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Nango E, Royant A, Kubo M, Nakane T, Wickstrand C, Kimura T, Tanaka T, Tono K, Song C, Tanaka R, Arima T, Yamashita A, Kobayashi J, Hosaka T, Mizohata E, Nogly P, Sugahara M, Nam D, Nomura T, Shimamura T, Im D, Fujiwara T, Yamanaka Y, Jeon B, Nishizawa T, Oda K, Fukuda M, Andersson R, Båth P, Dods R, Davidsson J, Matsuoka S, Kawatake S, Murata M, Nureki O, Owada S, Kameshima T, Hatsui T, Joti Y, Schertler G, Yabashi M, Bondar AN, Standfuss J, Neutze R, Iwata S. A three-dimensional movie of structural changes in bacteriorhodopsin. Science 2016; 354:1552-1557. [DOI: 10.1126/science.aah3497] [Citation(s) in RCA: 294] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 11/21/2016] [Indexed: 01/24/2023]
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Bondar AN, Fischer S, Smith JC. Water Pathways in the Bacteriorhodopsin Proton Pump. J Membr Biol 2010; 239:73-84. [DOI: 10.1007/s00232-010-9329-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 11/05/2010] [Indexed: 01/18/2023]
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Bondar AN, Baudry J, Suhai S, Fischer S, Smith JC. Key Role of Active-Site Water Molecules in Bacteriorhodopsin Proton-Transfer Reactions. J Phys Chem B 2008; 112:14729-41. [DOI: 10.1021/jp801916f] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ana-Nicoleta Bondar
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany, Molecular Biophysics Department, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, University of California at Irvine, Department of Physiology and Biophysics and the Center for Biomembrane Systems, Med. Sci. I, D-374, Irvine, California 92697-4560, University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge
| | - Jerome Baudry
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany, Molecular Biophysics Department, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, University of California at Irvine, Department of Physiology and Biophysics and the Center for Biomembrane Systems, Med. Sci. I, D-374, Irvine, California 92697-4560, University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge
| | - Sándor Suhai
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany, Molecular Biophysics Department, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, University of California at Irvine, Department of Physiology and Biophysics and the Center for Biomembrane Systems, Med. Sci. I, D-374, Irvine, California 92697-4560, University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge
| | - Stefan Fischer
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany, Molecular Biophysics Department, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, University of California at Irvine, Department of Physiology and Biophysics and the Center for Biomembrane Systems, Med. Sci. I, D-374, Irvine, California 92697-4560, University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge
| | - Jeremy C. Smith
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany, Molecular Biophysics Department, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, University of California at Irvine, Department of Physiology and Biophysics and the Center for Biomembrane Systems, Med. Sci. I, D-374, Irvine, California 92697-4560, University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge
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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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Iwasa T, Abe E, Yakura Y, Yoshida H, Kamo N. Tryptophan 171 in Pharaonis phoborhodopsin (sensory rhodopsin II) interacts with the chromophore retinal and its substitution with alanine or threonine slowed down the decay of M- and O-intermediate. Photochem Photobiol 2007; 83:328-35. [PMID: 17029563 DOI: 10.1562/2006-06-15-ra-928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Pharaonis phoborhodopsin (ppR), also called pharaonis sensory rhodopsin II, NpSRII, is a photoreceptor for the photophobic response of Natronomonas pharaonis. Tryptophan 182 (W182) of bacteriorhodopsin (bR) is near the chromophore retinal and has been suggested to interact with retinal during the photoreaction and also to be involved in the hydrogen-bonding network around the retinal. W182 of bR is conserved in ppR as tryptophan 171 (W171). To elucidate whether W171 of ppR interacts with retinal during the photoreaction and/or is involved in the hydrogen-bonding network as in bR, we formed W171-substituted mutants of ppR, W171A and W171T. Our low-temperature spectroscopic study has revealed that the substitution of W171 to Ala or Thr resulted in the stabilization of M- and O-intermediates. The stability of M and absorption spectral changes during the M-decay were different depending on the substituted residue. These findings suggest that W171 in ppR interacts with retinal and the degree of the interaction depends on the substituted residues, which might be rate determining in the M-decay. In addition, the involvement of W171 in the hydrogen-bonding network is suggested by the O-decay. We also found that glycerol slowed the decay of M and not of O.
