1
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Meng X, Ganapathy S, van Roemburg L, Post M, Brinks D. Voltage Imaging with Engineered Proton-Pumping Rhodopsins: Insights from the Proton Transfer Pathway. ACS PHYSICAL CHEMISTRY AU 2023; 3:320-333. [PMID: 37520318 PMCID: PMC10375888 DOI: 10.1021/acsphyschemau.3c00003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/13/2023] [Accepted: 04/13/2023] [Indexed: 08/01/2023]
Abstract
Voltage imaging using genetically encoded voltage indicators (GEVIs) has taken the field of neuroscience by storm in the past decade. Its ability to create subcellular and network level readouts of electrical dynamics depends critically on the kinetics of the response to voltage of the indicator used. Engineered microbial rhodopsins form a GEVI subclass known for their high voltage sensitivity and fast response kinetics. Here we review the essential aspects of microbial rhodopsin photocycles that are critical to understanding the mechanisms of voltage sensitivity in these proteins and link them to insights from efforts to create faster, brighter and more sensitive microbial rhodopsin-based GEVIs.
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Affiliation(s)
- Xin Meng
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
| | - Srividya Ganapathy
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
- Department
of Pediatrics & Cellular and Molecular Medicine, UCSD School of Medicine, La Jolla, California 92093, United States
| | - Lars van Roemburg
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
| | - Marco Post
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
| | - Daan Brinks
- Department
of Imaging Physics, Delft University of
Technology, 2628 CJ Delft, The
Netherlands
- Department
of Molecular Genetics, Erasmus University
Medical Center, 3015 GD Rotterdam, The Netherlands
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2
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Brown LS. Light-driven proton transfers and proton transport by microbial rhodopsins - A biophysical perspective. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183867. [PMID: 35051382 DOI: 10.1016/j.bbamem.2022.183867] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/30/2021] [Accepted: 01/10/2022] [Indexed: 12/31/2022]
Abstract
In the last twenty years, our understanding of the rules and mechanisms for the outward light-driven proton transport (and underlying proton transfers) by microbial rhodopsins has been changing dramatically. It transitioned from a very detailed atomic-level understanding of proton transport by bacteriorhodopsin, the prototypical proton pump, to a confounding variety of sequence motifs, mechanisms, directions, and modes of transport in its newly found homologs. In this review, we will summarize and discuss experimental data obtained on new microbial rhodopsin variants, highlighting their contribution to the refinement and generalization of the ideas crystallized in the previous century. In particular, we will focus on the proton transport (and transfers) vectoriality and their structural determinants, which, in many cases, remain unidentified.
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Affiliation(s)
- Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Ontario N1G 2W1, Canada.
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3
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Effects of Mutations of Lys41 and Asp102 of Bacteriorhodopsin. Biosci Biotechnol Biochem 2014; 75:1364-70. [DOI: 10.1271/bbb.110180] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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4
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Gerwert K, Freier E, Wolf S. The role of protein-bound water molecules in microbial rhodopsins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:606-13. [PMID: 24055285 DOI: 10.1016/j.bbabio.2013.09.006] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 09/08/2013] [Accepted: 09/10/2013] [Indexed: 02/06/2023]
Abstract
Protein-bound internal water molecules are essential features of the structure and function of microbial rhodopsins. Besides structural stabilization, they act as proton conductors and even proton storage sites. Currently, the most understood model system exhibiting such features is bacteriorhodopsin (bR). During the last 20 years, the importance of water molecules for proton transport has been revealed through this protein. It has been shown that water molecules are as essential as amino acids for proton transport and biological function. In this review, we present an overview of the historical development of this research on bR. We furthermore summarize the recently discovered protein-bound water features associated with proton transport. Specifically, we discuss a pentameric water/amino acid arrangement close to the protonated Schiff base as central proton-binding site, a protonated water cluster as proton storage site at the proton-release site, and a transient linear water chain at the proton uptake site. We highlight how protein conformational changes reposition or reorient internal water molecules, thereby guiding proton transport. Last, we compare the water positions in bR with those in other microbial rhodopsins to elucidate how protein-bound water molecules guide the function of microbial rhodopsins. 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)
- Klaus Gerwert
- Department of Biophysics, University of Bochum, ND 04 North, 44780 Bochum, Germany; Department of Biophysics, Chinese Academy of Sciences-Max-Planck Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS), 320 Yue Yang Lu, 200031 Shanghai, PR China.
