1
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Aoyama M, Katayama K, Kandori H. Unique hydrogen-bonding network in a viral channelrhodopsin. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149148. [PMID: 38906314 DOI: 10.1016/j.bbabio.2024.149148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/10/2024] [Accepted: 06/13/2024] [Indexed: 06/23/2024]
Abstract
Channelrhodopsins (CRs) are used as key tools in optogenetics, and novel CRs, either found from nature or engineered by mutation, have greatly contributed to the development of optogenetics. Recently CRs were discovered from viruses, and crystal structure of a viral CR, OLPVR1, reported a very similar water-containing hydrogen-bonding network near the retinal Schiff base to that of a light-driven proton-pump bacteriorhodopsin (BR). In both OLPVR1 and BR, nearly planar pentagonal cluster structures are comprised of five oxygen atoms, three oxygens from water molecules and two oxygens from the Schiff base counterions. The planar pentagonal cluster stabilizes a quadrupole, two positive charges at the Schiff base and an arginine, and two negative charges at the counterions, and thus plays important roles in light-gated channel function of OLPVR1 and light-driven proton pump function of BR. Despite similar pentagonal cluster structures, present FTIR analysis revealed different hydrogen-bonding networks between OLPVR1 and BR. The hydrogen bond between the protonated Schiff base and a water is stronger in OLPVR1 than in BR, and internal water molecules donate hydrogen bonds much weaker in OLPVR1 than in BR. In OLPVR1, the bridged water molecule between the Schiff base and counterions forms hydrogen bonds to D76 and D200 equally, while the hydrogen-bonding interaction is much stronger to D85 than to D212 in BR. The present interpretation is supported by the mutation results, where D76 and D200 equally work as the Schiff base counterions in OLPVR1, but D85 is the primary counterion in BR. This work reports highly sensitive hydrogen-bonding network in the Schiff base region, which would be closely related to each function through light-induced alterations of the network.
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Affiliation(s)
- Mako Aoyama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Kota Katayama
- 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
| | - 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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2
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Malakar P, Gholami S, Aarabi M, Rivalta I, Sheves M, Garavelli M, Ruhman S. Retinal photoisomerization versus counterion protonation in light and dark-adapted bacteriorhodopsin and its primary photoproduct. Nat Commun 2024; 15:2136. [PMID: 38459010 PMCID: PMC10923925 DOI: 10.1038/s41467-024-46061-w] [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: 09/20/2023] [Accepted: 02/08/2024] [Indexed: 03/10/2024] Open
Abstract
Discovered over 50 years ago, bacteriorhodopsin is the first recognized and most widely studied microbial retinal protein. Serving as a light-activated proton pump, it represents the archetypal ion-pumping system. Here we compare the photochemical dynamics of bacteriorhodopsin light and dark-adapted forms with that of the first metastable photocycle intermediate known as "K". We observe that following thermal double isomerization of retinal in the dark from bio-active all-trans 15-anti to 13-cis, 15-syn, photochemistry proceeds even faster than the ~0.5 ps decay of the former, exhibiting ballistic wave packet curve crossing to the ground state. In contrast, photoexcitation of K containing a 13-cis, 15-anti chromophore leads to markedly multi-exponential excited state decay including much slower stages. QM/MM calculations, aimed to interpret these results, highlight the crucial role of protonation, showing that the classic quadrupole counterion model poorly reproduces spectral data and dynamics. Single protonation of ASP212 rectifies discrepancies and predicts triple ground state structural heterogeneity aligning with experimental observations. These findings prompt a reevaluation of counter ion protonation in bacteriorhodopsin and contribute to the broader understanding of its photochemical dynamics.
