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Zerbetto M, Saint-Pierre C, Piserchia A, Torrengo S, Gambarelli S, Abergel D, Polimeno A, Gasparutto D, Sicoli G. Intrinsic Flexibility beyond the Highly Ordered DNA Tetrahedron: An Integrative Spectroscopic and Molecular Dynamics Approach. J Phys Chem Lett 2023; 14:10032-10038. [PMID: 37906734 DOI: 10.1021/acs.jpclett.3c02383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Since the introduction of DNA-based architectures, in the past decade, DNA tetrahedrons have aroused great interest. Applications of such nanostructures require structural control, especially in the perspective of their possible functionalities. In this work, an integrated approach for structural characterization of a tetrahedron structure is proposed with a focus on the fundamental biophysical aspects driving the assembly process. To address such an issue, spin-labeled DNA sequences are chemically synthesized, self-assembled, and then analyzed by Continuous-Wave (CW) and pulsed Electron Paramagnetic Resonance (EPR) spectroscopy. Interspin distance measurements based on PELDOR/DEER techniques combined with molecular dynamics (MD) thus revealed unexpected dynamic heterogeneity and flexibility of the assembled structures. The observation of flexibility in these ordered 3D structures demonstrates the sensitivity of this approach and its effectiveness in accessing the main dynamic and structural features with unprecedented resolution.
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Affiliation(s)
- Mirco Zerbetto
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Christine Saint-Pierre
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 17 rue des Martyrs, F-38000 Grenoble, France
| | - Andrea Piserchia
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Simona Torrengo
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 17 rue des Martyrs, F-38000 Grenoble, France
| | - Serge Gambarelli
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 17 rue des Martyrs, F-38000 Grenoble, France
| | - Daniel Abergel
- Laboratoire des biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Antonino Polimeno
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Didier Gasparutto
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 17 rue des Martyrs, F-38000 Grenoble, France
| | - Giuseppe Sicoli
- CNRS UMRS 8516, LASIRE, University of Lille, Avenue Paul Langevin - C4 building, F-59655 Villeneuve d'Ascq Cedex, France
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2
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Kojima K, Sudo Y. Convergent evolution of animal and microbial rhodopsins. RSC Adv 2023; 13:5367-5381. [PMID: 36793294 PMCID: PMC9923458 DOI: 10.1039/d2ra07073a] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/05/2023] [Indexed: 02/15/2023] Open
Abstract
Rhodopsins, a family of photoreceptive membrane proteins, contain retinal as a chromophore and were firstly identified as reddish pigments from frog retina in 1876. Since then, rhodopsin-like proteins have been identified mainly from animal eyes. In 1971, a rhodopsin-like pigment was discovered from the archaeon Halobacterium salinarum and named bacteriorhodopsin. While it was believed that rhodopsin- and bacteriorhodopsin-like proteins were expressed only in animal eyes and archaea, respectively, before the 1990s, a variety of rhodopsin-like proteins (called animal rhodopsins or opsins) and bacteriorhodopsin-like proteins (called microbial rhodopsins) have been progressively identified from various tissues of animals and microorganisms, respectively. Here, we comprehensively introduce the research conducted on animal and microbial rhodopsins. Recent analysis has revealed that the two rhodopsin families have common molecular properties, such as the protein structure (i.e., 7-transmembrane structure), retinal structure (i.e., binding ability to cis- and trans-retinal), color sensitivity (i.e., UV- and visible-light sensitivities), and photoreaction (i.e., triggering structural changes by light and heat), more than what was expected at the early stages of rhodopsin research. Contrastingly, their molecular functions are distinctively different (e.g., G protein-coupled receptors and photoisomerases for animal rhodopsins and ion transporters and phototaxis sensors for microbial rhodopsins). Therefore, based on their similarities and dissimilarities, we propose that animal and microbial rhodopsins have convergently evolved from their distinctive origins as multi-colored retinal-binding membrane proteins whose activities are regulated by light and heat but independently evolved for different molecular and physiological functions in the cognate organism.
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Affiliation(s)
- Keiichi Kojima
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University Japan
| | - Yuki Sudo
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University Japan
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3
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Lipid Dynamics in Diisobutylene-Maleic Acid (DIBMA) Lipid Particles in Presence of Sensory Rhodopsin II. Int J Mol Sci 2021; 22:ijms22052548. [PMID: 33806280 PMCID: PMC7961963 DOI: 10.3390/ijms22052548] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 01/01/2023] Open
Abstract
Amphiphilic diisobutylene/maleic acid (DIBMA) copolymers extract lipid-encased membrane proteins from lipid bilayers in a detergent-free manner, yielding nanosized, discoidal DIBMA lipid particles (DIBMALPs). Depending on the DIBMA/lipid ratio, the size of DIBMALPs can be broadly varied which makes them suitable for the incorporation of proteins of different sizes. Here, we examine the influence of the DIBMALP sizes and the presence of protein on the dynamics of encased lipids. As shown by a set of biophysical methods, the stability of DIBMALPs remains unaffected at different DIBMA/lipid ratios. Coarse-grained molecular dynamics simulations confirm the formation of viable DIBMALPs with an overall size of up to 35 nm. Electron paramagnetic resonance spectroscopy of nitroxides located at the 5th, 12th or 16th carbon atom positions in phosphatidylcholine-based spin labels reveals that the dynamics of enclosed lipids are not altered by the DIBMALP size. The presence of the membrane protein sensory rhodopsin II from Natronomonas pharaonis (NpSRII) results in a slight increase in the lipid dynamics compared to empty DIBMALPs. The light-induced photocycle shows full functionality of DIBMALPs-embedded NpSRII and a significant effect of the protein-to-lipid ratio during preparation on the NpSRII dynamics. This study indicates a possible expansion of the applicability of the DIBMALP technology on studies of membrane protein–protein interaction and oligomerization in a constraining environment.
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4
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Voskoboynikova N, Margheritis EG, Kodde F, Rademacher M, Schowe M, Budke-Gieseking A, Psathaki OE, Steinhoff HJ, Cosentino K. Evaluation of DIBMA nanoparticles of variable size and anionic lipid content as tools for the structural and functional study of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183588. [PMID: 33662362 DOI: 10.1016/j.bbamem.2021.183588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 12/16/2022]
Abstract
Amphiphilic maleic acid-containing polymers allow for the direct extraction of membrane proteins into stable, homogenous, water-soluble copolymer/lipid nanoparticles without the use of detergents. By adjusting the polymer/lipid ratio, the size of the nanoparticles can be tuned at convenience for the incorporation of protein complexes of different size. However, an increase in the size of the lipid nanoparticles may correlate with increased sample heterogeneity, thus hampering their application to spectroscopic and structural techniques where highly homogeneous samples are desirable. In addition, size homogeneity can be affected by low liposome solubilization efficiency by DIBMA, which carries a negative charge, in the presence of high lipid charge density. In this work, we apply biophysical tools to characterize the size and size heterogeneity of large (above 15 nm) lipid nanoparticles encased by the diisobutylene/maleic acid (DIBMA) copolymer at different DIBMA/lipid ratios and percentages of anionic lipids. Importantly, for nanoparticle preparations in the diameter range of 40 nm or below, the size homogeneity of the DIBMA/lipid nanoparticles (DIBMALPs) remains unchanged. In addition, we show that anionic lipids do not affect the production, size and size homogeneity of DIBMALPs. Furthermore, they do not affect the overall lipid dynamics in the membrane, and preserve the functionality of an enclosed membrane protein. This work strengthens the suitability of DIBMALPs as universal, native-like lipid environments for functional studies of membrane proteins and provide useful insight on the suitability of these systems for those structural techniques requiring highly homogeneous sample preparations.
