1
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Schubert L, Chen JL, Fritz T, Marxer F, Langner P, Hoffmann K, Gamiz-Hernandez AP, Kaila VRI, Schlesinger R, Heberle J. Proton Release Reactions in the Inward H + Pump NsXeR. J Phys Chem B 2023; 127:8358-8369. [PMID: 37729557 DOI: 10.1021/acs.jpcb.3c04100] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Directional ion transport across biological membranes plays a central role in many cellular processes. Elucidating the molecular determinants for vectorial ion transport is key to understanding the functional mechanism of membrane-bound ion pumps. The extensive investigation of the light-driven proton pump bacteriorhodopsin from Halobacterium salinarum(HsBR) enabled a detailed description of outward proton transport. Although the structure of inward-directed proton pumping rhodopsins is very similar to HsBR, little is known about their protonation pathway, and hence, the molecular reasons for the vectoriality of proton translocation remain unclear. Here, we employ a combined experimental and theoretical approach to tracking protonation steps in the light-driven inward proton pump xenorhodopsin from Nanosalina sp. (NsXeR). Time-resolved infrared spectroscopy reveals the transient deprotonation of D220 concomitantly with deprotonation of the retinal Schiff base. Our molecular dynamics simulations support a proton release pathway from the retinal Schiff base via a hydrogen-bonded water wire leading to D220 that could provide a putative gating point for the proton release and with allosteric interactions to the retinal Schiff base. Our findings support the key role of D220 in mediating proton release to the cytoplasmic side and provide evidence that this residue is not the primary proton acceptor of the proton transiently released by the retinal Schiff base.
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Affiliation(s)
- Luiz Schubert
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195Berlin, Germany
| | - Jheng-Liang Chen
- Genetic Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195Berlin, Germany
| | - Tobias Fritz
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Florina Marxer
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195Berlin, Germany
| | - Pit Langner
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195Berlin, Germany
| | - Kirsten Hoffmann
- Genetic Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195Berlin, Germany
| | - Ana P Gamiz-Hernandez
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ramona Schlesinger
- Genetic Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195Berlin, Germany
| | - Joachim Heberle
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195Berlin, Germany
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2
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Suzuki K, Del Carmen Marín M, Konno M, Bagherzadeh R, Murata T, Inoue K. Structural characterization of proton-pumping rhodopsin lacking a cytoplasmic proton donor residue by X-ray crystallography. J Biol Chem 2022; 298:101722. [PMID: 35151692 PMCID: PMC8927995 DOI: 10.1016/j.jbc.2022.101722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/05/2022] [Accepted: 02/08/2022] [Indexed: 01/10/2023] Open
Abstract
DTG/DTS rhodopsin, which was named based on a three-residue motif (DTG or DTS) that is important for its function, is a light-driven proton-pumping microbial rhodopsin using a retinal chromophore. In contrast to other light-driven ion-pumping rhodopsins, DTG/DTS rhodopsin does not have a cytoplasmic proton donor residue, such as Asp, Glu, or Lys. Because of the lack of cytoplasmic proton donor residue, proton directly binds to the retinal chromophore from the cytoplasmic solvent. However, mutational experiments that showed the complicated effects of mutations were not able to clarify the roles played by each residue, and the detail of proton uptake pathway is unclear because of the lack of structural information. To understand the proton transport mechanism of DTG/DTS rhodopsin, here we report the three-dimensional structure of one of the DTG/DTS rhodopsins, PspR from Pseudomonas putida, by X-ray crystallography. We show that the structure of the cytoplasmic side of the protein is significantly different from that of bacteriorhodopsin, the best-characterized proton-pumping rhodopsin, and large cytoplasmic cavities were observed. We propose that these hydrophilic cytoplasmic cavities enable direct proton uptake from the cytoplasmic solvent without the need for a specialized cytoplasmic donor residue. The introduction of carboxylic residues homologous to the cytoplasmic donors in other proton-pumping rhodopsins resulted in higher pumping activity with less pH dependence, suggesting that DTG/DTS rhodopsins are advantageous for producing energy and avoiding intracellular alkalization in soil and plant-associated bacteria.
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Affiliation(s)
- Kano Suzuki
- Department of Chemistry, Graduate School of Science, Chiba University, Inage, Chiba, Japan
| | | | - Masae Konno
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Reza Bagherzadeh
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Inage, Chiba, Japan; Membrane Protein Research and Molecular Chirality Research Centers, Chiba University, Inage, Chiba, Japan.
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba, Japan.
