the multiplexing advantage of FT-IR spectroscopy. We explored alternatives to the use of optical filters. Tilting the cryostat windows was effective in reducing the intensity of the second harmonic artifacts but tilting the sample windows was not, presumably by their close proximity to the focal point of the IR beam. We also introduce a simple numerical post-processing approach that can partially, but not fully, correct for second-harmonic ghost bands in FT-IR difference spectra.
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Affiliation(s)
- Shota Ito
- 1 Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan
| | - Hideki Kandori
- 1 Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan
- 2 OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Japan
| | - Victor A Lorenz-Fonfria
- 3 Institute of Molecular Science (ICMol), Universitat de València, Paterna, Spain
- 4 Department of Biochemistry and Molecular Biology, Universitat de València, Burjassot, Spain
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18
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Tomida S, Ito S, Inoue K, Kandori H. Hydrogen-bonding network at the cytoplasmic region of a light-driven sodium pump rhodopsin KR2. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:684-691. [PMID: 29852143 DOI: 10.1016/j.bbabio.2018.05.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/11/2018] [Accepted: 05/24/2018] [Indexed: 01/15/2023]
Abstract
Light-driven sodium-pumping rhodopsins are able to actively transport sodium ions. Structure/function studies of Krokinobacter eikastus rhodopsin 2 (KR2) identified N61 and G263 at the cytoplasmic surface constituting the "Ion-selectivity filter" for sodium ions, while retinal Schiff base acts as the light "Switch and Gate" for transport of sodium ions. Q123 is located between the two regions, and plays an important role for the pump function, which was implicated by functional, spectroscopic, X-ray crystallographic and computational studies. According to the atomic structure of KR2, Q123 is involved in the hydrogen-bonding network at the cytoplasmic region, together with S64, protein-bound waters, and peptide carbonyl of K255 bound to the chromophore. To gain the detailed structural information around Q123, here we compared light-induced difference Fourier-transform infrared (FTIR) spectra at 77 K between the wild-type (WT) and mutant proteins of KR2, such as Q123A, Q123V, and S64A. The obtained spectra were very similar between WT and these mutants, whereas the observed mutation effects enabled us to identify vibrations of the hydrogen-bonding network at the Q123 and S64 region. This is unique for KR2, not for the corresponding mutations in a light-driven proton-pump bacteriorhodopsin (BR). Hydrogen-bonding alteration is absent for the mutants of KR2, suggesting that proper inter-helical connectivity of helices B, C, and G is important for protein structural changes for sodium-pump function, which is controlled by the region around Q123.
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Affiliation(s)
- Sahoko Tomida
- 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
| | - Keiichi Inoue
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; Frontier Research Institute for Material Science, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.
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19
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Nomura Y, Ito S, Teranishi M, Ono H, Inoue K, Kandori H. Low-temperature FTIR spectroscopy provides evidence for protein-bound water molecules in eubacterial light-driven ion pumps. Phys Chem Chem Phys 2018; 20:3165-3171. [DOI: 10.1039/c7cp05674e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The present FTIR study showed that eubacterial light-driven H+, Na+ and Cl− pump rhodopsins contain strongly hydrogen-bonded water molecule, the functional determinant of light-driven proton pump. This explains well the asymmetric functional conversions of light-driven ion pumps.
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Affiliation(s)
- Yurika Nomura
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Showa-ku
- Japan
| | - Shota Ito
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Showa-ku
- Japan
| | - Miwako Teranishi
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Showa-ku
- Japan
| | - Hikaru Ono
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Showa-ku
- Japan
| | - Keiichi Inoue
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Showa-ku
- Japan
- OptoBioTechnology Research Center
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Showa-ku
- Japan
- OptoBioTechnology Research Center
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20
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pH-sensitive vibrational probe reveals a cytoplasmic protonated cluster in bacteriorhodopsin. Proc Natl Acad Sci U S A 2017; 114:E10909-E10918. [PMID: 29203649 DOI: 10.1073/pnas.1707993114] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Infrared spectroscopy has been used in the past to probe the dynamics of internal proton transfer reactions taking place during the functional mechanism of proteins but has remained mostly silent to protonation changes in the aqueous medium. Here, by selectively monitoring vibrational changes of buffer molecules with a temporal resolution of 6 µs, we have traced proton release and uptake events in the light-driven proton-pump bacteriorhodopsin and correlate these to other molecular processes within the protein. We demonstrate that two distinct chemical entities contribute to the temporal evolution and spectral shape of the continuum band, an unusually broad band extending from 2,300 to well below 1,700 cm-1 The first contribution corresponds to deprotonation of the proton release complex (PRC), a complex in the extracellular domain of bacteriorhodopsin where an excess proton is shared by a cluster of internal water molecules and/or ionic E194/E204 carboxylic groups. We assign the second component of the continuum band to the proton uptake complex, a cluster with an excess proton reminiscent to the PRC but located in the cytoplasmic domain and possibly stabilized by D38. Our findings refine the current interpretation of the continuum band and call for a reevaluation of the last proton transfer steps in bacteriorhodopsin.
