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Lukhele S, Cohen ÉA. Conserved residues within the HIV-1 Vpu transmembrane-proximal hinge region modulate BST2 binding and antagonism. Retrovirology 2017; 14:18. [PMID: 28288652 PMCID: PMC5348903 DOI: 10.1186/s12977-017-0345-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 03/05/2017] [Indexed: 11/10/2022] Open
Abstract
Background BST2 inhibits HIV-1 release by tethering nascent virions to the surface of infected cells. HIV-1 Vpu overcomes this restriction by removing BST2 from viral budding sites via BST2 intracellular trapping and sequestration, surface downregulation and/or displacement mechanisms. Vpu is composed of a short luminal tail, a transmembrane domain (TMD) and a cytoplasmic hinge region that is followed by two helices. BST2 counteraction relies on the ability of Vpu to physically bind BST2 through TMD interactions and recruit the clathrin-dependent trafficking machinery via a canonical acidic di-leucine signalling motif within the helix-2 of Vpu. The highly conserved Vpu transmembrane-proximal hinge region encompasses residues that resemble an acidic leucine-based trafficking motif, whose functional roles are currently ill-defined. In this study, we investigated the contribution of these residues towards Vpu-mediated BST2 antagonism. Results We show that while these conserved residues have no intrinsic activity on the cellular distribution of Vpu in the absence of BST2, they regulate the ability of Vpu to bind to BST2 and, consequently, govern both BST2-dependent trafficking properties of the protein as well as its co-localization with BST2. Moreover, these residues, particularly a glutamic acid residue positioned immediately following the TMD, are a determinant not only for efficient targeting of BST2, but also binding and degradation of CD4, another host membrane protein targeted by Vpu. Mechanistically, our data are consistent with a role of these residues in the maintenance of the Vpu TMD conformational configuration such that interactions with membrane-associated host targets are favoured. Conclusions Altogether, this work demonstrates an important regulatory role of the transmembrane-proximal Vpu hinge region residues towards enabling the protein to efficiently engage its target host proteins. Thus, this highly conserved, cytosolic Vpu hinge region may represent an attractive target for the development of anti-Vpu inhibitors. Electronic supplementary material The online version of this article (doi:10.1186/s12977-017-0345-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sabelo Lukhele
- Laboratory of Human Retrovirology, Institut de Recherches Cliniques de Montréal (IRCM), 110, Pine Avenue West, Montreal, QC, H2W 1R7, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, H3A 1A3, Canada
| | - Éric A Cohen
- Laboratory of Human Retrovirology, Institut de Recherches Cliniques de Montréal (IRCM), 110, Pine Avenue West, Montreal, QC, H2W 1R7, Canada. .,Division of Experimental Medicine, McGill University, Montreal, QC, H3A 1A3, Canada. .,Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, H3T 1J4, Canada.
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2
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Lazarova T, Mlynarczyk K, Querol E, Tenchov B, Filipek S, Padrós E. Identification of Specific Effect of Chloride on the Spectral Properties and Structural Stability of Multiple Extracellular Glutamic Acid Mutants of Bacteriorhodopsin. PLoS One 2016; 11:e0162952. [PMID: 27657718 PMCID: PMC5033488 DOI: 10.1371/journal.pone.0162952] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 08/31/2016] [Indexed: 11/18/2022] Open
Abstract
In the present work we combine spectroscopic, DSC and computational approaches to examine the multiple extracellular Glu mutants E204Q/E194Q, E204Q/E194Q/E9Q and E204Q/E194Q/E9Q/E74Q of bacteriorhodopsin by varying solvent ionic strength and composition. Absorption spectroscopy data reveal that the absorption maxima of multiple EC Glu mutants can be tuned by the chloride concentration in the solution. Visible Circular dichroism spectra imply that the specific binding of Cl- can modulate weakened exciton chromophore coupling and reestablish wild type-like bilobe spectral features of the mutants. The DSC data display reappearance of the reversible thermal transition, higher Tm of denaturation and an increase in the enthalpy of unfolding of the mutants in 1 M KCl solutions. Molecular dynamics simulations indicate high affinity binding of Cl- to Arg82 and to Gln204 and Gln194 residues in the mutants. Analysis of the experimental data suggests that simultaneous elimination of the negatively charged side chain of Glu194 and Glu204 is the major cause for mutants' alterations. Specific Cl- binding efficiently coordinates distorted hydrogen bonding interactions of the EC region and reconstitutes the conformation and structure stability of mutated bR in WT-like fashion.