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3
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Maag D, Mast T, Elstner M, Cui Q, Kubař T. O to bR transition in bacteriorhodopsin occurs through a proton hole mechanism. Proc Natl Acad Sci U S A 2021; 118:e2024803118. [PMID: 34561302 PMCID: PMC8488608 DOI: 10.1073/pnas.2024803118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2021] [Indexed: 12/27/2022] Open
Abstract
Extensive classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations are used to establish the structural features of the O state in bacteriorhodopsin (bR) and its conversion back to the bR ground state. The computed free energy surface is consistent with available experimental data for the kinetics and thermodynamics of the O to bR transition. The simulation results highlight the importance of the proton release group (PRG, consisting of Glu194/204) and the conserved arginine 82 in modulating the hydration level of the protein cavity. In particular, in the O state, deprotonation of the PRG and downward rotation of Arg82 lead to elevated hydration level and a continuous water network that connects the PRG to the protonated Asp85. Proton exchange through this water network is shown by ∼0.1-μs semiempirical QM/MM free energy simulations to occur through the generation and propagation of a proton hole, which is relayed by Asp212 and stabilized by Arg82. This mechanism provides an explanation for the observation that the D85S mutant of bacteriorhodopsin pumps chloride ions. The electrostatics-hydration coupling mechanism and the involvement of all titration states of water are likely applicable to many biomolecules involved in bioenergetic transduction.
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Affiliation(s)
- Denis Maag
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Thilo Mast
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
- Institute for Biological Interfaces, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Qiang Cui
- Department of Chemistry, Boston University, Boston, MA 02215
- Department of Physics, Boston University, Boston, MA 02215
- Department of Biomedical Engineering, Boston University, Boston, MA 02215
| | - Tomáš Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany;
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4
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Inoue K. Diversity, Mechanism, and Optogenetic Application of Light-Driven Ion Pump Rhodopsins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:89-126. [PMID: 33398809 DOI: 10.1007/978-981-15-8763-4_6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ion-transporting microbial rhodopsins are widely used as major molecular tools in optogenetics. They are categorized into light-gated ion channels and light-driven ion pumps. While the former passively transport various types of cations and anions in a light-dependent manner, light-driven ion pumps actively transport specific ions, such as H+, Na+, Cl-, against electrophysiological potential by using light energy. Since the ion transport by these pumps induces hyperpolarization of membrane potential and inhibit neural firing, light-driven ion-pumping rhodopsins are mostly applied as inhibitory optogenetics tools. Recent progress in genome and metagenome sequencing identified more than several thousands of ion-pumping rhodopsins from a wide variety of microbes, and functional characterization studies has been revealing many new types of light-driven ion pumps one after another. Since light-gated channels were reviewed in other chapters in this book, here the rapid progress in functional characterization, molecular mechanism study, and optogenetic application of ion-pumping rhodopsins were reviewed.
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Affiliation(s)
- Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Chiba, Japan.
- PRESTO, Japan Science and Technology Agency, Saitama, Japan.
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5
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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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6
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Conversion of a light-driven proton pump into a light-gated ion channel. Sci Rep 2015; 5:16450. [PMID: 26597707 PMCID: PMC4657025 DOI: 10.1038/srep16450] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 10/14/2015] [Indexed: 12/19/2022] Open
Abstract
Interest in microbial rhodopsins with ion pumping activity has been revitalized in the context of optogenetics, where light-driven ion pumps are used for cell hyperpolarization and voltage sensing. We identified an opsin-encoding gene (CsR) in the genome of the arctic alga Coccomyxa subellipsoidea C-169 that can produce large photocurrents in Xenopus oocytes. We used this property to analyze the function of individual residues in proton pumping. Modification of the highly conserved proton shuttling residue R83 or its interaction partner Y57 strongly reduced pumping power. Moreover, this mutation converted CsR at moderate electrochemical load into an operational proton channel with inward or outward rectification depending on the amino acid substitution. Together with molecular dynamics simulations, these data demonstrate that CsR-R83 and its interacting partner Y57 in conjunction with water molecules forms a proton shuttle that blocks passive proton flux during the dark-state but promotes proton movement uphill upon illumination.
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7
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Lórenz-Fonfría VA, Heberle J. Channelrhodopsin unchained: structure and mechanism of a light-gated cation channel. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:626-42. [PMID: 24212055 DOI: 10.1016/j.bbabio.2013.10.014] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 10/21/2013] [Accepted: 10/30/2013] [Indexed: 12/25/2022]
Abstract
The new and vibrant field of optogenetics was founded by the seminal discovery of channelrhodopsin, the first light-gated cation channel. Despite the numerous applications that have revolutionised neurophysiology, the functional mechanism is far from understood on the molecular level. An arsenal of biophysical techniques has been established in the last decades of research on microbial rhodopsins. However, application of these techniques is hampered by the duration and the complexity of the photoreaction of channelrhodopsin compared with other microbial rhodopsins. A particular interest in resolving the molecular mechanism lies in the structural changes that lead to channel opening and closure. Here, we review the current structural and mechanistic knowledge that has been accomplished by integrating the static structure provided by X-ray crystallography and electron microscopy with time-resolved spectroscopic and electrophysiological techniques. The dynamical reactions of the chromophore are effectively coupled to structural changes of the protein, as shown by ultrafast spectroscopy. The hierarchical sequence of structural changes in the protein backbone that spans the time range from 10(-12)s to 10(-3)s prepares the channel to open and, consequently, cations can pass. Proton transfer reactions that are associated with channel gating have been resolved. In particular, glutamate 253 and aspartic acid 156 were identified as proton acceptor and donor to the retinal Schiff base. The reprotonation of the latter is the critical determinant for channel closure. The proton pathway that eventually leads to proton pumping is also discussed. 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)
- Víctor A Lórenz-Fonfría
- Freie Universität Berlin, Experimental Molecular Biophysics, Arnimallee 14, 14195 Berlin, Germany
| | - Joachim Heberle
- Freie Universität Berlin, Experimental Molecular Biophysics, Arnimallee 14, 14195 Berlin, Germany.