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21
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Ito S, Sugita S, Inoue K, Kandori H. FTIR Analysis of a Light-driven Inward Proton-pumping Rhodopsin at 77 K. Photochem Photobiol 2017; 93:1381-1387. [DOI: 10.1111/php.12771] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/22/2017] [Indexed: 01/27/2023]
Affiliation(s)
- Shota Ito
- Department of Life Science and Applied Chemistry; Nagoya Institute of Technology; Showa-ku Nagoya Japan
| | - Shinya Sugita
- Department of Life Science and Applied Chemistry; Nagoya Institute of Technology; Showa-ku Nagoya Japan
| | - Keiichi Inoue
- Department of Life Science and Applied Chemistry; Nagoya Institute of Technology; Showa-ku Nagoya Japan
- OptoBioTechnology Research Center; Nagoya Institute of Technology; Showa-ku Nagoya Japan
- PRESTO; Japan Science and Technology Agency; Kawaguchi Saitama Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry; Nagoya Institute of Technology; Showa-ku Nagoya Japan
- OptoBioTechnology Research Center; Nagoya Institute of Technology; Showa-ku Nagoya Japan
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22
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Lórenz-Fonfría VA, Muders V, Schlesinger R, Heberle J. Changes in the hydrogen-bonding strength of internal water molecules and cysteine residues in the conductive state of channelrhodopsin-1. J Chem Phys 2015; 141:22D507. [PMID: 25494778 DOI: 10.1063/1.4895796] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Water plays an essential role in the structure and function of proteins, particularly in the less understood class of membrane proteins. As the first of its kind, channelrhodopsin is a light-gated cation channel and paved the way for the new and vibrant field of optogenetics, where nerve cells are activated by light. Still, the molecular mechanism of channelrhodopsin is not understood. Here, we applied time-resolved FT-IR difference spectroscopy to channelrhodopsin-1 from Chlamydomonas augustae. It is shown that the (conductive) P2(380) intermediate decays with τ ≈ 40 ms and 200 ms after pulsed excitation. The vibrational changes between the closed and the conductive states were analyzed in the X-H stretching region (X = O, S, N), comprising vibrational changes of water molecules, sulfhydryl groups of cysteine side chains and changes of the amide A of the protein backbone. The O-H stretching vibrations of "dangling" water molecules were detected in two different states of the protein using H2 (18)O exchange. Uncoupling experiments with a 1:1 mixture of H2O:D2O provided the natural uncoupled frequencies of the four O-H (and O-D) stretches of these water molecules, each with a very weakly hydrogen-bonded O-H group (3639 and 3628 cm(-1)) and with the other O-H group medium (3440 cm(-1)) to moderately strongly (3300 cm(-1)) hydrogen-bonded. Changes in amide A and thiol vibrations report on global and local changes, respectively, associated with the formation of the conductive state. Future studies will aim at assigning the respective cysteine group(s) and at localizing the "dangling" water molecules within the protein, providing a better understanding of their functional relevance in CaChR1.
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Affiliation(s)
| | - Vera Muders
- Genetic Biophysics, Freie Universität Berlin, 14195 Berlin, Germany
| | | | - Joachim Heberle
- Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany
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23
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Ogren JI, Yi A, Mamaev S, Li H, Lugtenburg J, DeGrip WJ, Spudich JL, Rothschild KJ. Comparison of the structural changes occurring during the primary phototransition of two different channelrhodopsins from Chlamydomonas algae. Biochemistry 2014; 54:377-88. [PMID: 25469620 PMCID: PMC4303311 DOI: 10.1021/bi501243y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Channelrhodopsins
(ChRs) from green flagellate algae function as
light-gated ion channels when expressed heterologously in mammalian
cells. Considerable interest has focused on understanding the molecular
mechanisms of ChRs to bioengineer their properties for specific optogenetic
applications such as elucidating the function of specific neurons
in brain circuits. While most studies have used channelrhodopsin-2
from Chlamydomonas reinhardtii (CrChR2), in this work low-temperature Fourier transform infrared-difference
spectroscopy is applied to study the conformational changes occurring
during the primary phototransition of the red-shifted ChR1 from Chlamydomonas augustae (CaChR1). Substitution
with isotope-labeled retinals or the retinal analogue A2, site-directed
mutagenesis, hydrogen–deuterium exchange, and H218O exchange were used to assign bands to the retinal
chromophore, protein, and internal water molecules. The primary phototransition
of CaChR1 at 80 K involves, in contrast to that of CrChR2, almost exclusively an all-trans to 13-cis isomerization of the retinal chromophore,
as in the primary phototransition of bacteriorhodopsin (BR). In addition,
significant differences are found for structural changes of the protein
and internal water(s) compared to those of CrChR2,
including the response of several Asp/Glu residues to retinal isomerization.
A negative amide II band is identified in the retinal ethylenic stretch
region of CaChR1, which reflects along with amide
I bands alterations in protein backbone structure early in the photocycle.