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Affiliation(s)
- Tatsuo Iwasa
- Department of Materials Science and Engineering, Muroran Institute of Technology, Muroran, Japan.
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Maeda A, Morgan JE, Gennis RB, Ebrey TG. Water as a cofactor in the unidirectional light-driven proton transfer steps in bacteriorhodopsin. Photochem Photobiol 2007; 82:1398-405. [PMID: 16634652 DOI: 10.1562/2006-01-16-ir-779] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Recent evidence for involvement of internal water molecules in the mechanism of bacteriorhodopsin is reviewed. Water O-H stretching vibration bands in the Fourier transform IR difference spectra of the L, M and N intermediates of bacteriorhodopsin were analyzed by photoreactions at cryogenic temperatures. A broad vibrational band in L was shown to be due to formation of a structure of water molecules connecting the Schiff base to the Thr46-Asp96 region. This structure disappears in the M intermediate, suggesting that it is involved in transient stabilization of the L intermediate prior to proton transfer from the Schiff base to Asp85. The interaction of the Schiff base with a water molecule is restored in the N intermediate. We propose that water is a critical mobile component of bacteriorhodopsin, forming organized structures in the transient intermediates during the photocycle and, to a large extent, determining the chemical behavior of these transient states.
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Affiliation(s)
- Akio Maeda
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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Morgan JE, Vakkasoglu AS, Gennis RB, Maeda A. Water structural changes in the L and M photocycle intermediates of bacteriorhodopsin as revealed by time-resolved step-scan Fourier transform infrared (FTIR) spectroscopy. Biochemistry 2007; 46:2787-96. [PMID: 17300175 PMCID: PMC3972897 DOI: 10.1021/bi0616596] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In previous Fourier transform infrared (FTIR) studies of the photocycle intermediates of bacteriorhodopsin at cryogenic temperatures, water molecules were observed in the L intermediate, in the region surrounded by protein residues between the Schiff base and Asp96. In the M intermediate, the water molecules had moved away toward the Phe219-Thr46 region. To evaluate the relevance of this scheme at room temperature, time-resolved FTIR difference spectra of bacteriorhodopsin, including the water O-H stretching vibration frequency regions, were recorded in the micro- and millisecond time ranges. Vibrational changes of weakly hydrogen-bonded water molecules were observed in L, M, and N. In each of these intermediates, the depletion of a water O-H stretching vibration at 3645 cm-1, originating from the initial unphotolyzed bacteriorhodopsin, was observed as a trough in the difference spectrum. This vibration is due to the dangling O-H group of a water molecule, which interacts with Asp85, and its absence in each of these intermediates indicates that there is perturbation of this O-H group. The formation of M is accompanied by the appearance of water O-H stretching vibrations at 3670 and 3657 cm-1, the latter of which persists to N. The 3670 cm-1 band of M is due to water molecules present in the region surrounded by Thr46, Asp96, and Phe219. The formation of L at 298 K is accompanied by the perturbations of Asp96 and the Schiff base, although in different ways from what is observed at 170 K. Changes in a broad water vibrational feature, centered around 3610 cm-1, are kinetically correlated with the L-M transition. These results imply that, even at room temperature, water molecules interact with Asp96 and the Schiff base in L, although with a less rigid structure than at cryogenic temperatures.
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Affiliation(s)
- Joel E. Morgan
- Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Room 2237, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180
| | - Ahmet S. Vakkasoglu
- Center for Biophysics and Computational Biology, University of Illinois at Urbana/Champaign, Urbana, IL, 61801
| | - Robert B. Gennis
- Center for Biophysics and Computational Biology, University of Illinois at Urbana/Champaign, Urbana, IL, 61801
- Department of Biochemistry, University of Illinois at Urbana/Champaign, Urbana, IL 61801
| | - Akio Maeda
- Department of Biochemistry, University of Illinois at Urbana/Champaign, Urbana, IL 61801
- Author to whom correspondence should be addressed. Phone and Fax: +81-774-22-8781.
