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Inoue K. Diversity, Mechanism, and Optogenetic Application of Light-Driven Ion Pump Rhodopsins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:89-126. [PMID: 33398809 DOI: 10.1007/978-981-15-8763-4_6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ion-transporting microbial rhodopsins are widely used as major molecular tools in optogenetics. They are categorized into light-gated ion channels and light-driven ion pumps. While the former passively transport various types of cations and anions in a light-dependent manner, light-driven ion pumps actively transport specific ions, such as H+, Na+, Cl-, against electrophysiological potential by using light energy. Since the ion transport by these pumps induces hyperpolarization of membrane potential and inhibit neural firing, light-driven ion-pumping rhodopsins are mostly applied as inhibitory optogenetics tools. Recent progress in genome and metagenome sequencing identified more than several thousands of ion-pumping rhodopsins from a wide variety of microbes, and functional characterization studies has been revealing many new types of light-driven ion pumps one after another. Since light-gated channels were reviewed in other chapters in this book, here the rapid progress in functional characterization, molecular mechanism study, and optogenetic application of ion-pumping rhodopsins were reviewed.
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Affiliation(s)
- Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Chiba, Japan.
- PRESTO, Japan Science and Technology Agency, Saitama, Japan.
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2
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Buhrke D, Hildebrandt P. Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy. Chem Rev 2019; 120:3577-3630. [PMID: 31814387 DOI: 10.1021/acs.chemrev.9b00429] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un- and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.
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Affiliation(s)
- David Buhrke
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
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3
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Daldrop JO, Saita M, Heyden M, Lorenz-Fonfria VA, Heberle J, Netz RR. Orientation of non-spherical protonated water clusters revealed by infrared absorption dichroism. Nat Commun 2018; 9:311. [PMID: 29358659 PMCID: PMC5778031 DOI: 10.1038/s41467-017-02669-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/15/2017] [Indexed: 11/09/2022] Open
Abstract
Infrared continuum bands that extend over a broad frequency range are a key spectral signature of protonated water clusters. They are observed for many membrane proteins that contain internal water molecules, but their microscopic mechanism has remained unclear. Here we compute infrared spectra for protonated and unprotonated water chains, discs, and droplets from ab initio molecular dynamics simulations. The continuum bands of the protonated clusters exhibit significant anisotropy for chains and discs, with increased absorption along the direction of maximal cluster extension. We show that the continuum band arises from the nuclei motion near the excess charge, with a long-ranged amplification due to the electronic polarizability. Our experimental, polarization-resolved light–dark difference spectrum of the light-driven proton pump bacteriorhodopsin exhibits a pronounced dichroic continuum band. Our results suggest that the protonated water cluster responsible for the continuum band of bacteriorhodopsin is oriented perpendicularly to the membrane normal. Protein-bound water clusters play a key role for proton transport and storage in molecular biology. Here, the authors show by simulations and experiments that the orientation of non-spherical protonated water clusters in bacteriorhodopsin is unveiled by polarization-resolved infrared spectroscopy.
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Affiliation(s)
- Jan O Daldrop
- Department of Physics, Freie Universität Berlin, 14195, Berlin, Germany
| | - Mattia Saita
- Department of Physics, Freie Universität Berlin, 14195, Berlin, Germany
| | - Matthias Heyden
- Max-Planck-Institut für Kohlenforschung, 45470, Mülheim an der Ruhr, Germany
| | | | - Joachim Heberle
- Department of Physics, Freie Universität Berlin, 14195, Berlin, Germany.
| | - Roland R Netz
- Department of Physics, Freie Universität Berlin, 14195, Berlin, Germany.
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4
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Giliberti V, Badioli M, Nucara A, Calvani P, Ritter E, Puskar L, Aziz EF, Hegemann P, Schade U, Ortolani M, Baldassarre L. Heterogeneity of the Transmembrane Protein Conformation in Purple Membranes Identified by Infrared Nanospectroscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1701181. [PMID: 28960799 DOI: 10.1002/smll.201701181] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 08/02/2017] [Indexed: 06/07/2023]
Abstract
Cell membranes are intrinsically heterogeneous, as the local protein and lipid distribution is critical to physiological processes. Even in template systems embedding a single protein type, like purple membranes, there can be a different local response to external stimuli or environmental factors, resulting in heterogeneous conformational changes. Despite the dramatic advances of microspectroscopy techniques, the identification of the conformation heterogeneity is still a challenging task. Tip-enhanced infrared nanospectroscopy is here used to identify conformational changes connected to the hydration state of the transmembrane proteins contained in a 50 nm diameter cell membrane area, without the need for fluorescent labels. In dried purple membrane monolayers, areas with fully hydrated proteins are found among large numbers of molecules with randomly distributed hydration states. Infrared nanospectroscopy results are compared to the spectra obtained with diffraction-limited infrared techniques based on the use of synchrotron radiation, in which the diffraction limit still prevents the observation of nanoscale heterogeneity.
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Affiliation(s)
- Valeria Giliberti
- Istituto Italiano di Tecnologia, Center for Life NanoScience, Viale Regina Elena 291, I-00161, Roma, Italy
| | - Michela Badioli
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 2, I-00185, Roma, Italy
| | - Alessandro Nucara
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 2, I-00185, Roma, Italy
| | - Paolo Calvani
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 2, I-00185, Roma, Italy
| | - Eglof Ritter
- Humboldt-Universität zu Berlin, Institut für Biologie, Invalidenstraße 42, D-10115, Berlin, Germany
| | - Ljiljana Puskar
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 15, 12489, Berlin, Germany
| | - Emad Flear Aziz
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 15, 12489, Berlin, Germany
| | - Peter Hegemann
- Humboldt-Universität zu Berlin, Institut für Biologie, Invalidenstraße 42, D-10115, Berlin, Germany
| | - Ulrich Schade
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 15, 12489, Berlin, Germany
| | - Michele Ortolani
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 2, I-00185, Roma, Italy
| | - Leonetta Baldassarre
- Istituto Italiano di Tecnologia, Center for Life NanoScience, Viale Regina Elena 291, I-00161, Roma, Italy
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 2, I-00185, Roma, Italy
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5
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Harder D, Hirschi S, Ucurum Z, Goers R, Meier W, Müller DJ, Fotiadis D. Engineering a Chemical Switch into the Light-driven Proton Pump Proteorhodopsin by Cysteine Mutagenesis and Thiol Modification. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601537] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daniel Harder
- Institute of Biochemistry and Molecular Medicine; University of Bern; 3012 Bern Switzerland
| | - Stephan Hirschi
- Institute of Biochemistry and Molecular Medicine; University of Bern; 3012 Bern Switzerland
| | - Zöhre Ucurum
- Institute of Biochemistry and Molecular Medicine; University of Bern; 3012 Bern Switzerland
| | - Roland Goers
- Department of Chemistry; University of Basel; 4056 Basel Switzerland
- Department of Biosystems Science and Engineering; ETH Zürich; 4058 Basel Switzerland
| | - Wolfgang Meier
- Department of Chemistry; University of Basel; 4056 Basel Switzerland
| | - Daniel J. Müller
- Department of Biosystems Science and Engineering; ETH Zürich; 4058 Basel Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine; University of Bern; 3012 Bern Switzerland
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6
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Harder D, Hirschi S, Ucurum Z, Goers R, Meier W, Müller DJ, Fotiadis D. Engineering a Chemical Switch into the Light-driven Proton Pump Proteorhodopsin by Cysteine Mutagenesis and Thiol Modification. Angew Chem Int Ed Engl 2016; 55:8846-9. [PMID: 27294681 DOI: 10.1002/anie.201601537] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/27/2016] [Indexed: 12/20/2022]
Abstract
For applications in synthetic biology, for example, the bottom-up assembly of biomolecular nanofactories, modules of specific and controllable functionalities are essential. Of fundamental importance in such systems are energizing modules, which are able to establish an electrochemical gradient across a vesicular membrane as an energy source for powering other modules. Light-driven proton pumps like proteorhodopsin (PR) are excellent candidates for efficient energy conversion. We have extended the versatility of PR by implementing an on/off switch based on reversible chemical modification of a site-specifically introduced cysteine residue. The position of this cysteine residue in PR was identified by structure-based cysteine mutagenesis combined with a proton-pumping assay using E. coli cells overexpressing PR and PR proteoliposomes. The identified PR mutant represents the first light-driven proton pump that can be chemically switched on/off depending on the requirements of the molecular system.