A decrease in the hydrogen bond strength of a weakly hydrogen bonded
internal water is detected in both CaChR1 and CrChR2, but the bands are much broader in CrChR2, indicating a more heterogeneous environment. Mutations involving
residues Glu169 and Asp299 (homologues of the Asp85 and Asp212 Schiff
base counterions, respectively, in BR) lead to the conclusion that
Asp299 is protonated during P1 formation and suggest that these residues
interact through a strong hydrogen bond that facilitates the transfer
of a proton from Glu169.
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Affiliation(s)
- John I Ogren
- Molecular Biophysics Laboratory, Photonics Center, and Department of Physics, Boston University , Boston, Massachusetts 02215, United States
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24
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Ono H, Inoue K, Abe-Yoshizumi R, Kandori H. FTIR Spectroscopy of a Light-Driven Compatible Sodium Ion-Proton Pumping Rhodopsin at 77 K. J Phys Chem B 2014; 118:4784-92. [DOI: 10.1021/jp500756f] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | - Keiichi Inoue
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
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25
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Debus RJ. Evidence from FTIR Difference Spectroscopy That D1-Asp61 Influences the Water Reactions of the Oxygen-Evolving Mn4CaO5 Cluster of Photosystem II. Biochemistry 2014; 53:2941-55. [DOI: 10.1021/bi500309f] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Richard J. Debus
- Department of Biochemistry, University of California, Riverside, California 92521, United States
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26
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Ito S, Kato HE, Taniguchi R, Iwata T, Nureki O, Kandori H. Water-containing hydrogen-bonding network in the active center of channelrhodopsin. J Am Chem Soc 2014; 136:3475-82. [PMID: 24512107 DOI: 10.1021/ja410836g] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Channelrhodopsin (ChR) functions as a light-gated ion channel in Chlamydomonas reinhardtii. Passive transport of cations by ChR is fundamentally different from the active transport by light-driven ion pumps such as archaerhodopsin, bacteriorhodopsin, and halorhodopsin. These microbial rhodopsins are important tools for optogenetics, where ChR is used to activate neurons by light, while the ion pumps are used for neural silencing. Ion-transport functions by these rhodopsins strongly depend on the specific hydrogen-bonding networks containing water near the retinal chromophore. In this work, we measured protein-bound water molecules in a chimeric ChR protein of ChR1 (helices A to E) and ChR2 (helices F and G) of Chlamydomonas reinhardtii using low-temperature FTIR spectroscopy at 77 K. We found that the active center of ChR possesses more water molecules (9 water vibrations) than those of other microbial (2-6 water vibrations) and animal (6-8 water vibrations) rhodopsins. We conclude that the protonated retinal Schiff base interacts with the counterion (Glu162) directly, without the intervening water molecule found in proton-pumping microbial rhodopsins. The present FTIR results and the recent X-ray structure of ChR reveal a unique hydrogen-bonding network around the active center of this light-gated ion channel.
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Affiliation(s)
- Shota Ito
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
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27
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Ernst OP, Lodowski DT, Elstner M, Hegemann P, Brown L, Kandori H. Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem Rev 2014; 114:126-63. [PMID: 24364740 PMCID: PMC3979449 DOI: 10.1021/cr4003769] [Citation(s) in RCA: 746] [Impact Index Per Article: 74.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Indexed: 12/31/2022]
Affiliation(s)
- Oliver P. Ernst
- Departments
of Biochemistry and Molecular Genetics, University of Toronto, 1 King’s College Circle, Medical Sciences Building, Toronto, Ontario M5S 1A8, Canada
| | - David T. Lodowski
- Center
for Proteomics and Bioinformatics, Case
Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Marcus Elstner
- Institute
for Physical Chemistry, Karlsruhe Institute
of Technology, Kaiserstrasse
12, 76131 Karlsruhe, Germany
| | - Peter Hegemann
- Institute
of Biology, Experimental Biophysics, Humboldt-Universität
zu Berlin, Invalidenstrasse
42, 10115 Berlin, Germany
| | - Leonid
S. Brown
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Hideki Kandori
- Department
of Frontier Materials, Nagoya Institute
of Technology, Showa-ku, Nagoya 466-8555, Japan
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Fukuda T, Muroda K, Kandori H. Detection of a protein-bound water vibration of halorhodopsin in aqueous solution. Biophysics (Nagoya-shi) 2013; 9:167-72. [PMID: 27493555 PMCID: PMC4629683 DOI: 10.2142/biophysics.9.167] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 12/04/2013] [Indexed: 01/14/2023] Open
Abstract
Protein-bound water molecules play crucial roles in their structure and function, but their detection is an experimental challenge, particularly in aqueous solution at room temperature. By applying attenuated total reflection (ATR) Fourier-transform infrared (FTIR) spectroscopy to a light-driven Cl(-) pump pharaonis halorhodopsin (pHR), here we detected an O-H stretching vibration of protein-bound water molecules in the active center. The pHR(Cl(-)) minus pHR(Br(-)) ATR-FTIR spectra show random fluctuation at 3600-3000 cm(-1), frequency window of water vibration, which can be interpreted in terms of dynamical fluctuation of aqueous water at room temperature. On the other hand, we observed a reproducible spectral feature at 3617 (+)/3630 (-) cm(-1) in the pHR(Cl(-)) minus pHR(Br(-)) spectrum, which is absent in the pHR(Cl(-)) minus pHR(Cl(-)) and in the pHR(Br(-)) minus pHR(Br(-)) spectra. The water O-H stretching vibrations of pHR(Cl(-)) and pHR(Br(-)) at 3617 and 3630 cm(-1), respectively, are confirmed by light-induced difference FTIR spectra in isotope water (H2 (18)O) at 77 K. The observed water molecule presumably binds to the active center of pHR, and alter its hydrogen bond during the Cl(-) pumping photocycle.