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Affiliation(s)
| | | | - Felix Kodde
- Department of Physics, University of Osnabrück, 49069 Osnabrück, Germany
| | - Malte Rademacher
- Department of Physics, University of Osnabrück, 49069 Osnabrück, Germany
| | - Maurice Schowe
- Department of Physics, University of Osnabrück, 49069 Osnabrück, Germany
| | - Annette Budke-Gieseking
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Germany
| | - Olympia-Ekaterini Psathaki
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Germany
| | | | - Katia Cosentino
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Germany.
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5
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Colbasevici A, Voskoboynikova N, Orekhov PS, Bozdaganyan ME, Karlova MG, Sokolova OS, Klare JP, Mulkidjanian AY, Shaitan KV, Steinhoff HJ. Lipid dynamics in nanoparticles formed by maleic acid-containing copolymers: EPR spectroscopy and molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183207. [PMID: 31987867 DOI: 10.1016/j.bbamem.2020.183207] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 12/11/2022]
Abstract
Amphiphilic maleic acid-containing copolymers account for a recent methodical breakthrough in the study of membrane proteins. Their application enables a detergent-free extraction of membrane proteins from lipid bilayers, yielding stable water-soluble, discoidal lipid bilayer particles with incorporated proteins, which are wrapped with copolymers. Although many studies confirm the potential of this approach for membrane protein research, the interactions between the maleic acid-containing copolymers and extracted lipids, as well as possible effects of the copolymers on lipid-embedded proteins deserve further scrutinization. Here, we combine electron paramagnetic resonance spectroscopy and coarse-grain molecular dynamics simulations to compare the distribution and dynamics of lipids in lipid particles of phospholipid bilayers encased either by an aliphatic diisobutylene/maleic acid copolymer (DIBMALPs) or by an aromatic styrene/maleic acid copolymer (SMALPs). Nitroxides located at the 5th, 12th or 16th carbon atom positions in phosphatidylcholine-based spin labels experience restrictions of their reorientational motion depending on the type of encasing copolymer. The dynamics of the lipids was less constrained in DIBMALPs than in SMALPs with the affinity of spin labeled lipids to the polymeric rim being more pronounced in SMALPs.
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Affiliation(s)
| | | | - Philipp S Orekhov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia; Sechenov University, Moscow 119146, Russia; Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Marine E Bozdaganyan
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia; Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Maria G Karlova
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Olga S Sokolova
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Johann P Klare
- Department of Physics, Osnabrueck University, 49069 Osnabrueck, Germany
| | - Armen Y Mulkidjanian
- Department of Physics, Osnabrueck University, 49069 Osnabrueck, Germany; A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Konstantin V Shaitan
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
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6
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Mosslehy W, Voskoboynikova N, Colbasevici A, Ricke A, Klose D, Klare JP, Mulkidjanian AY, Steinhoff HJ. Conformational Dynamics of Sensory Rhodopsin II in Nanolipoprotein and Styrene-Maleic Acid Lipid Particles. Photochem Photobiol 2019; 95:1195-1204. [PMID: 30849183 DOI: 10.1111/php.13096] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/03/2019] [Indexed: 02/01/2023]
Abstract
Styrene-maleic acid lipid particles (SMALPs) provide stable water-soluble nanocontainers for lipid-encased membrane proteins. Possible effects of the SMA-stabilized lipid environment on the interaction dynamics between functionally coupled membrane proteins remain to be elucidated. The photoreceptor sensory rhodopsin II, NpSRII and its cognate transducer, NpHtrII, of Natronomonas pharaonis form a transmembrane complex, NpSRII2 /NpHtrII2 that plays a key role in negative phototaxis and provides a unique model system to study the light-induced transfer of a conformational signal between two integral membrane proteins. Photon absorption induces transient structural changes in NpSRII comprising an outward movement of helix F that cause further conformational alterations in NpHtrII. We applied site-directed spin labeling and time-resolved optical and EPR spectroscopy to compare the conformational dynamics of NpSRII2 /NpHtrII2 reconstituted in SMALPs with that of nanolipoprotein particle and liposome preparations. NpSRII and NpSRII2 /NpHtrII2 show similar photocycles in liposomes and nanolipoprotein particles. An accelerated decay of the M photointermediate found for SMALPs can be explained by a high local proton concentration provided by the carboxylic groups of the SMA polymer. Light-induced large-scale conformational changes of NpSRII2 /NpHtrII2 observed in liposomes and nanolipoprotein particles are affected in SMALPs, indicating restrictions of the protein's conformational freedom.
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Affiliation(s)
- Wageiha Mosslehy
- Department of Physics, University of Osnabrück, Osnabrück, Germany
| | | | | | - Adrian Ricke
- Department of Physics, University of Osnabrück, Osnabrück, Germany
| | - Daniel Klose
- Department of Physics, University of Osnabrück, Osnabrück, Germany.,Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Johann P Klare
- Department of Physics, University of Osnabrück, Osnabrück, Germany
| | - Armen Y Mulkidjanian
- Department of Physics, University of Osnabrück, Osnabrück, Germany.,School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
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7
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Voskoboynikova N, Mosslehy W, Colbasevici A, Ismagulova TT, Bagrov DV, Akovantseva AA, Timashev PS, Mulkidjanian AY, Bagratashvili VN, Shaitan KV, Kirpichnikov MP, Steinhoff HJ. Characterization of an archaeal photoreceptor/transducer complex from Natronomonas pharaonis assembled within styrene–maleic acid lipid particles. RSC Adv 2017. [DOI: 10.1039/c7ra10756k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The archaeal receptor/transducer complex NpSRII/NpHtrII retains its integrity upon reconstitution in styrene–maleic acid lipid particles.
