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Bedendi G, De Moura Torquato LD, Webb S, Cadoux C, Kulkarni A, Sahin S, Maroni P, Milton RD, Grattieri M. Enzymatic and Microbial Electrochemistry: Approaches and Methods. ACS MEASUREMENT SCIENCE AU 2022; 2:517-541. [PMID: 36573075 PMCID: PMC9783092 DOI: 10.1021/acsmeasuresciau.2c00042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 06/17/2023]
Abstract
The coupling of enzymes and/or intact bacteria with electrodes has been vastly investigated due to the wide range of existing applications. These span from biomedical and biosensing to energy production purposes and bioelectrosynthesis, whether for theoretical research or pure applied industrial processes. Both enzymes and bacteria offer a potential biotechnological alternative to noble/rare metal-dependent catalytic processes. However, when developing these biohybrid electrochemical systems, it is of the utmost importance to investigate how the approaches utilized to couple biocatalysts and electrodes influence the resulting bioelectrocatalytic response. Accordingly, this tutorial review starts by recalling some basic principles and applications of bioelectrochemistry, presenting the electrode and/or biocatalyst modifications that facilitate the interaction between the biotic and abiotic components of bioelectrochemical systems. Focus is then directed toward the methods used to evaluate the effectiveness of enzyme/bacteria-electrode interaction and the insights that they provide. The basic concepts of electrochemical methods widely employed in enzymatic and microbial electrochemistry, such as amperometry and voltammetry, are initially presented to later focus on various complementary methods such as spectroelectrochemistry, fluorescence spectroscopy and microscopy, and surface analytical/characterization techniques such as quartz crystal microbalance and atomic force microscopy. The tutorial review is thus aimed at students and graduate students approaching the field of enzymatic and microbial electrochemistry, while also providing a critical and up-to-date reference for senior researchers working in the field.
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Affiliation(s)
- Giada Bedendi
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | | | - Sophie Webb
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Cécile Cadoux
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Amogh Kulkarni
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Selmihan Sahin
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Plinio Maroni
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Ross D. Milton
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Matteo Grattieri
- Dipartimento
di Chimica, Università degli Studi
di Bari “Aldo Moro”, via E. Orabona 4, Bari 70125, Italy
- IPCF-CNR
Istituto per i Processi Chimico Fisici, Consiglio Nazionale delle Ricerche, via E. Orabona 4, Bari 70125, Italy
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2
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Imaging and Force Spectroscopy of Single Transmembrane Proteins with the Atomic Force Microscope. Methods Mol Biol 2020. [PMID: 31218616 DOI: 10.1007/978-1-4939-9512-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The atomic force microscope (AFM) has opened avenues and provided opportunities to investigate biological soft matter and processes ranging from nanometer (nm) to millimeter (mm). The high temporal (millisecond) and spatial (nanometer) resolutions of the AFM are suited for studying many biological processes in their native conditions. The AFM cantilever-aptly termed as a "lab on a tip"-can be used as an imaging tool as well as a handle to manipulate single bonds and proteins. Recent examples have convincingly established AFM as a tool to study the mechanical properties and monitor processes of single proteins and cells with high sensitivity, thus affording insight into important mechanistic details. This chapter specifically focuses on practical and analytical protocols of single-molecule AFM methodologies related to high-resolution imaging and single-molecule force spectroscopy of transmembrane proteins in a lipid bilayer (reconstituted or native). Both these techniques are operator oriented, and require specialized working knowledge of the instrument, theory and practical skills.