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Affiliation(s)
- Tzvetana Lazarova
- Unitat de Biofísica, Departament de Bioquímica i de Biologia Molecular, Facultat de Medicina, and Centre d'Estudis en Biofísica, Universitat Autònoma de Barcelona, Barcelona, Spain
- * E-mail: (TL); (EP)
| | - Krzysztof Mlynarczyk
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Enric Querol
- Institut de Biomedicina i Biotecnologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Boris Tenchov
- Department of Medical Physics and Biophysics, Faculty of Medicine, Medical University – Sofia, Sofia, Bulgaria
| | - Slawomir Filipek
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Esteve Padrós
- Unitat de Biofísica, Departament de Bioquímica i de Biologia Molecular, Facultat de Medicina, and Centre d'Estudis en Biofísica, Universitat Autònoma de Barcelona, Barcelona, Spain
- * E-mail: (TL); (EP)
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Gomariz M, Martínez-García M, Santos F, Constantino M, Meseguer I, Antón J. Retinal-binding proteins mirror prokaryotic dynamics in multipond solar salterns. Environ Microbiol 2015; 17:514-26. [DOI: 10.1111/1462-2920.12709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 10/30/2014] [Accepted: 11/02/2014] [Indexed: 11/28/2022]
Affiliation(s)
- María Gomariz
- Department of Materials, Optics and Electronics; University Miguel Hernández of Elche; Alicante 03202 Spain
- Department of Physiology, Genetics, and Microbiology; University of Alicante; Alicante 03080 Spain
| | - Manuel Martínez-García
- Department of Physiology, Genetics, and Microbiology; University of Alicante; Alicante 03080 Spain
| | - Fernando Santos
- Department of Physiology, Genetics, and Microbiology; University of Alicante; Alicante 03080 Spain
| | - Marco Constantino
- Department of Physiology, Genetics, and Microbiology; University of Alicante; Alicante 03080 Spain
| | - Inmaculada Meseguer
- Department of Materials, Optics and Electronics; University Miguel Hernández of Elche; Alicante 03202 Spain
| | - Josefa Antón
- Department of Physiology, Genetics, and Microbiology; University of Alicante; Alicante 03080 Spain
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4
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Lazarova T, Mlynarczyk K, Filipek S, Kolinski M, Wassenaar TA, Querol E, Renugopalakrishnan V, Viswanathan S, Padrós E. The effect of triple glutamic mutations E9Q/E194Q/E204Q on the structural stability of bacteriorhodopsin. FEBS J 2013; 281:1181-95. [PMID: 24341610 DOI: 10.1111/febs.12694] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 11/21/2013] [Accepted: 12/12/2013] [Indexed: 10/25/2022]
Abstract
In the present study, we report on the structural features of the bacteriorhodopsin triple mutant E9Q/E194Q/E204Q (3Glu) of bacteriorhodopsin by combining experimental and molecular dynamics (MD) approaches. In 3Glu mutant, Glu9, Glu194 and Glu204 residues located at the extracellular side of the protein were mutated altogether to glutamines. UV-visible and differential scanning calorimetry experiments served as diagnostic tools for monitoring the resistance against thermal stress of the active site and the tertiary structures of the 3Glu. The analyses of the UV-visible thermal difference spectra demonstrate that the spectral forms at room temperature and the thermal unfolding path differ in the wild-type bacteriorhodopsin and the 3Glu. Even with these spectral differences, the thermal unfolding of the active site occurs at rather similar melting temperatures in both proteins. A noteworthy consequence of the mutations is the altered two-dimensional packing revealed by the lack of the pre-transition peak in differential scanning calorimetry traces of 3Glu mutant, as previously detected in wild-type and the corresponding single mutants. The infrared spectroscopy data agree with the loss of paracrystalinity, illustrating a substantial conversion of αII to αI helical conformation in the 3Glu mutant. Molecular dynamics simulations show higher dynamics flexibility of most of the extracellular regions of 3Glu, which may account for the somewhat lower tertiary structural stability of the mutated protein. Finally, hydrogen bond analysis reveals that the mutated Glu194 and Glu204 residues create ~ 50% less hydrogen bonds with water molecules compared to wild-type bacteriorhodopsin. These results exemplify the role of the water hydrogen-bonding network for structural integrity and conformational flexibility of bacteriorhodopsin.