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Affiliation(s)
- Daniel Harder
- Institute of Biochemistry and Molecular Medicine, University of Bern, 3012, Bern, Switzerland
| | - Stephan Hirschi
- Institute of Biochemistry and Molecular Medicine, University of Bern, 3012, Bern, Switzerland
| | - Zöhre Ucurum
- Institute of Biochemistry and Molecular Medicine, University of Bern, 3012, Bern, Switzerland
| | - Roland Goers
- Department of Chemistry, University of Basel, 4056, Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland
| | - Wolfgang Meier
- Department of Chemistry, University of Basel, 4056, Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, 3012, Bern, Switzerland.
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7
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Novel expression and characterization of a light driven proton pump archaerhodopsin 4 in a Halobacterium salinarum strain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:390-398. [DOI: 10.1016/j.bbabio.2014.12.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 12/22/2014] [Accepted: 12/25/2014] [Indexed: 11/19/2022]
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8
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García-Martínez J, Brunk M, Avalos J, Terpitz U. The CarO rhodopsin of the fungus Fusarium fujikuroi is a light-driven proton pump that retards spore germination. Sci Rep 2015; 5:7798. [PMID: 25589426 PMCID: PMC4295100 DOI: 10.1038/srep07798] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 12/18/2014] [Indexed: 12/29/2022] Open
Abstract
Rhodopsins are membrane-embedded photoreceptors found in all major taxonomic kingdoms using retinal as their chromophore. They play well-known functions in different biological systems, but their roles in fungi remain unknown. The filamentous fungus Fusarium fujikuroi contains two putative rhodopsins, CarO and OpsA. The gene carO is light-regulated, and the predicted polypeptide contains all conserved residues required for proton pumping. We aimed to elucidate the expression and cellular location of the fungal rhodopsin CarO, its presumed proton-pumping activity and the possible effect of such function on F. fujikuroi growth. In electrophysiology experiments we confirmed that CarO is a green-light driven proton pump. Visualization of fluorescent CarO-YFP expressed in F. fujikuroi under control of its native promoter revealed higher accumulation in spores (conidia) produced by light-exposed mycelia. Germination analyses of conidia from carO(-) mutant and carO(+) control strains showed a faster development of light-exposed carO(-) germlings. In conclusion, CarO is an active proton pump, abundant in light-formed conidia, whose activity slows down early hyphal development under light. Interestingly, CarO-related rhodopsins are typically found in plant-associated fungi, where green light dominates the phyllosphere. Our data provide the first reliable clue on a possible biological role of a fungal rhodopsin.
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Affiliation(s)
- Jorge García-Martínez
- Department of Genetics, Faculty of Biology, University of Seville, E-41012 Seville, Spain
| | - Michael Brunk
- Department of Biotechnology and Biophysics, Biocenter, Julius Maximilian University Würzburg, D-97074 Würzburg, Germany
| | - Javier Avalos
- Department of Genetics, Faculty of Biology, University of Seville, E-41012 Seville, Spain
| | - Ulrich Terpitz
- Department of Biotechnology and Biophysics, Biocenter, Julius Maximilian University Würzburg, D-97074 Würzburg, Germany
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9
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Mukhopadhyay S, Cohen SR, Marchak D, Friedman N, Pecht I, Sheves M, Cahen D. Nanoscale electron transport and photodynamics enhancement in lipid-depleted bacteriorhodopsin monomers. ACS NANO 2014; 8:7714-7722. [PMID: 25003581 DOI: 10.1021/nn500202k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Potential future use of bacteriorhodopsin (bR) as a solid-state electron transport (ETp) material requires the highest possible active protein concentration. To that end we prepared stable monolayers of protein-enriched bR on a conducting HOPG substrate by lipid depletion of the native bR. The ETp properties of this construct were then investigated using conducting probe atomic force microscopy at low bias, both in the ground dark state and in the M-like intermediate configuration, formed upon excitation by green light. Photoconductance modulation was observed upon green and blue light excitation, demonstrating the potential of these monolayers as optoelectronic building blocks. To correlate protein structural changes with the observed behavior, measurements were made as a function of pressure under the AFM tip, as well as humidity. The junction conductance is reversible under pressure changes up to ∼300 MPa, but above this pressure the conductance drops irreversibly. ETp efficiency is enhanced significantly at >60% relative humidity, without changing the relative photoactivity significantly. These observations are ascribed to changes in protein conformation and flexibility and suggest that improved electron transport pathways can be generated through formation of a hydrogen-bonding network.
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10
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Nakanishi T, Kanada S, Murakami M, Ihara K, Kouyama T. Large deformation of helix F during the photoreaction cycle of Pharaonis halorhodopsin in complex with azide. Biophys J 2013; 104:377-85. [PMID: 23442859 DOI: 10.1016/j.bpj.2012.12.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 12/08/2012] [Accepted: 12/11/2012] [Indexed: 02/01/2023] Open
Abstract
Halorhodopsin from Natronomonas pharaonis (pHR), a retinylidene protein that functions as a light-driven chloride ion pump, is converted into a proton pump in the presence of azide ion. To clarify this conversion, we investigated light-induced structural changes in pHR using a C2 crystal that was prepared in the presence of Cl(-) and subsequently soaked in a solution containing azide ion. When the pHR-azide complex was illuminated at pH 9, a profound outward movement (∼4 Å) of the cytoplasmic half of helix F was observed in a subunit with the EF loop facing an open space. This movement created a long water channel between the retinal Schiff base and the cytoplasmic surface, along which a proton could be transported. Meanwhile, the middle moiety of helix C moved inward, leading to shrinkage of the primary anion-binding site (site I), and the azide molecule in site I was expelled out to the extracellular medium. The results suggest that the cytoplasmic half of helix F and the middle moiety of helix C act as different types of valves for active proton transport.