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Affiliation(s)
- Partha Malakar
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Samira Gholami
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy
| | - Mohammad Aarabi
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy
| | - Ivan Rivalta
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy
- ENSL, CNRS, Laboratoire de Chimie UMR 5182, 46 allée d'Italie, 69364, Lyon, France
| | - Mordechai Sheves
- Department of Molecular Chemistry and Materials Science, The Weizmann Institute of Science, Rehovot, 7610001, Israel.
| | - Marco Garavelli
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy.
| | - Sanford Ruhman
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
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3
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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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4
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Hontani Y, Ganapathy S, Frehan S, Kloz M, de Grip WJ, Kennis JTM. Photoreaction Dynamics of Red-Shifting Retinal Analogues Reconstituted in Proteorhodopsin. J Phys Chem B 2019; 123:4242-4250. [PMID: 30998011 PMCID: PMC6526469 DOI: 10.1021/acs.jpcb.9b01136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Microbial rhodopsins
constitute a key protein family in optobiotechnological
applications such as optogenetics and voltage imaging. Spectral tuning
of rhodopsins into the deep-red and near-infrared spectral regions
is of great demand in such applications because more bathochromic
light into the near-infrared range penetrates deeper in living tissue.
Recently, retinal analogues have been successfully used in ion transporting
and fluorescent rhodopsins to achieve red-shifted absorption, activity,
and emission properties. Understanding their photochemical mechanism
is essential for further design of appropriate retinal analogues but
is yet only poorly understood for most retinal analogue pigments.
Here, we report the photoreaction dynamics of red-shifted analogue
pigments of the proton pump proteorhodopsin (PR) containing A2 (all-trans-3,4-dehydroretinal), MOA2 (all-trans-3-methoxy-3,4-dehydroretinal), or DMAR (all-trans-3-dimethylamino-16-nor-1,2,3,4-didehydroretinal), utilizing femto-
to submillisecond transient absorption spectroscopy. We found that
the A2 analogue photoisomerizes in 1.4, 3.0, and/or 13 ps upon 510
nm light illumination, which is comparable to the native retinal (A1)
in PR. On the other hand, the deprotonation of the A2 pigment Schiff
base was observed with a dominant time constant of 67 μs, which
is significantly slower than the A1 pigment. In the MOA2 pigment,
no isomerization or photoproduct formation was detected upon 520 nm
excitation, implying that all the excited molecules returned to the
initial ground state in 2.0 and 4.2 ps. The DMAR pigment showed very
slow excited state dynamics similar to the previously studied MMAR
pigment, but only very little photoproduct was formed. The low efficiency
of the photoproduct formation likely is the reason why DMAR analogue
pigments of PR showed very weak proton pumping activity.
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Affiliation(s)
- Yusaku Hontani
- Department of Physics and Astronomy , Vrije Universiteit , Amsterdam 1081 HV , The Netherlands
| | - Srividya Ganapathy
- Department of Biophysical Organic Chemistry, Leiden Institute of Chemistry, Gorlaeus Laboratories , Leiden University , Leiden 2300 RA , The Netherlands
| | - Sean Frehan
- Department of Physics and Astronomy , Vrije Universiteit , Amsterdam 1081 HV , The Netherlands
| | - Miroslav Kloz
- ELI-Beamlines , Institute of Physics , Na Slovance 2 , Praha 8 182 21 , Czech Republic
| | - Willem J de Grip
- Department of Biophysical Organic Chemistry, Leiden Institute of Chemistry, Gorlaeus Laboratories , Leiden University , Leiden 2300 RA , The Netherlands.,Department of Biochemistry , Radboud University Medical Center , Nijmegen 6500 HB , The Netherlands
| | - John T M Kennis
- Department of Physics and Astronomy , Vrije Universiteit , Amsterdam 1081 HV , The Netherlands
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5
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Singh M, Katayama K, Béjà O, Kandori H. Anion binding to mutants of the Schiff base counterion in heliorhodopsin 48C12. Phys Chem Chem Phys 2019; 21:23663-23671. [DOI: 10.1039/c9cp04102h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The anion binds as the direct H-bonding acceptor of the Schiff base in E107A, while E107Q indirectly accommodates an anion.