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Affiliation(s)
- Tzvetana Lazarova
- Unitat de Biofísica, Departament de Bioquímica i de Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona, Spain; Centre d'Estudis en Biofísica, Universitat Autònoma de Barcelona, Spain
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5
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Simón-Vázquez R, Domínguez M, Lórenz-Fonfría VA, Alvarez S, Bourdelande JL, de Lera AR, Padrós E, Perálvarez-Marín A. Probing a polar cluster in the retinal binding pocket of bacteriorhodopsin by a chemical design approach. PLoS One 2012; 7:e42447. [PMID: 22879987 PMCID: PMC3411786 DOI: 10.1371/journal.pone.0042447] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 07/06/2012] [Indexed: 11/24/2022] Open
Abstract
Bacteriorhodopsin has a polar cluster of amino acids surrounding the retinal molecule, which is responsible for light harvesting to fuel proton pumping. From our previous studies, we have shown that threonine 90 is the pivotal amino acid in this polar cluster, both functionally and structurally. In an attempt to perform a phenotype rescue, we have chemically designed a retinal analogue molecule to compensate the drastic effects of the T90A mutation in bacteriorhodopsin. This analogue substitutes the methyl group at position C13 of the retinal hydrocarbon chain by and ethyl group (20-methyl retinal). We have analyzed the effect of reconstituting the wild-type and the T90A mutant apoproteins with all-trans-retinal and its 20-methyl derivative (hereafter, 13-ethyl retinal). Biophysical characterization indicates that recovering the steric interaction between the residue 90 and retinal, eases the accommodation of the chromophore, however it is not enough for a complete phenotype rescue. The characterization of these chemically engineered chromoproteins provides further insight into the role of the hydrogen bond network and the steric interactions involving the retinal binding pocket in bacteriorhodopsin and other microbial sensory rhodopsins.
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Affiliation(s)
- Rosana Simón-Vázquez
- Departament de Bioquímica i de Biologia Molecular and Centre d'Estudis en Biofísica, Universitat Autònoma de Barcelona, Barcelona, Spain
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6
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Perálvarez-Marín A, Sepulcre F, Márquez M, Proietti MG, Padrós E. Combination of extended X-ray absorption fine structure spectroscopy with lipidic cubic phases for the study of cation binding in bacteriorhodopsin. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:1007-12. [PMID: 21667310 DOI: 10.1007/s00249-011-0714-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 05/10/2011] [Accepted: 05/18/2011] [Indexed: 10/18/2022]
Abstract
We have performed a quantitative X-ray absorption fine structure analysis of bacteriorhodopsin in purple membrane patches and in lipidic cubic phases regenerated with Mn(2+). Lipidic cubic phases and purple membrane results have been compared, demonstrating that the lipidic cubic phase process does not introduce relevant distortions in the local geometry of the cation binding sites. For both samples, we have observed similarities for Mn(2+) coordination in terms of type, number, and average distances of surrounding atoms, indicating a first coordination shell composed by 6 O atoms, and 3/4 C atoms located in the second coordination shell.
