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Hegemann P, Michel H. Dieter Oesterhelt (1940-2022): Life with light and color, pioneer of membrane protein research. Biophys Physicobiol 2023; 20:e201010. [PMID: 38362317 PMCID: PMC10865852 DOI: 10.2142/biophysico.bppb-v20.s010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 01/26/2023] Open
Affiliation(s)
| | - Hartmut Michel
- Max Planck Institute of Biophysics, Frankfurt 60438, Germany
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2
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Kataoka M. Structural studies of bacteriorhodopsin in BC era. Biophys Physicobiol 2023; 20:e201006. [PMID: 38362329 PMCID: PMC10865857 DOI: 10.2142/biophysico.bppb-v20.s006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/17/2023] [Indexed: 01/19/2023] Open
Abstract
It marked half a century since the discovery of bacteriorhodopsin two years ago. On this occasion, I have revisited historically important diffraction studies of this membrane protein, based on my recollections. X-ray diffraction and electron diffraction, and electron microscopy, described the low-resolution structure of bacteriorhodopsin within the purple membrane. Neutron diffraction was effective to assign the helical regions in the primary structure with 7 rods revealed by low-resolution structure as well as to describe the retinal position. Substantial conformational changes upon light illumination were clarified by the structures of various photointermediates. Early trials of time-resolved studies were also introduced. Models for the mechanism of light-driven proton pump based on the low-resolution structural studies are also described. Significantly, they are not far from the today's understanding. I believe that the spirit of the early research scientists in this field and the essence of their studies, which constitute the foundations of the field, still actively fertilizes current membrane protein research.
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Affiliation(s)
- Mikio Kataoka
- Nara Institute of Science and Technology, Ikoma, Nara 630-0189, Japan
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3
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Abstract
Research on type 1 rhodopsins spans now a history of 50 years. Originally, just archaeal ion pumps and sensors have been discovered. However, with modern genetic techniques and gene sequencing tools, more and more proteins were identified in all kingdoms of life. Spectroscopic and other biophysical studies revealed quite diverse functions. Ion pumps, sensors, and channels are imprinted in the same seven-helix transmembrane protein scaffold carrying a retinal prosthetic group. In this review, molecular biology methods are described, which enabled the elucidation of their function and structure leading to optogenetic applications.
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Affiliation(s)
- Martin Engelhard
- Department Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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4
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Li F, Egea PF, Vecchio AJ, Asial I, Gupta M, Paulino J, Bajaj R, Dickinson MS, Ferguson-Miller S, Monk BC, Stroud RM. Highlighting membrane protein structure and function: A celebration of the Protein Data Bank. J Biol Chem 2021; 296:100557. [PMID: 33744283 PMCID: PMC8102919 DOI: 10.1016/j.jbc.2021.100557] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 02/10/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
Biological membranes define the boundaries of cells and compartmentalize the chemical and physical processes required for life. Many biological processes are carried out by proteins embedded in or associated with such membranes. Determination of membrane protein (MP) structures at atomic or near-atomic resolution plays a vital role in elucidating their structural and functional impact in biology. This endeavor has determined 1198 unique MP structures as of early 2021. The value of these structures is expanded greatly by deposition of their three-dimensional (3D) coordinates into the Protein Data Bank (PDB) after the first atomic MP structure was elucidated in 1985. Since then, free access to MP structures facilitates broader and deeper understanding of MPs, which provides crucial new insights into their biological functions. Here we highlight the structural and functional biology of representative MPs and landmarks in the evolution of new technologies, with insights into key developments influenced by the PDB in magnifying their impact.
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Affiliation(s)
- Fei Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA; Department of Neurology, University of California San Francisco, San Francisco, California, USA
| | - Pascal F Egea
- Department of Biological Chemistry, School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Alex J Vecchio
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | | | - Meghna Gupta
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Joana Paulino
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Ruchika Bajaj
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Miles Sasha Dickinson
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Shelagh Ferguson-Miller
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Brian C Monk
- Sir John Walsh Research Institute and Department of Oral Sciences, University of Otago, North Dunedin, Dunedin, New Zealand
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA.
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5
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His57 controls the efficiency of ESR, a light-driven proton pump from Exiguobacterium sibiricum at low and high pH. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148328. [PMID: 33075275 DOI: 10.1016/j.bbabio.2020.148328] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/06/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022]
Abstract
ESR, a light-driven proton pump from Exiguobacterium sibiricum, contains a lysine residue (Lys96) in the proton donor site. Substitution of Lys96 with a nonionizable residue greatly slows reprotonation of the retinal Schiff base. The recent study of electrogenicity of the K96A mutant revealed that overall efficiency of proton transport is decreased in the mutant due to back reactions (Siletsky et al., BBA, 2019). Similar to members of the proteorhodopsin and xanthorhodopsin families, in ESR the primary proton acceptor from the Schiff base, Asp85, closely interacts with His57. To examine the role of His57 in the efficiency of proton translocation by ESR, we studied the effects of H57N and H57N/K96A mutations on the pH dependence of light-induced pH changes in suspensions of Escherichia coli cells, kinetics of absorption changes and electrogenic proton transfer reactions during the photocycle. We found that at low pH (<5) the proton pumping efficiency of the H57N mutant in E. coli cells and its electrogenic efficiency in proteoliposomes is substantially higher than in the WT, suggesting that interaction of His57 with Asp85 sets the low pH limit for H+ pumping in ESR. The electrogenic components that correspond to proton uptake were strongly accelerated at low pH in the mutant indicating that Lys96 functions as a very efficient proton donor at low pH. In the H57N/K96A mutant, a higher H+ pumping efficiency compared with K96A was observed especially at high pH, apparently from eliminating back reactions between Asp85 and the Schiff base by the H57N mutation.