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Affiliation(s)
- Manish Singh
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
- OptoBioTechnology Research Center
| | - Oded Béjà
- Faculty of Biology
- Technion – Israel Institute of Technology
- Haifa
- Israel
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
- OptoBioTechnology Research Center
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6
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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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7
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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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8
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Shigeta A, Ito S, Inoue K, Okitsu T, Wada A, Kandori H, Kawamura I. Solid-State Nuclear Magnetic Resonance Structural Study of the Retinal-Binding Pocket in Sodium Ion Pump Rhodopsin. Biochemistry 2017; 56:543-550. [PMID: 28040890 DOI: 10.1021/acs.biochem.6b00999] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The recently identified Krokinobacter rhodopsin 2 (KR2) functions as a light-driven sodium ion pump. The structure of the retinal-binding pocket of KR2 offers important insights into the mechanisms of KR2, which has motif of Asn112, Asp116, and Gln123 (NDQ) that is common among sodium ion pump rhodopsins but is unique among other microbial rhodopsins. Here we present solid-state nuclear magnetic resonance (NMR) characterization of retinal and functionally important residues in the vicinity of retinal in the ground state. We assigned chemical shifts of retinal C14 and C20 atoms, and Tyr218Cζ, Lys255Cε, and the protonated Schiff base of KR2 in lipid environments at acidic and neutral pH. 15N NMR signals of the protonated Schiff base showed a twist around the N-Cε bond under neutral conditions, compared with other microbial rhodopsins. These data indicated that the location of the counterion Asp116 is one helical pitch toward the cytoplasmic side. In acidic environments, the 15N Schiff base signal was shifted to a lower field, indicating that protonation of Asp116 induces reorientation during interactions between the Schiff base and Asp116. In addition, the Tyr218 residue in the vicinity of retinal formed a weak hydrogen bond with Asp251, a temporary Na+-binding site during the photocycle. These features may indicate unique mechanisms of sodium ion pumps.
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Affiliation(s)
- Arisu Shigeta
- Graduate School of Engineering, Yokohama National University , Hodogaya-ku, Yokohama 240-8501, Japan
| | - Shota Ito
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.,PRESTO, Japan Science and Technology Agency (JST) , 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Takashi Okitsu
- Department of Organic Chemistry for Life Science, Kobe Pharmaceutical University , Higashinada-ku, Kobe 658-8558, Japan
| | - Akimori Wada
- Department of Organic Chemistry for Life Science, Kobe Pharmaceutical University , Higashinada-ku, Kobe 658-8558, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Izuru Kawamura
- Graduate School of Engineering, Yokohama National University , Hodogaya-ku, Yokohama 240-8501, Japan
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9
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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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10
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Yamashita H, Inoue K, Shibata M, Uchihashi T, Sasaki J, Kandori H, Ando T. Role of trimer-trimer interaction of bacteriorhodopsin studied by optical spectroscopy and high-speed atomic force microscopy. J Struct Biol 2013; 184:2-11. [PMID: 23462099 DOI: 10.1016/j.jsb.2013.02.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 12/22/2012] [Accepted: 02/12/2013] [Indexed: 10/27/2022]
Abstract
Bacteriorhodopsin (bR) trimers form a two-dimensional hexagonal lattice in the purple membrane of Halobacterium salinarum. However, the physiological significance of forming the lattice has long been elusive. Here, we study this issue by comparing properties of assembled and non-assembled bR trimers using directed mutagenesis, high-speed atomic force microscopy (HS-AFM), optical spectroscopy, and a proton pumping assay. First, we show that the bonds formed between W12 and F135 amino acid residues are responsible for trimer-trimer association that leads to lattice assembly; the lattice is completely disrupted in both W12I and F135I mutants. HS-AFM imaging reveals that both crystallized D96N and non-crystallized D96N/W12I mutants undergo a large conformational change (i.e., outward E-F loop displacement) upon light-activation. However, lattice disruption significantly reduces the rate of conformational change under continuous light illumination. Nevertheless, the quantum yield of M-state formation, measured by low-temperature UV-visible spectroscopy, and proton pumping efficiency are unaffected by lattice disruption. From these results, we conclude that trimer-trimer association plays essential roles in providing bound retinal with an appropriate environment to maintain its full photo-reactivity and in maintaining the natural photo-reaction pathway.