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Affiliation(s)
- Alex Perálvarez-Marín
- Unitat de Biofísica, Departament de Bioquímica i de Biologia Molecular and Centre d'Estudis en Biofísica, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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7
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Ranaghan MJ, Shima S, Ramos L, Poulin DS, Whited G, Rajasekaran S, Stuart JA, Albert AD, Birge RR. Photochemical and thermal stability of green and blue proteorhodopsins: implications for protein-based bioelectronic devices. J Phys Chem B 2011; 114:14064-70. [PMID: 20964279 DOI: 10.1021/jp106633w] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The photochemical and thermal stability of the detergent-solubilized blue- and green-absorbing proteorhodpsins, BPR and GPR, respectively, are investigated to determine the viability of these proteins for photonic device applications. Photochemical stability is studied by using pulsed laser excitation and differential UV-vis spectroscopy to assign the photocyclicity. GPR, with a cyclicity of 7 × 10(4) photocycles protein(-1), is 4-5 times more stable than BPR (9 × 10(3) photocycles protein(-1)), but is less stable than native bacteriorhodopsin (9 × 10(5) photocycles protein(-1)) or the 4-keto-bacteriorhodopsin analogue (1 × 10(5) photocycles protein(-1)). The thermal stabilities are assigned by using differential scanning calorimetry and thermal bleaching experiments. Both proteorhodopsins display excellent thermal stability, with melting temperatures above 85 °C, and remain photochemically stable up to 75 °C. The biological relevance of our results is also discussed. The lower cyclicity of BPR is found to be adequate for the long-term biological function of the host organism at ocean depths of 50 m or more.
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Affiliation(s)
- Matthew J Ranaghan
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, Connecticut 06269, USA
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8
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Lazarova T, Querol E, Padrós E. Coupling between the retinal thermal isomerization and the Glu194 residue of bacteriorhodopsin. Photochem Photobiol 2009; 85:617-23. [PMID: 19267876 DOI: 10.1111/j.1751-1097.2008.00534.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glu194 is a residue located at the end of F helix on the extracellular side of the light-induced proton pump bacteriorhodopsin (BR). Currently, it is well recognized that Glu194 and Glu204 residues, along with water clusters, constitute the proton release group of BR. Here we report that the replacement of Glu194 for Gln affects not only the photocycle of the protein but also has tremendous effect on the all-trans to 13-cis thermal isomerization. We studied the pH dependence of the dark adaptation of the E194Q mutant and performed HPLC analysis of the isomer compositions of the light- and partially dark-adapted states of the mutant at several pH values. Our data confirmed that E194Q exhibits extremely slow dark adaptation over a wide range of pH. HPLC data showed that a significantly larger concentration of all-trans isomer was present in the samples of the E194Q mutant even after prolonged dark adaptation. After 14 days in the dark the 13-cis to all-trans ratio was 1:3 in the mutant, compared to 2:1 in the wild type. These data clearly indicate the involvement of Glu194 in control of the rate of all-trans to 13-cis thermal isomerization.
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Affiliation(s)
- Tzvetana Lazarova
- Departament de Bioquímica i de Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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9
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Wassenaar TA, Daura X, Padrós E, Mark AE. Calcium binding to the purple membrane: A molecular dynamics study. Proteins 2009; 74:669-81. [PMID: 18704943 DOI: 10.1002/prot.22182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The purple membrane (PM) is a specialized membrane patch found in halophilic archaea, containing the photoreceptor bacteriorhodopsin (bR). It is long known that calcium ions bind to the PM, but their position and role remain elusive to date. Molecular dynamics simulations in conjunction with a highly detailed model of the PM have been used to investigate the stability of calcium ions placed at three proposed cation binding sites within bR, one near the Schiff base, one in the region of the proton release group, and one near Glu9. The simulations suggest that, of the sites investigated, the binding of calcium ions was most likely at the proton release group. Binding in the region of the Schiff base, while possible, was associated with significant changes in local geometry. Calcium ions placed near Glu9 in the interior of bR (simultaneously to a Ca(2+) near the Schiff base and another one near the Glu194-Glu204 site) were not stable. The results obtained are discussed in relation to recent experimental observations and theoretical considerations.