| | - Erik Freier
- Department of Biophysics, University of Bochum, ND 04 North, 44780 Bochum, Germany
| | - Steffen Wolf
- Department of Biophysics, Chinese Academy of Sciences-Max-Planck Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS), 320 Yue Yang Lu, 200031 Shanghai, PR China
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5
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Tamogami J, Kikukawa T, Miyauchi S, Muneyuki E, Kamo N. A Tin Oxide Transparent Electrode Provides the Means for Rapid Time-resolved pH Measurements: Application to Photoinduced Proton Transfer of Bacteriorhodopsin and Proteorhodopsin. Photochem Photobiol 2009; 85:578-89. [DOI: 10.1111/j.1751-1097.2008.00520.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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6
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Wang Z, Bai J, Xu Y. The effect of charged lipids on bacteriorhodopsin membrane reconstitution and its photochemical activities. Biochem Biophys Res Commun 2008; 371:814-7. [DOI: 10.1016/j.bbrc.2008.04.141] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2008] [Accepted: 04/28/2008] [Indexed: 11/25/2022]
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7
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Lanyi JK. Proton transfers in the bacteriorhodopsin photocycle. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:1012-8. [PMID: 16376293 DOI: 10.1016/j.bbabio.2005.11.003] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2005] [Revised: 11/08/2005] [Accepted: 11/10/2005] [Indexed: 11/23/2022]
Abstract
The steps in the mechanism of proton transport in bacteriorhodopsin include examples for most kinds of proton transfer reactions that might occur in a transmembrane pump: proton transfer via a bridging water molecule, coupled protonation/deprotonation of two buried groups separated by a considerable distance, long-range proton migration over a hydrogen-bonded aqueous chain, and capture as well as release of protons at the membrane-water interface. The conceptual and technical advantages of this system have allowed close examination of many of these model reactions, some at an atomic level.
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Affiliation(s)
- Janos K Lanyi
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA.
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8
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Jaakola VP, Rehn M, Moeller M, Alexiev U, Goldman A, Turner GJ. G-protein-coupled receptor domain overexpression in Halobacterium salinarum: long-range transmembrane interactions in heptahelical membrane proteins. Proteins 2006; 60:412-23. [PMID: 15971205 DOI: 10.1002/prot.20498] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The aminergic alpha(2b)-adrenergic receptor (alpha(2b)-AR) third intracellular loop (alpha(2b)-AR 3i) mediates receptor subcellular compartmentalization and signal transduction processes via ligand-dependent interaction with G(i)- and G(o)- proteins. To understand the structural origins of these processes we engineered several lengths of alpha(2b)-AR 3i into the third intracellular loop of the proton pump bacteriorhodopsin (bR) and produced the fusion proteins in quantities suitable for physical studies. The fusion proteins were expressed in the Archaeon Halobacterium salinarum and purified. A highly expressed fusion protein was crystallized from bicelles and diffracted to low resolution on an in-house diffractometer. The bR-alpha(2b)-AR 3i(203-292) protein possessed a photocycle slightly perturbed from that of the wild-type bR. The first half of the fusion protein photocycle, correlated with proton release, is accelerated by a factor of 3, whereas the second half, correlated with proton uptake, is slightly slower than wild-type bR. In addition, there is a large decrease in the pK(a), (from 9.6 to 8.3) of the terminal proton release group in the unphotolyzed state of bR-alpha(2b)-AR 3i as deduced from the pH-dependence of the M-formation. Perturbation of a cytoplasmic loop has thus resulted in the perturbation of proton release at the extracellular surface. The current work indicates that long-range and highly coupled intramolecular interactions exist that are capable of "transducing" structural perturbations (e.g., signals) across the cellular membrane. This gene fusion approach may have general applicability for physical studies of G-protein-coupled receptor domains in the context of the bR structural scaffold.