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6
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Singh A, Singh AK. Haloarchaea: worth exploring for their biotechnological potential. Biotechnol Lett 2017; 39:1793-1800. [PMID: 28900776 DOI: 10.1007/s10529-017-2434-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 09/07/2017] [Indexed: 12/14/2022]
Abstract
Halophilic archaea are unique microorganisms adapted to survive under high salt conditions and biomolecules produced by them may possess unusual properties. Haloarchaeal metabolites are stable at high salt and temperature conditions that are useful for industrial applications. Proteins and enzymes of this group of archaea are functional under salt concentrations at which bacterial counterparts fail to be active. Such properties makes haloarchaeal enzymes suitable for salt-based applications and their use under dehydrating conditions. For example, bacteriorhodopsin or the purple membrane protein present in halophilic archaea has the most recognizable applications in photoelectric devices, artificial retinas, holograms etc. Haloarchaea are also useful for bioremediation of polluted hypersaline areas. Polyhydroxyalkanoates and exopolysccharides produced by these microorganisms are biodegradable and have the potential to replace commercial non-degradable plastics and polymers. Moreover, halophilic archaea have excellent potential to be used as drug delivery systems and for nanobiotechnology by virtue of their gas vesicles and S-layer glycoproteins. Despite of possible applications of halophilic archaea, laboratory-to-industrial transition of these potential candidates is yet to be established.
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Affiliation(s)
- Aparna Singh
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, 390002, Gujarat, India.
| | - Anil K Singh
- Department of Biotechnology, Shree M & N. Virani Science College, Rajkot, 360005, Gujarat, India
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7
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Photonic Potential of Haloarchaeal Pigment Bacteriorhodopsin for Future Electronics: A Review. Curr Microbiol 2017; 74:996-1002. [DOI: 10.1007/s00284-017-1271-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 05/23/2017] [Indexed: 10/19/2022]
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8
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Chen HM, Jheng KR, Yu AD. Direct, label-free, selective, and sensitive microbial detection using a bacteriorhodopsin-based photoelectric immunosensor. Biosens Bioelectron 2017; 91:24-31. [PMID: 27987407 DOI: 10.1016/j.bios.2016.12.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/30/2016] [Accepted: 12/12/2016] [Indexed: 11/19/2022]
Abstract
A photoelectric immunosensor using purple membranes (PM) as the transducer, which contains photoactive bacteriorhodopsin, is here first demonstrated for direct and label-free microbial detection. Biotinylated polyclonal antibodies against Escherichia coli were immobilized on a PM-coated electrode through further surface biotinylation and bridging avidin or NeutrAvidin. The photocurrent generated by the antibody-coated sensor was reduced after incubation with E. coli K-12 cultures, with the reduction level increased with the culture populations. The immunosensor prepared via NeutrAvidin exhibited much better selectivity than the one prepared via avidin, recognizing almost none of the tested Gram-positive bacteria. Cultures with populations ranging from 1 to 107CFU/10mL were detected in a single step without any preprocessing. Both AFM and Raman analysis confirmed the layer-by-layer fabrication of the antibody-coated substrates as well as the binding of microorganisms. By investigating the effect of illumination orientation and simulating the photocurrent responses with an equivalent circuit model containing a chemical capacitance, we suggest that the photocurrent reduction was primarily caused by the light-shielding effect of the captured bacteria. Using the current fabrication technique, versatile bacteriorhodopsin-based photoelectric immunosensors can be readily prepared to detect a wide variety of biological cells.
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Affiliation(s)
- Hsiu-Mei Chen
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan.
| | - Kai-Ru Jheng
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan
| | - An-Dih Yu
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan
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9
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Govorunova EG, Koppel LA. The Road to Optogenetics: Microbial Rhodopsins. BIOCHEMISTRY (MOSCOW) 2016; 81:928-40. [PMID: 27682165 DOI: 10.1134/s0006297916090029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Optogenetics technology (using light-sensitive microbial proteins to control animal cell physiology) is becoming increasingly popular in laboratories around the world. Among these proteins, particularly important are rhodopsins that transport ions across the membrane and are used in optogenetics to regulate membrane potential by light, mostly in neurons. Although rhodopsin ion pumps transport only one charge per captured photon, channelrhodopsins are capable of more efficient passive transport. In this review, we follow the history of channelrhodopsin discovery in flagellate algae and discuss the latest addition to the channelrhodopsin family, channels with anion, rather than cation, selectivity.
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Affiliation(s)
- E G Govorunova
- Lomonosov Moscow State University, School of Biology, Moscow, 119991, Russia.
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10
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Amdursky N, Kundu PK, Ahrens J, Huppert D, Klajn R. Noncovalent Interactions with Proteins Modify the Physicochemical Properties of a Molecular Switch. Chempluschem 2015; 81:44-48. [DOI: 10.1002/cplu.201500417] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/16/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Nadav Amdursky
- Department of Organic Chemistry; Weizmann Institute of Science; Rehovot 76100 Israel
- Department of Materials & Interfaces; Weizmann Institute of Science; Rehovot 76100 Israel
| | - Pintu K. Kundu
- Department of Organic Chemistry; Weizmann Institute of Science; Rehovot 76100 Israel
| | - Johannes Ahrens
- Department of Organic Chemistry; Weizmann Institute of Science; Rehovot 76100 Israel
| | - Dan Huppert
- School of Chemistry; Tel Aviv University; Tel Aviv 69978 Israel
| | - Rafal Klajn
- Department of Organic Chemistry; Weizmann Institute of Science; Rehovot 76100 Israel
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11
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Petrovskaya LE, Balashov SP, Lukashev EP, Imasheva ES, Gushchin IY, Dioumaev AK, Rubin AB, Dolgikh DA, Gordeliy VI, Lanyi JK, Kirpichnikov MP. ESR — A retinal protein with unusual properties from Exiguobacterium sibiricum. BIOCHEMISTRY (MOSCOW) 2015; 80:688-700. [DOI: 10.1134/s000629791506005x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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12
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Balashov SP, Imasheva ES, Dioumaev A, Wang JM, Jung KH, Lanyi JK. Light-driven Na(+) pump from Gillisia limnaea: a high-affinity Na(+) binding site is formed transiently in the photocycle. Biochemistry 2014; 53:7549-61. [PMID: 25375769 PMCID: PMC4263435 DOI: 10.1021/bi501064n] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 10/17/2014] [Indexed: 02/06/2023]
Abstract
A group of microbial retinal proteins most closely related to the proton pump xanthorhodopsin has a novel sequence motif and a novel function. Instead of, or in addition to, proton transport, they perform light-driven sodium ion transport, as reported for one representative of this group (KR2) from Krokinobacter. In this paper, we examine a similar protein, GLR from Gillisia limnaea, expressed in Escherichia coli, which shares some properties with KR2 but transports only Na(+). The absorption spectrum of GLR is insensitive to Na(+) at concentrations of ≤3 M. However, very low concentrations of Na(+) cause profound differences in the decay and rise time of photocycle intermediates, consistent with a switch from a "Na(+)-independent" to a "Na(+)-dependent" photocycle (or photocycle branch) at ∼60 μM Na(+). The rates of photocycle steps in the latter, but not the former, are linearly dependent on Na(+) concentration. This suggests that a high-affinity Na(+) binding site is created transiently after photoexcitation, and entry of Na(+) from the bulk to this site redirects the course of events in the remainder of the cycle. A greater concentration of Na(+) is needed for switching the reaction path at lower pH. The data suggest therefore competition between H(+) and Na(+) to determine the two alternative pathways. The idea that a Na(+) binding site can be created at the Schiff base counterion is supported by the finding that upon perturbation of this region in the D251E mutant, Na(+) binds without photoexcitation. Binding of Na(+) to the mutant shifts the chromophore maximum to the red like that of H(+), which occurs in the photocycle of the wild type.