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Affiliation(s)
- Tetsuya Fukuda
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Kosuke Muroda
- 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
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29
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Furutani Y, Kandori H. Hydrogen-bonding changes of internal water molecules upon the actions of microbial rhodopsins studied by FTIR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:598-605. [PMID: 24041645 DOI: 10.1016/j.bbabio.2013.09.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 09/04/2013] [Accepted: 09/06/2013] [Indexed: 11/27/2022]
Abstract
Microbial rhodopsins are classified into type-I rhodopsins, which utilize light energy to perform wide varieties of function, such as proton pumping, ion pumping, light sensing, cation channels, and so on. The crystal structures of several type-I rhodopsins were solved and the molecular mechanisms have been investigated based on the atomic structures. However, the crystal structures of proteins of interest are not always available and the basic architectures are sometimes quite similar, which obscures how the proteins achieve different functions. Stimulus-induced difference FTIR spectroscopy is a powerful tool to detect minute structural changes providing a clue for elucidating the molecular mechanisms. In this review, the studies on type-I rhodopsins from fungi and marine bacteria, whose crystal structures have not been solved yet, were summarized. Neurospora rhodopsin and Leptosphaeria rhodopsin found from Fungi have sequence similarity. The former has no proton pumping function, while the latter has. Proteorhodopsin is another example, whose proton pumping machinery is altered at alkaline and acidic conditions. We described how the structural changes of protein were different and how water molecules were involved in them. We reviewed the results on dynamics of the internal water molecules in pharaonis halorhodopsin as well. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
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Affiliation(s)
- Yuji Furutani
- Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan; Department of Structural Molecular Science, The Graduate University for Advanced Studies (SOKENDAI), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan; PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.
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30
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Rich PR, Maréchal A. Functions of the hydrophilic channels in protonmotive cytochrome c oxidase. J R Soc Interface 2013; 10:20130183. [PMID: 23864498 PMCID: PMC3730678 DOI: 10.1098/rsif.2013.0183] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 06/03/2013] [Indexed: 01/31/2023] Open
Abstract
The structures and functions of hydrophilic channels in electron-transferring membrane proteins are discussed. A distinction is made between proton channels that can conduct protons and dielectric channels that are non-conducting but can dielectrically polarize in response to the introduction of charge changes in buried functional centres. Functions of the K, D and H channels found in A1-type cytochrome c oxidases are reviewed in relation to these ideas. Possible control of function by dielectric channels and their evolutionary relation to proton channels is explored.
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Affiliation(s)
- Peter R Rich
- Glynn Laboratory of Bioenergetics, Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK.
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31
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Pal R, Sekharan S, Batista VS. Spectral Tuning in Halorhodopsin: The Chloride Pump Photoreceptor. J Am Chem Soc 2013; 135:9624-7. [DOI: 10.1021/ja404600z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Rhitankar Pal
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut
06520-8107, United States
| | - Sivakumar Sekharan
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut
06520-8107, United States
| | - Victor S. Batista
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut
06520-8107, United States
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32
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Ito H, Sumii M, Kawanabe A, Fan Y, Furutani Y, Brown LS, Kandori H. Comparative FTIR study of a new fungal rhodopsin. J Phys Chem B 2012; 116:11881-9. [PMID: 22973982 DOI: 10.1021/jp306993a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacteriorhodopsin (BR) is a light-driven proton pump of halophilic Archaea , and BR-like proton-pumping rhodopsins have been discovered in Bacteria and Eucarya as well. Leptosphaeria rhodopsin (LR) and Phaeosphaeria Rhodopsin 2 (PhaeoRD2) are both fungal rhodopsins in such a functional class, even though they belong to different branches of the phylogenetic tree. In this study, we compared light-induced structural changes in the K, L, and M photointermediates for PhaeoRD2, LR, and BR using low-temperature Fourier transform infrared (FTIR) spectroscopy. We observed a strongly hydrogen-bonded water molecule in PhaeoRD2 (water O-D stretch in D(2)O at 2258 cm(-1)) as well as in LR and BR. This observation provided additional experimental evidence to the concept that strongly hydrogen-bonded water molecule is the functional determinant of light-driven proton pumping. The difference FTIR spectra for all the K, L, and M states are surprisingly similar between PhaeoRD2 and LR, but not for BR. PhaeoRD2 is more homologous to LR than to BR, but the difference is small. The amino acid identities between PhaeoRD2 and LR, and between PhaeoRD2 and BR are 34.5% and 30.2%, respectively. In addition, the amino acids uniquely identical for the fungal rhodopsins are located rather far from the retinal chromophore. In fact, the amino acid identities within 4 Å from retinal are the same among PhaeoRD2, LR, and BR. For more than 100 amino acids located within 12 Å from retinal, the identities are 48.7% between PhaeoRD2 and LR, 46.0% between PhaeoRD2 and BR, and 47.8% between LR and BR. These results suggest that protein core structures are equally different among the three rhodopsins. Thus, the identical FTIR spectra between PhaeoRD2 and LR (but not BR), even for the K state, indicate that fungal rhodopsins possess some common structural motif and dynamics not obvious from the amino acid sequences.