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3
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Robson T, Shah DSH, Solovyova AS, Lakey JH. Modular Protein Engineering Approach to the Functionalization of Gold Nanoparticles for Use in Clinical Diagnostics. ACS APPLIED NANO MATERIALS 2018; 1:3590-3599. [PMID: 30101217 PMCID: PMC6083416 DOI: 10.1021/acsanm.8b00737] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 06/28/2018] [Indexed: 05/21/2023]
Abstract
Functional protein-gold nanoparticle (AuNP) conjugates have a wide variety of applications including biosensing and drug delivery. Correct protein orientation, which is important to maintain functionality on the nanoparticle surface, can be difficult to achieve in practice, and dedicated protein scaffolds have been used on planar gold surfaces to drive the self-assembly of oriented protein arrays. Here we use the transmembrane domain of Escherichia coli outer membrane protein A (OmpATM) to create protein-AuNP conjugates. The addition of a single cysteine residue into a periplasmic loop, to create cysOmpATM, drives oriented assembly and increased equilibrium binding. As the protein surface concentration increases, the sulfur-gold bond in cysOmpATM creates a more densely populated AuNP surface than the poorly organized wtOmpATM layer. The functionalization of AuNP improved both their stability and homogeneity. This was further exploited using multidomain protein chimeras, based on cysOmpATM, which were shown to form ordered protein arrays with their functional domains displayed away from the AuNP surface. A fusion with protein G was shown to specifically bind antibodies via their Fc region. Next, an in vitro selected single chain antibody (scFv)-cysOmpATM fusion protein, bound to AuNP, detected influenza A nucleoprotein, a widely used antigen in diagnostic assays. Finally, using the same scFv-cysOmpATM-AuNP conjugates, a prototype lateral flow assay for influenza demonstrated the utility of fully recombinant self-assembling sensor layers. By simultaneously removing the need for both animal antibodies and a separate immobilization procedure, this technology could greatly simplify the development of a range of in vitro diagnostics.
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Affiliation(s)
- Timothy Robson
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle
upon Tyne NE2 4HH, U.K.
| | - Deepan S. H. Shah
- Orla
Protein Technologies Ltd., Biosciences Centre, International Centre for Life, Times Square, Newcastle upon Tyne NE1 4EP, U.K.
| | - Alexandra S. Solovyova
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle
upon Tyne NE2 4HH, U.K.
| | - Jeremy H. Lakey
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle
upon Tyne NE2 4HH, U.K.
- E-mail:
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4
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Sidhu A, Ristic D, Sánchez H, Wyman C. The Recombination Mediator BRCA2: Architectural Plasticity of Recombination Intermediates Revealed by Single-Molecule Imaging (SFM/TIRF). Methods Enzymol 2018; 600:347-374. [DOI: 10.1016/bs.mie.2017.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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5
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Lettieri R, Di Giorgio F, Colella A, Magnusson R, Bjorefors F, Placidi E, Palleschi A, Venanzi M, Gatto E. DPPTE Thiolipid Self-Assembled Monolayer: A Critical Assay. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:11560-11572. [PMID: 27689538 DOI: 10.1021/acs.langmuir.6b01912] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Supported lipid membranes represent an elegant way to design a fluid interface able to mimic the physicochemical properties of biological membranes, with potential biotechnological applications. In this work, a diacyl phospholipid, the 1,2-dipalmitoyl-sn-glycero-3-phosphothioethanol (DPPTE), functionalized with a thiol group, was immobilized on a gold surface. In this molecule, the thiol group, responsible for the Au-S bond (45 kJ/mol) is located on the phospholipid polar head, letting the hydrophobic chain protrude from the film. This system is widely used in the literature but is no less challenging, since its characterization is not complete, as several discordant data have been obtained. In this work, the film was characterized by cyclic voltammetry blocking experiments, to verify the SAM formation, and by reductive desorption measurements, to estimate the molecular density of DPPTE on the gold surface. This value has been compared to that obtained by quartz crystal microbalance measurements. Ellipsometry and impedance spectroscopy measurements have been performed to obtain information about the monolayer thickness and capacitance. The film morphology was investigated by atomic force microscopy. Finally, Monte Carlo simulations were carried out, in order to gain molecular information about the morphologies of the DPPTE SAM and compare them to the experimental results. We demonstrate that DPPTE molecules, incubated 18 h below the phase transition temperature (T = 41.1 ± 0.4 °C) in ethanol solution, are able to form a self-assembled monolayer on the gold surface, with domain structures of different order, which have never been reported before. Our results make possible rationalization of the scattered results so far obtained on this system, giving a new insight into the formation of phospholipids SAMs on a gold surface.