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8
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Friedman R, Nachliel E, Gutman M. Protein surface dynamics: interaction with water and small solutes. J Biol Phys 2013; 31:433-52. [PMID: 23345909 DOI: 10.1007/s10867-005-0171-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Previous time resolved measurements had indicated that protons could propagate on the surface of a protein, or a membrane, by a special mechanism that enhances the shuttle of the proton towards a specific site [1]. It was proposed that a proper location of residues on the surface contributes to the proton shuttling function. In the present study, this notion was further investigated using molecular dynamics, with only the mobile charge replaced by Na(+) and Cl(-) ions. A molecular dynamics simulation of a small globular protein (the S6 of the bacterial ribosome) was carried out in the presence of explicit water molecules and four pairs of Na(+) and Cl(-) ions. A 10 ns simulation indicated that the ions and the protein's surface were in equilibrium, with rapid passage of the ions between the protein's surface and the bulk. Yet it was noted that, close to some domains, the ions extended their duration near the surface, suggesting that the local electrostatic potential prevented them from diffusing to the bulk. During the time frame in which the ions were detained next to the surface, they could rapidly shuttle between various attractor sites located under the electrostatic umbrella. Statistical analysis of molecular dynamics and electrostatic potential/entropy consideration indicated that the detainment state is an energetic compromise between attractive forces and entropy of dilution. The similarity between the motion of free ions next to a protein and the proton transfer on the protein's surface are discussed.
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Affiliation(s)
- Ran Friedman
- Laser Laboratory for Fast Reactions in Biology, Department of Biochemistry, The George S. Wise Faculty for Life Sciences, Tel Aviv University, Tel Aviv, Israel
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9
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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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10
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Low temperature FTIR spectroscopy provides new insights in the pH-dependent proton pathway of proteorhodopsin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1583-90. [DOI: 10.1016/j.bbabio.2011.09.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 08/25/2011] [Accepted: 09/05/2011] [Indexed: 11/15/2022]
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11
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Lórenz-Fonfría VA, Kandori H, Padrós E. Probing specific molecular processes and intermediates by time-resolved Fourier transform infrared spectroscopy: application to the bacteriorhodopsin photocycle. J Phys Chem B 2011; 115:7972-85. [PMID: 21615095 DOI: 10.1021/jp201739w] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a general approach for probing the kinetics of specific molecular processes in proteins by time-resolved Fourier transform infrared (IR) spectroscopy. Using bacteriorhodopsin (bR) as a model we demonstrate that by appropriately monitoring some selected IR bands it is possible obtaining the kinetics of the most important events occurring in the photocycle, namely changes in the chromophore and the protein backbone conformation, and changes in the protonation state of the key residues implicated in the proton transfers. Besides confirming widely accepted views of the bR photocycle, our analysis also sheds light into some disputed issues: the degree of retinal torsion in the L intermediate to respect the ground state; the possibility of a proton transfer from Asp85 to Asp212; the relationship between the protonation/deprotonation of Asp85 and the proton release complex; and the timing of the protein backbone dynamics. By providing a direct way to estimate the kinetics of photocycle intermediates the present approach opens new prospects for a robust quantitative kinetic analysis of the bR photocycle, which could also benefit the study of other proteins involved in photosynthesis, in phototaxis, or in respiratory chains.
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Affiliation(s)
- Víctor A Lórenz-Fonfría
- Unitat de Biofísica, Departament de Bioquímica i de Biologia Molecular, and Centre d'Estudis en Biofísica, Universitat Autònoma de Barcelona, Barcelona 08193, Spain.