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Affiliation(s)
- Hiroyasu Ito
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya 466-8555, Japan
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33
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Saito K, Kandori H, Ishikita H. Factors that differentiate the H-bond strengths of water near the Schiff bases in bacteriorhodopsin and Anabaena sensory rhodopsin. J Biol Chem 2012; 287:34009-18. [PMID: 22865888 DOI: 10.1074/jbc.m112.388348] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacteriorhodopsin (BR) functions as a light-driven proton pump, whereas Anabaena sensory rhodopsin (ASR) is believed to function as a photosensor despite the high similarity in their protein sequences. In Fourier transform infrared (FTIR) spectroscopic studies, the lowest O-D stretch for D(2)O was observed at ∼2200 cm(-1) in BR but was significantly higher in ASR (>2500 cm(-1)), which was previously attributed to a water molecule near the Schiff base (W402) that is H-bonded to Asp-85 in BR and Asp-75 in ASR. We investigated the factors that differentiate the lowest O-D stretches of W402 in BR and ASR. Quantum mechanical/molecular mechanical calculations reproduced the H-bond geometries of the crystal structures, and the calculated O-D stretching frequencies were corroborated by the FTIR band assignments. The potential energy profiles indicate that the smaller O-D stretching frequency in BR originates from the significantly higher pK(a)(Asp-85) in BR relative to the pK(a)(Asp-75) in ASR, which were calculated to be 1.5 and -5.1, respectively. The difference is mostly due to the influences of Ala-53, Arg-82, Glu-194-Glu-204, and Asp-212 on pK(a)(Asp-85) in BR and the corresponding residues Ser-47, Arg-72, Ser-188-Asp-198, and Pro-206 on pK(a)(Asp-75) in ASR. Because these residues participate in proton transfer pathways in BR but not in ASR, the presence of a strongly H-bonded water molecule near the Schiff base ultimately results from the proton-pumping activity in BR.
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Affiliation(s)
- Keisuke Saito
- 202 Building E, Career-Path Promotion Unit for Young Life Scientists, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Kyoto 606-8501, Japan
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34
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Herz J, Verhoefen MK, Weber I, Bamann C, Glaubitz C, Wachtveitl J. Critical role of Asp227 in the photocycle of proteorhodopsin. Biochemistry 2012; 51:5589-600. [PMID: 22738119 DOI: 10.1021/bi3003764] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The photocycle of the proton acceptor complex mutant D227N of the bacterial retinal protein proteorhodopsin is investigated employing steady state pH-titration experiments in the UV-visible range as well as femtosecond-pump-probe spectroscopy and flash photolysis in the visible spectral range. The evaluation of the pH-dependent spectra showed that the neutralization of the charge at position 227 has a remarkable influence on the ground state properties of the protein. Both the pK(a) values of the primary proton acceptor and of the Schiff base are considerably decreased. Femtosecond-time-resolved measurements demonstrate that the general S(1) deactivation pathway; that is, the K-state formation is preserved in the D227N mutant. However, the pH-dependence of the reaction rate is lost by the substitution of Asp227 with an asparagine. Also no significant kinetic differences are observed upon deuteration. This is explained by the lack of a strongly hydrogen-bonded water in the vicinity of Asp97, Asp227, and the Schiff base or a change in the hydrogen bonding of it (Ikeda et al. (2007) Biochemistry 46, 5365-5373). The flash photolysis measurements prove a considerably elongated photocycle with pronounced pH-dependence. Interestingly, at pH 9 the M-state is visible until the end of the reaction cycle, leading to the conclusion that the mutation does not only lower the pK(a) of the Schiff base in the unphotolyzed ground state but also prevents an efficient reprotonation reaction.