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Affiliation(s)
- Sergei P. Balashov
- Department
of Physiology and Biophysics, University
of California, Irvine, California 92697, United States
| | - Eleonora S. Imasheva
- Department
of Physiology and Biophysics, University
of California, Irvine, California 92697, United States
| | - Andrei
K. Dioumaev
- Department
of Physiology and Biophysics, University
of California, Irvine, California 92697, United States
| | - Jennifer M. Wang
- Department
of Physiology and Biophysics, University
of California, Irvine, California 92697, United States
| | - Kwang-Hwan Jung
- Department
of Life Science and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Shinsu-Dong 1, Mapo-Gu, Seoul 121-742, Korea
| | - Janos K. Lanyi
- Department
of Physiology and Biophysics, University
of California, Irvine, California 92697, United States
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13
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Schulten K, Humphrey W, Logunov I, Sheves M, Xu D. Molecular Dynamics Studies of Bacteriorhodopsin's Photocycles. Isr J Chem 2013. [DOI: 10.1002/ijch.199500042] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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14
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Chou KC. A molecular piston mechanism of pumping protons by bacteriorhodopsin. Amino Acids 2013; 7:1-17. [PMID: 24185969 DOI: 10.1007/bf00808442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/1993] [Accepted: 12/20/1993] [Indexed: 10/26/2022]
Abstract
In this review the proton-pumping mechanism proposed recently for bacteriorhodopsin [Chou, K. C. (1993) Journal of Protein Chemistry, 12: 337-350] is illustrated in terms of a phenomenological model. According to the model, theβ-ionone of the retinal chromophore in bacteriorhodopsin can be phenomenologically imagined as a molecular "piston". The photon capture by bacteriorhodopsin would "pull" it up while the spontaneous decrease in potential energy would "push" it down so that it would be up and down alternately during the photocycle process. When it is pulled up, the gate of pore is open and the water channel for the proton translocation is through; when it is pushed down, the gate of pore is closed and the water channel is shut up. Such a model not only is quite consistent with experimental observations, but also provides useful insights and a different view to elucidate the protonpumping mechanism of bacteriorhodopsin. The essence of the model might be useful in investigating the mechanism of ion-channels of other membrane proteins.
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Affiliation(s)
- K C Chou
- Computational Chemistry, Upjohn Laboratories, 49001-4940, Kalamazoo, Michigan, USA
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15
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Grote M, Engelhard M, Hegemann P. Of ion pumps, sensors and channels - perspectives on microbial rhodopsins between science and history. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:533-45. [PMID: 23994288 DOI: 10.1016/j.bbabio.2013.08.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 08/20/2013] [Accepted: 08/22/2013] [Indexed: 10/26/2022]
Abstract
We present a historical overview of research on microbial rhodopsins ranging from the 1960s to the present date. Bacteriorhodopsin (BR), the first identified microbial rhodopsin, was discovered in the context of cell and membrane biology and shown to be an outward directed proton transporter. In the 1970s, BR had a big impact on membrane structural research and bioenergetics, that made it to a model for membrane proteins and established it as a probe for the introduction of various biophysical techniques that are widely used today. Halorhodopsin (HR), which supports BR physiologically by transporting negatively charged Cl⁻ into the cell, is researched within the microbial rhodopsin community since the late 1970s. A few years earlier, the observation of phototactic responses in halobacteria initiated research on what are known today as sensory rhodopsins (SR). The discovery of the light-driven ion channel, channelrhodopsin (ChR), serving as photoreceptors for behavioral responses in green alga has complemented inquiries into this photoreceptor family. Comparing the discovery stories, we show that these followed quite different patterns, albeit the objects of research being very similar. The stories of microbial rhodopsins present a comprehensive perspective on what can nowadays be considered one of nature's paradigms for interactions between organisms and light. Moreover, they illustrate the unfolding of this paradigm within the broader conceptual and instrumental framework of the molecular life sciences. 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)
- Mathias Grote
- Institut für Philosophie, Literatur-, Wissenschafts- und Technikgeschichte, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany.