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Affiliation(s)
- Tsjerk A Wassenaar
- Department of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 9747 AG Groningen, The Netherlands
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10
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Influence of proline on the thermostability of the active site and membrane arrangement of transmembrane proteins. Biophys J 2008; 95:4384-95. [PMID: 18658225 DOI: 10.1529/biophysj.108.136747] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proline residues play a fundamental and subtle role in the dynamics, structure, and function in many membrane proteins. Temperature derivative spectroscopy and differential scanning calorimetry have been used to determine the effect of proline substitution in the structural stability of the active site and transmembrane arrangement of bacteriorhodopsin. We have analyzed the Pro-to-Ala mutation for the helix-embedded prolines Pro50, Pro91, and Pro186 in the native membrane environment. This information has been complemented with the analysis of the respective crystallographic structures by the FoldX force field. Differential scanning calorimetry allowed us to determine distorted membrane arrangement for P50A and P186A. The protein stability was severely affected for P186A and P91A. In the case of Pro91, a single point mutation is capable of strongly slowing down the conformational diffusion along the denaturation coordinate, becoming a barrier-free downhill process above 371 K. Temperature derivative spectroscopy, applied for first time to study thermal stability of proteins, has been used to monitor the stability of the active site of bacteriorhodopsin. The mutation of Pro91 and Pro186 showed the most striking effects on the retinal binding pocket. These residues are the Pro in closer contact to the active site (activation energies for retinal release of 60.1 and 76.8 kcal/mol, respectively, compared to 115.8 kcal/mol for WT). FoldX analysis of the protein crystal structures indicates that the Pro-to-Ala mutations have both local and long-range effects on the structural stability of residues involved in the architecture of the protein and the active site and in the proton pumping function. Thus, this study provides a complete overview of the substitution effect of helix-embedded prolines in the thermodynamic and dynamic stability of a membrane protein, also related to its structure and function.
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11
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Role of extracellular glutamic acids in the stability and energy landscape of bacteriorhodopsin. Biophys J 2008; 95:3407-18. [PMID: 18621827 DOI: 10.1529/biophysj.108.131904] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteriorhodopsin (BR), a specialized nanomachine, converts light energy into a proton gradient to power Halobacterium salinarum. In this work, we analyze the mechanical stability of a BR triple mutant in which three key extracellular residues, Glu(9), Glu(194), and Glu(204), were mutated simultaneously to Gln. These three Glu residues are involved in a network of hydrogen bonds, in cation binding, and form part of the proton release pathway of BR. Changes in these features and the robust photocycle dynamics of wild-type (WT) BR are apparent when the three extracellular Glu residues are mutated to Gln. It is speculated that such functional changes of proteins go hand in hand with changes in their mechanical properties. Here, we apply single-molecule dynamic force spectroscopy to investigate how the Glu to Gln mutations change interactions, reaction pathways, and the energy barriers of the structural regions of WT BR. The altered heights and positions of individual energy barriers unravel the changes in the mechanical and the unfolding kinetic properties of the secondary structures of WT BR. These changes in the mechanical unfolding energy landscape cause the proton pump to choose unfolding pathways differently. We suggest that, in a similar manner, the changed mechanical properties of mutated BR alter the functional energy landscape favoring different reaction pathways in the light-induced proton pumping mechanism.
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12
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Saitô H, Naito A. NMR studies on fully hydrated membrane proteins, with emphasis on bacteriorhodopsin as a typical and prototype membrane protein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3145-61. [PMID: 17964534 DOI: 10.1016/j.bbamem.2007.08.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2007] [Revised: 08/24/2007] [Accepted: 08/29/2007] [Indexed: 11/30/2022]
Abstract
The 3D structures or dynamic feature of fully hydrated membrane proteins are very important at ambient temperature, in relation to understanding their biological activities, although their data, especially from the flexible portions such as surface regions, are unavailable from X-ray diffraction or cryoelectron microscope at low temperature. In contrast, high-resolution solid-state NMR spectroscopy has proved to be a very convenient alternative means to be able to reveal their dynamic structures. To clarify this problem, we describe here how we are able to reveal such structures and dynamic features, based on intrinsic probes from high-resolution solid-state NMR studies on bacteriorhodopsin (bR) as a typical membrane protein in 2D crystal, regenerated preparation in lipid bilayer and detergents. It turned out that their dynamic features are substantially altered upon their environments where bR is present. We further review NMR applications to study structure and dynamics of a variety of membrane proteins, including sensory rhodopsin, rhodopsin, photoreaction centers, diacylglycerol kinases, etc.