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Affiliation(s)
- Julia Herz
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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35
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Muroda K, Nakashima K, Shibata M, Demura M, Kandori H. Protein-bound water as the determinant of asymmetric functional conversion between light-driven proton and chloride pumps. Biochemistry 2012; 51:4677-84. [PMID: 22583333 DOI: 10.1021/bi300485r] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Bacteriorhodopsin (BR) and halorhodopsin (HR) are light-driven outward proton and inward chloride pumps, respectively. They have similar protein architecture, being composed of seven-transmembrane helices that bind an all-trans-retinal. BR can be converted into a chloride pump by a single amino acid replacement at position 85, suggesting that BR and HR share a common transport mechanism, and the ionic specificity is determined by the amino acid at that position. However, HR cannot be converted into a proton pump by the corresponding reverse mutation. Here we mutated 6 and 10 amino acids of HR into BR-like, whereas such multiple HR mutants never pump protons. Light-induced Fourier transform infrared spectroscopy revealed that hydrogen bonds of the retinal Schiff base and water are both strong for BR and both weak for HR. Multiple HR mutants exhibit strong hydrogen bonds of the Schiff base, but the hydrogen bond of water is still weak. We concluded that the cause of nonfunctional conversion of HR is the lack of strongly hydrogen-bonded water, the functional determinant of the proton pump.
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Affiliation(s)
- Kosuke Muroda
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan
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36
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Katayama K, Furutani Y, Imai H, Kandori H. Protein-bound water molecules in primate red- and green-sensitive visual pigments. Biochemistry 2012; 51:1126-33. [PMID: 22260165 DOI: 10.1021/bi201676y] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein-bound water molecules play crucial roles in the structure and function of proteins. The functional role of water molecules has been discussed for rhodopsin, the light sensor for twilight vision, on the basis of X-ray crystallography, Fourier transform infrared (FTIR) spectroscopy, and a radiolytic labeling method, but nothing is known about the protein-bound waters in our color visual pigments. Here we apply low-temperature FTIR spectroscopy to monkey red (MR)- and green (MG)-sensitive color pigments at 77 K and successfully identify water vibrations using D(2)O and D(2)(18)O in the whole midinfrared region. The observed water vibrations are 6-8 for MR and MG, indicating that several water molecules are present near the retinal chromophore and change their hydrogen bonds upon retinal photoisomerization. In this sense, color visual pigments possess protein-bound water molecules essentially similar to those of rhodopsin. The absence of strongly hydrogen-bonded water molecules (O-D stretch at <2400 cm(-1)) is common between rhodopsin and color pigments, which greatly contrasts with the case of proton-pumping microbial rhodopsins. On the other hand, two important differences are observed in water signal between rhodopsin and color pigments. First, the water vibrations are identical between the 11-cis and 9-cis forms of rhodopsin, but different vibrational bands are observed at >2550 cm(-1) for both MR and MG. Second, strongly hydrogen-bonded water molecules (2303 cm(-1) for MR and 2308 cm(-1) for MG) are observed for the all-trans form after retinal photoisomerization, which is not the case for rhodopsin. These specific features of MR and MG can be explained by the presence of water molecules in the Cl(-)-biding site, which are located near positions C11 and C9 of the retinal chromophore. The averaged frequencies of the observed water O-D stretching vibrations for MR and MG are lower as the λ(max) is red-shifted, suggesting that water molecules are involved in the color tuning of our vision.
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Affiliation(s)
- Kota Katayama
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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37
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Clair ECS, Ogren JI, Mamaev S, Kralj JM, Rothschild KJ. Conformational changes in the archaerhodopsin-3 proton pump: detection of conserved strongly hydrogen bonded water networks. J Biol Phys 2011; 38:153-68. [PMID: 23277676 DOI: 10.1007/s10867-011-9246-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Accepted: 10/25/2011] [Indexed: 11/30/2022] Open
Abstract
Archaerhodopsin-3 (AR3) is a light-driven proton pump from Halorubrum sodomense, but little is known about its photocycle. Recent interest has focused on AR3 because of its ability to serve both as a high-performance, genetically-targetable optical silencer of neuronal activity and as a membrane voltage sensor. We examined light-activated structural changes of the protein, retinal chromophore, and internal water molecules during the photocycle of AR3. Low-temperature and rapid-scan time-resolved FTIR-difference spectroscopy revealed that conformational changes during formation of the K, M, and N photocycle intermediates are similar, although not identical, to bacteriorhodopsin (BR). Positive/negative bands in the region above 3,600 cm( - 1), which have previously been assigned to structural changes of weakly hydrogen bonded internal water molecules, were substantially different between AR3 and BR. This included the absence of positive bands recently associated with a chain of proton transporting water molecules in the cytoplasmic channel and a weakly hydrogen bonded water (W401), which is part of a hydrogen-bonded pentagonal cluster located near the retinal Schiff base. However, many of the broad IR continuum absorption changes below 3,000 cm( - 1) assigned to networks of water molecules involved in proton transport through cytoplasmic and extracellular portions in BR were very similar in AR3. This work and subsequent studies comparing BR and AR3 structural changes will help identify conserved elements in BR-like proton pumps as well as bioengineer AR3 to optimize neural silencing and voltage sensing.