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12
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Jiang X, Engelhard M, Ataka K, Heberle J. Molecular Impact of the Membrane Potential on the Regulatory Mechanism of Proton Transfer in Sensory Rhodopsin II. J Am Chem Soc 2010; 132:10808-15. [DOI: 10.1021/ja102295g] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiue Jiang
- Department of Chemistry, Biophysical Chemistry (PC III), Bielefeld University, 33615 Bielefeld, Germany, MaxPlanck Institute of Molecular Physiology, 44221 Dortmund, Germany, Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany, and Japan Science and Technology Agency, 102-0075, Tokyo, Japan
| | - Martin Engelhard
- Department of Chemistry, Biophysical Chemistry (PC III), Bielefeld University, 33615 Bielefeld, Germany, MaxPlanck Institute of Molecular Physiology, 44221 Dortmund, Germany, Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany, and Japan Science and Technology Agency, 102-0075, Tokyo, Japan
| | - Kenichi Ataka
- Department of Chemistry, Biophysical Chemistry (PC III), Bielefeld University, 33615 Bielefeld, Germany, MaxPlanck Institute of Molecular Physiology, 44221 Dortmund, Germany, Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany, and Japan Science and Technology Agency, 102-0075, Tokyo, Japan
| | - Joachim Heberle
- Department of Chemistry, Biophysical Chemistry (PC III), Bielefeld University, 33615 Bielefeld, Germany, MaxPlanck Institute of Molecular Physiology, 44221 Dortmund, Germany, Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany, and Japan Science and Technology Agency, 102-0075, Tokyo, Japan
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13
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Phatak P, Frähmcke JS, Wanko M, Hoffmann M, Strodel P, Smith J, Suhai S, Bondar AN, Elstner M. Long-distance proton transfer with a break in the bacteriorhodopsin active site. J Am Chem Soc 2009; 131:7064-78. [PMID: 19405533 PMCID: PMC2746972 DOI: 10.1021/ja809767v] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacteriorhodopsin is a proton-pumping membrane protein found in the plasma membrane of the archaeon Halobacterium salinarium. Light-induced isomerization of the retinal chromophore from all-trans to 13-cis leads to a sequence of five conformation-coupled proton transfer steps and the net transport of one proton from the cytoplasmic to the extracellular side of the membrane. The mechanism of the long-distance proton transfer from the primary acceptor Asp85 to the extracellular proton release group during the O --> bR is poorly understood. Experiments suggest that this long-distance transfer could involve a transient state [O] in which the proton resides on the intermediate carrier Asp212. To assess whether the transient protonation of Asp212 participates in the deprotonation of Asp85, we performed hybrid Quantum Mechanics/Molecular Mechanics proton transfer calculations using different protein structures and with different retinal geometries and active site water molecules. The structural models were assessed by computing UV-vis excitation energies and C=O vibrational frequencies. The results indicate that a transient [O] conformer with protonated Asp212 could indeed be sampled during the long-distance proton transfer to the proton release group. Our calculations suggest that, in the starting proton transfer state O, the retinal is strongly twisted and at least three water molecules are present in the active site.
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Affiliation(s)
- Prasad Phatak
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, D-38106 Braunschweig, Germany
| | - Jan S. Frähmcke
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, D-38106 Braunschweig, Germany
| | - Marius Wanko
- BCCMS, Universität Bremen, D-28334 Bremen, Germany
| | | | - Paul Strodel
- Accelrys Ltd., Cambridge CB4 0WN, United Kingdom
| | - Jeremy Smith
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120, Heidelberg, Germany
- Center for Molecular Biophysics, Oak Ridge National Laboratory, PO BOX 2008 MS6164, Oak Ridge, Tennessee 37831, USA
- Department of Biochemistry and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Ave, Knoxville Tennessee 37996, USA
| | - Sándor Suhai
- Molecular Biophysics Department, German Cancer Research Institute, Im Neuheimer Feld 280, D-69120, Heidelberg, Germany
| | - Ana-Nicoleta Bondar
- Molecular Biophysics Department, German Cancer Research Institute, Im Neuheimer Feld 280, D-69120, Heidelberg, Germany
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120, Heidelberg, Germany
- Department of Physiology and Biophysics and the Center for Biomembrane Systems, University of California at Irvine, Med. Sci. I, D-347, Irvine, CA 92697, USA
| | - Marcus Elstner
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, D-38106 Braunschweig, Germany
- Molecular Biophysics Department, German Cancer Research Institute, Im Neuheimer Feld 280, D-69120, Heidelberg, Germany
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14
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Kitade Y, Furutani Y, Kamo N, Kandori H. Proton Release Group of pharaonis Phoborhodopsin Revealed by ATR-FTIR Spectroscopy. Biochemistry 2009; 48:1595-603. [DOI: 10.1021/bi801984u] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuya Kitade
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, and Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Yuji Furutani
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, and Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Naoki Kamo
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, and Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, and Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
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15
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Barth A. Infrared spectroscopy of proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:1073-101. [PMID: 17692815 DOI: 10.1016/j.bbabio.2007.06.004] [Citation(s) in RCA: 2864] [Impact Index Per Article: 168.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Revised: 06/18/2007] [Accepted: 06/19/2007] [Indexed: 12/12/2022]
Abstract
This review discusses the application of infrared spectroscopy to the study of proteins. The focus is on the mid-infrared spectral region and the study of protein reactions by reaction-induced infrared difference spectroscopy.
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Affiliation(s)
- Andreas Barth
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden.