| | - Martin Engelhard
- Max Planck Institut für Molekulare Physiologie, Otto Hahn Str. 11, 44227 Dortmund, Germany
| | - Peter Hegemann
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
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16
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Balashov SP, Petrovskaya LE, Imasheva ES, Lukashev EP, Dioumaev AK, Wang JM, Sychev SV, Dolgikh DA, Rubin AB, Kirpichnikov MP, Lanyi JK. Breaking the carboxyl rule: lysine 96 facilitates reprotonation of the Schiff base in the photocycle of a retinal protein from Exiguobacterium sibiricum. J Biol Chem 2013; 288:21254-21265. [PMID: 23696649 DOI: 10.1074/jbc.m113.465138] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A lysine instead of the usual carboxyl group is in place of the internal proton donor to the retinal Schiff base in the light-driven proton pump of Exiguobacterium sibiricum (ESR). The involvement of this lysine in proton transfer is indicated by the finding that its substitution with alanine or other residues slows reprotonation of the Schiff base (decay of the M intermediate) by more than 2 orders of magnitude. In these mutants, the rate constant of the M decay linearly decreases with a decrease in proton concentration, as expected if reprotonation is limited by the uptake of a proton from the bulk. In wild type ESR, M decay is biphasic, and the rate constants are nearly pH-independent between pH 6 and 9. Proton uptake occurs after M formation but before M decay, which is especially evident in D2O and at high pH. Proton uptake is biphasic; the amplitude of the fast phase decreases with a pKa of 8.5 ± 0.3, which reflects the pKa of the donor during proton uptake. Similarly, the fraction of the faster component of M decay decreases and the slower one increases, with a pKa of 8.1 ± 0.2. The data therefore suggest that the reprotonation of the Schiff base in ESR is preceded by transient protonation of an initially unprotonated donor, which is probably the ε-amino group of Lys-96 or a water molecule in its vicinity, and it facilitates proton delivery from the bulk to the reaction center of the protein.
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Affiliation(s)
- Sergei P Balashov
- From the Department of Physiology and Biophysics, University of California, Irvine, California 92697,.
| | - Lada E Petrovskaya
- the Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia, and.
| | - Eleonora S Imasheva
- From the Department of Physiology and Biophysics, University of California, Irvine, California 92697
| | - Evgeniy P Lukashev
- the Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Andrei K Dioumaev
- From the Department of Physiology and Biophysics, University of California, Irvine, California 92697
| | - Jennifer M Wang
- From the Department of Physiology and Biophysics, University of California, Irvine, California 92697
| | - Sergey V Sychev
- the Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia, and
| | - Dmitriy A Dolgikh
- the Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia, and; the Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Andrei B Rubin
- the Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Mikhail P Kirpichnikov
- the Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia, and; the Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Janos K Lanyi
- From the Department of Physiology and Biophysics, University of California, Irvine, California 92697,.
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17
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Grote M. Purple matter, membranes and 'molecular pumps' in rhodopsin research (1960s-1980s). JOURNAL OF THE HISTORY OF BIOLOGY 2013; 46:331-368. [PMID: 22907707 DOI: 10.1007/s10739-012-9333-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In the context of 1960s research on biological membranes, scientists stumbled upon a curiously coloured material substance, which became called the "purple membrane." Interactions with the material as well as chemical analyses led to the conclusion that the microbial membrane contained a photoactive molecule similar to rhodopsin, the light receptor of animals' retinae. Until 1975, the find led to the formation of novel objects in science, and subsequently to the development of a field in the molecular life sciences that comprised biophysics, bioenergetics as well as membrane and structural biology. Furthermore, the purple membrane and bacteriorhodopsin, as the photoactive membrane transport protein was baptized, inspired attempts at hybrid bio-optical engineering throughout the 1980s. A central motif of the research field was the identification of a functional biological structure, such as a membrane, with a reactive material substance that could be easily prepared and manipulated. Building on this premise, early purple membrane research will be taken as a case in point to understand the appearance and transformation of objects in science through work with material substances. Here, the role played by a perceptible material and its spontaneous change of colour, or reactivity, casts a different light on objects and experimental practices in the late twentieth century molecular life sciences. With respect to the impact of chemical working and thinking, the purple membrane and rhodopsins represent an influential domain straddling the life and chemical sciences as well as bio- and material technologies, which has received only little historical and philosophical attention. Re-drawing the boundary between the living and the non-enlivened, these researches explain and model organismic activity through the reactivity of macromolecular structures, and thus palpable material substances.
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Affiliation(s)
- Mathias Grote
- Institut für Philosophie, Literatur-, Wissenschafts- und Technikgeschichte, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany,
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18
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Aspartate-histidine interaction in the retinal schiff base counterion of the light-driven proton pump of Exiguobacterium sibiricum. Biochemistry 2012; 51:5748-62. [PMID: 22738070 DOI: 10.1021/bi300409m] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the distinctive features of eubacterial retinal-based proton pumps, proteorhodopsins, xanthorhodopsin, and others, is hydrogen bonding of the key aspartate residue, the counterion to the retinal Schiff base, to a histidine. We describe properties of the recently found eubacterium proton pump from Exiguobacterium sibiricum (named ESR) expressed in Escherichia coli, especially features that depend on Asp-His interaction, the protonation state of the key aspartate, Asp85, and its ability to accept a proton from the Schiff base during the photocycle. Proton pumping by liposomes and E. coli cells containing ESR occurs in a broad pH range above pH 4.5. Large light-induced pH changes indicate that ESR is a potent proton pump. Replacement of His57 with methionine or asparagine strongly affects the pH-dependent properties of ESR. In the H57M mutant, a dramatic decrease in the quantum yield of chromophore fluorescence emission and a 45 nm blue shift of the absorption maximum with an increase in the pH from 5 to 8 indicate deprotonation of the counterion with a pK(a) of 6.3, which is also the pK(a) at which the M intermediate is observed in the photocycle of the protein solubilized in detergent [dodecyl maltoside (DDM)]. This is in contrast with the case for the wild-type protein, for which the same experiments show that the major fraction of Asp85 is deprotonated at pH >3 and that it protonates only at low pH, with a pK(a) of 2.3. The M intermediate in the wild-type photocycle accumulates only at high pH, with an apparent pK(a) of 9, via deprotonation of a residue interacting with Asp85, presumably His57. In liposomes reconstituted with ESR, the pK(a) values for M formation and spectral shifts are 2-3 pH units lower than in DDM. The distinctively different pH dependencies of the protonation of Asp85 and the accumulation of the M intermediate in the wild-type protein versus the H57M mutant indicate that there is strong Asp-His interaction, which substantially lowers the pK(a) of Asp85 by stabilizing its deprotonated state.