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11
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Sattig T, Rickert C, Bamberg E, Steinhoff HJ, Bamann C. Light-Induced Movement of the Transmembrane Helix B in Channelrhodopsin-2. Angew Chem Int Ed Engl 2013; 52:9705-8. [DOI: 10.1002/anie.201301698] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 06/12/2013] [Indexed: 11/06/2022]
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12
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Sattig T, Rickert C, Bamberg E, Steinhoff HJ, Bamann C. Light-Induced Movement of the Transmembrane Helix B in Channelrhodopsin-2. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301698] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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13
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Hussain S, Franck JM, Han S. Transmembrane Protein Activation Refined by Site-Specific Hydration Dynamics. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201206147] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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Hussain S, Franck JM, Han S. Transmembrane protein activation refined by site-specific hydration dynamics. Angew Chem Int Ed Engl 2013; 52:1953-8. [PMID: 23307344 DOI: 10.1002/anie.201206147] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 09/18/2012] [Indexed: 11/11/2022]
Affiliation(s)
- Sunyia Hussain
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93016, USA
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15
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Zocher M, Roos C, Wegmann S, Bosshart PD, Dötsch V, Bernhard F, Müller DJ. Single-molecule force spectroscopy from nanodiscs: an assay to quantify folding, stability, and interactions of native membrane proteins. ACS NANO 2012; 6:961-71. [PMID: 22196235 DOI: 10.1021/nn204624p] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Single-molecule force spectroscopy (SMFS) can quantify and localize inter- and intramolecular interactions that determine the folding, stability, and functional state of membrane proteins. To conduct SMFS the membranes embedding the membrane proteins must be imaged and localized in a rather time-consuming manner. Toward simplifying the investigation of membrane proteins by SMFS, we reconstituted the light-driven proton pump bacteriorhodopsin into lipid nanodiscs. The advantage of using nanodiscs is that membrane proteins can be handled like water-soluble proteins and characterized with similar ease. SMFS characterization of bacteriorhodopsin in native purple membranes and in nanodiscs reveals no significant alterations of structure, function, unfolding intermediates, and strengths of inter- and intramolecular interactions. This demonstrates that lipid nanodiscs provide a unique approach for in vitro studies of native membrane proteins using SMFS and open an avenue to characterize membrane proteins by a wide variety of SMFS approaches that have been established on water-soluble proteins.
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Affiliation(s)
- Michael Zocher
- Biosystems Science and Engineering (BSSE), ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
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16
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Pan Y, Brown L, Konermann L. Hydrogen exchange mass spectrometry of bacteriorhodopsin reveals light-induced changes in the structural dynamics of a biomolecular machine. J Am Chem Soc 2011; 133:20237-44. [PMID: 22043856 DOI: 10.1021/ja206197h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Many proteins act as molecular machines that are fuelled by a nonthermal energy source. Examples include transmembrane pumps and stator-rotor complexes. These systems undergo cyclic motions (CMs) that are being driven along a well-defined conformational trajectory. Superimposed on these CMs are thermal fluctuations (TFs) that are coupled to stochastic motions of the solvent. Here we explore whether the TFs of a molecular machine are affected by the occurrence of CMs. Bacteriorhodopsin (BR) is a light-driven proton pump that serves as a model system in this study. The function of BR is based on a photocycle that involves trans/cis isomerization of a retinal chromophore, as well as motions of transmembrane helices. Hydrogen/deuterium exchange (HDX) mass spectrometry was used to monitor the TFs of BR, focusing on the monomeric form of the protein. Comparative HDX studies were conducted under illumination and in the dark. The HDX kinetics of BR are dramatically accelerated in the presence of light. The isotope exchange rates and the number of backbone amides involved in EX2 opening transitions increase roughly 2-fold upon illumination. In contrast, light/dark control experiments on retinal-free protein produced no discernible differences. It can be concluded that the extent of TFs in BR strongly depends on photon-driven CMs. The light-induced differences in HDX behavior are ascribed to protein destabilization. Specifically, the thermodynamic stability of the dark-adapted protein is estimated to be 5.5 kJ mol(-1) under the conditions of our work. This value represents the free energy difference between the folded state F and a significantly unfolded conformer U. Illumination reduces the stability of F by 2.2 kJ mol(-1). Mechanical agitation caused by isomerization of the chromophore is transferred to the surrounding protein scaffold, and subsequently, the energy dissipates into the solvent. Light-induced retinal motions therefore act analogously to an internal heat source that promotes the occurrence of TFs. Overall, our data highlight the potential of HDX methods for probing the structural dynamics of molecular machines under "engine on" and "engine off" conditions.
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Affiliation(s)
- Yan Pan
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7
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17
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ATP synthase superassemblies in animals and plants: Two or more are better. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1185-97. [PMID: 21679683 DOI: 10.1016/j.bbabio.2011.05.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 05/30/2011] [Accepted: 05/31/2011] [Indexed: 12/11/2022]
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18
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Proton transfer via a transient linear water-molecule chain in a membrane protein. Proc Natl Acad Sci U S A 2011; 108:11435-9. [PMID: 21709261 DOI: 10.1073/pnas.1104735108] [Citation(s) in RCA: 156] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
High-resolution protein ground-state structures of proton pumps and channels have revealed internal protein-bound water molecules. Their possible active involvement in protein function has recently come into focus. An illustration of the formation of a protonated protein-bound water cluster that is actively involved in proton transfer was described for the membrane protein bacteriorhodopsin (bR) [Garczarek F, Gerwert K (2006) Nature 439:109-112]. Here we show through a combination of time-resolved FTIR spectroscopy and molecular dynamics simulations that three protein-bound water molecules are rearranged by a protein conformational change that resulted in a transient Grotthuss-type proton-transfer chain extending through a hydrophobic protein region of bR. This transient linear water chain facilitates proton transfer at an intermediate conformation only, thereby directing proton transfer within the protein. The rearrangement of protein-bound water molecules that we describe, from inactive positions in the ground state to an active chain in an intermediate state, appears to be energetically favored relative to transient incorporation of water molecules from the bulk. Our discovery provides insight into proton-transfer mechanisms through hydrophobic core regions of ubiquitous membrane spanning proteins such as G-protein coupled receptors or cytochrome C oxidases.