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Affiliation(s)
| | - W. Mosslehy
- Department of Physics
- University of Osnabrück
- Osnabrück
- Germany
| | - A. Colbasevici
- Department of Physics
- University of Osnabrück
- Osnabrück
- Germany
| | - T. T. Ismagulova
- Department of Bioengineering
- Faculty of Biology
- Lomonosov Moscow State University
- Moscow
- Russia
| | - D. V. Bagrov
- Department of Bioengineering
- Faculty of Biology
- Lomonosov Moscow State University
- Moscow
- Russia
| | - A. A. Akovantseva
- Institute of Photonic Technologies of Research Center “Crystallography and Photonics” of RAS
- Moscow
- Russia
| | - P. S. Timashev
- Institute for Regenerative Medicine of I. M. Sechenov First Moscow State Medical University
- Moscow
- Russia
- Institute of Photonic Technologies of Research Center “Crystallography and Photonics” of RAS
- Moscow
| | | | - V. N. Bagratashvili
- Institute of Photonic Technologies of Research Center “Crystallography and Photonics” of RAS
- Moscow
- Russia
| | - K. V. Shaitan
- Department of Bioengineering
- Faculty of Biology
- Lomonosov Moscow State University
- Moscow
- Russia
| | - M. P. Kirpichnikov
- Department of Bioengineering
- Faculty of Biology
- Lomonosov Moscow State University
- Moscow
- Russia
| | - H.-J. Steinhoff
- Department of Physics
- University of Osnabrück
- Osnabrück
- Germany
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8
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Inoue K, Ono H, Kandori H. Na+ Transport by a Sodium Ion Pump Rhodopsin is Resistant to Environmental Change: A Comparison of the Photocycles of the Na+ and Li+ Transport Processes. CHEM LETT 2015. [DOI: 10.1246/cl.141023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology
- OptoBioTechnology Research Center, Nagoya Institute of Technology
- PRESTO, Japan Science and Technology Agency
| | - Hikaru Ono
- Department of Frontier Materials, Nagoya Institute of Technology
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology
- OptoBioTechnology Research Center, Nagoya Institute of Technology
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9
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Orban-Glaß I, Voskoboynikova N, Busch KB, Klose D, Rickert C, Mosslehy W, Roder F, Wilkens V, Piehler J, Engelhard M, Steinhoff HJ, Klare JP. Clustering and dynamics of phototransducer signaling domains revealed by site-directed spin labeling electron paramagnetic resonance on SRII/HtrII in membranes and nanodiscs. Biochemistry 2014; 54:349-62. [PMID: 25489970 DOI: 10.1021/bi501160q] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In halophilic archaea the photophobic response is mediated by the membrane-embedded 2:2 photoreceptor/-transducer complex SRII/HtrII, the latter being homologous to the bacterial chemoreceptors. Both systems bias the rotation direction of the flagellar motor via a two-component system coupled to an extended cytoplasmic signaling domain formed by a four helical antiparallel coiled-coil structure. For signal propagation by the HAMP domains connecting the transmembrane and cytoplasmic domains, it was suggested that a two-state thermodynamic equilibrium found for the first HAMP domain in NpSRII/NpHtrII is shifted upon activation, yet signal propagation along the coiled-coil transducer remains largely elusive, including the activation mechanism of the coupled kinase CheA. We investigated the dynamic and structural properties of the cytoplasmic tip domain of NpHtrII in terms of signal transduction and putative oligomerization using site-directed spin labeling electron paramagnetic resonance spectroscopy. We show that the cytoplasmic tip domain of NpHtrII is engaged in a two-state equilibrium between a dynamic and a compact conformation like what was found for the first HAMP domain, thus strengthening the assumption that dynamics are the language of signal transfer. Interspin distance measurements in membranes and on isolated 2:2 photoreceptor/transducer complexes in nanolipoprotein particles provide evidence that archaeal photoreceptor/-transducer complexes analogous to chemoreceptors form trimers-of-dimers or higher-order assemblies even in the absence of the cytoplasmic components CheA and CheW, underlining conservation of the overall mechanistic principles underlying archaeal phototaxis and bacterial chemotaxis systems. Furthermore, our results revealed a significant influence of the NpHtrII signaling domain on the NpSRII photocycle kinetics, providing evidence for a conformational coupling of SRII and HtrII in these complexes.
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Affiliation(s)
- Ioan Orban-Glaß
- Macromolecular Structure Group, Department of Physics, University of Osnabrück , Barbarastrasse 7, 49076 Osnabrück, Germany
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10
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Ward R, Pliotas C, Branigan E, Hacker C, Rasmussen A, Hagelueken G, Booth IR, Miller S, Lucocq J, Naismith JH, Schiemann O. Probing the structure of the mechanosensitive channel of small conductance in lipid bilayers with pulsed electron-electron double resonance. Biophys J 2014; 106:834-42. [PMID: 24559986 PMCID: PMC3944623 DOI: 10.1016/j.bpj.2014.01.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 01/03/2014] [Accepted: 01/07/2014] [Indexed: 01/16/2023] Open
Abstract
Mechanosensitive channel proteins are important safety valves against osmotic shock in bacteria, and are involved in sensing touch and sound waves in higher organisms. The mechanosensitive channel of small conductance (MscS) has been extensively studied. Pulsed electron-electron double resonance (PELDOR or DEER) of detergent-solubilized protein confirms that as seen in the crystal structure, the outer ring of transmembrane helices do not pack against the pore-forming helices, creating an apparent void. The relevance of this void to the functional form of MscS in the bilayer is the subject of debate. Here, we report PELDOR measurements of MscS reconstituted into two lipid bilayer systems: nanodiscs and bicelles. The distance measurements from multiple mutants derived from the PELDOR data are consistent with the detergent-solution arrangement of the protein. We conclude, therefore, that the relative positioning of the transmembrane helices is preserved in mimics of the cell bilayer, and that the apparent voids are not an artifact of detergent solution but a property of the protein that will have to be accounted for in any molecular mechanism of gating.
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Affiliation(s)
- Richard Ward
- Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Scotland
| | - Christos Pliotas
- Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Scotland
| | - Emma Branigan
- Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Scotland
| | - Christian Hacker
- School of Medicine, University of St. Andrews, St. Andrews, Scotland
| | - Akiko Rasmussen
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland
| | - Gregor Hagelueken
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Ian R Booth
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland
| | - Samantha Miller
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland
| | - John Lucocq
- School of Medicine, University of St. Andrews, St. Andrews, Scotland
| | - James H Naismith
- Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Scotland.
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany; Centre for Biomolecular Sciences, University of St. Andrews, St. Andrews, Scotland.
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11
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Inoue K, Tsukamoto T, Sudo Y. Molecular and evolutionary aspects of microbial sensory rhodopsins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:562-77. [PMID: 23732219 DOI: 10.1016/j.bbabio.2013.05.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 05/14/2013] [Accepted: 05/16/2013] [Indexed: 02/03/2023]
Abstract
Retinal proteins (~rhodopsins) are photochemically reactive membrane-embedded proteins, with seven transmembrane α-helices which bind the chromophore retinal (vitamin A aldehyde). They are widely distributed through all three biological kingdoms, eukarya, bacteria and archaea, indicating the biological significance of the retinal proteins. Light absorption by the retinal proteins triggers a photoisomerization of the chromophore, leading to the biological function, light-energy conversion or light-signal transduction. This article reviews molecular and evolutionary aspects of the light-signal transduction by microbial sensory receptors and their related proteins. 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)
- Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Takashi Tsukamoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Yuki Sudo
- Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan; Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan; Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki, Japan.