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Grote M, O'Malley MA. Enlightening the life sciences: the history of halobacterial and microbial rhodopsin research. FEMS Microbiol Rev 2011; 35:1082-99. [DOI: 10.1111/j.1574-6976.2011.00281.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Brünger A, Schulten Z, Schulten K. A Network Thermodynamic Investigation of Stationary and Non-Stationary Proton Transport Through Proteins. ACTA ACUST UNITED AC 2011. [DOI: 10.1524/zpch.1983.136.136.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Lo KM, Jones SS, Hackett NR, Khorana HG. Specific amino acid substitutions in bacterioopsin: Replacement of a restriction fragment in the structural gene by synthetic DNA fragments containing altered codons. Proc Natl Acad Sci U S A 2010; 81:2285-9. [PMID: 16593452 PMCID: PMC345043 DOI: 10.1073/pnas.81.8.2285] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To study the mechanism of light-dependent proton translocation by bacteriorhodopsin, we have introduced single-codon changes in the gene so as to produce the following specific amino acid substitutions in the protein: Tyr-185 to Phe, Pro-186 to Leu, Trp-189 to Phe, Ser-193 to Ala, and Glu-194 to Gln. The strategy involved replacement of a 62-base-pair restriction fragment by synthetic DNA duplexes containing the modified nucleotide sequences. This required a unique restriction site (Xho I) at Ile-203 which was created by oligonucleotide-directed point mutagenesis. The six DNA duplexes corresponding to the modified native and mutant restriction fragments were all prepared by DNA ligase-catalyzed joining of chemically synthesized deoxyribooligonucleotides. The bacterioopsin expression plasmids reconstructed by using the synthetic DNA fragments were characterized by restriction analysis and DNA sequence determination. An extremely rapid, efficient, and general method for purification of the synthetic oligonucleotides and of DNA fragments was developed.
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Affiliation(s)
- K M Lo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
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Betlach M, Pfeifer F, Friedman J, Boyer HW. Bacterio-opsin mutants of Halobacterium halobium. Proc Natl Acad Sci U S A 2010; 80:1416-20. [PMID: 16593291 PMCID: PMC393608 DOI: 10.1073/pnas.80.5.1416] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bacterio-opsin (bop) gene of Halobacterium halobium R1 has been cloned with about 40 kilobases of flanking genomic sequence. The 40-kilobase segment is derived from the (G+C)-rich fraction of the chromosome and is not homologous to the major (pHH1) or minor endogenous covalently closed circular DNA species of H. halobium. A 5.1-kilobase Pst I fragment containing the bop gene was subcloned in pBR322 and a partial restriction map was determined. Defined restriction fragments of this clone were used as probes to analyze the defects associated with the bop gene in 12 bacterio-opsin mutants. Eleven out of 12 of the mutants examined had inserts ranging from 350 to 3,000 base pairs either in the bop gene or up to 1,400 base pairs upstream. The positions of the inserts were localized to four regions in the 5.1-kilobase genomic fragment: within the gene (one mutant), in a region that overlaps the 5' end of the gene (seven mutants), and in two different upstream regions (three mutants). Two revertants of the mutant with the most distal insert had an additional insert in the same region. The polar effects of these inserts are discussed in terms of inactivation of a regulatory gene or disruption of part of a coordinately expressed operon. Given the defined nature of the bop mRNA-i.e., it has a 5' leader sequence of three ribonucleotides-these observations indicate that the bop mRNA might be processed from a large mRNA transcript.
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Affiliation(s)
- M Betlach
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143
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Dumont ME, Wiggins JW, Hayward SB. Location of platinum binding sites on bacteriorhodopsin by electron diffraction. Proc Natl Acad Sci U S A 2010; 78:2947-51. [PMID: 16593014 PMCID: PMC319476 DOI: 10.1073/pnas.78.5.2947] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A platinum-containing derivative of bacteriorhodopsin has been prepared by treating purple membranes with glycyl-L-methionatoplatinum. Low-dose electron diffraction was used to identify Pt binding sites in the 5.6 A resolution reconstruction of the bacteriorhodopsin unit cell in projection. This is a necessary first step in the use of the Pt derivative for identifying the parts of the amino acid sequence corresponding to the alpha helices in the bacteriorhodopsin structure and for obtaining phases for reflections out to 3.5 A resolution by the method of heavy-atom isomorphous replacement. The largest peak in a Fourier difference map between platinum-labeled and native purple membrane is larger than the spurious features expected to arise from errors in measurements of diffraction intensities.
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Affiliation(s)
- M E Dumont
- Department of Biophysics, The Johns Hopkins University, Baltimore, Maryland 21218
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Draheim JE, Cassim JY. Large Scale Global Structural Changes of the Purple Membrane during the Photocycle. Biophys J 2010; 47:497-507. [PMID: 19431590 DOI: 10.1016/s0006-3495(85)83943-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Both the solution and the oriented film absorption and circular dichroic spectra of the bacteriorhodopsin (bR(568)) and M(412) intermediate of the purple membrane photocycle were compared over the wavelength region 800-183 nm to assess structural changes during this photocycle. The main findings are (a) loss of the excitonic interaction among the chromophoric retinal transitions indicating disordering of the retinal orientations in the membrane and distortions of the membrane hexagonal crystal lattice, (b) structural change of the chromophoric retinal, (c) changes in the key interactions between the retinal and specific groups in the local environment of the apoprotein, (d) significant changes of the tertiary structure of the bR with negligible secondary structure involvement, and (e) a net tilting of the rodlike segments of the bR polypeptides away from the membrane normal. These findings are in accord with large scale global structural changes of the membrane during the photocycle and with structural metastability of the bR molecules. An important implication of these changes is the possibility of transmembrane retinal-regulated pulsating channels during the photocycle. The significance of this possibility in respect to models for the proton translocation function of this membrane is discussed.
