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Yamashita H, Inoue K, Shibata M, Uchihashi T, Sasaki J, Kandori H, Ando T. Role of trimer-trimer interaction of bacteriorhodopsin studied by optical spectroscopy and high-speed atomic force microscopy. J Struct Biol 2013; 184:2-11. [PMID: 23462099 DOI: 10.1016/j.jsb.2013.02.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 12/22/2012] [Accepted: 02/12/2013] [Indexed: 10/27/2022]
Abstract
Bacteriorhodopsin (bR) trimers form a two-dimensional hexagonal lattice in the purple membrane of Halobacterium salinarum. However, the physiological significance of forming the lattice has long been elusive. Here, we study this issue by comparing properties of assembled and non-assembled bR trimers using directed mutagenesis, high-speed atomic force microscopy (HS-AFM), optical spectroscopy, and a proton pumping assay. First, we show that the bonds formed between W12 and F135 amino acid residues are responsible for trimer-trimer association that leads to lattice assembly; the lattice is completely disrupted in both W12I and F135I mutants. HS-AFM imaging reveals that both crystallized D96N and non-crystallized D96N/W12I mutants undergo a large conformational change (i.e., outward E-F loop displacement) upon light-activation. However, lattice disruption significantly reduces the rate of conformational change under continuous light illumination. Nevertheless, the quantum yield of M-state formation, measured by low-temperature UV-visible spectroscopy, and proton pumping efficiency are unaffected by lattice disruption. From these results, we conclude that trimer-trimer association plays essential roles in providing bound retinal with an appropriate environment to maintain its full photo-reactivity and in maintaining the natural photo-reaction pathway.
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Affiliation(s)
- Hayato Yamashita
- Department of Physics, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
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Rhinow D, Chizhik I, Baumann RP, Noll F, Hampp N. Crystallinity of Purple Membranes Comprising the Chloride-Pumping Bacteriorhodopsin Variant D85T and Its Modulation by pH and Salinity. J Phys Chem B 2010; 114:15424-8. [DOI: 10.1021/jp108502p] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel Rhinow
- Max-Planck-Institute of Biophysics, Department of Structural Biology, Max-von-Laue-Str. 3, D-60438 Frankfurt, Germany, Philipps-University of Marburg, Department of Chemistry, Hans-Meerwein-Str. Bldg. H, D-35032 Marburg, Germany, and Material Sciences Center, D-35032 Marburg, Germany
| | - Ivan Chizhik
- Max-Planck-Institute of Biophysics, Department of Structural Biology, Max-von-Laue-Str. 3, D-60438 Frankfurt, Germany, Philipps-University of Marburg, Department of Chemistry, Hans-Meerwein-Str. Bldg. H, D-35032 Marburg, Germany, and Material Sciences Center, D-35032 Marburg, Germany
| | - Roelf-Peter Baumann
- Max-Planck-Institute of Biophysics, Department of Structural Biology, Max-von-Laue-Str. 3, D-60438 Frankfurt, Germany, Philipps-University of Marburg, Department of Chemistry, Hans-Meerwein-Str. Bldg. H, D-35032 Marburg, Germany, and Material Sciences Center, D-35032 Marburg, Germany
| | - Frank Noll
- Max-Planck-Institute of Biophysics, Department of Structural Biology, Max-von-Laue-Str. 3, D-60438 Frankfurt, Germany, Philipps-University of Marburg, Department of Chemistry, Hans-Meerwein-Str. Bldg. H, D-35032 Marburg, Germany, and Material Sciences Center, D-35032 Marburg, Germany
| | - Norbert Hampp
- Max-Planck-Institute of Biophysics, Department of Structural Biology, Max-von-Laue-Str. 3, D-60438 Frankfurt, Germany, Philipps-University of Marburg, Department of Chemistry, Hans-Meerwein-Str. Bldg. H, D-35032 Marburg, Germany, and Material Sciences Center, D-35032 Marburg, Germany
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El Kirat K, Morandat S, Dufrêne YF. Nanoscale analysis of supported lipid bilayers using atomic force microscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:750-65. [DOI: 10.1016/j.bbamem.2009.07.026] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Revised: 07/17/2009] [Accepted: 07/23/2009] [Indexed: 12/11/2022]
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Sasaki T, Aizawa T, Kamiya M, Kikukawa T, Kawano K, Kamo N, Demura M. Effect of Chloride Binding on the Thermal Trimer−Monomer Conversion of Halorhodopsin in the Solubilized System. Biochemistry 2009; 48:12089-95. [DOI: 10.1021/bi901380c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takanori Sasaki
- Faculty of Life Science, Hokkaido University, Sapporo 060-0810, Japan
- School of Science and Technology, Meiji University, Tama-ku, Kawasaki-shi, Kanagawa 214-8571, Japan
| | - Tomoyasu Aizawa