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16
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Friedman R, Nachliel E, Gutman M. Molecular dynamics of a protein surface: ion-residues interactions. Biophys J 2005; 89:768-81. [PMID: 15894639 PMCID: PMC1366628 DOI: 10.1529/biophysj.105.058917] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2005] [Accepted: 04/28/2005] [Indexed: 11/18/2022] Open
Abstract
Time-resolved measurements indicated that protons could propagate on the surface of a protein or a membrane by a special mechanism that enhanced the shuttle of the proton toward a specific site. It was proposed that a suitable location of residues on the surface contributes to the proton shuttling function. In this study, this notion was further investigated by the use of molecular dynamics simulations, where Na(+) and Cl(-) are the ions under study, thus avoiding the necessity for quantum mechanical calculations. Molecular dynamics simulations were carried out using as a model a few Na(+) and Cl(-) ions enclosed in a fully hydrated simulation box with a small globular protein (the S6 of the bacterial ribosome). Three independent 10-ns-long simulations indicated that the ions and the protein's surface were in equilibrium, with rapid passage of the ions between the protein's surface and the bulk. However, it was noted that close to some domains the ions extended their duration near the surface, thus suggesting that the local electrostatic potential hindered their diffusion to the bulk. During the time frame in which the ions were detained next to the surface, they could rapidly shuttle between various attractor sites located under the electrostatic umbrella. Statistical analysis of the molecular dynamics and electrostatic potential/entropy consideration indicated that the detainment state is an energetic compromise between attractive forces and entropy of dilution. The similarity between the motion of free ions next to a protein and the proton transfer on the protein's surface are discussed.
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Affiliation(s)
- Ran Friedman
- Laser Laboratory for Fast Reactions in Biology, Department of Biochemistry, The George S. Wise Faculty for Life Sciences, Tel Aviv University, Israel
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17
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Shibata A, Sakata A, Ueno S, Hori T, Minami K, Baba Y, Kamo N. Regeneration and inhibition of proton pumping activity of bacteriorhodopsin blue membrane by cationic amine anesthetics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2005; 1669:17-25. [PMID: 15842995 DOI: 10.1016/j.bbamem.2005.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2004] [Revised: 02/03/2005] [Accepted: 02/04/2005] [Indexed: 11/15/2022]
Abstract
Bacteriorhodopsin (bR) is the prototype of an integral membrane protein with seven membrane-spanning alpha-helices and serves as a model of the G-protein-coupled drug receptors. This study is aimed at reaching a greater understanding of the role of amine local anesthetic cations on the proton transport in the bR protein, and furthermore, the functional role of "the cation" in the proton pumping mechanism. The effect of the amine anesthetic cations on the proton pump in the bR blue membrane was compared with those by divalent (Ca2+, Mg2+ and Mn2+) and monovalent metal cations (Li+, Na+, K+ and Cs+), which are essential for the correct functioning of the proton pumping of the bR protein. The results suggest that the interacting site of the divalent cation to the bR membrane may differ from that of the monovalent metal cation. The electric current profile of the bR blue membrane in the presence of the amine anesthetic cations was biphasic, involving the generation and inhibition of the proton pumping activity in a concentration-dependent manner. The extent of the regeneration of the proton pump by the additives increased in the order of monovalent metal cation<monovalent amine anesthetic cation<divalent metal cation. We found that organic cations such as the amine anesthetics can also regenerate the proton pump in the bR protein. The inhibition of proton transport in the bR protein by the anesthetic cations was elucidated using the wild type, the E204Q and the D96N mutated bRs. The hydrophobic interaction of the amine anesthetics with the bR protein plays an important part in inhibiting the bR proton pump.
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Affiliation(s)
- Akira Shibata
- Faculty of Pharmaceutical Sciences, The University of Tokushima, Shomachi, Tokushima 770-8505, Japan.
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18
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Cao ZW, Xue Y, Han LY, Xie B, Zhou H, Zheng CJ, Lin HH, Chen YZ. MoViES: molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids. Nucleic Acids Res 2004; 32:W679-85. [PMID: 15215475 PMCID: PMC441522 DOI: 10.1093/nar/gkh384] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Analysis of vibrational motions and thermal fluctuational dynamics is a widely used approach for studying structural, dynamic and functional properties of proteins and nucleic acids. Development of a freely accessible web server for computation of vibrational and thermal fluctuational dynamics of biomolecules is thus useful for facilitating the relevant studies. We have developed a computer program for computing vibrational normal modes and thermal fluctuational properties of proteins and nucleic acids and applied it in several studies. In our program, vibrational normal modes are computed by using modified AMBER molecular mechanics force fields, and thermal fluctuational properties are computed by means of a self-consistent harmonic approximation method. A web version of our program, MoViES (Molecular Vibrations Evaluation Server), was set up to facilitate the use of our program to study vibrational dynamics of proteins and nucleic acids. This software was tested on selected proteins, which show that the computed normal modes and thermal fluctuational bond disruption probabilities are consistent with experimental findings and other normal mode computations. MoViES can be accessed at http://ang.cz3.nus.edu.sg/cgi-bin/prog/norm.pl.