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12
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Klare JP, Steinhoff HJ. Structural Information from Spin-Labelled Membrane-Bound Proteins. STRUCTURAL INFORMATION FROM SPIN-LABELS AND INTRINSIC PARAMAGNETIC CENTRES IN THE BIOSCIENCES 2013. [DOI: 10.1007/430_2012_88] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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13
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Abstract
Solid-state NMR spectroscopy proved to be a versatile tool for characterization of structure and dynamics of complex biochemical systems. In particular, magic angle spinning (MAS) solid-state NMR came to maturity for application towards structural elucidation of biological macromolecules. Current challenges in applying solid-state NMR as well as progress achieved recently will be discussed in the following chapter focusing on conceptual aspects important for structural elucidation of proteins.
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Affiliation(s)
- Henrik Müller
- Institute of Physical Biology, Heinrich-Heine-University of Düsseldorf, 40225, Düsseldorf, Germany
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14
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Gradmann S, Ader C, Heinrich I, Nand D, Dittmann M, Cukkemane A, van Dijk M, Bonvin AMJJ, Engelhard M, Baldus M. Rapid prediction of multi-dimensional NMR data sets. JOURNAL OF BIOMOLECULAR NMR 2012; 54:377-387. [PMID: 23143278 DOI: 10.1007/s10858-012-9681-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 10/31/2012] [Indexed: 06/01/2023]
Abstract
We present a computational environment for Fast Analysis of multidimensional NMR DAta Sets (FANDAS) that allows assembling multidimensional data sets from a variety of input parameters and facilitates comparing and modifying such "in silico" data sets during the various stages of the NMR data analysis. The input parameters can vary from (partial) NMR assignments directly obtained from experiments to values retrieved from in silico prediction programs. The resulting predicted data sets enable a rapid evaluation of sample labeling in light of spectral resolution and structural content, using standard NMR software such as Sparky. In addition, direct comparison to experimental data sets can be used to validate NMR assignments, distinguish different molecular components, refine structural models or other parameters derived from NMR data. The method is demonstrated in the context of solid-state NMR data obtained for the cyclic nucleotide binding domain of a bacterial cyclic nucleotide-gated channel and on membrane-embedded sensory rhodopsin II. FANDAS is freely available as web portal under WeNMR ( http://www.wenmr.eu/services/FANDAS ).
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Affiliation(s)
- Sabine Gradmann
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan CH, Utrecht, The Netherlands
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15
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Stehle J, Scholz F, Löhr F, Reckel S, Roos C, Blum M, Braun M, Glaubitz C, Dötsch V, Wachtveitl J, Schwalbe H. Characterization of the ground state dynamics of proteorhodopsin by NMR and optical spectroscopies. JOURNAL OF BIOMOLECULAR NMR 2012; 54:401-413. [PMID: 23160927 DOI: 10.1007/s10858-012-9684-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 11/02/2012] [Indexed: 06/01/2023]
Abstract
We characterized the dynamics of proteorhodopsin (PR), solubilized in diC7PC, a detergent micelle, by liquid-state NMR spectroscopy at T = 323 K. Insights into the dynamics of PR at different time scales could be obtained and dynamic hot spots could be identified at distinct, functionally relevant regions of the protein, including the BC loop, the EF loop, the N-terminal part of helix F and the C-terminal part of helix G. We further characterize the dependence of the photocycle on different detergents (n-Dodecyl β-D-maltoside DDM; 1,2-diheptanoyl-sn-glycero-3-phosphocholine diC7PC) by ultrafast time-resolved UV/VIS spectroscopy. While the photocycle intermediates of PR in diC7PC and DDM exhibit highly similar spectral characteristics, significant changes in the population of these intermediates are observed. In-situ NMR experiments have been applied to characterize structural changes during the photocycle. Light-induced chemical shift changes detected during the photocycle in diC7PC are very small, in line with the changes in the population of intermediates in the photocycle of proteorhodopsin in diC7PC, where the late O-intermediate populated in DDM is missing and the population is shifted towards an equilibrium of intermediates states (M, N, O) without accumulation of a single populated intermediate.
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Affiliation(s)
- Jochen Stehle
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt, Germany
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16
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Wang J, Sasaki J, Tsai AL, Spudich JL. HAMP domain signal relay mechanism in a sensory rhodopsin-transducer complex. J Biol Chem 2012; 287:21316-25. [PMID: 22511775 DOI: 10.1074/jbc.m112.344622] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The phototaxis receptor complex composed of sensory rhodopsin II (SRII) and the transducer subunit HtrII mediates photorepellent responses in haloarchaea. Light-activated SRII transmits a signal through two HAMP switch domains (HAMP1 and HAMP2) in HtrII that bridge the photoreceptive membrane domain of the complex and the cytoplasmic output kinase-modulating domain. HAMP domains, widespread signal relay modules in prokaryotic sensors, consist of four-helix bundles composed of two helices, AS1 and AS2, from each of two dimerized transducer subunits. To examine their molecular motion during signal transmission, we incorporated SRII-HtrII dimeric complexes in nanodiscs to allow unrestricted probe access to the cytoplasmic side HAMP domains. Spin-spin dipolar coupling measurements confirmed that in the nanodiscs, SRII photoactivation induces helix movement in the HtrII membrane domain diagnostic of transducer activation. Labeling kinetics of a fluorescein probe in monocysteine-substituted HAMP1 mutants revealed a light-induced shift of AS2 against AS1 by one-half α-helix turn with minimal other changes. An opposite shift of AS2 against AS1 in HAMP2 at the corresponding positions supports the proposal from x-ray crystal structures by Airola et al. (Airola, M. V., Watts, K. J., Bilwes, A. M., and Crane, B. R. (2010) Structure 18, 436-448) that poly-HAMP chains undergo alternating opposite interconversions to relay the signal. Moreover, we found that haloarchaeal cells expressing a HAMP2-deleted SRII-HtrII exhibit attractant phototaxis, opposite from the repellent phototaxis mediated by the wild-type di-HAMP SRII-HtrII complex. The opposite conformational changes and corresponding opposite output signals of HAMP1 and HAMP2 imply a signal transmission mechanism entailing small shifts in helical register between AS1 and AS2 alternately in opposite directions in adjacent HAMPs.