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19
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Yang J, Aslimovska L, Glaubitz C. Molecular Dynamics of Proteorhodopsin in Lipid Bilayers by Solid-State NMR. J Am Chem Soc 2011; 133:4874-81. [DOI: 10.1021/ja109766n] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jun Yang
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Goethe University Frankfurt/M., Max-von-Laue Strasse 9, 60438 Frankfurt/M., Germany
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, The Chinese Academy of Sciences, Wuhan 430071, China
| | - Lubica Aslimovska
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Goethe University Frankfurt/M., Max-von-Laue Strasse 9, 60438 Frankfurt/M., Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Goethe University Frankfurt/M., Max-von-Laue Strasse 9, 60438 Frankfurt/M., Germany
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20
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Buchsteiner A, Hauβ T, Dante S, Dencher NA. Alzheimer's disease amyloid-β peptide analogue alters the ps-dynamics of phospholipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:1969-76. [DOI: 10.1016/j.bbamem.2010.06.024] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 06/23/2010] [Accepted: 06/28/2010] [Indexed: 11/26/2022]
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21
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Chu LK, El-Sayed MA. Kinetics of the M-Intermediate in the Photocycle of Bacteriorhodopsin upon Chemical Modification with Surfactants. Photochem Photobiol 2010; 86:316-23. [DOI: 10.1111/j.1751-1097.2009.00666.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Antoranz Contera S, Voïtchovsky K, Ryan JF. Controlled ionic condensation at the surface of a native extremophile membrane. NANOSCALE 2010; 2:222-229. [PMID: 20644798 DOI: 10.1039/b9nr00248k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
At the nanoscale level biological membranes present a complex interface with the solvent. The functional dynamics and relative flexibility of membrane components together with the presence of specific ionic effects can combine to create exciting new phenomena that challenge traditional theories such as the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory or models interpreting the role of ions in terms of their ability to structure water (structure making/breaking). Here we investigate ionic effects at the surface of a highly charged extremophile membrane composed of a proton pump (bacteriorhodopsin) and archaeal lipids naturally assembled into a 2D crystal. Using amplitude-modulation atomic force microscopy (AM-AFM) in solution, we obtained sub-molecular resolution images of ion-induced surface restructuring of the membrane. We demonstrate the presence of a stiff cationic layer condensed at its extracellular surface. This layer cannot be explained by traditional continuum theories. Dynamic force spectroscopy experiments suggest that it is produced by electrostatic correlation mediated by a Manning-type condensation of ions. In contrast, the cytoplasmic surface is dominated by short-range repulsive hydration forces. These findings are relevant to archaeal bioenergetics and halophilic adaptation. Importantly, they present experimental evidence of a natural system that locally controls its interactions with the surrounding medium and challenges our current understanding of biological interfaces.
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Affiliation(s)
- Sonia Antoranz Contera
- University of Oxford, Bionanotechnology IRC, Clarendon Laboratory, Physics Department, Parks Road, OX1 3PU, Oxford, UK.
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Pieper J. Time-resolved quasielastic neutron scattering studies of native photosystems. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1804:83-8. [PMID: 19782773 DOI: 10.1016/j.bbapap.2009.09.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Revised: 09/14/2009] [Accepted: 09/16/2009] [Indexed: 10/20/2022]
Abstract
The internal molecular dynamics of proteins plays an important role in a number of functional processes in native photosystems. Prominent examples include the photocycle of bacteriorhodopsin and electron transfer in the reaction center of plant photosystem II. In this regard, the recently developed technique of time-resolved quasielastic neutron scattering with laser excitation opens up new perspectives for the study of protein/membrane dynamics in specific functional states of even complex systems. The first direct observation of a functionally modulated protein dynamics has just recently been reported for the model system bacteriorhodopsin (Pieper et al., Phys. Rev. Lett. 100, 2008, 228103.), where a transient softening of the protein was observed on a timescale of approximately 1 ms along with the large-scale structural change in the M-intermediate of bacteriorhodopsin. In contrast, photosystem II membrane fragments with inhibited electron transfer show a suppression of protein dynamics approximately 160 mus after the actinic laser flash (Pieper and Renger, Biochemistry 48, 2009, 6111). This effect may reflect aggregation-like conformational changes capable of dissipation of excess excitation energy to prevent photodamage in the absence of Q(A)-->Q(B) electron transfer. These findings indicate that proteins exhibit a remarkable flexibility to accommodate different functional processes. This contribution will discuss methodical aspects, challenges, and recent applications of laser-excited, time-resolved quasielastic neutron scattering.
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Affiliation(s)
- Jörg Pieper
- Max-Volmer-Laboratories for Biophysical Chemistry, Technische Universität Berlin, 10623 Berlin, Germany.
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Seelert H, Dani DN, Dante S, Hauss T, Krause F, Schäfer E, Frenzel M, Poetsch A, Rexroth S, Schwassmann HJ, Suhai T, Vonck J, Dencher NA. From protons to OXPHOS supercomplexes and Alzheimer's disease: structure-dynamics-function relationships of energy-transducing membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:657-71. [PMID: 19281792 DOI: 10.1016/j.bbabio.2009.02.028] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Revised: 02/20/2009] [Accepted: 02/20/2009] [Indexed: 11/29/2022]
Abstract
By the elucidation of high-resolution structures the view of the bioenergetic processes has become more precise. But in the face of these fundamental advances, many problems are still unresolved. We have examined a variety of aspects of energy-transducing membranes from large protein complexes down to the level of protons and functional relevant picosecond protein dynamics. Based on the central role of the ATP synthase for supplying the biological fuel ATP, one main emphasis was put on this protein complex from both chloroplast and mitochondria. In particular the stoichiometry of protons required for the synthesis of one ATP molecule and the supramolecular organisation of ATP synthases were examined. Since formation of supercomplexes also concerns other complexes of the respiratory chain, our work was directed to unravel this kind of organisation, e.g. of the OXPHOS supercomplex I(1)III(2)IV(1), in terms of structure and function. Not only the large protein complexes or supercomplexes work as key players for biological energy conversion, but also small components as quinones which facilitate the transfer of electrons and protons. Therefore, their location in the membrane profile was determined by neutron diffraction. Physico-chemical features of the path of protons from the generators of the electrochemical gradient to the ATP synthase, as well as of their interaction with the membrane surface, could be elucidated by time-resolved absorption spectroscopy in combination with optical pH indicators. Diseases such as Alzheimer's dementia (AD) are triggered by perturbation of membranes and bioenergetics as demonstrated by our neutron scattering studies.
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Affiliation(s)
- H Seelert
- Department of Chemistry, Technische Universität Darmstadt, Petersenstrasse 22, D-64287 Darmstadt, Germany.