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Affiliation(s)
- Raffaella Lettieri
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata , 00133 Rome, Italy
| | - Floriana Di Giorgio
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata , 00133 Rome, Italy
| | - Alessandra Colella
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata , 00133 Rome, Italy
| | - Roger Magnusson
- Department of Physics, Chemistry and Biology (IFM), University of Linköping , 581 83 Linköping, Sweden
| | - Fredrik Bjorefors
- Ångström Laboratory, Department of Chemistry, Uppsala University , Box 538, SE-75121 Uppsala, Sweden
| | - Ernesto Placidi
- Institute of Structure of Matter, CNR, Department of Physics, University of Rome Tor Vergata , 00133 Rome, Italy
| | - Antonio Palleschi
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata , 00133 Rome, Italy
| | - Mariano Venanzi
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata , 00133 Rome, Italy
| | - Emanuela Gatto
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata , 00133 Rome, Italy
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6
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Pissinis DE, Diaz C, Maza E, Bonini IC, Barrantes FJ, Salvarezza RC, Schilardi PL. Functional nicotinic acetylcholine receptor reconstitution in Au(111)-supported thiolipid monolayers. NANOSCALE 2015; 7:15789-15797. [PMID: 26355753 DOI: 10.1039/c5nr04109k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The insertion and function of the muscle-type nicotinic acetylcholine receptor (nAChR) in Au(111)-supported thiolipid self-assembled monolayers have been studied by atomic force microscopy (AFM), surface plasmon resonance (SPR), and electrochemical techniques. It was possible for the first time to resolve the supramolecular arrangement of the protein spontaneously inserted in a thiolipid monolayer in an aqueous solution. Geometric supramolecular arrays of nAChRs were observed, most commonly in a triangular form compatible with three nAChR dimers of ∼20 nm each. Addition of the full agonist carbamoylcholine activated and opened the nAChR ion channel, as revealed by the increase in capacitance relative to that of the nAChR-thiolipid system under basal conditions. Thus, the self-assembled system appears to be a viable biomimetic model to measure ionic conductance mediated by ion-gated ion channels under different experimental conditions, with potential applications in biotechnology and pharmacology.
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Affiliation(s)
- Diego E Pissinis
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), CONICET - Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CC16, Suc. 4, La Plata, Buenos Aires, Argentina.
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7
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Chada N, Sigdel KP, Gari RRS, Matin TR, Randall LL, King GM. Glass is a Viable Substrate for Precision Force Microscopy of Membrane Proteins. Sci Rep 2015; 5:12550. [PMID: 26228793 PMCID: PMC4521160 DOI: 10.1038/srep12550] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 07/02/2015] [Indexed: 12/01/2022] Open
Abstract
Though ubiquitous in optical microscopy, glass has long been overlooked as a specimen supporting surface for high resolution atomic force microscopy (AFM) investigations due to its roughness. Using bacteriorhodopsin from Halobacterium salinarum and the translocon SecYEG from Escherichia coli, we demonstrate that faithful images of 2D crystalline and non-crystalline membrane proteins in lipid bilayers can be obtained on microscope cover glass following a straight-forward cleaning procedure. Direct comparison between AFM data obtained on glass and on mica substrates show no major differences in image fidelity. Repeated association of the ATPase SecA with the cytoplasmic protrusion of SecYEG demonstrates that the translocon remains competent for binding after tens of minutes of continuous AFM imaging. This opens the door for precision long-timescale investigations of the active translocase in near-native conditions and, more generally, for integration of high resolution biological AFM with many powerful optical techniques that require non-birefringent substrates.
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Affiliation(s)
- Nagaraju Chada
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, Missouri 65211 USA
| | - Krishna P Sigdel
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, Missouri 65211 USA
| | | | - Tina Rezaie Matin
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, Missouri 65211 USA
| | - Linda L Randall
- Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri 65211 USA
| | - Gavin M King
- 1] Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, Missouri 65211 USA [2] Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri 65211 USA
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8
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Sun W, Kewalramani S, Hujsak K, Zhang H, Bedzyk MJ, Dravid VP, Thaxton CS. Mesophase in a thiolate-containing diacyl phospholipid self-assembled monolayer. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:3232-3241. [PMID: 25695627 DOI: 10.1021/la504822q] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Maintaining the intrinsic features of mesophases is critically important when employing phospholipid self-assemblies to mimic biomembranes. Inorganic solid surfaces provide platforms to support, guide, and analyze organic self-assemblies but impose upon them a tendency to form well-ordered phases not often found in biomembranes. To address this, we measured mesophase formation in a thiolate self-assembled monolayer (SAM) of diacyl phospholipid, 1,2-dipalmitoyl-sn-glycero-3-phosphothioethanol (DPPTE) on Au(111), and provide thermodynamic analysis on the mixing behavior of inequivalent DPPTE acyl chains. Our work has uncovered three fundamental issues that enable mesophase formation: (1) Elimination of templating effects of the solid surface, (2) Weakening intermolecular and molecule-substrate interactions in adsorbates, and (3) Equilibrium through entropy-driven self-assembly. Thus, our work provides a more holistic understanding of phase behavior, from liquid phases to mesophases to highly crystalline phases, in organic self-assemblies on solid surfaces, which may extend their applications in nanodevices and to the wider fields of biology and medicine.