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Balashov SP, Govindjee R, Ebrey TG. Redshift of the purple membrane absorption band and the deprotonation of tyrosine residues at high pH: Origin of the parallel photocycles of trans-bacteriorhodopsin. Biophys J 2010; 60:475-90. [PMID: 19431801 DOI: 10.1016/s0006-3495(91)82074-4] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
At high pH (> 8) the 570 nm absorption band of all-trans bacteriorhodopsin (bR) in purple membrane undergoes a small (1.5 nm) shift to longer wavelengths, which causes a maximal increase in absorption at 615 nm. The pK of the shift is 9.0 in the presence of 167 mM KCl, and its intrinsic pK is approximately 8.3. The red shift of the trans-bR absorption spectrum correlates with the appearance of the fast component in the light-induced L to M transition, and absorption increases at 238 and 297 nm which are apparently caused by the deprotonation of a tyrosine residue and red shift of the absorption of tryptophan residues. This suggests that the deprotonation of a tyrosine residue with an exceptionally low pK (pK(a) approximately 8.3) is responsible for the absorption shift of the chromophore band and fast M formation. The pH and salt dependent equilibrium between the two forms of bR, "neutral" and "alkaline," bR <--> bR(a), results in two parallel photocycles of trans-bR at high pH, differing in the rate of the L to M transition. In the pH range 10-11.8 deprotonation of two more tyrosine residues is observed with pK's approximately 10.3 and 11.3 (in 167 mM KCL). Two simple models discussing the role of the pH induced tyrosine deprotonation in the photocycle and proton pumping are presented.It is suggested that the shifts of the absorption bands at high pH are due to the appearance of a negatively charged group inside the protein (tyrosinate) which causes electrochromic shifts of the chromophore and protein absorption bands due to the interaction with the dipole moments in the ground and excited states of bR (Stark effect). This effect gives evidence for a significant change in the dipole moment of the chromophore of bR upon excitation.Under illumination alkaline bR forms, besides the usual photocycle intermediates, a long-lived species with absorption maximum at 500 nm (P500). P500 slowly converts into bR(a) in the dark. Upon illumination P500 is transformed into an intermediate having an absorption maximum at 380 nm (P380). P380 can be reconverted to P500 by blue light illumination or by incubation in the dark.
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Affiliation(s)
- S P Balashov
- Department of Physiology and Biophysics, University of Illinois, Urbana, Illinois 61801 USA
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Seiff F, Wallat I, Westerhausen J, Heyn MP. Location of chemically modified lysine 41 in the structure of bacteriorhodopsin by neutron diffraction. Biophys J 2010; 50:629-35. [PMID: 19431687 DOI: 10.1016/s0006-3495(86)83502-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Purple membranes were prepared in which bacteriorhodopsin was labeled at lysine 41 with phenylisothiocyanate (PITC) and with perdeuterated PITC. The in-plane position of this small label containing only five deuterons was determined from the differences between the neutron diffraction intensities of the two samples. At 8.7-A resolution the Fourier difference map revealed a well-defined site between helices 3 and 4. This position was confirmed by a refinement procedure in reciprocal space. Model calculations showed that the observed difference density had the right amplitude for the label. Thus it is possible to locate a small group in a large protein structure by replacing as few as five hydrogens by deuterium. The observed location of PITC restricts the number of possibilities for the assignment of helix B in the sequence (to which lysine 41 is attached) to one of the seven helices of the structure. Taking into account the size of the label and the length of the lysine side chain our result excludes helices 1, 2, and 7 as candidates for B.
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Abstract
We summarize the predictions of the exciton model that was originally proposed to explain the observed biphasic band shape of its CD spectrum in the visible region of bacteriorhodopsin (bR). It is shown that to reconcile these predictions with the observed results on the linear dichroism, the retinal isomerization time and, the retinal-retinal distance, the biphasic nature of the observed CD spectrum of bR becomes itself an evidence against the exciton model because of the uncertainty principle.Reduced bR (RbR), which retains its hexagonal structure, shows a monophasic CD spectrum with relatively small rotational strength as compared to bR. This is shown to disagree with predictions made by the exciton model. The results could best be explained in terms of retinal-protein heterogeneity leading to two or more types of bR in which their retinals suffer opposite sense of intramolecular rotational distortion along their retinal long axis. Such a retinal-protein heterogeneity disappears in reduced bR which is known to have a planar (nondistorted) retinal conjugated system, resulting in a monophasic CD with reduced rotational strength, as observed.
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Affiliation(s)
- S Wu
- Department of Chemistry and Biochemistry University of California-Los Angeles, California 90024 USA
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Gibson NJ, Cassim JY. Nature of forces stabilizing the transmembrane protein bacteriorhodopsin in purple membrane. Biophys J 2010; 56:769-80. [PMID: 19431748 DOI: 10.1016/s0006-3495(89)82724-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Analysis of the far-ultraviolet solution and the oriented-film circular dichroic (CD) spectra of the purple membrane (PM) has indicated that the alpha-helical segments of its sole protein bacteriorhodopsin (bR) can undergo a significant tilting from the normal to the membrane plane during light-dependent hydroxylamine-mediated bleaching of the bR. However, this drastic change in tertiary structure is free of any observable secondary structural changes. This phenomenon can provide an excellent means for studying the relative contributions of forces responsible for the stability of this transmembrane protein within the membrane bilayer. Perturbation of the PM by varying degrees of papain digestion (resulting in changes in the bR ranging from only an elimination of the long COOH-terminal tail to the additional eliminations of the short NH(2)-terminal tail and a number of linkage amino acids between the helical segments of the bR) and by chemical cross-linking with dimethyl adipimidate (resulting primarily in the formation of intramolecular cross-links) resulted in a significant increase in this bleaching-induced tilting in all cases except the one in which only the COOH-tail was eliminated. The most severe perturbation (2-wk papain digestion) increased the net tilt angle per segment from 24 to 39 degrees with no indication of any secondary structural changes. Although these perturbations drastically reduced the structural stability of the bR to bleaching, they caused virtually no observable changes in the intramolecular structure of the bR or the supramolecular structure of the PM based on analysis of extensive absorption, linear dichroic, and CD spectra. In addition, study of the bleaching rates for the perturbed PM samples indicated that a linear correlation exists between the calculated initial bleaching rates and the net tilt angles.Considering the forces generally assumed to account for the stability of transmembrane proteins in membranes, (a) intersegmental hydrogen bonding and electrostatic interactions, (b) electrostatic interactions between hydrophilic polypeptide segments extending outside the bilayer and the many charged lipid heads of the bilayer, and (c) hydrophobic interactions, it is clear that the results of the bleaching experiments eliminate all but perhaps the last as contributing significantly to the bR stability in the PM. Furthermore, they provide more compelling evidence than previously available that the bR is capable of undergoing relatively large retinyldiene-controlled tertiary structural changes and that the chromophoric retinal serves as the most important factor in the native bR structural stability. This dynamic view of the bR bears directly on models proposed for bR function, favoring those in which protein structural metastability, rather than rigidity, is an essential factor. The proteinquake or deformation wave model proposed by this laboratory falls into this category.