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Pieper J, Buchsteiner A, Dencher NA, Lechner RE, Hauß T. Light-induced Modulation of Protein Dynamics During the Photocycle of Bacteriorhodopsin. Photochem Photobiol 2009; 85:590-7. [DOI: 10.1111/j.1751-1097.2008.00501.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Schäfer G, Shastri S, Verhoefen MK, Vogel V, Glaubitz C, Wachtveitl J, Mäntele W. Characterizing the Structure and Photocycle of PR 2D Crystals with CD and FTIR Spectroscopy. Photochem Photobiol 2009; 85:529-34. [DOI: 10.1111/j.1751-1097.2008.00491.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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27
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Hemoglobin senses body temperature. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 38:589-600. [PMID: 19238378 DOI: 10.1007/s00249-009-0410-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Revised: 01/20/2009] [Accepted: 01/29/2009] [Indexed: 10/21/2022]
Abstract
UNLABELLED When aspirating human red blood cells (RBCs) into 1.3 mum pipettes (DeltaP = -2.3 kPa), a transition from blocking the pipette below a critical temperature T(c) = 36.3 +/- 0.3 degrees C to passing it above the T(c) occurred (micropipette passage transition). With a 1.1 mum pipette no passage was seen which enabled RBC volume measurements also above T(c). With increasing temperature RBCs lost volume significantly faster below than above a T(c) = 36.4 +/- 0.7 (volume transition). Colloid osmotic pressure (COP) measurements of RBCs in autologous plasma (25 degrees C < or = T < or = 39.5 degrees C) showed a T (c) at 37.1 +/- 0.2 degrees C above which the COP rapidly decreased (COP transition). In NMR T(1)-relaxation time measurements, the T(1) of RBCs in autologous plasma changed from a linear (r = 0.99) increment below T(c) = 37 +/- 1 degrees C at a rate of 0.023 s/K into zero slope above T(c) (RBC T(1) transition). IN CONCLUSION An amorphous hemoglobin-water gel formed in the spherical trail, the residual partial sphere of the aspirated RBC. At T(c), a sudden fluidization of the gel occurs. All changes mentioned above happen at a distinct T(c) close to body temperature. The T(c) is moved +0.8 degrees C to higher temperatures when a D(2)O buffer is used. We suggest a mechanism similar to a "glass transition" or a "colloidal phase transition". At T(c), the stabilizing Hb bound water molecules reach a threshold number enabling a partial Hb unfolding. Thus, Hb senses body temperature which must be inscribed in the primary structure of hemoglobin and possibly other proteins.
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Bondar AN, Baudry J, Suhai S, Fischer S, Smith JC. Key Role of Active-Site Water Molecules in Bacteriorhodopsin Proton-Transfer Reactions. J Phys Chem B 2008; 112:14729-41. [DOI: 10.1021/jp801916f] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ana-Nicoleta Bondar
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany, Molecular Biophysics Department, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, University of California at Irvine, Department of Physiology and Biophysics and the Center for Biomembrane Systems, Med. Sci. I, D-374, Irvine, California 92697-4560, University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge
| | - Jerome Baudry
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany, Molecular Biophysics Department, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, University of California at Irvine, Department of Physiology and Biophysics and the Center for Biomembrane Systems, Med. Sci. I, D-374, Irvine, California 92697-4560, University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge
| | - Sándor Suhai
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany, Molecular Biophysics Department, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, University of California at Irvine, Department of Physiology and Biophysics and the Center for Biomembrane Systems, Med. Sci. I, D-374, Irvine, California 92697-4560, University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge
| | - Stefan Fischer
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany, Molecular Biophysics Department, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, University of California at Irvine, Department of Physiology and Biophysics and the Center for Biomembrane Systems, Med. Sci. I, D-374, Irvine, California 92697-4560, University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge
| | - Jeremy C. Smith
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany, Molecular Biophysics Department, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, University of California at Irvine, Department of Physiology and Biophysics and the Center for Biomembrane Systems, Med. Sci. I, D-374, Irvine, California 92697-4560, University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge
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Dioumaev AK, Lanyi JK. Switch from conventional to distributed kinetics in the bacteriorhodopsin photocycle. Biochemistry 2008; 47:11125-33. [PMID: 18821776 PMCID: PMC2692533 DOI: 10.1021/bi801247e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Below 195 K, the bacteriorhodopsin photocycle could not be adequately described with exponential kinetics [Dioumaev, A. K., and Lanyi, J. K. (2007) Proc. Natl. Acad. Sci. U.S.A. 104, 9621-9626] but required distributed kinetics, previously found in hemoglobin and myoglobin at temperatures below the vitrification point of the surrounding solvent. The aim of this study is to determine which factors cause the switch from this low-temperature regime to the conventional kinetics observed at ambient temperature. The photocycle was monitored by time-resolved FTIR between 180 and 280 K, using the D96N mutant. Depending on the temperature, decay and temporal redistribution of two or three intermediates (L, M, and N) were observed. Above approximately 245 K, an abrupt change in the kinetic behavior of the photocycle takes place. It does not affect the intermediates present but greatly accelerates their decay. Below approximately 240 K, a kinetic pattern with partial decay that cannot be explained by conventional kinetics, but suggesting distributed kinetics, was dominant, while above approximately 250 K, there were no significant deviations from exponential behavior. The approximately 245 K critical point is >/=10 K below the freezing point of interbilayer water, and we were unable to correlate it with any FTIR-detectable transition of the lipids. Therefore, we attribute the change from distributed to conventional kinetics to a thermodynamic phase transition in the protein. Most probably, it is related to the freezing and thawing of internal fluctuations of the protein, known as the dynamic phase transition, although in bacteriorhodopsin the latter is usually believed to take place at least 15 K below the observed critical temperature of approximately 245 K.
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Affiliation(s)
- Andrei K Dioumaev
- Department of Physiology and Biophysics, University of California, Irvine, California 92697-4560, USA.
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30
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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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Pieper J, Buchsteiner A, Dencher NA, Lechner RE, Hauss T. Transient protein softening during the working cycle of a molecular machine. PHYSICAL REVIEW LETTERS 2008; 100:228103. [PMID: 18643463 DOI: 10.1103/physrevlett.100.228103] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Indexed: 05/26/2023]
Abstract
Proper functioning of proteins usually requires a certain internal flexibility provided by stochastic structural fluctuations on the picosecond time scale. In contrast with conventional steady-state experiments, we report on a novel type of (laser-neutron) pump-probe experiment combining in situ activation of protein function with a time-dependent test of protein dynamics using quasielastic neutron scattering. A "transient protein softening" is shown to occur during the photocycle of bacteriorhodopsin as a direct proof for the functional significance of protein flexibility.
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Affiliation(s)
- Jörg Pieper
- Max-Volmer-Laboratories for Biophysical Chemistry, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany.