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Affiliation(s)
- Z W Cao
- Department of Computational Science, National University of Singapore, Blk SOC1, Level 7, 3 Science Drive 2, Singapore 117543, Singapore
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19
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Abstract
Fourier transform infrared and Raman spectroscopy, solid-state NMR, and X-ray crystallography have contributed detailed information about the structural changes in the proton transport cycle of the light-driven pump, bacteriorhodopsin. The results over the past few years add up to a step-by-step description of the configurational changes of the photoisomerized retinal, how these changes result in internal proton transfers and the release of a proton to the extracellular surface and uptake on the other side, as well as the conservation and transformation of excess free energy during the cycle.
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Affiliation(s)
- Janos K Lanyi
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, USA.
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20
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Tatulian SA. Attenuated Total Reflection Fourier Transform Infrared Spectroscopy: A Method of Choice for Studying Membrane Proteins and Lipids†. Biochemistry 2003; 42:11898-907. [PMID: 14556620 DOI: 10.1021/bi034235+] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Suren A Tatulian
- Biomolecular Science Center and Department of Molecular Biology and Microbiology, University of Central Florida, Orlando, Florida 32826, USA.
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21
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Nyquist RM, Heitbrink D, Bolwien C, Gennis RB, Heberle J. Direct observation of protonation reactions during the catalytic cycle of cytochrome c oxidase. Proc Natl Acad Sci U S A 2003; 100:8715-20. [PMID: 12851460 PMCID: PMC166378 DOI: 10.1073/pnas.1530408100] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2003] [Indexed: 11/18/2022] Open
Abstract
Cytochrome c oxidase, the terminal protein in the respiratory chain, converts oxygen into water and helps generate the electrochemical gradient used in the synthesis of ATP. The catalytic action of cytochrome c oxidase involves electron transfer, proton transfer, and O2 reduction. These events trigger specific molecular changes at the active site, which, in turn, influence changes throughout the protein, including alterations of amino acid side chain orientations, hydrogen bond patterns, and protonation states. We have used IR difference spectroscopy to investigate such modulations for the functional intermediate states E, R2,Pm, and F. These spectra reveal deprotonation of its key glutamic acid E286 in the E and in the Pm states. The consecutive deprotonation and reprotonation of E286 twice within one catalytic turnover illustrates the role of this residue as a proton shuttle. In addition, the spectra point toward deprotonation of a redox-active tyrosine, plausibly Y288, in the F intermediate. Structural insights into the molecular mechanism of catalysis based on the subtle molecular changes observed with IR difference spectroscopy are discussed.
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Affiliation(s)
- Rebecca M Nyquist
- Forschungszentrum Jülich, IBI-2: Structural Biology, 52425 Jülich, Germany
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22
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Azéma L, Lakhdar-Ghazal F, Sygusch J, Blonski C. Characterization of proton abstraction steps in enzymatic reactions by Fourier transform infrared spectroscopy. Anal Biochem 2003; 318:142-5. [PMID: 12782042 DOI: 10.1016/s0003-2697(03)00165-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- L Azéma
- Groupe de Chimie Organique Biologique, LSPCMIB UMR CNRS 5068, Université Paul Sabatier, Bât IIR1, 118 route de Narbonne, 31062 Toulouse Cedex 4, France
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23
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Ueno S, Shibata A, Yorimitsu A, Baba Y, Kamo N. Redox potentials of the oriented film of the wild-type, the E194Q-, E204Q- and D96N-mutated bacteriorhodopsins. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1609:109-14. [PMID: 12507765 DOI: 10.1016/s0005-2736(02)00660-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The redox potentials of the oriented films of the wild-type, the E194Q-, E204Q- and D96N-mutated bacteriorhodopsins (bR), prepared by adsorbing purple membrane (PM) sheets or its mutant on a Pt electrode, have been examined. The redox potentials (V) of the wild-type bR were -470 mV for the 13-cis configuration of the retinal Shiff base in bR and -757 mV for the all-trans configuration in H(2)O, and -433 mV for the 13-cis configuration and -742 mV for the all-trans configuration in D(2)O. The solvent isotope effect (DeltaV=V(D(2)O)-V(H(2)O)), which shifts the redox potential to a higher value, originates from the cooperative rearrangements of the extensively hydrogen-bonded water molecules around the protonated C=N part in the retinal Schiff base. The redox potential of bR was much higher for the 13-cis configuration than that for the all-trans configuration. The redox potentials for the E194Q mutant in the extracellular region were -507 mV for the 13-cis configuration and -788 mV for the all-trans configuration; and for the E204Q mutant they were -491 mV for the 13-cis configuration and -769 mV for the all-trans configuration. Replacement of the Glu(194) or Glu(204) residues by Gln weakened the electron withdrawing interaction to the protonated C=N bond in the retinal Schiff base. The E204 residue is less linked with the hydrogen-bonded network of the proton release pathway compared with E194. The redox potentials of the D96N mutant in the cytoplasmic region were -471 mV for the 13-cis configuration and -760 mV for the all-trans configuration which were virtually the same as those of the wild-type bR, indicating that the D to N point mutation of the 96 residue had no influence on the interaction between the D96 residue and the C=N part in the Schiff base under the light-adapted condition. The results suggest that the redox potential of bR is closely correlated to the hydrogen-bonded network spanning from the retinal Schiff base to the extracellular surface of bR in the proton transfer pathway.