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Affiliation(s)
- Wangqiang Sun
- †Department of Urology, Feinberg School of Medicine, Northwestern University, 303 East Chicago Avenue, Chicago, Illinois 60611, United States
- §Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior, Chicago, Illinois 60611, United States
- #Hubei Provincial Key Laboratory of Green Materials for Light Industry, Hubei University of Technology, Wuhan 430068, China
| | - Sumit Kewalramani
- ∥Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States
| | - Karl Hujsak
- ∥Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States
| | - Heng Zhang
- †Department of Urology, Feinberg School of Medicine, Northwestern University, 303 East Chicago Avenue, Chicago, Illinois 60611, United States
- §Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior, Chicago, Illinois 60611, United States
| | - Michael J Bedzyk
- ∥Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States
- ⊥Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Vinayak P Dravid
- ∥Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States
| | - C Shad Thaxton
- †Department of Urology, Feinberg School of Medicine, Northwestern University, 303 East Chicago Avenue, Chicago, Illinois 60611, United States
- §Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior, Chicago, Illinois 60611, United States
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9
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Le Brun AP, Soliakov A, Shah DSH, Holt SA, McGill A, Lakey JH. Engineered self-assembling monolayers for label free detection of influenza nucleoprotein. Biomed Microdevices 2015; 17:9951. [PMID: 25860669 PMCID: PMC4392172 DOI: 10.1007/s10544-015-9951-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Integrating nanotechnology into useable devices requires a combination of bottom up and top down methodology. Often the techniques to measure and control these different components are entirely different, so methods that can analyse the nanoscale component in situ are of increasing importance. Here we describe a strategy that employs a self-assembling monolayer of engineered protein chimeras to display an array of oriented antibodies (IgG) on a microelectronic device for the label free detection of influenza nucleoprotein. The structural and functional properties of the bio-interface were characterised by a range of physical techniques including surface plasmon resonance, quartz-crystal microbalance and neutron reflectometry. This combination of methods reveals a 13.5 nm thick engineered-monolayer that (i) self-assembles on gold surfaces, (ii) captures IgG with high affinity in a defined orientation and (iii) specifically recognises the influenza A nucleoprotein. Furthermore we also show that this non-covalent self-assembled structure can render the dissociation of bound IgG irreversible by chemical crosslinking in situ without affecting the IgG function. The methods can thus describe in detail the transition from soluble engineered molecules with nanometre dimensions to an array that demonstrates the principles of a working influenza sensor.