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Abstract
We used neutron scattering and specific hydrogen-deuterium labeling to investigate the thermal dynamics of isotope-labeled amino acids and retinal, predominantly in the active core and extracellular moiety of bacteriorhodopsin (BR) in the purple membrane and the dynamical response to hydration. Measurements on two neutron spectrometers allowed two populations of motions to be characterized. The lower amplitude motions were found to be the same for both the labeled amino acids and retinal of BR and the global membrane. The larger amplitude dynamics of the labeled part, however, were found to be more resilient than the average membrane, suggesting their functional importance. The response to hydration was characterized, showing that the labeled part of BR is not shielded from hydration effects. The results suggest that the inhibition of high-amplitude motions by lowering hydration may play a key role in the slowing down of the photocycle and the proton pumping activity of BR.
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Wood K, Plazanet M, Gabel F, Kessler B, Oesterhelt D, Zaccai G, Weik M. Dynamics of hydration water in deuterated purple membranes explored by neutron scattering. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 37:619-26. [PMID: 18286273 PMCID: PMC2755797 DOI: 10.1007/s00249-008-0285-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Revised: 01/22/2008] [Accepted: 01/31/2008] [Indexed: 11/29/2022]
Abstract
The function and dynamics of proteins depend on their direct environment, and much evidence has pointed to a strong coupling between water and protein motions. Recently however, neutron scattering measurements on deuterated and natural-abundance purple membrane (PM), hydrated in H2O and D2O, respectively, revealed that membrane and water motions on the ns-ps time scale are not directly coupled below 260 K (Wood et al. in Proc Natl Acad Sci USA 104:18049-18054, 2007). In the initial study, samples with a high level of hydration were measured. Here, we have measured the dynamics of PM and water separately, at a low-hydration level corresponding to the first layer of hydration water only. As in the case of the higher hydration samples previously studied, the dynamics of PM and water display different temperature dependencies, with a transition in the hydration water at 200 K not triggering a transition in the membrane at the same temperature. Furthermore, neutron diffraction experiments were carried out to monitor the lamellar spacing of a flash-cooled deuterated PM stack hydrated in H2O as a function of temperature. At 200 K, a sudden decrease in lamellar spacing indicated the onset of long-range translational water diffusion in the second hydration layer as has already been observed on flash-cooled natural-abundance PM stacks hydrated in D2O (Weik et al. in J Mol Biol 275:632-634, 2005), excluding thus a notable isotope effect. Our results reinforce the notion that membrane-protein dynamics may be less strongly coupled to hydration water motions than the dynamics of soluble proteins.
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Affiliation(s)
- K Wood
- Laboratoire de Biophysique Moléculaire, Institut de Biologie Structurale CEA-CNRS-UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
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Coupling of protein and hydration-water dynamics in biological membranes. Proc Natl Acad Sci U S A 2007; 104:18049-54. [PMID: 17986611 DOI: 10.1073/pnas.0706566104] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The dynamical coupling between proteins and their hydration water is important for the understanding of macromolecular function in a cellular context. In the case of membrane proteins, the environment is heterogeneous, composed of lipids and hydration water, and the dynamical coupling might be more complex than in the case of the extensively studied soluble proteins. Here, we examine the dynamical coupling between a biological membrane, the purple membrane (PM), and its hydration water by a combination of elastic incoherent neutron scattering, specific deuteration, and molecular dynamics simulations. Examining completely deuterated PM, hydrated in H(2)O, allowed the direct experimental exploration of water dynamics. The study of natural abundance PM in D(2)O focused on membrane dynamics. The temperature-dependence of atomic mean-square displacements shows inflections at 120 K and 260 K for the membrane and at 200 K and 260 K for the hydration water. Because transition temperatures are different for PM and hydration water, we conclude that ps-ns hydration water dynamics are not directly coupled to membrane motions on the same time scale at temperatures <260 K. Molecular-dynamics simulations of hydrated PM in the temperature range from 100 to 296 K revealed an onset of hydration-water translational diffusion at approximately 200 K, but no transition in the PM at the same temperature. Our results suggest that, in contrast to soluble proteins, the dynamics of the membrane protein is not controlled by that of hydration water at temperatures <260 K. Lipid dynamics may have a stronger impact on membrane protein dynamics than hydration water.
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Corcelli A, Lobasso S, Saponetti MS, Leopold A, Dencher NA. Glycocardiolipin modulates the surface interaction of the proton pumped by bacteriorhodopsin in purple membrane preparations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:2157-63. [PMID: 17669358 DOI: 10.1016/j.bbamem.2007.06.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2006] [Revised: 06/29/2007] [Accepted: 06/29/2007] [Indexed: 10/23/2022]
Abstract
Glycocardiolipin is an archaeal analogue of mitochondrial cardiolipin, having an extraordinary affinity for bacteriorhodopsin, the photoactivated proton pump in the purple membrane of Halobacterium salinarum. Here purple membranes have been isolated by osmotic shock from either cells or envelopes of Hbt. salinarum. We show that purple membranes isolated from envelopes have a lower content of glycocardiolipin than standard purple membranes isolated from cells. The properties of bacteriorhodopsin in the two different purple membrane preparations are compared; although some differences in the absorption spectrum and the kinetic of the dark adaptation process are present, the reduction of native membrane glycocardiolipin content does not significantly affect the photocycle (M-intermediate rise and decay) as well as proton pumping of bacteriorhodopsin. However, interaction of the pumped proton with the membrane surface and its equilibration with the aqueous bulk phase are altered.
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Affiliation(s)
- Angela Corcelli
- Dipartimento di Biochimica medica, biologia medica e fisica medica. Università degli Studi di Bari, Piazza G. Cesare, I-70124 Bari, Italy
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Buchsteiner A, Lechner RE, Hauss T, Dencher NA. Relationship Between Structure, Dynamics and Function of Hydrated Purple Membrane Investigated by Neutron Scattering and Dielectric Spectroscopy. J Mol Biol 2007; 371:914-23. [PMID: 17599349 DOI: 10.1016/j.jmb.2007.05.092] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2007] [Revised: 05/21/2007] [Accepted: 05/29/2007] [Indexed: 10/23/2022]
Abstract
We investigated the influence of hydration water on the relationship between structure, dynamics and function in a biological membrane system. For the example of the purple membrane (PM) with its protein bacteriorhodopsin (BR), a light-driven proton pump, complementary information from neutron diffraction, quasi-elastic neutron scattering (QENS) and dielectric spectroscopy will form a comprehensive picture of the structural and dynamic behavior of the PM in the temperature range between 150 and 290 K. Temperature- and humidity-dependent changes in the membrane system influence the accessibility of the different photocycle intermediates of BR. The melting of the 'freezing bound water' between 220 and 250 K could be related to the transition from the M1 to the M2 intermediate, which represents the key step in the photocycle. The dynamic transition in the vicinity of 180 K was shown to be necessary to ensure that the M1 intermediate can be populated and that the melting of crystallized bulk water above 255 K enables the completion of the photocycle.