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Affiliation(s)
- Jihong Wang
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, Houston, Texas 77030, USA
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17
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Mansoor SE, Dewitt MA, Farrens DL. Distance mapping in proteins using fluorescence spectroscopy: the tryptophan-induced quenching (TrIQ) method. Biochemistry 2010; 49:9722-31. [PMID: 20886836 DOI: 10.1021/bi100907m] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Studying the interplay between protein structure and function remains a daunting task. Especially lacking are methods for measuring structural changes in real time. Here we report our most recent improvements to a method that can be used to address such challenges. This method, which we now call tryptophan-induced quenching (TrIQ), provides a straightforward, sensitive, and inexpensive way to address questions of conformational dynamics and short-range protein interactions. Importantly, TrIQ only occurs over relatively short distances (∼5-15 Å), making it complementary to traditional fluorescence resonance energy transfer (FRET) methods that occur over distances too large for precise studies of protein structure. As implied in the name, TrIQ measures the efficient quenching induced in some fluorophores by tryptophan (Trp). We present here our analysis of the TrIQ effect for five different fluorophores that span a range of sizes and spectral properties. Each probe was attached to four different cysteine residues on T4 lysozyme, and the extent of TrIQ caused by a nearby Trp was measured. Our results show that, at least for smaller probes, the extent of TrIQ is distance dependent. Moreover, we also demonstrate how TrIQ data can be analyzed to determine the fraction of fluorophores involved in a static, nonfluorescent complex with Trp. Based on this analysis, our study shows that each fluorophore has a different TrIQ profile, or "sphere of quenching", which correlates with its size, rotational flexibility, and the length of attachment linker. This TrIQ-based "sphere of quenching" is unique to every Trp-probe pair and reflects the distance within which one can expect to see the TrIQ effect. Thus,TrIQ provides a straightforward, readily accessible approach for mapping distances within proteins and monitoring conformational changes using fluorescence spectroscopy.
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Affiliation(s)
- Steven E Mansoor
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239-3098, United States
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18
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Jiang X, Engelhard M, Ataka K, Heberle J. Molecular Impact of the Membrane Potential on the Regulatory Mechanism of Proton Transfer in Sensory Rhodopsin II. J Am Chem Soc 2010; 132:10808-15. [DOI: 10.1021/ja102295g] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiue Jiang
- Department of Chemistry, Biophysical Chemistry (PC III), Bielefeld University, 33615 Bielefeld, Germany, MaxPlanck Institute of Molecular Physiology, 44221 Dortmund, Germany, Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany, and Japan Science and Technology Agency, 102-0075, Tokyo, Japan
| | - Martin Engelhard
- Department of Chemistry, Biophysical Chemistry (PC III), Bielefeld University, 33615 Bielefeld, Germany, MaxPlanck Institute of Molecular Physiology, 44221 Dortmund, Germany, Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany, and Japan Science and Technology Agency, 102-0075, Tokyo, Japan
| | - Kenichi Ataka
- Department of Chemistry, Biophysical Chemistry (PC III), Bielefeld University, 33615 Bielefeld, Germany, MaxPlanck Institute of Molecular Physiology, 44221 Dortmund, Germany, Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany, and Japan Science and Technology Agency, 102-0075, Tokyo, Japan
| | - Joachim Heberle
- Department of Chemistry, Biophysical Chemistry (PC III), Bielefeld University, 33615 Bielefeld, Germany, MaxPlanck Institute of Molecular Physiology, 44221 Dortmund, Germany, Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany, and Japan Science and Technology Agency, 102-0075, Tokyo, Japan
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19
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Etzkorn M, Seidel K, Li L, Martell S, Geyer M, Engelhard M, Baldus M. Complex formation and light activation in membrane-embedded sensory rhodopsin II as seen by solid-state NMR spectroscopy. Structure 2010; 18:293-300. [PMID: 20223212 DOI: 10.1016/j.str.2010.01.011] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2009] [Revised: 12/23/2009] [Accepted: 01/22/2010] [Indexed: 11/18/2022]
Abstract
Microbial rhodopsins execute diverse biological functions in the cellular membrane. A mechanistic understanding of their functional profile is, however, still limited. We used solid-state NMR (ssNMR) spectroscopy to study structure and dynamics of a 2 x 400 amino acid sensory rhodopsin/transducer (SRII/HtrII) complex from Natronomonas pharaonis in a natural membrane environment. We found a receptor-transducer binding interface in the ground state that significantly extends beyond the available X-ray structure. This binding domain involves the EF loop of the receptor and stabilizes the functionally relevant, directly adjacent HAMP domain of the transducer. Using 2D ssNMR difference spectroscopy, we identified protein residues that may act as a functional module around the retinal binding site during the early events of protein activation. These latter protein segments, the inherent plasticity of the HAMP domain, and the observation of an extended SRII/HtrII membrane-embedded interface may be crucial components for optimal signal relay efficiency across the cell membrane.
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Affiliation(s)
- Manuel Etzkorn
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany
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20
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Oberbarnscheidt L, Janissen R, Martell S, Engelhard M, Oesterhelt F. Single-Molecule Force Spectroscopy Measures Structural Changes Induced by Light Activation and Transducer Binding in Sensory Rhodopsin II. J Mol Biol 2009; 394:383-90. [DOI: 10.1016/j.jmb.2009.07.083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 07/27/2009] [Accepted: 07/28/2009] [Indexed: 11/16/2022]
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21
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Klare JP, Steinhoff HJ. Spin labeling EPR. PHOTOSYNTHESIS RESEARCH 2009; 102:377-390. [PMID: 19728138 DOI: 10.1007/s11120-009-9490-7] [Citation(s) in RCA: 169] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2008] [Accepted: 08/14/2009] [Indexed: 05/28/2023]
Abstract
Site-directed spin labeling in combination with electron paramagnetic resonance spectroscopy has emerged as an efficient tool to elucidate the structure and conformational dynamics of biomolecules under native-like conditions. This article summarizes the basics as well as recent progress of site-directed spin labeling. Continuous wave EPR spectra analyses and pulse EPR techniques are reviewed with special emphasis on applications to the sensory rhodopsin-transducer complex mediating the photophobic response of the halophilic archaeum Natronomonas pharaonis and the photosynthetic reaction center from Rhodobacter sphaeroides R26.