- Faculty of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Masakatsu Kamiya
- Faculty of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Takashi Kikukawa
- Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Keiichi Kawano
- Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Naoki Kamo
- College of Pharmaceutical Sciences, Matsuyama University, Bunkyo-cho, Matsuyama 790-8578, Japan
| | - Makoto Demura
- Faculty of Life Science, Hokkaido University, Sapporo 060-0810, Japan
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Sasaki T, Kubo M, Kikukawa T, Kamiya M, Aizawa T, Kawano K, Kamo N, Demura M. Halorhodopsin fromNatronomonas pharaonisForms a Trimer Even in the Presence of a Detergent, Dodecyl-β-d-maltoside. Photochem Photobiol 2009; 85:130-6. [DOI: 10.1111/j.1751-1097.2008.00406.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Whitehead TA, Meadows AL, Clark DS. Controlling the self-assembly of a filamentous hyperthermophilic chaperone by an engineered capping protein. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2008; 4:956-960. [PMID: 18576281 DOI: 10.1002/smll.200700848] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- Timothy A Whitehead
- Department of Chemical Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
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7
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Medalsy I, Dgany O, Sowwan M, Cohen H, Yukashevska A, Wolf SG, Wolf A, Koster A, Almog O, Marton I, Pouny Y, Altman A, Shoseyov O, Porath D. SP1 protein-based nanostructures and arrays. NANO LETTERS 2008; 8:473-477. [PMID: 18193911 DOI: 10.1021/nl072455t] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Controlled formation of complex nanostructures is one of the main goals of nanoscience and nanotechnology. Stable Protein 1 (SP1) is a boiling-stable ring protein complex, 11 nm in diameter, which self-assembles from 12 identical monomers. SP1 can be utilized to form large ordered arrays; it can be easily modified by genetic engineering to produce various mutants; it is also capable of binding gold nanoparticles (GNPs) and thus forming protein-GNP chains made of alternating SP1s and GNPs. We report the formation and the protocols leading to the formation of those nanostructures and their characterization by transmission electron microscopy, atomic force microscopy, and electrostatic force microscopy. Further control over the GNP interdistances within the protein-GNP chains may lead to the formation of nanowires and structures that may be useful for nanoelectronics.
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Affiliation(s)
- Izhar Medalsy
- Physical Chemistry Department and Center for Nanoscience and Nanotechnology, The Hebrew University, Jerusalem 91904, Israel
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Sletmoen M, Skjåk-Braek G, Stokke BT. Mapping enzymatic functionalities of mannuronan C-5 epimerases and their modular units by dynamic force spectroscopy. Carbohydr Res 2005; 340:2782-95. [PMID: 16246317 DOI: 10.1016/j.carres.2005.09.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2005] [Revised: 09/26/2005] [Accepted: 09/28/2005] [Indexed: 11/30/2022]
Abstract
Alginates are (1-->4)-linked structural copolyuronans consisting of beta-D-mannuronic acid (M) and its C-5 epimer alpha-L-guluronic acid (G). The residue sequence variation is introduced in a unique postpolymerisation step catalysed by a family of C-5 epimerases named AlgE enzymes. The seven known AlgE's are composed of two modules, designated A and R, present in different number. The molecular details of the structure-function relationship of these seven epimerases, introducing specific residue sequences, are not understood. In this study, single-molecular pair interactions between alginate and AlgE enzymes were investigated using dynamic force spectroscopy. The AlgE enzymes AlgE4 and AlgE6, the recombinant construct PKA1 composed of A- and R-modules from various AlgE's, as well as separate R- and A-modules were studied. The strength of the protein-mannuronan interaction, when applying a loading rate of 0.6 nN/s, varied from 73 pN (AlgE4) to 144 pN (A-module). The determined potential width, that is, the distance from the activation barrier to the bound substrate molecule, was 0.23 nm for AlgE4, 0.19 nm for AlgE6 and 0.1 nm for the A-module. No attraction was observed between the R-module and the substrate. The observations indicate that the A-module contains the substrate binding site and that the R-module modulates the enzyme-substrate binding strength. The observed AlgE4-polymer residence times, two orders of magnitude longer than expected from kcat reported for AlgE4, not observed for PKA1, led us to propose a processive mode of action of AlgE4.