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Marx D. Proton transfer 200 years after von Grotthuss: insights from ab initio simulations. Chemphyschem 2007; 7:1848-70. [PMID: 16929553 DOI: 10.1002/cphc.200600128] [Citation(s) in RCA: 601] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In the last decade, ab initio simulations and especially Car-Parrinello molecular dynamics have significantly contributed to the improvement of our understanding of both the physical and chemical properties of water, ice, and hydrogen-bonded systems in general. At the heart of this family of in silico techniques lies the crucial idea of computing the many-body interactions by solving the electronic structure problem "on the fly" as the simulation proceeds, which circumvents the need for pre-parameterized potential models. In particular, the field of proton transfer in hydrogen-bonded networks greatly benefits from these technical advances. Here, several systems of seemingly quite different nature and of increasing complexity, such as Grotthuss diffusion in water, excited-state proton-transfer in solution, phase transitions in ice, and protonated water networks in the membrane protein bacteriorhodopsin, are discussed in the realms of a unifying viewpoint.
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Affiliation(s)
- Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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Balashov SP, Ebrey TG. Trapping and Spectroscopic Identification of the Photointermediates of Bacteriorhodopsin at Low Temperatures¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2001)0730453tasiot2.0.co2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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39
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Saitô H, Kawase Y, Kira A, Yamamoto K, Tanio M, Yamaguchi S, Tuzi S, Naito A. Surface and Dynamic Structures of Bacteriorhodopsin in a 2D Crystal, a Distorted or Disrupted Lattice, as Revealed by Site-directed Solid-state 13C NMR†. Photochem Photobiol 2007; 83:253-62. [PMID: 17576344 DOI: 10.1562/2006.06-12-ir-917] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The 3D structure of bacteriorhodopsin (bR) obtained by X-ray diffraction or cryo-electron microscope studies is not always sufficient for a picture at ambient temperature where dynamic behavior is exhibited. For this reason, a site-directed solid-state 13C NMR study of fully hydrated bR from purple membrane (PM), or a distorted or disrupted lattice, is very valuable in order to gain insight into the dynamic picture. This includes the surface structure, at the physiologically important ambient temperature. Almost all of the 13C NMR signals are available from [3-13C]Ala or [1-13C]Val-labeled bR from PM, although the 13C NMR signals from the surface areas, including loops and transmembrane alpha-helices near the surface (8.7 angstroms depth), are suppressed for preparations labeled with [1-13C]Gly, Ala, Leu, Phe, Tyr, etc. due to a failure of the attempted peak-narrowing by making use of the interfered frequency of the frequency of fluctuation motions with the frequency of magic angle spinning. In particular, the C-terminal residues, 226-235, are present as the C-terminal alpha-helix which is held together with the nearby loops to form a surface complex, although the remaining C-terminal residues undergo isotropic motion even in a 2D crystalline lattice (PM) under physiological conditions. Surprisingly, the 13C NMR signals could be further suppressed even from [3-13C]Ala- or [1-13C]Val-bR, due to the acquired fluctuation motions with correlation times in the order of 10(-4) to 10(-5) s, when the 2D lattice structure is instantaneously distorted or completely disrupted, either in photo-intermediate, removed retinal or when embedded in the lipid bilayers.
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Affiliation(s)
- Hazime Saitô
- Department of Life Science, Himeji Institute of Technology, University of Hyogo, Hyogo, Japan.
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40
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Mathias G, Marx D. Structures and spectral signatures of protonated water networks in bacteriorhodopsin. Proc Natl Acad Sci U S A 2007; 104:6980-5. [PMID: 17438299 PMCID: PMC1855365 DOI: 10.1073/pnas.0609229104] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Indexed: 11/18/2022] Open
Abstract
Networks of internal water molecules are thought to provide proton transfer pathways in many enzymatic and photosynthetic reactions. Extremely broad absorption continua observed in recent IR spectroscopic measurements on the photodriven proton pump bacteriorhodopsin (BR) suggest such networks may also serve as proton storage and release sites for these reactions. By combining electronic structure calculations with molecular mechanical force fields, we examine the dynamics and the resulting IR spectra of two protonated water networks, H+.(H2O)3 and H+.(H2O)4, in the release pocket of the initial state of BR, which possibly serve as proton donors to the extracellular surface. For both network sizes, topologically similar structures are found, which are anchored at residues E194 and E204 and stabilized by additional hydrogen bonds from neighboring protein side chains. These protonated water networks assume neither the classic Zundel nor Eigen motives but prefer wire-like topologies. Upon gauging calculated IR spectra of finite clusters with experimental gas-phase data, it is possible to link spectral features computed for these chain-like structures in the initial state of the BR photocycle to the measured absorption continua, in particular for the larger H+.(H2O)4 network. Furthermore, the free energy of proton dislocation along these chains is found to be within the range that is easily accessible at room temperature because of fluctuations.
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Affiliation(s)
- Gerald Mathias
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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41
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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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42
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Sato Y, Hata M, Neya S, Hoshino T. Computational Analysis of the Proton Translocation from Asp96 to Schiff Base in Bacteriorhodopsin. J Phys Chem B 2006; 110:22804-12. [PMID: 17092031 DOI: 10.1021/jp0632081] [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: 11/28/2022]
Abstract
The potential energy change during the M --> N process in bacteriorhodopsin has been evaluated by ab initio quantum chemical and advanced quantum chemical calculations following molecular dynamics (MD) simulations. Many previous experimental studies have suggested that the proton transfer from Asp96 to the Schiff base occurs under the following two conditions: (1) the hydrogen bond between Thr46 and Asp96 breaks and Thr46 is detached from Asp96 and (2) a stable chain of four water molecules spans an area from Asp96 --> Schiff base. In this work, we successfully reproduced the proton-transfer process occurring under these two conditions by molecular dynamics and quantum chemical calculations. The quantum chemical computation revealed that the proton transfer from Asp96 to Shiff base occurs in two-step reactions via an intermediate in which an H(3)O(+) appears around Ala215. The activation energy for the proton transfer in the first reaction was calculated to be 9.7 kcal/mol, which enables fast and efficient proton pump action. Further QM/MM (quantum mechanical/molecular mechanical) and FMO (fragment molecular orbital) calculations revealed that the potential energy change during the proton transfer is tightly regulated by the composition and the geometry of the surrounding amino acid residues of bacteriorhodopsin. Here, we report in detail the Asp96 --> Schiff base proton translocation mechanism of bacteriorhodopsin. Additionally, we discuss the effectiveness of combining quantum chemical calculations with truncated cluster models followed by advanced quantum chemical calculations applied to a whole protein to elucidate its reaction mechanism.