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Affiliation(s)
- Johann P Klare
- Physics Department, University of Osnabrück, Barbarastr. 7, 49076, Osnabrück, Germany
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22
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Verhoefen MK, Lenz MO, Amarie S, Klare JP, Tittor J, Oesterhelt D, Engelhard M, Wachtveitl J. Primary Reaction of Sensory Rhodopsin II Mutant D75N and the Influence of Azide. Biochemistry 2009; 48:9677-83. [DOI: 10.1021/bi901197c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mirka-Kristin Verhoefen
- Institute of Physical and Theoretical Chemistry, Institute of Biophysics, Johann Wolfgang Goethe-University Frankfurt, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Martin O. Lenz
- Institute of Physical and Theoretical Chemistry, Institute of Biophysics, Johann Wolfgang Goethe-University Frankfurt, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Sergiu Amarie
- Institute of Physical and Theoretical Chemistry, Institute of Biophysics, Johann Wolfgang Goethe-University Frankfurt, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Johann P. Klare
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44139 Dortmund, Germany
| | - Jörg Tittor
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Dieter Oesterhelt
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Martin Engelhard
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44139 Dortmund, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Institute of Biophysics, Johann Wolfgang Goethe-University Frankfurt, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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23
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Laohpongspaisan C, Rungrotmongkol T, Intharathep P, Malaisree M, Decha P, Aruksakunwong O, Sompornpisut P, Hannongbua S. Why amantadine loses its function in influenza m2 mutants: MD simulations. J Chem Inf Model 2009; 49:847-52. [PMID: 19281265 DOI: 10.1021/ci800267a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular dynamics simulations of the drug-resistant M2 mutants, A30T, S31N, and L26I, were carried out to investigate the inhibition of M2 activity using amantadine (AMT). The closed and open channel conformations were examined via non- and triply protonated H37. For the nonprotonated state, these mutants exhibited zero water density in the conducting region, and AMT was still bound to the channel pore. Thus, water transport is totally suppressed, similar to the wild-type channel. In contrast, the triply protonated states of the mutants exhibited a different water density and AMT position. A30T and L26I both have a greater water density compared to the wild-type M2, while for the A30T system, AMT is no longer inside the pore. Hydrogen bonding between AMT and H37 crucial for the bioactivity is entirely lost in the open conformation. The elimination of this important interaction of these mutations is responsible for the lost of AMT's function in influenza A M2. This is different for the S31N mutant in which AMT was observed to locate at the pore opening region and bond with V27 instead of S31.
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Affiliation(s)
- Chittima Laohpongspaisan
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
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24
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Sensory rhodopsin II/transducer complex formation in detergent and in lipid bilayers studied with FRET. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:522-31. [DOI: 10.1016/j.bbamem.2008.11.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Revised: 11/10/2008] [Accepted: 11/10/2008] [Indexed: 11/21/2022]
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25
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Structural refinement of membrane proteins by restrained molecular dynamics and solvent accessibility data. Biophys J 2008; 95:5349-61. [PMID: 18676641 DOI: 10.1529/biophysj.108.142984] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
We present an approach for incorporating solvent accessibility data from electron paramagnetic resonance experiments in the structural refinement of membrane proteins through restrained molecular dynamics simulations. The restraints have been parameterized from oxygen (PiO(2)) and nickel-ethylenediaminediacetic acid (PiNiEdda) collision frequencies, as indicators of lipid or aqueous exposed spin-label sites. These are enforced through interactions between a pseudoatom representation of the covalently attached Nitroxide spin-label and virtual "solvent" particles corresponding to O(2) and NiEdda in the surrounding environment. Interactions were computed using an empirical potential function, where the parameters have been optimized to account for the different accessibilities of the spin-label pseudoatoms to the surrounding environment. This approach, "pseudoatom-driven solvent accessibility refinement", was validated by refolding distorted conformations of the Streptomyces lividans potassium channel (KcsA), corresponding to a range of 2-30 A root mean-square deviations away from the native structure. Molecular dynamics simulations based on up to 58 electron paramagnetic resonance restraints derived from spin-label mutants were able to converge toward the native structure within 1-3 A root mean-square deviations with minimal computational cost. The use of energy-based ranking and structure similarity clustering as selection criteria helped in the convergence and identification of correctly folded structures from a large number of simulations. This approach can be applied to a variety of integral membrane protein systems, regardless of oligomeric state, and should be particularly useful in calculating conformational changes from a known reference crystal structure.
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Schneider R, Ader C, Lange A, Giller K, Hornig S, Pongs O, Becker S, Baldus M. Solid-State NMR Spectroscopy Applied to a Chimeric Potassium Channel in Lipid Bilayers. J Am Chem Soc 2008; 130:7427-35. [DOI: 10.1021/ja800190c] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Robert Schneider
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, and Institut für Neurale Signalverarbeitung, Zentrum für Molekulare Neurobiologie, Universität Hamburg, Falkenried 94, 20251 Hamburg, Germany
| | - Christian Ader
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, and Institut für Neurale Signalverarbeitung, Zentrum für Molekulare Neurobiologie, Universität Hamburg, Falkenried 94, 20251 Hamburg, Germany
| | - Adam Lange
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, and Institut für Neurale Signalverarbeitung, Zentrum für Molekulare Neurobiologie, Universität Hamburg, Falkenried 94, 20251 Hamburg, Germany
| | - Karin Giller
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, and Institut für Neurale Signalverarbeitung, Zentrum für Molekulare Neurobiologie, Universität Hamburg, Falkenried 94, 20251 Hamburg, Germany
| | - Sönke Hornig
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, and Institut für Neurale Signalverarbeitung, Zentrum für Molekulare Neurobiologie, Universität Hamburg, Falkenried 94, 20251 Hamburg, Germany
| | - Olaf Pongs
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, and Institut für Neurale Signalverarbeitung, Zentrum für Molekulare Neurobiologie, Universität Hamburg, Falkenried 94, 20251 Hamburg, Germany
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, and Institut für Neurale Signalverarbeitung, Zentrum für Molekulare Neurobiologie, Universität Hamburg, Falkenried 94, 20251 Hamburg, Germany
| | - Marc Baldus
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, and Institut für Neurale Signalverarbeitung, Zentrum für Molekulare Neurobiologie, Universität Hamburg, Falkenried 94, 20251 Hamburg, Germany
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Kawamura I, Yoshida H, Ikeda Y, Yamaguchi S, Tuzi S, Saitô H, Kamo N, Naito A. Dynamics change of phoborhodopsin and transducer by activation: study using D75N mutant of the receptor by site-directed solid-state 13C NMR. Photochem Photobiol 2008; 84:921-30. [PMID: 18363620 DOI: 10.1111/j.1751-1097.2008.00326.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pharaonis phoborhodopsin (ppR or sensory rhodopsin II) is a negative phototaxis receptor of Natronomonas pharaonis, and forms a complex, which transmits the photosignal into cytoplasm, with its cognate transducer (pHtrII). We examined a possible local dynamics change of ppR and its D75N mutant complexed with pHtrII, using solid-state (13)C NMR of [3-(13)C]Ala- and [1-(13)C]Val-labeled preparations. We distinguished Ala C(beta) (13)C signals of relatively static stem (Ala221) in the C-terminus of the receptors from those of flexible tip (Ala228, 234, 236 and 238), utilizing a mutant with truncated C-terminus. The local fluctuation frequency at the C-terminal tip was appreciably decreased when ppR was bound to pHtrII, while it was increased when D75N, that mimics the signaling state because of disrupted salt bridge between C and G helices prerequisite for the signal transfer, was bound to pHtrII. This signal change may be considered with the larger dissociation constant of the complex between pHtrII and M-state of ppR. At the same time, it turned out that fluctuation frequency of cytoplasmic portion of pHtrII is lowered when ppR is replaced by D75N in the complex with pHtrII. This means that the C-terminal tip partly participates in binding with the linker region of pHtrII in the dark, but this portion might be released at the signaling state leading to mutual association of the two transducers in the cytoplasmic regions within the ppR/pHtrII complex.