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Affiliation(s)
- Veli-Pekka Jaakola
- Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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9
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Brown LS, Jung KH. Bacteriorhodopsin-like proteins of eubacteria and fungi: the extent of conservation of the haloarchaeal proton-pumping mechanism. Photochem Photobiol Sci 2006; 5:538-46. [PMID: 16761082 DOI: 10.1039/b514537f] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A stereotypical image of a retinal-binding proton pump derived from extensive studies of halobacterial ion-transporting and sensory rhodopsins is a fast-cycling protein which possesses two strategically placed carboxylic acids serving as proton donor and acceptor for the retinal Schiff base. We review recent biophysical and bioinformatic data on the novel eubacterial and eucaryotic rhodopsins to analyze the extent of conservation of the haloarchaeal mechanism of transmembrane proton transport. We show that only the most essential elements of the haloarchaeal proton-pumping machinery are conserved universally, and that a mere presence of these elements in primary structures does not guarantee the proton-pumping ability.
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Affiliation(s)
- Leonid S Brown
- Department of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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10
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Saitô H, Yamaguchi S, Ogawa K, Tuzi S, Márquez M, Sanz C, Padrós E. Glutamic acid residues of bacteriorhodopsin at the extracellular surface as determinants for conformation and dynamics as revealed by site-directed solid-state 13C NMR. Biophys J 2004; 86:1673-81. [PMID: 14990495 PMCID: PMC1304003 DOI: 10.1016/s0006-3495(04)74236-8] [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: 12/22/2022] Open
Abstract
We recorded (13)C NMR spectra of [3-(13)C]Ala- and [1-(13)C]Val-labeled bacteriorhodopsin (bR) and a variety of its mutants, E9Q, E74Q, E194Q/E204Q (2Glu), E9Q/E194Q/E204Q (3Glu), and E9Q/E74Q/E194Q/E204Q (4Glu), to clarify contributions of the extracellular (EC) Glu residues to the conformation and dynamics of bR. Replacement of Glu-9 or Glu-74 and Glu-194/204 at the EC surface by glutamine(s) induced significant conformational changes in the cytoplasmic (CP) surface structure. These changes occurred in the C-terminal alpha-helix and loops, and also those of the EC surface, as viewed from (13)C NMR spectra of [3-(13)C]Ala- and [1-(13)C]Val-labeled proteins. Additional conformational changes in the transmembrane alpha-helices were induced as modified retinal-protein interactions for multiple mutants involving the E194Q/E204Q pair. Significant dynamic changes were induced for the triple or quadruple mutants, as shown by broadened (13)C NMR peaks of [1-(13)C]Val-labeled proteins. These changes were due to acquired global fluctuation motions of the order of 10(-4)-10(-5) s as a result of disorganized trimeric form. In such mutants (13)C NMR signals from Val residues of [1-(13)C]Val-labeled triple and quadruple mutants near the CP and EC surfaces (including 8.7-A depth from the surface) were substantially suppressed, as shown by comparative (13)C NMR studies with and without 40 micro M Mn(2+) ion. We conclude that these Glu residues at the EC surface play an important role in maintaining the native secondary structure of bR in the purple membrane.
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Affiliation(s)
- Hazime Saitô
- Department of Life Science, Graduate School of Science, Himeji Institute of Technology, Harima Science Garden City, Kamgiori, Hyogo, Japan 678-1297.