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Affiliation(s)
- Hayato Yamashita
- Department of Physics, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
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11
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Tamogami J, Kikukawa T, Nara T, Shimono K, Demura M, Kamo N. Photoinduced proton release in proteorhodopsin at low pH: the possibility of a decrease in the pK(a) of Asp227. Biochemistry 2012; 51:9290-301. [PMID: 23095117 DOI: 10.1021/bi300940p] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteorhodopsin (PR) is one of the microbial rhodopsins that are found in marine eubacteria and likely functions as an outward light-driven proton pump. Previously, we [Tamogami, J., et al. (2009) Photochem. Photobiol.85, 578-589] reported the occurrence of a photoinduced proton transfer in PR between pH 5 and 10 using a transparent ITO (indium-tin oxide) or SnO(2) electrode that works as a time-resolving pH electrode. In the study presented here, the proton transfer at low pH (<4) was investigated. Under these conditions, Asp97, the primary counterion to the protonated Schiff base, is protonated. We observed a first proton release that was followed by an uptake; during this process, however, the M intermediate did not form. Through the use of experiments with several PR mutants, we found that Asp227 played an essential role in proton release. This residue corresponds to the Asp212 residue of bacteriorhodopsin, the so-called secondary Schiff base counterion. We estimated the pK(a) of this residue in both the dark and the proton-releasing photoproduct to be ~3.0 and ~2.3, respectively. The pK(a) value of Asp227 in the dark was also estimated spectroscopically and was approximately equal to that determined with the ITO experiments, which may imply the possibility of the release of a proton from Asp227. In the absence of Cl(-), we observed the proton release in D227N and found that Asp97, the primary counterion, played a key role. It is inferred that the negative charge is required to stabilize the photoproducts through the deprotonation of Asp227 (first choice), the binding of Cl(-) (second choice), or the deprotonation of Asp97. The photoinduced proton release (possibly by the decrease in the pK(a) of the secondary counterion) in acidic media was also observed in other microbial rhodopsins with the exception of the Anabaena sensory rhodopsin, which lacks the dissociable residue at the position of Asp212 of BR or Asp227 of PR and halorhodopsin. The implication of this pK(a) decrease is discussed.
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Affiliation(s)
- Jun Tamogami
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan.
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12
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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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13
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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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14
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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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15
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Zhou P, Tian F, Zou J, Ren Y, Liu X, Shang Z. Do Halide Motifs Stabilize Protein Architecture? J Phys Chem B 2010; 114:15673-86. [DOI: 10.1021/jp105259d] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Peng Zhou
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, College of Bioengineering, Chongqing University, Chongqing 400044, China, Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China, Department of Biological and Chemical Engineering, Chongqing Education College, Chongqing 400067, China, and Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United
| | - Feifei Tian
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, College of Bioengineering, Chongqing University, Chongqing 400044, China, Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China, Department of Biological and Chemical Engineering, Chongqing Education College, Chongqing 400067, China, and Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United
| | - Jianwei Zou
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, College of Bioengineering, Chongqing University, Chongqing 400044, China, Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China, Department of Biological and Chemical Engineering, Chongqing Education College, Chongqing 400067, China, and Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United
| | - Yanrong Ren