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Affiliation(s)
- Anton P. Le Brun
- />Bragg Institute, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232 Australia
| | - Andrei Soliakov
- />Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH UK
- />Fujifilm Diosynth, Belasis Avenue, Billingham, Cleveland TS23 1LH UK
| | - Deepan S. H. Shah
- />Orla Protein Technologies Ltd, Biosciences Centre, International Centre for Life, Times Square, Newcastle upon Tyne, NE1 4EP UK
| | - Stephen A. Holt
- />Bragg Institute, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232 Australia
| | - Alison McGill
- />Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH UK
- />Fujifilm Diosynth, Belasis Avenue, Billingham, Cleveland TS23 1LH UK
| | - Jeremy H. Lakey
- />Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH UK
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10
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Arunmanee W, Harris JR, Lakey JH. Outer membrane protein F stabilised with minimal amphipol forms linear arrays and LPS-dependent 2D crystals. J Membr Biol 2014; 247:949-56. [PMID: 24585057 PMCID: PMC4196048 DOI: 10.1007/s00232-014-9640-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 02/11/2014] [Indexed: 11/30/2022]
Abstract
Amphipols (APol) are polymers which can solubilise and stabilise membrane proteins (MP) in aqueous solutions. In contrast to conventional detergents, APol are able to keep MP soluble even when the free APol concentration is very low. Outer membrane protein F (OmpF) is the most abundant MP commonly found in the outer membrane (OM) of Escherichia coli. It plays a vital role in the transport of hydrophilic nutrients, as well as antibiotics, across the OM. In the present study, APol was used to solubilise OmpF to characterize its interactions with molecules such as lipopolysaccharides (LPS) or colicins. OmpF was reconstituted into APol by the removal of detergents using Bio-Beads followed by size-exclusion chromatography (SEC) to remove excess APol. OmpF/APol complexes were then analysed by SEC, dynamic light scattering (DLS) and transmission electron microscopy (TEM). TEM showed that in the absence of free APol-OmpF associated as long filaments with a thickness of ~6 nm. This indicates that the OmpF trimers lie on their sides on the carbon EM grid and that they also favour side by side association. The formation of filaments requires APol and occurs very rapidly. Addition of LPS to OmpF/APol complexes impeded filament formation and the trimers form 2D sheets which mimic the OM. Consequently, free APol is undoubtedly required to maintain the homogeneity of OmpF in solutions, but 'minimum APol' provides a new phase, which can allow weaker protein-protein and protein-lipid interactions characteristic of native membranes to take place and thus control 1D-2D crystallisation.
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Affiliation(s)
- Wanatchaporn Arunmanee
- Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
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11
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Le Brun A, Clifton LA, Halbert CE, Lin B, Meron M, Holden PJ, Lakey JH, Holt SA. Structural characterization of a model gram-negative bacterial surface using lipopolysaccharides from rough strains of Escherichia coli. Biomacromolecules 2013; 14:2014-22. [PMID: 23617615 PMCID: PMC3679557 DOI: 10.1021/bm400356m] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 04/18/2013] [Indexed: 12/29/2022]
Abstract
Lipopolysaccharides (LPS) make up approximately 75% of the Gram-negative bacterial outer membrane (OM) surface, but because of the complexity of the molecule, there are very few model OMs that include LPS. The LPS molecule consists of lipid A, which anchors the LPS within the OM, a core polysaccharide region, and a variable O-antigen polysaccharide chain. In this work we used RcLPS (consisting of lipid A plus the first seven sugars of the core polysaccharide) from a rough strain of Escherichia coli to form stable monolayers of LPS at the air-liquid interface. The vertical structure RcLPS monolayers were characterized using neutron and X-ray reflectometry, while the lateral structure was investigated using grazing incidence X-ray diffraction and Brewster angle microscopy. It was found that RcLPS monolayers at surface pressures of 20 mN m(-1) and above are resolved as hydrocarbon tails, an inner headgroup, and an outer headgroup of polysaccharide with increasing solvation from tails to outer headgroups. The lateral organization of the hydrocarbon lipid chains displays an oblique hexagonal unit cell at all surface pressures, with only the chain tilt angle changing with surface pressure. This is in contrast to lipid A, which displays hexagonal or, above 20 mN m(-1), distorted hexagonal packing. This work provides the first complete structural analysis of a realistic E. coli OM surface model.
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Affiliation(s)
- Anton
P. Le Brun
- Bragg Institute, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Luke A. Clifton
- ISIS Neutron Facility, STFC Rutherford
Appleton Laboratory, Didcot, Oxfordshire
OX11 0QX, United Kingdom
| | - Candice E. Halbert
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37831, United States
| | - Binhua Lin
- Consortium
of Advanced Radiation
Sources (CARS), University of Chicago,
Chicago, Illinois 60637, United States
| | - Mati Meron
- Consortium
of Advanced Radiation
Sources (CARS), University of Chicago,
Chicago, Illinois 60637, United States
| | - Peter J. Holden
- Bragg Institute, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Jeremy H. Lakey
- Institute for Cell and Molecular
Biosciences, Newcastle University, Framlington
Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Stephen A. Holt
- Bragg Institute, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
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12
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Sapra KT. Atomic force microscopy and spectroscopy to probe single membrane proteins in lipid bilayers. Methods Mol Biol 2013; 974:73-110. [PMID: 23404273 DOI: 10.1007/978-1-62703-275-9_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The atomic force microscope (AFM) has opened vast avenues hitherto inaccessible to the biological scientist. The high temporal (millisecond) and spatial (nanometer) resolutions of the AFM are suited for studying many biological processes in their native conditions. The AFM cantilever stylus is aptly termed as a "lab on a tip" owing to its versatility as an imaging tool as well as a handle to manipulate single bonds and proteins. Recent examples assert that the AFM can be used to study the mechanical properties and monitor processes of single proteins and single cells, thus affording insight into important mechanistic details. This chapter specifically focuses on practical and analytical protocols of single-molecule AFM methodologies related to high-resolution imaging and single-molecule force spectroscopy of membrane proteins. Both these techniques are operator oriented, and require specialized working knowledge of the instrument, theoretical, and practical skills.