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Affiliation(s)
- Izuru Kawamura
- Graduate School of Engineering, Yokohama National University, Hodogaya-ku, Yokohama, Japan
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28
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Hayashi K, Sudo Y, Jee J, Mishima M, Hara H, Kamo N, Kojima C. Structural Analysis of the Phototactic Transducer Protein HtrII Linker Region from Natronomonas pharaonis,. Biochemistry 2007; 46:14380-90. [DOI: 10.1021/bi701837n] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kokoro Hayashi
- Laboratory of Biophysics, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma, Nara 630-0192, Japan, Laboratory of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences and Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0812, Japan, and ESR Division of Bruker Biospin K. K., Tsukuba, Ibaraki 305-0051, Japan
| | - Yuki Sudo
- Laboratory of Biophysics, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma, Nara 630-0192, Japan, Laboratory of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences and Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0812, Japan, and ESR Division of Bruker Biospin K. K., Tsukuba, Ibaraki 305-0051, Japan
| | - JunGoo Jee
- Laboratory of Biophysics, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma, Nara 630-0192, Japan, Laboratory of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences and Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0812, Japan, and ESR Division of Bruker Biospin K. K., Tsukuba, Ibaraki 305-0051, Japan
| | - Masaki Mishima
- Laboratory of Biophysics, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma, Nara 630-0192, Japan, Laboratory of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences and Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0812, Japan, and ESR Division of Bruker Biospin K. K., Tsukuba, Ibaraki 305-0051, Japan
| | - Hideyuki Hara
- Laboratory of Biophysics, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma, Nara 630-0192, Japan, Laboratory of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences and Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0812, Japan, and ESR Division of Bruker Biospin K. K., Tsukuba, Ibaraki 305-0051, Japan
| | - Naoki Kamo
- Laboratory of Biophysics, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma, Nara 630-0192, Japan, Laboratory of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences and Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0812, Japan, and ESR Division of Bruker Biospin K. K., Tsukuba, Ibaraki 305-0051, Japan
| | - Chojiro Kojima
- Laboratory of Biophysics, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma, Nara 630-0192, Japan, Laboratory of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences and Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0812, Japan, and ESR Division of Bruker Biospin K. K., Tsukuba, Ibaraki 305-0051, Japan
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29
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Taniguchi Y, Ikehara T, Kamo N, Watanabe Y, Yamasaki H, Toyoshima Y. Application of fluorescence resonance energy transfer (FRET) to investigation of light-induced conformational changes of the phoborhodopsin/transducer complex. Photochem Photobiol 2007; 83:311-6. [PMID: 16978044 DOI: 10.1562/2006-06-15-ra-922] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The photoreceptor phoborhodopsin (ppR; also called sensory rhodopsin II) forms a complex with its cognate the Halobacterial transducer II (pHtrII) in the membrane, through which changes in the environmental light conditions are transmitted to the cytoplasm in Natronomonas pharaonis to evoke negative phototaxis. We have applied a fluorescence resonance energy transfer (FRET)-based method for investigation of the light-induced conformational changes of the ppR/pHtrII complex. Several far-red dyes were examined as possible fluorescence donors or acceptors because of the absence of the spectral overlap of these dyes with all the photointermediates of ppR. The flash-induced changes of distances between the donor and an acceptor linked to cysteine residues which were genetically introduced at given positions in pHtrII(1-159) and ppR were determined from FRET efficiency changes. The dye-labeled complex was studied as solubilized in 0.1% n-dodecyl-beta-D-maltoside (DDM). The FRET-derived changes in distances from V78 and A79 in pHtrII to V185 in ppR were consistent with the crystal structure data (Moukhametzianov, R. et al. [2006] Nature, 440, 115-119). The distance from D102 in pHtrII linker region to V185 in ppR increased by 0.33 angstroms upon the flash excitation. These changes arose within 70 ms (the dead time of instrument) and decayed with a rate of 1.1 +/- 0.2 s. Thus, sub-angstrom-scale distance changes in the ppR/pHtrII complex were detected with this FRET-based method using far-red fluorescent dyes; this method should be a valuable tool to investigate conformation changes in the transducer, in particular its dynamics.
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Affiliation(s)
- Yukinori Taniguchi
- Nano-biotechnology Research Center, and Department of Bioscience, School of Science & Technology, Kwansei Gakuin University, Sanda, Hyogo, Japan.
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Baldus M. ICMRBS founder's medal 2006: biological solid-state NMR, methods and applications. JOURNAL OF BIOMOLECULAR NMR 2007; 39:73-86. [PMID: 17657566 DOI: 10.1007/s10858-007-9177-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Accepted: 06/26/2007] [Indexed: 05/16/2023]
Abstract
Solid-state NMR (ssNMR) provides increasing possibilities to study structure and dynamics of biomolecular systems. Our group has been interested in developing ssNMR-based approaches that are applicable to biomolecules of increasing molecular size and complexity without the need of specific isotope-labelling. Methodological aspects ranging from spectral assignments to the indirect detection of proton-proton contacts in multi-dimensional ssNMR are discussed and applied to (membrane) protein complexes.
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Affiliation(s)
- Marc Baldus
- Research Group Solid-state NMR, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany.
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Taniguchi Y, Ikehara T, Kamo N, Yamasaki H, Toyoshima Y. Dynamics of Light-Induced Conformational Changes of the Phoborhodopsin/Transducer Complex Formed in then-Dodecyl β-d-Maltoside Micelle. Biochemistry 2007; 46:5349-57. [PMID: 17432830 DOI: 10.1021/bi602482s] [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: 11/29/2022]
Abstract
A complex of photoreceptor phoborhodopsin (ppR; also called sensory rhodopsin II) and its cognate halobacterial transducer II (pHtrII) existing in the plasma membrane mediates the light signal to the cytoplasm in the earliest step of negative phototaxis in Natronomonas pharaonis. We have investigated the dynamics of the light-induced conformational changes of the ppR/pHtrII(1-159) complex formed in the presence of 0.1% n-dodecyl beta-d-maltoside (DDM) by a fluorescence resonance energy transfer (FRET) based method. Fluorescence donor and acceptor dyes were linked to cysteine residues genetically introduced at given positions in pHtrII and ppR. The light-induced FRET efficiency changes for various pairs of dye-labeled cysteine residues were determined to examine dynamics of movements of given residues in the transmembrane and the linker region including the HAMP domain in pHtrII induced by photoexcitation of ppR. Upon flash excitation of ppR, FRET efficiency changed depending on pairs of the labeled cysteine residues. The distances between V185 in ppR and the five given residues (102 through 141) in the pHtrII linker region estimated from the FRET efficiency increased by 0.3-0.8 A; on the other hand, the distances between S31 in ppR and the five residues in pHtrII decreased. The changes arose within 70 ms (the dead time of instrument) and decayed at a rate of 1.1 +/- 0.2 s. Azide significantly increased the decay rate of light-induced FRET efficiency changes by accelerating the decay of the M state of ppR. The decay rate of FRET efficiency changes coincided with the rate of recovery of the ppR to the initial state but not the decay of the M state. We conclude that the light-induced conformational change of pHtrII occurs before, at the formation or during the M state, and its relaxation is coupled tightly with the decay of the O state of ppR in the 1:1 complex formed in the DDM micelle.