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Lanyi JK, Schobert B. Structural changes in the L photointermediate of bacteriorhodopsin. J Mol Biol 2006; 365:1379-92. [PMID: 17141271 PMCID: PMC1851893 DOI: 10.1016/j.jmb.2006.11.016] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2006] [Revised: 10/27/2006] [Accepted: 11/03/2006] [Indexed: 11/25/2022]
Abstract
The L to M reaction of the bacteriorhodopsin photocycle includes the crucial proton transfer from the retinal Schiff base to Asp85. In spite of the importance of the L state in deciding central issues of the transport mechanism in this pump, the serious disagreements among the three published crystallographic structures of L have remained unresolved. Here, we report on the X-ray diffraction structure of the L state, to 1.53-1.73 A resolutions, from replicate data sets collected from six independent crystals. Unlike earlier studies, the partial occupancy refinement uses diffraction intensities from the same crystals before and after the illumination to produce the trapped L state. The high reproducibility of inter-atomic distances, and bond angles and torsions of the retinal, lends credibility to the structural model. The photoisomerized 13-cis retinal in L is twisted at the C(13)=C(14) and C(15)=NZ double-bonds, and the Schiff base does not lose its connection to Wat402 and, therefore, to the proton acceptor Asp85. The protonation of Asp85 by the Schiff base in the L-->M reaction is likely to occur, therefore, via Wat402. It is evident from the structure of the L state that various conformational changes involving hydrogen-bonding residues and bound water molecules begin to propagate from the retinal to the protein at this stage already, and in both extracellular and cytoplasmic directions. Their rationales in the transport can be deduced from the way their amplitudes increase in the intermediates that follow L in the reaction cycle, and from the proton transfer reactions with which they are associated.
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Affiliation(s)
- Janos K Lanyi
- Department of Physiology & Biophysics, University of California, Irvine, CA 92697, USA.
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Maeda A, Morgan JE, Gennis RB, Ebrey TG. Water as a Cofactor in the Unidirectional Light-Driven Proton Transfer Steps in Bacteriorhodopsin. Photochem Photobiol 2006. [DOI: 10.1111/j.1751-1097.2006.tb09791.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Lanyi JK. Proton transfers in the bacteriorhodopsin photocycle. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:1012-8. [PMID: 16376293 DOI: 10.1016/j.bbabio.2005.11.003] [Citation(s) in RCA: 158] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2005] [Revised: 11/08/2005] [Accepted: 11/10/2005] [Indexed: 11/23/2022]
Abstract
The steps in the mechanism of proton transport in bacteriorhodopsin include examples for most kinds of proton transfer reactions that might occur in a transmembrane pump: proton transfer via a bridging water molecule, coupled protonation/deprotonation of two buried groups separated by a considerable distance, long-range proton migration over a hydrogen-bonded aqueous chain, and capture as well as release of protons at the membrane-water interface. The conceptual and technical advantages of this system have allowed close examination of many of these model reactions, some at an atomic level.
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Affiliation(s)
- Janos K Lanyi
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA.
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Lanyi JK. What is the real crystallographic structure of the L photointermediate of bacteriorhodopsin? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2004; 1658:14-22. [PMID: 15282169 DOI: 10.1016/j.bbabio.2004.03.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2004] [Revised: 03/16/2004] [Accepted: 03/16/2004] [Indexed: 11/21/2022]
Abstract
In the last few years, three laboratories have reported three entirely different crystallographic models for the L photointermediate of bacteriorhodopsin. All are from X-ray diffraction of illuminated crystals that contain L in photostationary states created at similar cryogenic temperatures. This article compares the models and their implications, the crystallographic statistics and the methods used to derive them, as well as their agreement with non-crystallographic information.
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Affiliation(s)
- Janos K Lanyi
- Department of Physiology and Biophysics, College of Medicine, University of California, 349-D Medical Science, Irvine, CA 92697-4560, USA.
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