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11
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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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12
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Hendler RW, Bose S. Interconversions among four M-intermediates in the bacteriorhodopsin photocycle. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:3518-24. [PMID: 12919316 DOI: 10.1046/j.1432-1033.2003.03731.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Halobacterium salinarum displays four distinct kinetic forms of M-intermediate in its bacteriorhodopsin photocycle. In wild-type, there are mainly two species with time constants near 2 and 5 ms. Under various kinds of stress, two other species arise with time constants near 10 and 70 ms. We show that these four species are interconvertible. Increases in membrane hydrophobicity convert the slower to faster forms. Perturbations caused by Triton X-100 or mutations convert faster to slower forms. The fastest form requires a hydrophobic membrane environment near a ring of four charged aspartate residues in the trimer, namely Asp36, Asp38, Asp102, and Asp104 in the cytoplasmic loop regions. Interconversions of the 2-ms and 5-ms species of the wild-type are accomplished by pH-changes. The potential significance of these findings is discussed.
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Affiliation(s)
- Richard W Hendler
- Laboratory of Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892-0510, USA.
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13
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Friedman R, Nachliel E, Gutman M. The role of small intraprotein cavities in the catalytic cycle of bacteriorhodopsin. Biophys J 2003; 85:886-96. [PMID: 12885636 PMCID: PMC1303210 DOI: 10.1016/s0006-3495(03)74528-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The last phase of the proton transfer cycle of bacteriorhodopsin calls for a passage of a proton from D38 to D96. This reaction utilizes a narrow shaft approximately 10-A long that connects the two carboxylates that cross through a very hydrophobic domain. As the shaft is too narrow to be permanently hydrated, there are two alternatives for the proton propagation into the channel. The proton may propagate through the shaft without solvation at the expense of a high electrostatic barrier; alternatively, the shaft will expand to accommodate some water molecules, thus lowering the Born energy for the insertion of the charge into the protein (B. Schätzler, N. A. Dencher, J. Tittor, D. Oesterhelt, S. Yaniv-Checover, E. Nachliel, and G. Gutman, 2003, BIOPHYS: J. 84:671-686). A comparative study of nine published crystal-structures of bacteriorhodopsin identified, next to the shaft, microcavities in the protein whose position and surrounding atoms are common to the reported structures. Some of the cavities either shrink or expand during the photocycle. It is argued that the plasticity of the cavities provides a working space needed for the transient solvation of the shaft, thus reducing the activation energy necessary for the solvation of the shaft. This suggestion is corroborated by the recent observations of Klink et al. (B. U. Klink, R. Winter, M. Engelhard, and I. Chizhov, 2002, BIOPHYS: J. 83:3490-3498) that the late phases of the photocycle (tau >/=1 ms) are strongly inhibited by external pressure.
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Affiliation(s)
- Ran Friedman
- Laser Laboratory for Fast Reactions in Biology, Department of Biochemistry, Tel Aviv University, Tel Aviv 69978, Israel
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14
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Schobert B, Brown LS, Lanyi JK. Crystallographic structures of the M and N intermediates of bacteriorhodopsin: assembly of a hydrogen-bonded chain of water molecules between Asp-96 and the retinal Schiff base. J Mol Biol 2003; 330:553-70. [PMID: 12842471 DOI: 10.1016/s0022-2836(03)00576-x] [Citation(s) in RCA: 142] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An M intermediate of wild-type bacteriorhodopsin and an N intermediate of the V49A mutant were accumulated in photostationary states at pH 5.6 and 295 K, and their crystal structures determined to 1.52A and 1.62A resolution, respectively. They appear to be M(1) and N' in the sequence, M(1)<-->M(2)<-->M'(2)<-->N<-->N'-->O-->BR, where M(1), M(2), and M'(2) contain an unprotonated retinal Schiff base before and after a reorientation switch and after proton release to the extracellular surface, while N and N' contain a reprotonated Schiff base, before and after reprotonation of Asp96 from the cytoplasmic surface. In M(1), we detect a cluster of three hydrogen-bonded water molecules at Asp96, not present in the BR state. In M(2), whose structure we reported earlier, one of these water molecules intercalates between Asp96 and Thr46. In N', the cluster is transformed into a single-file hydrogen-bonded chain of four water molecules that connects Asp96 to the Schiff base. We find a network of three water molecules near residue 219 in the crystal structure of the non-illuminated F219L mutant, where the residue replacement creates a cavity. This suggests that the hydration of the cytoplasmic region we observe in N' might have occurred spontaneously, beginning at an existing water molecule as nucleus, in the cavities from residue rearrangements in the photocycle.