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Affiliation(s)
- Hazime Saitô
- Center for Quantum Life Sciences, Hiroshima University, Higashi-Hiroshima 739-8526, Japan.
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13
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Voïtchovsky K, Contera SA, Ryan JF. Electrostatic and steric interactions determine bacteriorhodopsin single-molecule biomechanics. Biophys J 2007; 93:2024-37. [PMID: 17513362 PMCID: PMC1959538 DOI: 10.1529/biophysj.106.101469] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Bacteriorhodopsin (bR) is a haloarchaeal membrane protein that converts the energy of single photons into large structural changes to directionally pump protons across purple membrane. This is achieved by a complex combination of local dynamic interactions controlling bR biomechanics at the submolecular level, producing efficient amplification of the retinal photoisomerization. Using single molecule force spectroscopy at different salt concentrations, we show that tryptophan (Trp) residues use steric specific interactions to create a rigid scaffold in bR extracellular region and are responsible for the main unfolding barriers. This scaffold, which encloses the retinal, controls bR local mechanical properties and anchors the protein into the membrane. Furthermore, the stable Trp-based network allows ion binding to two specific sites on the extracellular loops (BC and FG), which are involved in proton release and lateral transport. In contrast, the cytoplasmic side of bR is mainly governed by relatively weak nonspecific electrostatic interactions that provide the flexibility necessary for large cytoplasmic structural rearrangements during the photocycle. The presence of an extracellular Trp-based network tightly enclosing the retinal seems common to most haloarchaeal rhodopsins, and could be relevant to their exceptional efficiency.
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Affiliation(s)
- Kislon Voïtchovsky
- Bionanotechnology Interdisciplinary Research Collaboration, Department of Physics, Clarendon Laboratory, University of Oxford, Oxford, United Kingdom
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14
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Sepulcre F, Cordomí A, Proietti MG, Perez JJ, García J, Querol E, Padrós E. X-ray absorption and molecular dynamics study of cation binding sites in the purple membrane. Proteins 2007; 67:360-74. [PMID: 17266122 DOI: 10.1002/prot.21273] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The present work describes the results of a study aimed at identifying candidate cation binding sites on the extracellular region of bacteriorhodopsin, including a site near the retinal pocket. The approach used is a combined effort involving computational chemistry methods (computation of cation affinity maps and molecular dynamics) together with the Extended X-Ray Absorption Fine Structure (EXAFS) technique to obtain relevant information about the local structure of the protein in the neighborhood of Mn(2+) ions in different affinity binding sites. The results permit the identification of a high-affinity binding site where the ion is coordinated simultaneously to Asp212(-) and Asp85(-). Comparison of EXAFS data of the wild type protein with the quadruple mutant E9Q/E74Q/E194Q/E204Q at pH 7.0 and 10.0 demonstrate that extracellular glutamic acid residues are involved in cation binding.
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Affiliation(s)
- Francesc Sepulcre
- Departament d'Enginyeria Agroalimentària i Biotecnologia, Escola Superior d'Agricultura de Barcelona, Universitat Politècnica de Catalunya, Barcelona, Spain.