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Affiliation(s)
- Satoru Ueno
- Faculty of Pharmaceutical Sciences, Tokushima University, Tokushima, Japan
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24
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Schätzler B, Dencher NA, Tittor J, Oesterhelt D, Yaniv-Checover S, Nachliel E, Gutman M. Subsecond proton-hole propagation in bacteriorhodopsin. Biophys J 2003; 84:671-86. [PMID: 12524320 PMCID: PMC1302648 DOI: 10.1016/s0006-3495(03)74887-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The dynamics of proton transfer between the surface of purple membrane and the aqueous bulk have recently been investigated by the Laser Induced Proton Pulse Method. Following a Delta-function release of protons to the bulk, the system was seen to regain its state of equilibrium within a few hundreds of microseconds. These measurements set the time frame for the relaxation of any state of acid-base disequilibrium between the bacteriorhodopsin's surface and the bulk. It was also deduced that the released protons react with the various proton binding within less than 10 micro s. In the present study, we monitored the photocycle and the proton-cycle of photo-excited bacteriorhodopsin, in the absence of added buffer, and calculated the proton balance between the Schiff base and the bulk phase in a time-resolved mode. It was noticed that the late phase of the M decay (beyond 1 ms) is characterized by a slow (subsecond) relaxation of disequilibrium, where the Schiff base is already reprotonated but the pyranine still retains protons. Thus, it appears that the protonation of D96 is a slow rate-limiting process that generates a "proton hole" in the cytoplasmic section of the protein. The velocity of the hole propagation is modulated by the ionic strength of the solution and by selective replacements of charged residues on the interhelical loops of the protein, at domains that seems to be remote from the intraprotein proton conduction trajectory.
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Affiliation(s)
- Bettina Schätzler
- Laser Laboratory for Fast Reactions in Biology, Department of Biochemistry, Tel Aviv University, Israel
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25
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Wise KJ, Gillespie NB, Stuart JA, Krebs MP, Birge RR. Optimization of bacteriorhodopsin for bioelectronic devices. Trends Biotechnol 2002; 20:387-94. [PMID: 12175770 DOI: 10.1016/s0167-7799(02)02023-1] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Bacteriorhodopsin (BR) is the photoactive proton pump found in the purple membrane of the salt marsh archaeon Halobacterium salinarum. Evolution has optimized this protein for high photochemical efficiency, thermal stability and cyclicity, as the organism must be able to function in a hot, stagnant and resource-limited environment. Photonic materials generated via organic chemistry have yet to surpass the native protein in terms of quantum efficiency or cyclicity. However, the native protein still lacks the overall efficiency necessary for commercial viability and virtually all successful photonic devices using bacteriorhodopsin are based on chemical or genetic variants of the native protein. We show that genetic engineering can provide significant improvement in the device capabilities of proteins and, in the case of bacteriorhodopsin, a 700-fold improvement has been realized in volumetric data storage. We conclude that semi-random mutagenesis and directed evolution will play a prominent role in future efforts in bioelectronic optimization.
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Affiliation(s)
- Kevin J Wise
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
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26
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Friedrich T, Geibel S, Kalmbach R, Chizhov I, Ataka K, Heberle J, Engelhard M, Bamberg E. Proteorhodopsin is a light-driven proton pump with variable vectoriality. J Mol Biol 2002; 321:821-38. [PMID: 12206764 DOI: 10.1016/s0022-2836(02)00696-4] [Citation(s) in RCA: 190] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Proteorhodopsin, a homologue of archaeal bacteriorhodopsin (BR), belongs to a newly identified family of retinal proteins from marine bacteria, which could play an important role in the energy balance of the biosphere. We cloned the cDNA sequence of proteorhodopsin by chemical gene synthesis, expressed the protein in Escherichia coli cells, purified and reconstituted the protein in its functional active state. The photocycle characteristics were determined by time-resolved absorption and Fourier transform infrared (FT-IR) spectroscopy. The pH-dependence of the absorption spectrum indicates that the pK(a) of the primary acceptor of the Schiff base proton (Asp97) is 7.68. Generally, the photocycle of proteorhodopsin is similar to that of BR, although an L-like photocycle intermediate was not detectable. Whereas at pH>7 an M-like intermediate is formed upon illumination, at pH 5 no M-like intermediate could be detected. As the photocycle kinetics do not change between the acidic and alkaline state of proteorhodopsin, the only difference between these two forms is the protonation status of Asp97. This is corroborated by time-resolved FT-IR spectroscopy, which demonstrates that proton transfer from the retinal Schiff base to Asp97 is observed at alkaline pH, but the other vibrational changes are essentially pH-independent.After reconstitution into proteoliposomes, light-induced proton currents of proteorhodopsin were measured in a compound membrane system where proteoliposomes were adsorbed to planar lipid bilayers. Our results show that proteorhodopsin is a light-driven proton pump with characteristics similar to those of BR at alkaline pH. However, at acidic pH, the direction of proton pumping is inverted. Complementary experiments were carried out on proteorhodopsin expressed heterologously in Xenopus laevis oocytes under voltage clamp conditions. The following results were obtained. (1) At alkaline pH, proteorhodopsin mediates outwardly directed proton pumping like BR. (2) The direction of proton pumping can be inverted, when Asp97 is protonated. (3) The current can be inverted by changes of the polarity of the applied voltage. (4) The light intensity-dependence of the photocurrents leads to the conclusion that the alkaline form of proteorhodopsin shows efficient proton pumping after sequential excitation by two photons.