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, College of Bioengineering, Chongqing University, Chongqing 400044, China, Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China, Department of Biological and Chemical Engineering, Chongqing Education College, Chongqing 400067, China, and Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United
| | - Xiuhong Liu
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, College of Bioengineering, Chongqing University, Chongqing 400044, China, Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China, Department of Biological and Chemical Engineering, Chongqing Education College, Chongqing 400067, China, and Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United
| | - Zhicai Shang
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, College of Bioengineering, Chongqing University, Chongqing 400044, China, Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China, Department of Biological and Chemical Engineering, Chongqing Education College, Chongqing 400067, China, and Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United
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16
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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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17
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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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18
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Photoreactions and structural changes of anabaena sensory rhodopsin. SENSORS 2009; 9:9741-804. [PMID: 22303148 PMCID: PMC3267196 DOI: 10.3390/s91209741] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Revised: 10/14/2009] [Accepted: 10/23/2009] [Indexed: 12/05/2022]
Abstract
Anabaena sensory rhodopsin (ASR) is an archaeal-type rhodopsin found in eubacteria. The gene encoding ASR forms a single operon with ASRT (ASR transducer) which is a 14 kDa soluble protein, suggesting that ASR functions as a photochromic sensor by activating the soluble transducer. This article reviews the detailed photoreaction processes of ASR, which were studied by low-temperature Fourier-transform infrared (FTIR) and UV-visible spectroscopy. The former research reveals that the retinal isomerization is similar to bacteriorhodopsin (BR), but the hydrogen-bonding network around the Schiff base and cytoplasmic region is different. The latter study shows the stable photoproduct of the all-trans form is 100% 13-cis, and that of the 13-cis form is 100% all-trans. These results suggest that the structural changes of ASR in the cytoplasmic domain play important roles in the activation of the transducer protein, and photochromic reaction is optimized for its sensor function.
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19
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Yoshitsugu M, Yamada J, Kandori H. Color-changing mutation in the E-F loop of proteorhodopsin. Biochemistry 2009; 48:4324-30. [PMID: 19334675 DOI: 10.1021/bi900228a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
It is usually assumed that only amino acids located near the retinal chromophore are responsible for color tuning of rhodopsins. However, we recently found that replacement of Ala178 with Arg in the E-F loop of proteorhodopsin (PR), an archaeal-type rhodopsin in marine bacteria, shifts the lambda(max) from 525 to 545 nm at neutral pH [Yoshitsugu, M., Shibata, M., Ikeda, D., Furutani, Y., and Kandori, H. (2008) Angew. Chem., Int. Ed. 47, 3923-3926]. Since the location of Ala178 is distant from the retinal chromophore (approximately 25 A), the molecular mechanism of the unusual mutation effect on color tuning is intriguing. Here we studied this mechanism by using additional mutations and some analytical methods. Introduction of Arg into the corresponding amino acid in bacteriorhodopsin (BR, M163R mutant) does not change the absorption spectra, indicating that the effect is specific to PR. Introduction of Arg into the A-B or C-D loop yields little (3 nm) or no color change, respectively. T177R and P180R mutants exhibited absorption spectra identical to that of the wild type, while N176R and S179R mutants exhibit lambda(max) values of 528 and 535 nm, respectively. Therefore, the observed color change is position-specific, being fully effective at position 178 and half-effective at position 179. Salt affects the absorption spectra of wild-type and A178R PR similarly. FTIR spectroscopy at 77 K indicated similar chromophore structures for wild-type and A178R PR, and A178R PR pumps protons normally. We infer that the E-F loop has a unique structure in PR and the mutation of Ala178 disrupts the structure that includes the transmembrane region, leading to the observed changes in color and pK(a).