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Affiliation(s)
- Marit Sletmoen
- Biophysics and Medical Technology, Department of Physics, The Norwegian University of Science and Technology, NTNU, NO-7491 Trondheim, Norway
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Cisneros DA, Oesterhelt D, Müller DJ. Probing Origins of Molecular Interactions Stabilizing the Membrane Proteins Halorhodopsin and Bacteriorhodopsin. Structure 2005; 13:235-42. [PMID: 15698567 DOI: 10.1016/j.str.2004.12.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2004] [Revised: 11/30/2004] [Accepted: 12/02/2004] [Indexed: 11/18/2022]
Abstract
Single-molecule atomic force microscopy and spectroscopy were applied to detect molecular interactions stabilizing the structure of halorhodopsin (HR), a light-driven chloride pump from Halobacterium salinarum. Because of the high structural and sequence similarities between HR and bacteriorhodopsin, we compared their unfolding pathways and polypeptide regions that established structurally stable segments against unfolding. Unfolding pathways and structural segments stabilizing the proteins both exhibited a remarkably high similarity. This suggests that different amino acid compositions can establish structurally indistinguishable energetic barriers. These stabilizing domains rather result from comprehensive interactions of all amino acids within a structural region than from specific interactions. However, one additional unfolding barrier located within a short segment of helix E was detected for HR. This barrier correlated with a Pi-bulk interaction, which locally disrupts helix E and divides a structural stabilizing segment.
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Dufrêne YF, Müller DJ. Microbial Surfaces Investigated Using Atomic Force Microscopy. METHODS IN MICROBIOLOGY 2004. [DOI: 10.1016/s0580-9517(04)34006-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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Dufrêne YF. Recent progress in the application of atomic force microscopy imaging and force spectroscopy to microbiology. Curr Opin Microbiol 2003; 6:317-23. [PMID: 12831910 DOI: 10.1016/s1369-5274(03)00058-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Atomic force microscopy imaging and force spectroscopy have recently opened a range of novel applications in microbiology. During the past two years, rapid advances have been made using atomic force microscopy to visualize the surface structure of two-dimensional bacterial protein crystals, biofilms and individual cells in physiological conditions. There has also been remarkable progress in using force spectroscopy to measure biomolecular interactions and physical properties of microbial surfaces. Specific highlights include the imaging and manipulation of membrane proteins at the subnanometer level, the observation of the surface of living cells at high resolution, the mapping of local properties such as surface charges, the measurement of elastic properties of cell-surface constituents and the probing of cellular interactions using functionalized probes.
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Affiliation(s)
- Yves F Dufrêne
- Unité de chimie des interfaces, Université catholique de Louvain, Croix du Sud 2/18, B-1348 Louvain-la-Neuve, Belgium.
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Abstract
Halorhodopsin, a light-driven halide pump, is the second archaeal rhodopsin involved in ion pumping to be studied at high resolution by X-ray crystallography. Like its cousin bacteriorhodopsin, halorhodopsin couples vectorial ion transport to the isomerisation state of a covalently linked retinal. Given the similarity and interconvertability of these two ion pumps, a unified mechanism for ion translocation by archaeal rhodopsins is now emerging.
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Affiliation(s)
- Lars-Oliver Essen
- Department of Chemistry, Philipps University, Hans-Meerwein-Strasse, D-35032 Marburg, Germany.
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Müller DJ, Janovjak H, Lehto T, Kuerschner L, Anderson K. Observing structure, function and assembly of single proteins by AFM. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2002; 79:1-43. [PMID: 12225775 DOI: 10.1016/s0079-6107(02)00009-3] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Single molecule experiments provide insight into the individuality of biological macromolecules, their unique function, reaction pathways, trajectories and molecular interactions. The exceptional signal-to-noise ratio of the atomic force microscope allows individual proteins to be imaged under physiologically relevant conditions at a lateral resolution of 0.5-1nm and a vertical resolution of 0.1-0.2nm. Recently, it has become possible to observe single molecule events using this technique. This capability is reviewed on various water-soluble and membrane proteins. Examples of the observation of function, variability, and assembly of single proteins are discussed. Statistical analysis is important to extend conclusions derived from single molecule experiments to protein species. Such approaches allow the classification of protein conformations and movements. Recent developments of probe microscopy techniques allow simultaneous measurement of multiple signals on individual macromolecules, and greatly extend the range of experiments possible for probing biological systems at the molecular level. Biologists exploring molecular mechanisms will benefit from a burgeoning of scanning probe microscopes and of their future combination with molecular biological experiments.
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Affiliation(s)
- Daniel J Müller
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Pfotenhauer Str. 108, D-01307 Dresden, Germany.
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