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Affiliation(s)
- N J Gibson
- Department of Microbiology and Program in Biophysics, College of Biological Sciences, The Ohio State University, Columbus, Ohio 43210
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Otomo J, Tomioka A, Kinosita K, Miyata H, Takenaka Y, Kouyama T, Ikegami A. Chromophore of Bacteriorhodopsin is Closer to the Cytoplasmic Surface of Purple Membrane: Fluorescence Energy Transfer on Oriented Membrane Sheets. Biophys J 2010; 54:57-64. [PMID: 19431725 DOI: 10.1016/s0006-3495(88)82930-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Transmembrane location of the retinal chromophore, either native or reduced in situ to a fluorescent derivative, of the purple membrane of Halobacterium halobium was investigated with fluorescence energy transfer techniques. Single sheets of purple membrane, either native or reduced with borohydride, were adsorbed on polylysine-coated glass; the orientation, whether the exposed surfaces were cytoplasmic or extracellular, was controlled by adjusting the pH of the membrane suspension before the adsorption. On the exposed surface of the reduced membrane, a layer of cytochrome c, hemoglobin, or ferritin was deposited. The rate of excitation energy transfer from the fluorescent chromophore in the membrane to the colored protein was greater when the protein was on the cytoplasmic surface of the membrane than when it was on the extracellular surface. Analysis in which uniform distribution of the protein on the surface was assumed showed that the reduced chromophore is situated at a depth of <1.5 nm from the cytoplasmic surface. The location of the native retinal chromophore was examined by depositing a small amount of tris(2,2'-bipyridyl)ruthenium(II) complex on the native membrane adsorbed on the glass. Energy transfer from the luminescent complex to the retinal chromosphore was more efficient on the cytoplasmic surface than on the extracellular surface, suggesting that the native chromophore is also on the cytoplasmic side. From these and previous results we conclude that the chromophore, whether native or reduced, of bacteriorhodopsin is located at a depth of 1.0 +/- 0.3 nm from the cytoplasmic surface of purple membrane.
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Engelman DM. An Implication of the Structure of Bacteriorhodopsin: Globular Membrane Proteins are Stabilized by Polar Interactions. Biophys J 2010; 37:187-8. [PMID: 19431470 DOI: 10.1016/s0006-3495(82)84662-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Kometani T, Kinosita K, Furuno T, Kouyama T, Ikegami A. Transmembrane location of retinal in purple membrane: fluorescence energy transfer in maximally packed donor-acceptor systems. Biophys J 2010; 52:509-17. [PMID: 19431704 DOI: 10.1016/s0006-3495(87)83240-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Transmembrane location of the retinal chromophore in the purple membrane of Halobacterium halobium was investigated in three different systems in which excitation energy transfer between the chromophore and external dye molecules condensed on the membrane surfaces was observed. In system ii, the energy donor was the retinal chromophore converted in situ to a fluorescent derivative. The fluorescent membranes were embedded in solid cobalt-EDTA, which served as energy acceptors. System iii was similar to system ii, except that the acceptors were tris(2,2'-bipyridyl)ruthenium(II) complex in solid form. The positively charged ruthenium complex had a radius of 0.7 nm, whereas the cobalt complex in system ii was smaller (radius approximately 0.4 nm) and negatively charged. System iv was stacked sheets of native purple membrane with interspersed ruthenium complex; energy transfer from the luminescent ruthenuim complex to the native retinal chromophore was observed. The energy transfer rates in these three systems, and in two additional systems already described (Kouyama, T., K. Kinosita, Jr., and A. Ikegami, 1983, J. Mol. Biol., 165:91-107), were all consistent with a location of the retinal chromophore at a depth of 1.0 +/- 0.3 nm from a surface of the purple membrane. All the analyses in the present work involved an assumption that contacts between the external dye molecules and membrane surfaces were maximal; the depth values obtained cannot be underestimates. The chromophore therefore must be outside the middle one-third of the thickness, approximately 4.5 nm, of the purple membrane.
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Huang JY, Lewis A. Determination of the absolute orientation of the retinylidene chromophore in purple membrane by a second-harmonic interference technique. Biophys J 2010; 55:835-42. [PMID: 19431740 DOI: 10.1016/s0006-3495(89)82883-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The absolute direction of the retinal chromophore of bacterio-rhodopsin relative to the membrane plane is investigated by using an optical second-harmonic interference technique. Compared with the known adsorbed geometry of free retinylidene Schiff base on a glass substrate, our data indicate the beta-ionone ring of the chromophore of bacteriorhodopsin points away from the cytoplasmic surface of the purple membrane. The implication of this finding is discussed in light of other chemical and structural results on bacteriorhodopsin.
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Butt HJ. Measuring local surface charge densities in electrolyte solutions with a scanning force microscope. Biophys J 2010; 63:578-82. [PMID: 19431843 DOI: 10.1016/s0006-3495(92)81601-6] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
To show that local surface charge densities can be measured with a scanning force microscope purple membranes adsorbed to alumina were imaged in electrolyte solutions. Force versus distance curves were measured on purple membranes and on the bare alumina with standard silicon nitride tips. By comparing the electrostatic force measured on both substances, the surface charge density of purple membranes could be calculated from the known charge density of alumina. The charge density of purple membranes was estimated to be -0.05 C/m(2).