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Affiliation(s)
- Erica C Saint Clair
- Department of Physics, Photonics Center and Molecular Biophysics Laboratory, Boston University, Boston, MA 02215 USA
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38
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Shibata M, Uchihashi T, Yamashita H, Kandori H, Ando T. Structural Changes in Bacteriorhodopsin in Response to Alternate Illumination Observed by High-Speed Atomic Force Microscopy. Angew Chem Int Ed Engl 2011; 50:4410-3. [DOI: 10.1002/anie.201007544] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Indexed: 11/09/2022]
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39
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Shibata M, Uchihashi T, Yamashita H, Kandori H, Ando T. Structural Changes in Bacteriorhodopsin in Response to Alternate Illumination Observed by High-Speed Atomic Force Microscopy. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007544] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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40
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Mizuno M, Sudo Y, Homma M, Mizutani Y. Direct Observation of the Structural Change of Tyr174 in the Primary Reaction of Sensory Rhodopsin II. Biochemistry 2011; 50:3170-80. [DOI: 10.1021/bi101817y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, 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
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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41
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Kawanabe A, Furutani Y, Jung KH, Kandori H. An inward proton transport using Anabaena sensory rhodopsin. J Microbiol 2011; 49:1-6. [PMID: 21369972 DOI: 10.1007/s12275-011-0547-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Accepted: 01/14/2011] [Indexed: 11/24/2022]
Abstract
ATP is synthesized by an enzyme that utilizes proton motive force and thus nature creates various proton pumps. The best understood proton pump is bacteriorhodopsin (BR), an outward-directed light-driven proton pump in Halobacterium salinarum. Many archaeal and eubacterial rhodopsins are now known to show similar proton transport activity. Proton pumps must have a specific mechanism to exclude transport in the reverse direction to maintain a proton gradient, and in the case of BR, a highly hydrophobic cytoplasmic domain may constitute such machinery. Although an inward proton pump has neither been created naturally nor artificially, we recently reported that an inward-directed proton transport can be engineered from a bacterial rhodopsin by a single amino acid replacement Anabaena sensory rhodopsin (ASR) is a photochromic sensor in freshwater cyanobacteria, possessing little proton transport activity. When we replace Asp217 at the cytoplasmic domain (distance ∼ 15 Å from the retinal chromophore) to Glu, ASR is converted into an inward proton transport, driven by absorption of a single photon. FTIR spectra clearly show an increased proton affinity for Glu217, which presumably controls the unusual directionality opposite to normal proton pumps.
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Affiliation(s)
- Akira Kawanabe
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
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42
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Suzuki Y, Yokokawa M, Yoshimura SH, Takeyasu K. Biological Application of Fast-Scanning Atomic Force Microscopy. SCANNING PROBE MICROSCOPY IN NANOSCIENCE AND NANOTECHNOLOGY 2 2011. [DOI: 10.1007/978-3-642-10497-8_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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43
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Affiliation(s)
- Hrvoje Petek
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh Pennsylvania 15260, United States, and Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui, China
| | - Jin Zhao
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh Pennsylvania 15260, United States, and Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui, China
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44
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Hirano K, Yokogawa D, Sato H, Sakaki S. An Analysis of 3D Solvation Structure in Biomolecules: Application to Coiled Coil Serine and Bacteriorhodopsin. J Phys Chem B 2010; 114:7935-41. [DOI: 10.1021/jp911470p] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kenji Hirano
- Department of Molecular Engineering, Kyoto University, Kyoto 615-8510, Japan, and Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Daisuke Yokogawa
- Department of Molecular Engineering, Kyoto University, Kyoto 615-8510, Japan, and Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Kyoto University, Kyoto 615-8510, Japan, and Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Shigeyoshi Sakaki
- Department of Molecular Engineering, Kyoto University, Kyoto 615-8510, Japan, and Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
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45
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Hashimoto K, Choi AR, Furutani Y, Jung KH, Kandori H. Low-Temperature FTIR Study of Gloeobacter Rhodopsin: Presence of Strongly Hydrogen-Bonded Water and Long-Range Structural Protein Perturbation upon Retinal Photoisomerization. Biochemistry 2010; 49:3343-50. [DOI: 10.1021/bi100184k] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kyohei Hashimoto
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Ah Reum Choi
- Department of Life Science and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul 121-742, Korea
| | - Yuji Furutani
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Kwang-Hwan Jung
- Department of Life Science and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul 121-742, Korea
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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46
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Yamada K, Kawanabe A, Kandori H. Importance of Alanine at Position 178 in Proteorhodopsin for Absorption of Prevalent Ambient Light in the Marine Environment. Biochemistry 2010; 49:2416-23. [DOI: 10.1021/bi9020204] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Keisuke Yamada
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Akira Kawanabe
- 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
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47
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Shibata M, Yamashita H, Uchihashi T, Kandori H, Ando T. High-speed atomic force microscopy shows dynamic molecular processes in photoactivated bacteriorhodopsin. NATURE NANOTECHNOLOGY 2010; 5:208-12. [PMID: 20154686 DOI: 10.1038/nnano.2010.7] [Citation(s) in RCA: 200] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 01/08/2010] [Indexed: 05/24/2023]
Abstract
Dynamic changes in protein conformation in response to external stimuli are important in biological processes, but it has proved difficult to directly visualize such structural changes under physiological conditions. Here, we show that high-speed atomic force microscopy can be used to visualize dynamic changes in stimulated proteins. High-resolution movies of a light-driven proton pump, bacteriorhodopsin, reveal that, upon illumination, a cytoplasmic portion of each bacteriorhodopsin monomer is brought into contact with adjacent trimers. The bacteriorhodopsin-bacteriorhodopsin interaction in the transiently formed assembly engenders both positive and negative cooperative effects in the decay kinetics as the initial bacteriorhodopsin recovers and, as a consequence, the turnover rate of the photocycle is maintained constant, on average, irrespective of the light intensity. These results confirm that high-resolution visualization is a powerful approach for studying elaborate biomolecular processes under realistic conditions.