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15
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Shibata A, Sakata A, Ueno S, Hori T, Minami K, Baba Y, Kamo N. Regeneration and inhibition of proton pumping activity of bacteriorhodopsin blue membrane by cationic amine anesthetics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2005; 1669:17-25. [PMID: 15842995 DOI: 10.1016/j.bbamem.2005.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2004] [Revised: 02/03/2005] [Accepted: 02/04/2005] [Indexed: 11/15/2022]
Abstract
Bacteriorhodopsin (bR) is the prototype of an integral membrane protein with seven membrane-spanning alpha-helices and serves as a model of the G-protein-coupled drug receptors. This study is aimed at reaching a greater understanding of the role of amine local anesthetic cations on the proton transport in the bR protein, and furthermore, the functional role of "the cation" in the proton pumping mechanism. The effect of the amine anesthetic cations on the proton pump in the bR blue membrane was compared with those by divalent (Ca2+, Mg2+ and Mn2+) and monovalent metal cations (Li+, Na+, K+ and Cs+), which are essential for the correct functioning of the proton pumping of the bR protein. The results suggest that the interacting site of the divalent cation to the bR membrane may differ from that of the monovalent metal cation. The electric current profile of the bR blue membrane in the presence of the amine anesthetic cations was biphasic, involving the generation and inhibition of the proton pumping activity in a concentration-dependent manner. The extent of the regeneration of the proton pump by the additives increased in the order of monovalent metal cation<monovalent amine anesthetic cation<divalent metal cation. We found that organic cations such as the amine anesthetics can also regenerate the proton pump in the bR protein. The inhibition of proton transport in the bR protein by the anesthetic cations was elucidated using the wild type, the E204Q and the D96N mutated bRs. The hydrophobic interaction of the amine anesthetics with the bR protein plays an important part in inhibiting the bR proton pump.
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Affiliation(s)
- Akira Shibata
- Faculty of Pharmaceutical Sciences, The University of Tokushima, Shomachi, Tokushima 770-8505, Japan.
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Sepulcre F, Proietti MG, Benfatto M, Della Longa S, García J, Padrós E. A quantitative XANES analysis of the calcium high-affinity binding site of the purple membrane. Biophys J 2005; 87:513-20. [PMID: 15240484 PMCID: PMC1304372 DOI: 10.1529/biophysj.103.030080] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this article we report x-ray absorption measurements of Ca(2+)-substituted bacteriorhodopsin. We present a detailed study of the absorption spectrum close to the absorption edge that is very sensitive to the site geometry. We combined ab initio calculations of the x-ray absorption cross section based on a full multiple scattering approach, with a best fit of the experimental data performed by changing the cluster geometry. The Ca(2+)-bacteriorhodopsin environment is composed of six oxygen atoms showing a distorted orthorhombic symmetry, whereas the Ca(2+) in water solution has a regular octahydrated first sphere of coordination. Our results are in good agreement with previous molecular models suggesting that the high-affinity cationic site could be in the proximity of the retinal pocket. Our results provide strong direct evidence of the specific binding site of the metal cation in bacteriorhodopsin.
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Affiliation(s)
- Francesc Sepulcre
- Departament d'Enginyeria Agroalimentària i Biotecnologia, Escola Superior d'Agricultura, Universitat Politècnica de Catalunya, Barcelona, Spain.
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17
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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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Heyes CD, Reynolds KB, El-Sayed MA. Eu3+binding to europium-regenerated bacteriorhodopsin upon delipidation and monomerization. FEBS Lett 2004; 562:207-10. [PMID: 15044027 DOI: 10.1016/s0014-5793(04)00182-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2004] [Revised: 02/10/2004] [Accepted: 02/16/2004] [Indexed: 11/27/2022]
Abstract
We have studied the effect of monomerization of the purple membrane lattice, as well as removal of 75% of the lipids, on the binding properties of Eu(3+) ions. We found that delipidation and monomerization do not cause the cations to lose their binding ability to the protein. This suggests that the three most strongly bound Eu(3+) cations do not bind to the lipids, but directly bind to the protein. Furthermore, we found that delipidation actually causes a slight increase in the binding affinity. This is likely a result of reduced aggregation of europium-regenerated bacteriorhodopsin (bR) upon lipid removal causing more exposure of the binding sites to the Eu(3+) cations. These results, taken with those from our previous publication [Heyes and El-Sayed, Biophys. J. 85 (2003) 426-434], might suggest that the cations remain bound upon delipidation of bR, but have no effect on the function. This is discussed with respect to the role of cations in the function of native bR.