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Affiliation(s)
- K Tanuj Sapra
- Department of Chemistry, University of Oxford, Oxford, UK.
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13
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Clifton LA, Johnson CL, Solovyova AS, Callow P, Weiss KL, Ridley H, Le Brun AP, Kinane CJ, Webster JRP, Holt SA, Lakey JH. Low resolution structure and dynamics of a colicin-receptor complex determined by neutron scattering. J Biol Chem 2011; 287:337-346. [PMID: 22081604 PMCID: PMC3249085 DOI: 10.1074/jbc.m111.302901] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Proteins that translocate across cell membranes need to overcome a significant hydrophobic barrier. This is usually accomplished via specialized protein complexes, which provide a polar transmembrane pore. Exceptions to this include bacterial toxins, which insert into and cross the lipid bilayer itself. We are studying the mechanism by which large antibacterial proteins enter Escherichia coli via specific outer membrane proteins. Here we describe the use of neutron scattering to investigate the interaction of colicin N with its outer membrane receptor protein OmpF. The positions of lipids, colicin N, and OmpF were separately resolved within complex structures by the use of selective deuteration. Neutron reflectivity showed, in real time, that OmpF mediates the insertion of colicin N into lipid monolayers. This data were complemented by Brewster Angle Microscopy images, which showed a lateral association of OmpF in the presence of colicin N. Small angle neutron scattering experiments then defined the three-dimensional structure of the colicin N-OmpF complex. This revealed that colicin N unfolds and binds to the OmpF-lipid interface. The implications of this unfolding step for colicin translocation across membranes are discussed.
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Affiliation(s)
- Luke A Clifton
- ISIS Spallation Neutron Source, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - Christopher L Johnson
- Institute for Cell and Molecular Biosciences, The Medical School, University of Newcastle, Framlington Place, Newcastle-upon-Tyne NE2 4HH, United Kingdom
| | - Alexandra S Solovyova
- Institute for Cell and Molecular Biosciences, The Medical School, University of Newcastle, Framlington Place, Newcastle-upon-Tyne NE2 4HH, United Kingdom
| | - Phil Callow
- Partnership for Structural Biology, Institut Laue Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | - Kevin L Weiss
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Helen Ridley
- Institute for Cell and Molecular Biosciences, The Medical School, University of Newcastle, Framlington Place, Newcastle-upon-Tyne NE2 4HH, United Kingdom
| | - Anton P Le Brun
- Institute for Cell and Molecular Biosciences, The Medical School, University of Newcastle, Framlington Place, Newcastle-upon-Tyne NE2 4HH, United Kingdom
| | - Christian J Kinane
- ISIS Spallation Neutron Source, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - John R P Webster
- ISIS Spallation Neutron Source, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - Stephen A Holt
- ISIS Spallation Neutron Source, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - Jeremy H Lakey
- Institute for Cell and Molecular Biosciences, The Medical School, University of Newcastle, Framlington Place, Newcastle-upon-Tyne NE2 4HH, United Kingdom.