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Affiliation(s)
- Thomas Friedrich
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry, Kennedyallee 70, D-60596 Frankfurt am Main, Germany
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27
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Lazarova T, Sanz C, Sepulcre F, Querol E, Padrós E. Specific effects of chloride on the photocycle of E194Q and E204Q mutants of bacteriorhodopsin as measured by FTIR spectroscopy. Biochemistry 2002; 41:8176-83. [PMID: 12069610 DOI: 10.1021/bi025654u] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Low-temperature Fourier transform infrared spectroscopy has been used to study mutants of Glu194 and Glu204, two amino acids that are involved in proton release to the extracellular side of bacteriorhodopsin. Difference spectra of films of E194Q, E204Q, E194Q/E204Q, E9Q/E194Q/E204Q, and E9Q/E74Q/E194Q/E204Q at 243, 277, and 293 K and several pH values were obtained by continuous illumination. A specific effect of Cl(-) ions was found for the mutants, promoting a N-like intermediate at alkaline pH and an O' intermediate at neutral or acid pH. The apparent pK(a) of Asp85 in the M intermediate was found to be decreased for E194Q in the presence of Cl(-) (pK(a) of 7.6), but it was unchanged for E204Q, as compared to wild-type. In the absence of Cl(-) (i.e., in the presence of SO(4)(2)(-)), mutation of Glu194 or of Glu204 produces M- (or M(N), M(G))-like intermediates under all of the conditions examined. The absence of N, O, and O' intermediates suggests a long-range effect of the mutation. Furthermore, it is suggested that Cl(-) acts by reaching the interior of the protein, rather than producing surface effects. The effect of low water content was also examined, in the presence of Cl(-). Similar spectra corresponding to the M(1) intermediate were found for dry samples of both mutants, indicating that the effects of the mutations or of Cl(-) ions are confined to the second part of the photocycle. The water O-H stretching data further confirms altered photocycles and the effect of Cl(-) on the accumulation of the N intermediate.
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Affiliation(s)
- Tzvetana Lazarova
- Unitat de Biofísica, Departament de Bioquímica i de Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Barcelona 08193, Spain
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28
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Tittor J, Paula S, Subramaniam S, Heberle J, Henderson R, Oesterhelt D. Proton translocation by bacteriorhodopsin in the absence of substantial conformational changes. J Mol Biol 2002; 319:555-65. [PMID: 12051928 DOI: 10.1016/s0022-2836(02)00307-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Unlike wild-type bacteriorhodopsin (BR), the BR triple mutant D96G/F171C/F219L has been shown to undergo only minor structural rearrangements during its photocycle. Nonetheless, the mutant is capable of transporting protons at a rate of 125(+/-40) H+/BR per minute under light-saturating conditions. Light adaptation of the triple mutant's retinal proceeds in a pH-dependent manner up to a maximum of 63% all-trans. These two findings imply that the transport activity of the triple mutant comprises 66% of the wild-type activity. Time-resolved spectroscopy reveals that the identity and sequence of intermediates in the photocycle of the triple mutant in the all-trans configuration correspond to that of wild-type BR. The only differences relate to a slower rise and decay of the M and O intermediates, and a significant spectral contribution from a 13-cis component. No indication for accumulation of the N intermediate is found under a variety of conditions that normally favor the formation of this species in wild-type BR. The Fourier transform infrared (FTIR) spectrum of the M intermediate in the triple mutant resembles that of wild type. Minor changes in the amide I region during the photocycle suggest that only small movements of the protein backbone occur. Electron microscopy reveals large differences in conformation between the unilluminated state of the mutant protein and wild-type but no light-induced changes in time-resolved measurements. Evidently, proton transport by the triple mutant does not require the major conformational rearrangements that occur on the same time-scale with wild-type. Thus, we conclude that large conformational changes observed in the photocycle of the wild-type and many BR mutants are not a prerequisite for the change in accessibility of the Schiff base nitrogen atom that must occur during vectorial catalysis to allow proton transport.
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Affiliation(s)
- J Tittor
- Max-Planck-Institut für Biochemie, 82152 Martinsried, Germany.
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