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Affiliation(s)
- Maiko Yoshitsugu
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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20
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Nakashima K, Nakamura T, Takeuchi S, Shibata M, Demura M, Tahara T, Kandori H. Properties of the Anion-Binding Site of pharaonis Halorhodopsin Studied by Ultrafast Pump−Probe Spectroscopy and Low-Temperature FTIR Spectroscopy. J Phys Chem B 2009; 113:8429-34. [DOI: 10.1021/jp902596k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Keisuke Nakashima
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Hirosawa, Wako 351-0198, Japan, and Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Takumi Nakamura
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Hirosawa, Wako 351-0198, Japan, and Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Satoshi Takeuchi
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Hirosawa, Wako 351-0198, Japan, and Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Mikihiro Shibata
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Hirosawa, Wako 351-0198, Japan, and Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Makoto Demura
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Hirosawa, Wako 351-0198, Japan, and Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Tahei Tahara
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Hirosawa, Wako 351-0198, Japan, and Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Hirosawa, Wako 351-0198, Japan, and Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
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21
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Yoshimoto J, Sandoval CA, Saito S. Aqua-aminoorganoboron Catalyst: Engineering Single Water Molecule to Act as an Acid Catalyst in Nitro Aldol Reaction. CHEM LETT 2008. [DOI: 10.1246/cl.2008.1294] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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22
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Suzuki D, Sudo Y, Furutani Y, Takahashi H, Homma M, Kandori H. Structural Changes of Salinibacter Sensory Rhodopsin I upon Formation of the K and M Photointermediates. Biochemistry 2008; 47:12750-9. [DOI: 10.1021/bi801358b] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daisuke Suzuki
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan, and Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
| | - Yuki Sudo
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan, and Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
| | - Yuji Furutani
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan, and Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
| | - Hazuki Takahashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan, and Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan, and Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
| | - Hideki Kandori
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan, and Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
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23
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Kawanabe A, Furutani Y, Yoon SR, Jung KH, Kandori H. FTIR Study of the L Intermediate of Anabaena Sensory Rhodopsin: Structural Changes in the Cytoplasmic Region. Biochemistry 2008; 47:10033-40. [DOI: 10.1021/bi800941a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Akira Kawanabe
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan, and Department of Life Science and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Shinsu-Dong 1, Mapo-Gu, Seoul, 121-742, Korea
| | - Yuji Furutani
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan, and Department of Life Science and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Shinsu-Dong 1, Mapo-Gu, Seoul, 121-742, Korea
| | - Sa Ryong Yoon
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan, and Department of Life Science and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Shinsu-Dong 1, Mapo-Gu, Seoul, 121-742, Korea
| | - Kwang-Hwan Jung
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan, and Department of Life Science and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Shinsu-Dong 1, Mapo-Gu, Seoul, 121-742, Korea
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan, and Department of Life Science and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Shinsu-Dong 1, Mapo-Gu, Seoul, 121-742, Korea
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24
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Influence of proline on the thermostability of the active site and membrane arrangement of transmembrane proteins. Biophys J 2008; 95:4384-95. [PMID: 18658225 DOI: 10.1529/biophysj.108.136747] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proline residues play a fundamental and subtle role in the dynamics, structure, and function in many membrane proteins. Temperature derivative spectroscopy and differential scanning calorimetry have been used to determine the effect of proline substitution in the structural stability of the active site and transmembrane arrangement of bacteriorhodopsin. We have analyzed the Pro-to-Ala mutation for the helix-embedded prolines Pro50, Pro91, and Pro186 in the native membrane environment. This information has been complemented with the analysis of the respective crystallographic structures by the FoldX force field. Differential scanning calorimetry allowed us to determine distorted membrane arrangement for P50A and P186A. The protein stability was severely affected for P186A and P91A. In the case of Pro91, a single point mutation is capable of strongly slowing down the conformational diffusion along the denaturation coordinate, becoming a barrier-free downhill process above 371 K. Temperature derivative spectroscopy, applied for first time to study thermal stability of proteins, has been used to monitor the stability of the active site of bacteriorhodopsin. The mutation of Pro91 and Pro186 showed the most striking effects on the retinal binding pocket. These residues are the Pro in closer contact to the active site (activation energies for retinal release of 60.1 and 76.8 kcal/mol, respectively, compared to 115.8 kcal/mol for WT). FoldX analysis of the protein crystal structures indicates that the Pro-to-Ala mutations have both local and long-range effects on the structural stability of residues involved in the architecture of the protein and the active site and in the proton pumping function. Thus, this study provides a complete overview of the substitution effect of helix-embedded prolines in the thermodynamic and dynamic stability of a membrane protein, also related to its structure and function.