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Affiliation(s)
- Brigitte Schobert
- Department of Physiology and Biophysics, University of California, D345 Medical Science I, Irvine, CA 92697, USA
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15
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Lanyi JK. Molecular Mechanism of Ion Transport in Bacteriorhodopsin: Insights from Crystallographic, Spectroscopic, Kinetic, and Mutational Studies. J Phys Chem B 2000. [DOI: 10.1021/jp0023718] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Janos K. Lanyi
- Department of Physiology & Biophysics, University of California, Irvine, California 92697
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16
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Brown LS. Reconciling crystallography and mutagenesis: a synthetic approach to the creation of a comprehensive model for proton pumping by bacteriorhodopsin. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1460:49-59. [PMID: 10984590 DOI: 10.1016/s0005-2728(00)00129-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
As a result of the number of new high-resolution structures of the pigment and some of its photointermediates, a realistic model for the functioning of bacteriorhodopsin seems to be finally emerging. However, lack of structural information for some of the key functional states, and contradictions between some published structural models, argue for the use of the synthetic approach, one that includes use of data from both crystallographic and mutagenesis studies. The role of mutagenesis in this synthetic approach falls into two categories. First, to provide additional structural information, and second, to test the predictions of structural models by studying mutant phenotypes. This review urges critical comparisons of the structural and mutagenesis data, as there are problems with their selective and indiscriminate use.
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Affiliation(s)
- L S Brown
- Department of Physiology and Biophysics, University of California, 92697-4560, Irvine, CA, USA.
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17
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Balashov SP. Protonation reactions and their coupling in bacteriorhodopsin. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1460:75-94. [PMID: 10984592 DOI: 10.1016/s0005-2728(00)00131-6] [Citation(s) in RCA: 130] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Light-induced changes of the proton affinities of amino acid side groups are the driving force for proton translocation in bacteriorhodopsin. Recent progress in obtaining structures of bacteriorhodopsin and its intermediates with an increasingly higher resolution, together with functional studies utilizing mutant pigments and spectroscopic methods, have provided important information on the molecular architecture of the proton transfer pathways and the key groups involved in proton transport. In the present paper I consider mechanisms of light-induced proton release and uptake and intramolecular proton transport and mechanisms of modulation of proton affinities of key groups in the framework of these data. Special attention is given to some important aspects that have surfaced recently. These are the coupling of protonation states of groups involved in proton transport, the complex titration of the counterion to the Schiff base and its origin, the role of the transient protonation of buried groups in catalysis of the chromophore's thermal isomerization, and the relationship between proton affinities of the groups and the pH dependencies of the rate constants of the photocycle and proton transfer reactions.
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Affiliation(s)
- S P Balashov
- Center for Biophysics and Computational Biology, Department of Cell and Structural Biology, University of Illinois at Urbana-Champaign, B107 CLSL, 601 S. Goodwin Ave., 61801, Urbana, IL, USA.
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18
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Abstract
Internal water molecules are considered to play a crucial role in the functional processes of proton pump proteins. They may participate in hydrogen-bonding networks inside proteins that constitute proton pathways. In addition, they could participate in the switch reaction by mediating an essential proton transfer at the active site. Nevertheless, little has been known about the structure and function of internal water molecules in such proteins. Recent progress in infrared spectroscopy and X-ray crystallography provided new information on water molecules inside bacteriorhodopsin, the light-driven proton pump. The accumulated knowledge on bacteriorhodopsin in the last decade of the 20th century will lead to a realistic picture of internal water molecules at work in the 21st century. In this review, I describe how the role of water molecules has been studied in bacteriorhodopsin, and what should be known about the role of water molecules in the future.