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Affiliation(s)
- Yoshiharu Sato
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan
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44
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Brzezinski P, Adelroth P. Design principles of proton-pumping haem-copper oxidases. Curr Opin Struct Biol 2006; 16:465-72. [PMID: 16842995 DOI: 10.1016/j.sbi.2006.06.012] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2006] [Revised: 06/12/2006] [Accepted: 06/30/2006] [Indexed: 11/20/2022]
Abstract
Transmembrane electrochemical proton gradients are used to store free energy in biological systems, and to drive the synthesis of biomolecules and transmembrane transport. These gradients are maintained by membrane-bound proton transporters that employ free energy provided by, for example, electron transfer or light. In recent years, the structures of several membrane proteins involved in proton translocation have been determined, and indicate that both protein-bound water molecules and protonatable amino acid residues play central roles in transmembrane proton conduction. From these structures, in combination with functional studies, have emerged general principles of proton transfer across membranes and control mechanisms for such reactions, in particular with regard to the electron-transfer-driven proton pump cytochrome c oxidase.
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Affiliation(s)
- Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden.
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45
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Efremov R, Gordeliy VI, Heberle J, Büldt G. Time-resolved microspectroscopy on a single crystal of bacteriorhodopsin reveals lattice-induced differences in the photocycle kinetics. Biophys J 2006; 91:1441-51. [PMID: 16731567 PMCID: PMC1518640 DOI: 10.1529/biophysj.106.083345] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The determination of the intermediate state structures of the bacteriorhodopsin photocycle has lead to an unprecedented level of understanding of the catalytic process exerted by a membrane protein. However, the crystallographic structures of the intermediate states are only relevant if the working cycle is not impaired by the crystal lattice. Therefore, we applied visible and Fourier transform infrared spectroscopy (FTIR) microspectroscopy with microsecond time resolution to compare the photoreaction of a single bacteriorhodopsin crystal to that of bacteriorhodopsin residing in the native purple membrane. The analysis of the FTIR difference spectra of the resolved intermediate states reveals great similarity in structural changes taking place in the crystal and in PM. However, the kinetics of the photocycle are significantly altered in the three-dimensional crystal as compared to PM. Strikingly, the L state decay is accelerated in the crystal, whereas the M decay is delayed. The physical origin of this deviation and the implications for trapping of intermediate states are discussed. As a methodological advance, time-resolved step-scan FTIR spectroscopy on a single protein crystal is demonstrated for the first time which may be used in the future to gauge the functionality of other crystallized proteins with the molecular resolution of vibrational spectroscopy.
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Affiliation(s)
- R Efremov
- Forschungszentrum Jülich, IBI-2: Structural Biology, 52425 Jülich, Germany
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46
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Kessler M, Gottschalk KE, Janovjak H, Muller DJ, Gaub HE. Bacteriorhodopsin Folds into the Membrane against an External Force. J Mol Biol 2006; 357:644-54. [PMID: 16434052 DOI: 10.1016/j.jmb.2005.12.065] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2005] [Revised: 12/15/2005] [Accepted: 12/17/2005] [Indexed: 10/25/2022]
Abstract
Despite their crucial importance for cellular function, little is known about the folding mechanisms of membrane proteins. Recently details of the folding energy landscape were elucidated by atomic force microscope (AFM)-based single molecule force spectroscopy. Upon unfolding and extraction of individual membrane proteins energy barriers in structural elements such as loops and helices were mapped and quantified with the precision of a few amino acids. Here we report on the next logical step: controlled refolding of single proteins into the membrane. First individual bacteriorhodopsin monomers were partially unfolded and extracted from the purple membrane by pulling at the C-terminal end with an AFM tip. Then by gradually lowering the tip, the protein was allowed to refold into the membrane while the folding force was recorded. We discovered that upon refolding certain helices are pulled into the membrane against a sizable external force of several tens of picoNewton. From the mechanical work, which the helix performs on the AFM cantilever, we derive an upper limit for the Gibbs free folding energy. Subsequent unfolding allowed us to analyze the pattern of unfolding barriers and corroborate that the protein had refolded into the native state.
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Affiliation(s)
- Max Kessler
- Chair of Applied Physics and Center for NanoScience, Ludwig-Maximilians Universität, Amalienstrasse 54, 80799 München, Germany
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47
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Quasielastic Neutron Scattering in Biology, Part II: Applications. NEUTRON SCATTERING IN BIOLOGY 2006. [DOI: 10.1007/3-540-29111-3_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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48
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Garczarek F, Gerwert K. Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy. Nature 2005; 439:109-12. [PMID: 16280982 DOI: 10.1038/nature04231] [Citation(s) in RCA: 419] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Accepted: 09/08/2005] [Indexed: 11/09/2022]
Abstract
Much progress has been made in our understanding of water molecule reactions on surfaces, proton solvation in gas-phase water clusters and proton transfer through liquids. Compared with our advanced understanding of these physico-chemical systems, much less is known about individual water molecules and their cooperative behaviour in heterogeneous proteins during enzymatic reactions. Here we use time-resolved Fourier transform infrared spectroscopy (trFTIR) and in situ H2(18)O/H2(16)O exchange FTIR to determine how the membrane protein bacteriorhodopsin uses the interplay among strongly hydrogen-bonded water molecules, a water molecule with a dangling hydroxyl group and a protonated water cluster to transfer protons. The precise arrangement of water molecules in the protein matrix results in a controlled Grotthuss proton transfer, in contrast to the random proton migration that occurs in liquid water. Our findings support the emerging paradigm that intraprotein water molecules are as essential for biological functions as amino acids.
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Affiliation(s)
- Florian Garczarek
- Lehrstuhl für Biophysik, Ruhr-Universität Bochum, D-44780 Bochum, Germany
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49
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Bakker HJ, Gilijamse JJ, Lock AJ. Energy Transfer in Single Hydrogen-Bonded Water Molecules. Chemphyschem 2005; 6:1146-56. [PMID: 15887193 DOI: 10.1002/cphc.200400606] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We study the structure and dynamics of hydrogen-bonded complexes of H2O/HDO and acetone dissolved in carbon tetrachloride by probing the response of the O-H stretching vibrations with linear mid-infrared spectroscopy and femtosecond mid-infrared pump-probe spectroscopy. We find that the hydrogen bonds in these complexes break and reform with a characteristic time scale of approximately 1 ps. These hydrogen-bond dynamics are observed to play an important role in the equilibration of vibrational energy over the two O-H groups of the H2O molecule. For both H2O and HDO, the O-H stretching vibrational excitation relaxes with a time constant of 6.3+/-0.3 ps, and the molecular reorientation has a time constant of 6+/-1 ps.
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Affiliation(s)
- Huib J Bakker
- FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands.
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50
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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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