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Affiliation(s)
- Yukinori Taniguchi
- Nano-biotechnology Research Center and Department of Bioscience, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo, Japan
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Mennes N, Klare JP, Chizhov I, Seidel R, Schlesinger R, Engelhard M. Expression of the halobacterial transducer protein HtrII from Natronomonas pharaonis in Escherichia coli. FEBS Lett 2007; 581:1487-94. [PMID: 17368449 DOI: 10.1016/j.febslet.2007.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2007] [Revised: 03/02/2007] [Accepted: 03/02/2007] [Indexed: 11/21/2022]
Abstract
Archaeal phototaxis is mediated by sensory rhodopsins which form complexes with their cognate transducers. Whereas the receptors sensory rhodopsin I and sensory rhodopsin II (SRII) have been expressed in Escherichia coli (E. coli) only shortened fragments of HtrII from Natronomonas pharaonis (NpHtrII) are available. Here we describe the heterologous expression of full length NpHtrII which was achieved in yields of up to 0.9 mg per litre cell culture. Gel filtration analysis reveals the tendency of the transducer to form dimers and higher-order oligomers which was also observed when complexed to NpSRII. A circular dichroism (CD) spectrum of NpHtrII is comparable to those obtained for the E. coli chemoreceptors indicating a similar folding with predominantly alpha-helical structure. NpHtrII dissociates from the NpSRII/HtrII complex with an apparent K(D) of about 0.6 microM. Photocycle kinetics of the complex is comparable to that obtained for NpSRII in complex with a truncated transducer with slight differences in the M-decay. The data indicate that the heterologously expressed NpHtrII adopt a native like structure, providing the means for elucidating transmembrane signal transduction and activation of microbial signalling cascades.
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Affiliation(s)
- Nadine Mennes
- Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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33
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Etzkorn M, Martell S, Andronesi O, Seidel K, Engelhard M, Baldus M. Sekundärstruktur, Dynamik und Topologie eines Sieben-Helix-Rezeptors in nativer Membranumgebung, untersucht mit Festkörper-NMR-Spektroskopie. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200602139] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Etzkorn M, Martell S, Andronesi OC, Seidel K, Engelhard M, Baldus M. Secondary Structure, Dynamics, and Topology of a Seven-Helix Receptor in Native Membranes, Studied by Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2007; 46:459-62. [PMID: 17001715 DOI: 10.1002/anie.200602139] [Citation(s) in RCA: 179] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Manuel Etzkorn
- Max-Planck-Institut für Biophysikalische Chemie, Abteilung für NMR-basierte Strukturbiologie, Am Fassberg 11, 37077 Göttingen, Germany
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Inoue K, Sasaki J, Spudich JL, Terazima M. Laser-induced transient grating analysis of dynamics of interaction between sensory rhodopsin II D75N and the HtrII transducer. Biophys J 2006; 92:2028-40. [PMID: 17189313 PMCID: PMC1861795 DOI: 10.1529/biophysj.106.097493] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The interaction between sensory rhodopsin II (SRII) and its transducer HtrII was studied by the time-resolved laser-induced transient grating method using the D75N mutant of SRII, which exhibits minimal visible light absorption changes during its photocycle, but mediates normal phototaxis responses. Flash-induced transient absorption spectra of transducer-free D75N and D75N joined to 120 amino-acid residues of the N-terminal part of the SRII transducer protein HtrII (DeltaHtrII) showed only one spectrally distinct K-like intermediate in their photocycles, but the transient grating method resolved four intermediates (K(1)-K(4)) distinct in their volumes. D75N bound to HtrII exhibited one additional slower kinetic species, which persists after complete recovery of the initial state as assessed by absorption changes in the UV-visible region. The kinetics indicate a conformationally changed form of the transducer portion (designated Tr*), which persists after the photoreceptor returns to the unphotolyzed state. The largest conformational change in the DeltaHtrII portion was found to cause a DeltaHtrII-dependent increase in volume rising in 8 micros in the K(4) state and a drastic decrease in the diffusion coefficient (D) of K(4) relatively to those of the unphotolyzed state and Tr*. The magnitude of the decrease in D indicates a large structural change, presumably in the solvent-exposed HAMP domain of DeltaHtrII, where rearrangement of interacting molecules in the solvent would substantially change friction between the protein and the solvent.
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Affiliation(s)
- Keiichi Inoue
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
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Sudo Y, Spudich JL. Three strategically placed hydrogen-bonding residues convert a proton pump into a sensory receptor. Proc Natl Acad Sci U S A 2006; 103:16129-34. [PMID: 17050685 PMCID: PMC1637548 DOI: 10.1073/pnas.0607467103] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2006] [Indexed: 11/18/2022] Open
Abstract
In haloarchaea, light-driven ion transporters have been modified by evolution to produce sensory receptors that relay light signals to transducer proteins controlling motility behavior. The proton pump bacteriorhodopsin and the phototaxis receptor sensory rhodopsin II (SRII) differ by 74% of their residues, with nearly all conserved residues within the photoreactive retinal-binding pocket in the membrane-embedded center of the proteins. Here, we show that three residues in bacteriorhodopsin replaced by the corresponding residues in SRII enable bacteriorhodopsin to efficiently relay the retinal photoisomerization signal to the SRII integral membrane transducer (HtrII) and induce robust phototaxis responses. A single replacement (Ala-215-Thr), bridging the retinal and the membrane-embedded surface, confers weak phototaxis signaling activity, and the additional two (surface substitutions Pro-200-Thr and Val-210-Tyr), expected to align bacteriorhodopsin and HtrII in similar juxtaposition as SRII and HtrII, greatly enhance the signaling. In SRII, the three residues form a chain of hydrogen bonds from the retinal's photoisomerized C(13)=C(14) double bond to residues in the membrane-embedded alpha-helices of HtrII. The results suggest a chemical mechanism for signaling that entails initial storage of energy of photoisomerization in SRII's hydrogen bond between Tyr-174, which is in contact with the retinal, and Thr-204, which borders residues on the SRII surface in contact with HtrII, followed by transfer of this chemical energy to drive structural transitions in the transducer helices. The results demonstrate that evolution accomplished an elegant but simple conversion: The essential differences between transport and signaling proteins in the rhodopsin family are far less than previously imagined.
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Affiliation(s)
- Yuki Sudo
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, TX 77030
| | - John L. Spudich
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, TX 77030
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