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Affiliation(s)
- Colin D Heyes
- Laser Dynamics Laboratory, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
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19
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Affiliation(s)
- Colin D. Heyes
- Laser Dynamics Laboratory, School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
| | - Mostafa A. El-Sayed
- Laser Dynamics Laboratory, School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
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20
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Heyes CD, El-Sayed MA. Proton transfer reactions in native and deionized bacteriorhodopsin upon delipidation and monomerization. Biophys J 2003; 85:426-34. [PMID: 12829497 PMCID: PMC1303098 DOI: 10.1016/s0006-3495(03)74487-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
We have investigated the role of the native lipids on bacteriorhodopsin (bR) proton transfer and their connection with the cation-binding role. We observe that both the efficiency of M formation and the kinetics of M rise and decay depend on the lipids and lattice but, as the lipids are removed, the cation binding is a much less important factor for the proton pumping function. Upon 75% delipidation using 3-[(cholamidopropyl)dimethylammonio]-propanesulfonate (CHAPS), the M formation and decay kinetics are much slower than the native, and the efficiency of M formation is approximately 30%-40% that of the native. Upon monomerization of bR by Trition X-100, the efficiency of M recovers close to that of the native (depending on pH), M formation is approximately 10 times faster, and M decay kinetics are comparable to native at pH 7. The same results on the M intermediate are observed if deionized blue bR (deI bbR) is treated with these detergents (with or without pH buffers present), even though deionized blue bR containing all the lipids has no photocycle. This suggests that the cation(s) has a role in native bR that is different than in delipidated or monomerized bR, even so far as to suggest that the cation(s) becomes unimportant to the function as the lipids are removed.
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Affiliation(s)
- Colin D Heyes
- Laser Dynamics Laboratory, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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21
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Lazarova T, Sanz C, Sepulcre F, Querol E, Padrós E. Specific effects of chloride on the photocycle of E194Q and E204Q mutants of bacteriorhodopsin as measured by FTIR spectroscopy. Biochemistry 2002; 41:8176-83. [PMID: 12069610 DOI: 10.1021/bi025654u] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Low-temperature Fourier transform infrared spectroscopy has been used to study mutants of Glu194 and Glu204, two amino acids that are involved in proton release to the extracellular side of bacteriorhodopsin. Difference spectra of films of E194Q, E204Q, E194Q/E204Q, E9Q/E194Q/E204Q, and E9Q/E74Q/E194Q/E204Q at 243, 277, and 293 K and several pH values were obtained by continuous illumination. A specific effect of Cl(-) ions was found for the mutants, promoting a N-like intermediate at alkaline pH and an O' intermediate at neutral or acid pH. The apparent pK(a) of Asp85 in the M intermediate was found to be decreased for E194Q in the presence of Cl(-) (pK(a) of 7.6), but it was unchanged for E204Q, as compared to wild-type. In the absence of Cl(-) (i.e., in the presence of SO(4)(2)(-)), mutation of Glu194 or of Glu204 produces M- (or M(N), M(G))-like intermediates under all of the conditions examined. The absence of N, O, and O' intermediates suggests a long-range effect of the mutation. Furthermore, it is suggested that Cl(-) acts by reaching the interior of the protein, rather than producing surface effects. The effect of low water content was also examined, in the presence of Cl(-). Similar spectra corresponding to the M(1) intermediate were found for dry samples of both mutants, indicating that the effects of the mutations or of Cl(-) ions are confined to the second part of the photocycle. The water O-H stretching data further confirms altered photocycles and the effect of Cl(-) on the accumulation of the N intermediate.
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Affiliation(s)
- Tzvetana Lazarova
- Unitat de Biofísica, Departament de Bioquímica i de Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Barcelona 08193, Spain
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