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Affiliation(s)
- Mikihiro Shibata
- Department of Physics, Kanazawa University, Kanazawa 920-1192, Japan
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48
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Kawanabe A, Furutani Y, Jung KH, Kandori H. Engineering an inward proton transport from a bacterial sensor rhodopsin. J Am Chem Soc 2010; 131:16439-44. [PMID: 19848403 DOI: 10.1021/ja904855g] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
ATP is synthesized by an enzyme that utilizes proton motive force, and thus, nature has created various proton pumps. The best-understood proton pump is bacteriorhodopsin (BR), an outward-directed, light-driven proton pump in Halobacterium salinarum. Many archaeal and eubacterial rhodopsins are now known to show similar proton transport activity. We previously converted BR into an inward-directed chloride ion pump, but an inward proton pump has never been created. Proton pumps must have a specific mechanism to exclude transport in the reverse direction in order to maintain a proton gradient, and in the case of BR, a highly hydrophobic cytoplasmic domain may constitute such machinery. Here we report that an inward-directed proton transport can be engineered from a bacterial rhodopsin by a single amino acid replacement. Anabaena sensory rhodopsin (ASR) is a photochromic sensor in freshwater cyanobacteria that possesses little proton pump activity. When we replaced Asp217 in the cytoplasmic domain (a distance of approximately 15 A from the retinal chromophore) by Glu, ASR exhibited an inward proton transport activity driven by absorption of a single photon. FTIR spectra clearly showed an increased proton affinity for Glu217, which presumably controls the unusual directionality opposite to that in normal proton pumps.
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Affiliation(s)
- Akira Kawanabe
- Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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Gross R, Wolf MMN, Schumann C, Friedman N, Sheves M, Li L, Engelhard M, Trentmann O, Neuhaus HE, Diller R. Primary photoinduced protein response in bacteriorhodopsin and sensory rhodopsin II. J Am Chem Soc 2010; 131:14868-78. [PMID: 19778046 DOI: 10.1021/ja904218n] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Essential for the biological function of the light-driven proton pump, bacteriorhodopsin (BR), and the light sensor, sensory rhodopsin II (SRII), is the coupling of the activated retinal chromophore to the hosting protein moiety. In order to explore the dynamics of this process we have performed ultrafast transient mid-infrared spectroscopy on isotopically labeled BR and SRII samples. These include SRII in D(2)O buffer, BR in H(2)(18)O medium, SRII with (15)N-labeled protein, and BR with (13)C(14)(13)C(15)-labeled retinal chromophore. Via observed shifts of infrared difference bands after photoexcitation and their kinetics we provide evidence for nonchromophore bands in the amide I and the amide II region of BR and SRII. A band around 1550 cm(-1) is very likely due to an amide II vibration. In the amide I region, contributions of modes involving exchangeable protons and modes not involving exchangeable protons can be discerned. Observed bands in the amide I region of BR are not due to bending vibrations of protein-bound water molecules. The observed protein bands appear in the amide I region within the system response of ca. 0.3 ps and in the amide II region within 3 ps, and decay partially in both regions on a slower time scale of 9-18 ps. Similar observations have been presented earlier for BR5.12, containing a nonisomerizable chromophore (R. Gross et al. J. Phys. Chem. B 2009, 113, 7851-7860). Thus, the results suggest a common mechanism for ultrafast protein response in the artificial and the native system besides isomerization, which could be induced by initial chromophore polarization.
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Affiliation(s)
- Ruth Gross
- University of Kaiserslautern, Department of Physics, Erwin-Schrodinger-Strasse, 67663 Kaiserslautern, Germany
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Kawaguchi S, Kambara O, Shibata M, Kandori H, Tominaga K. Low-frequency dynamics of bacteriorhodopsin studied by terahertz time-domain spectroscopy. Phys Chem Chem Phys 2010; 12:10255-62. [DOI: 10.1039/b927397b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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