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Affiliation(s)
- H Kandori
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, 606-8502, Kyoto, Japan.
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19
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Dencher NA, Sass HJ, Büldt G. Water and bacteriorhodopsin: structure, dynamics, and function. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1460:192-203. [PMID: 10984600 DOI: 10.1016/s0005-2728(00)00139-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A wealth of information has been gathered during the past decades that water molecules do play an important role in the structure, dynamics, and function of bacteriorhodopsin (bR) and purple membrane. Light-induced structural alterations in bR as detected by X-ray and neutron diffraction at low and high resolution are discussed in relationship to the mechanism of proton pumping. The analysis of high resolution intermediate structures revealed photon-induced rearrangements of water molecules and hydrogen bonds concomitant with conformational changes in the chromophore and the protein. These observations led to an understanding of key features of the pumping mechanism, especially the vectoriality and the different modes of proton translocation in the proton release and uptake domain of bR. In addition, water molecules influence the function of bR via equilibrium fluctuations, which must occur with adequate amplitude so that energy barriers between conformational states can be overcome.
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Affiliation(s)
- N A Dencher
- Technische Universität Darmstadt, Institute of Biochemistry, Physical Biochemistry, Petersenstrasse 22, D-64287 Darmstadt, Germany.
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20
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Krebs MP, Isenbarger TA. Structural determinants of purple membrane assembly. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1460:15-26. [PMID: 10984587 DOI: 10.1016/s0005-2728(00)00126-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The purple membrane is a two-dimensional crystalline lattice formed by bacteriorhodopsin and lipid molecules in the cytoplasmic membrane of Halobacterium salinarum. High-resolution structural studies, in conjunction with detailed knowledge of the lipid composition, make the purple membrane one of the best models for elucidating the forces that are responsible for the assembly and stability of integral membrane protein complexes. In this review, recent mutational efforts to identify the structural features of bacteriorhodopsin that determine its assembly in the purple membrane are discussed in the context of structural, calorimetric and reconstitution studies. Quantitative evidence is presented that interactions between transmembrane helices of neighboring bacteriorhodopsin molecules contribute to purple membrane assembly. However, other specific interactions, particularly between bacteriorhodopsin and lipid molecules, may provide the major driving force for assembly. Elucidating the molecular basis of protein-protein and protein-lipid interactions in the purple membrane may provide insights into the formation of integral membrane protein complexes in other systems.
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Affiliation(s)
- M P Krebs
- Department of Biomolecular Chemistry, University of Wisconsin Medical School, 53706-1532, Madison, WI, USA.
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21
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Abstract
Adding Ca2+ or other cations to deionized bacteriorhodopsin causes a blue to purple color shift, a result of deprotonation of Asp85. It has been proposed by different groups that the protonation state of Asp85 responds to the binding of Ca2+ either 1) directly at a specific site in the protein or 2) indirectly through the rise of the surface pH. We tested the idea of specific binding of Ca2+ and found that the surface pH, as determined from the ionization state of eosin covalently linked to engineered cysteine residues, rises about equally at both extracellular and cytoplasmic surfaces when only one Ca2+ is added. This precludes binding to a specific site and suggests that rather than decreasing the pKa of Asp85 by direct interaction, Ca2+ increases the surface pH by binding to anionic lipid groups. As Ca2+ is added the surface pH rises, but deprotonation of Asp85 occurs only when the surface pH approaches its pKa. The nonlinear relationship between Ca2+ binding and deprotonation of Asp85 from this effect is different in the wild-type protein and in various mutants and explains the observed complex and varied spectral titration curves.
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Affiliation(s)
- G Váró
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, USA
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