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Yoshitsugu M, Shibata M, Ikeda D, Furutani Y, Kandori H. Color change of proteorhodopsin by a single amino acid replacement at a distant cytoplasmic loop. Angew Chem Int Ed Engl 2008; 47:3923-6. [PMID: 18404767 DOI: 10.1002/anie.200705989] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Maiko Yoshitsugu
- Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan
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26
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Morgan JE, Gennis RB, Maeda A. A role for internal water molecules in proton affinity changes in the Schiff base and Asp85 for one-way proton transfer in bacteriorhodopsin. Photochem Photobiol 2008; 84:1038-45. [PMID: 18557823 DOI: 10.1111/j.1751-1097.2008.00377.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Light-induced proton pumping in bacteriorhodospin is carried out through five proton transfer steps. We propose that the proton transfer to Asp85 from the Schiff base in the L-to-M transition is accompanied by the relocation of a water cluster on the cytoplasmic side of the Schiff base from a site close to the Schiff base in L to the Phe219-Thr46 region in M. The water cluster present in L, formed at 170 K, is more rigid than that at room temperature. This may be responsible for blocking the conversion of L to M at 170 K. In the photocycle at room temperature, this water cluster returns to the site close to the Schiff base in N, with a rigid structure similar to that of L at 170 K. The increase in the proton affinity of Asp85, which is a prerequisite for the one-way proton transfer in the M-to-N transition, is suggested to be facilitated by a structural change which disrupts interactions between Asp212 and the Schiff base, and between Asp212 and Arg82. We propose that this liberation of Asp212 is accompanied by a rearrangement of the structure of water molecules between Asp85 and Asp212, stabilizing the protonated Asp85 in M.
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Affiliation(s)
- Joel E Morgan
- Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
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27
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Ito M, Sudo Y, Furutani Y, Okitsu T, Wada A, Homma M, Spudich JL, Kandori H. Steric constraint in the primary photoproduct of sensory rhodopsin II is a prerequisite for light-signal transfer to HtrII. Biochemistry 2008; 47:6208-15. [PMID: 18479149 DOI: 10.1021/bi8003507] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sensory rhodopsin II (SRII, also called pharaonis phoborhodopsin, ppR) is responsible for negative phototaxis in Natronomonas pharaonis. Photoisomerization of the retinal chromophore from all- trans to 13- cis initiates conformational changes in the protein, leading to activation of the cognate transducer protein (HtrII). We previously observed enhancement of the C 14-D stretching vibration of the retinal chromophore at 2244 cm (-1) upon formation of the K state and interpreted that a steric constraint occurs at the C 14D group in SRII K. Here, we identify the counterpart of the C 14D group as Thr204, because the C 14-D stretching signal disappeared in T204A, T204S, and T204C mutants as well as a C 14-HOOP (hydrogen out-of-plane) vibration at 864 cm (-1). Although the K state of the wild-type bacteriorhodopsin (BR), a light-driven proton pump, possesses neither 2244 nor 864 cm (-1) bands, both signals appeared for the K state of a triple mutant of BR that functions as a light sensor (P200T/V210Y/A215T). We found a positive correlation between these vibrational amplitudes of the C 14 atom at 77 K and the physiological phototaxis response. These observations strongly suggest that the steric constraint between the C 14 group of retinal and Thr204 of the protein is a prerequisite for light-signal transduction by SRII.
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Affiliation(s)
- Motohiro Ito
- Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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28
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Yoshitsugu M, Shibata M, Ikeda D, Furutani Y, Kandori H. Color Change of Proteorhodopsin by a Single Amino Acid Replacement at a Distant Cytoplasmic Loop. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705989] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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