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Affiliation(s)
- H J Butt
- Max-Planck-Institut für Biophysik, Kennedyallee 70, 6000 Frankfurt a. M. 70, Germany
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Jansson M, Wårell K, Levander F, James P. Membrane Protein Identification: N-Terminal Labeling of Nontryptic Membrane Protein Peptides Facilitates Database Searching. J Proteome Res 2007; 7:659-65. [DOI: 10.1021/pr070545t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maria Jansson
- Department of Protein Technology, BMC D13, Lund University, Lund SE-221 84, Sweden
| | - Kristofer Wårell
- Department of Protein Technology, BMC D13, Lund University, Lund SE-221 84, Sweden
| | - Fredrik Levander
- Department of Protein Technology, BMC D13, Lund University, Lund SE-221 84, Sweden
| | - Peter James
- Department of Protein Technology, BMC D13, Lund University, Lund SE-221 84, Sweden
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Abstract
Since high-resolution structural data are still scarce, different kinds of theoretical structure prediction algorithms are of major importance in membrane protein biochemistry. But how well do the current prediction methods perform? Which structural features can be predicted and which cannot? And what can we expect in the next few years?
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Affiliation(s)
- Arne Elofsson
- Center for Biomembrane Research, Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
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Sakiyama T, Aya A, Embutsu M, Imamura K, Nakanishi K. Protease susceptibility of β-lactoglobulin adsorbed on stainless steel surface as evidence of contribution of its specific segment to adsorption. J Biosci Bioeng 2006; 101:434-9. [PMID: 16781474 DOI: 10.1263/jbb.101.434] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2005] [Accepted: 03/01/2006] [Indexed: 11/17/2022]
Abstract
beta-Lactoglobulin (beta-Lg) is a major constituent of fouling deposits in the dairy industry. To determine the interaction between beta-Lg and stainless steel surfaces, beta-Lg irreversibly adsorbed on stainless steel particles was subjected to lysyl endopeptidase treatment and the course of fragmentation was compared with that observed for beta-Lg in solution. The results showed a distinct difference between the courses of fragmentation: a fragment (residues 102-135) was liberated readily from beta-Lg in solution but scarcely from beta-Lg irreversibly adsorbed on stainless steel particles. This result strongly suggests that residues 102-135 include a segment primarily responsible for the interaction of beta-Lg with stainless steel surfaces. This supports our previous results [Sakiyama et al., J. Biosci. Bioeng., 88, 536-541 (1999)] that showed that residues 125-135 of beta-Lg have a strong affinity toward stainless steel surfaces and probably a major contribution to the adsorption of beta-Lg.
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Affiliation(s)
- Takaharu Sakiyama
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Japan.
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Karnaukhova E, Vasileiou C, Wang A, Berova N, Nakanishi K, Borhan B. Circular dichroism of heterochromophoric and partially regenerated purple membrane: Search for exciton coupling. Chirality 2005; 18:72-83. [PMID: 16385624 DOI: 10.1002/chir.20222] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In order to determine the origin of the bisignate CD spectra of native purple membrane, heterochromophoric analogues containing bacteriorhodopsin regenerated with native all-trans-retinal and retinal analogues were investigated. The data collected for the purple membrane samples containing two different chromophores suggest the additive character of the CD spectra. This conclusion was supported by a series of spectra using 5,6-dihydroretinal and 3-dehydroretinal and by using 33% regenerated PM in buffer and in presence of osmolytes. Our results support the idea of conformational heterogeneity of the chromophores in the bR in the trimer, suggesting that the three bR subunits in the trimer are not conformationally equal, and therefore, the bisignate CD spectrum of bR in the purple membrane occurs rather due to a superposition of the CD spectra from variously distorted bR subunits in the trimer than interchromophoric exciton-coupling interactions.
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Affiliation(s)
- Elena Karnaukhova
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20892, USA
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Abstract
Opioids have been used and abused by humans for centuries. The mu opioid receptor represents the high affinity binding site for opioid narcotics with high abuse liability such as morphine, codeine and fentanyl. Heroin (diacetylmorphine), a semi-synthetic derivative of morphine, crosses the blood-brain barrier more readily than morphine due to its increased hydrophobicity. Once in the brain heroin is hydrolyzed to morphine, which acts at the mu opioid receptor and results in euphoria, thus conferring the reinforcing properties of heroin. Using molecular biology techniques, the mu opioid receptors from several species have been cloned. This article reviews recent progress in this area, with respect to the two major cellular functions of the mu opioid receptor: reduction of intracellular cAMP concentration by inhibiting adenylyl cyclase activity, and inhibition of neuronal firing by modulating membrane ion channels.
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Affiliation(s)
- L Yu
- Department of Medical and Molecualr Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA.
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42
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Lee DC, Herzyk E, Chapman D. Structure of bacteriorhodopsin investigated using Fourier transform infrared spectroscopy and proteolytic digestion. Biochemistry 2002. [DOI: 10.1021/bi00392a029] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Tóth-Boconádi R, Hristova S, Keszthelyi L. Diamines reverse the direction on the bacteriorhodopsin proton pump. FEBS Lett 2001. [DOI: 10.1016/0014-5793(86)80153-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Skulachev VP. The dual role of rhodopsin in vision: light-driven charge translocation and formation of long-lived photoproducts. FEBS Lett 2001. [DOI: 10.1016/0014-5793(82)80928-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Evidence for the protonation of two internal carboxylic groups during the photocycle of bacteriorhodopsin. FEBS Lett 2001. [DOI: 10.1016/0014-5793(82)80021-5] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Pabst R, Ringsdorf H, Koch H, Dose K. Light-driven proton transport of bacteriorhodopsin incorporated into long-term stable liposomes of a polymerizable sulfolipid. FEBS Lett 2001. [DOI: 10.1016/0014-5793(83)80866-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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