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14
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Le Brun AP, Holt SA, Shah DS, Majkrzak CF, Lakey JH. The structural orientation of antibody layers bound to engineered biosensor surfaces. Biomaterials 2011; 32:3303-11. [DOI: 10.1016/j.biomaterials.2011.01.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Accepted: 01/08/2011] [Indexed: 10/18/2022]
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15
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Engel A. Imaging and interrogating native membrane proteins using the atomic force microscope. Methods Mol Biol 2011; 736:153-167. [PMID: 21660727 DOI: 10.1007/978-1-61779-105-5_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Membrane proteins exist in a lipid bilayer and provide for cell-cell communication, transport solutes, and convert energies. Detergents are used to extract membrane proteins and keep them in solution for purification and subsequent analyses. The atomic force microscope (AFM) is a powerful tool for imaging and manipulating membrane proteins in their native state without the necessity to solubilize them. It allows membranes that are adsorbed to flat solid supports to be raster-scanned in physiological solutions with an atomically sharp tip. Therefore, AFM is capable of observing biological molecular machines at work. Superb images of native membranes have been recorded, and a quantitative interpretation of the data acquired using the AFM tip has become possible. In addition, multifunctional probes to simultaneously acquire information on the topography and electrical properties of membrane proteins have been produced. This progress is discussed here and fosters expectations for future developments and applications of AFM and single-molecule force spectroscopy.
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Affiliation(s)
- Andreas Engel
- Maurice E. Müller Institute for Structural Biology, Biozentrum, University of Basel, Basel, Switzerland.
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16
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Cooke MJ, Zahir T, Phillips SR, Shah DSH, Athey D, Lakey JH, Shoichet MS, Przyborski SA. Neural differentiation regulated by biomimetic surfaces presenting motifs of extracellular matrix proteins. J Biomed Mater Res A 2010; 93:824-32. [PMID: 19653304 DOI: 10.1002/jbm.a.32585] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The interaction between cells and the extracellular matrix (ECM) is essential during development. To elucidate the function of ECM proteins on cell differentiation, we developed biomimetic surfaces that display specific ECM peptide motifs in a controlled manner. Presentation of ECM domains for collagen, fibronectin, and laminin influenced the formation of neurites by differentiating PC12 cells. The effect of these peptide sequences was also tested on the development of adult neural stem/progenitor cells. In this system, collagen I and fibronectin induced the formation of beta-III-tubulin positive cells, whereas collagen IV reduced such differentiation. Biomimetic surfaces composed of multiple peptide types enabled the combinatorial effects of various ECM motifs to be studied. Surfaces displaying combined motifs were often predictable as a result of the synergistic effects of ECM peptides studied in isolation. For example, the additive effects of fibronectin and laminin resulted in greater expression of beta-III-tubulin positive cells, whereas the negative effect of the collagen IV domain was canceled out by coexpression of collagen I. However, simultaneous expression of certain ECM domains was less predictable. These data highlight the complexity of the cellular response to combined ECM signals and the need to study the function of ECM domains individually and in combination.
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Affiliation(s)
- M J Cooke
- North East England Stem Cell Institute (NESCI), School of Biological and Biomedical Science, University of Durham, South Road, Durham DH1 3LE, United Kingdom
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17
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Lakey JH. Neutrons for biologists: a beginner's guide, or why you should consider using neutrons. J R Soc Interface 2009; 6 Suppl 5:S567-73. [PMID: 19656821 DOI: 10.1098/rsif.2009.0156.focus] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
From the structures of isolated protein complexes to the molecular dynamics of whole cells, neutron methods can achieve a resolution in complex systems that is inaccessible to other techniques. Biology is fortunate in that it is rich in water and hydrogen, and this allows us to exploit the differential sensitivity of neutrons to this element and its major isotope, deuterium. Furthermore, neutrons exhibit wave properties that allow us to use them in similar ways to light, X-rays and electrons. This review aims to explain the basics of biological neutron science to encourage its greater use in solving difficult problems in the life sciences.
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Affiliation(s)
- Jeremy H Lakey
- Institute for Cell and Molecular Biosciences, University of Newcastle, Framlington Place, Newcastle-upon-Tyne NE2 4HH, UK.
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18
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Shinozaki Y, Sumitomo K, Tsuda M, Koizumi S, Inoue K, Torimitsu K. Direct observation of ATP-induced conformational changes in single P2X(4) receptors. PLoS Biol 2009; 7:e1000103. [PMID: 19419241 PMCID: PMC2675908 DOI: 10.1371/journal.pbio.1000103] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Accepted: 03/19/2009] [Indexed: 12/04/2022] Open
Abstract
The ATP-gated P2X4 receptor is a cation channel, which is important in various pathophysiological events. The architecture of the P2X4 receptor in the activated state and how to change its structure in response to ATP binding are not fully understood. Here, we analyze the architecture and ATP-induced structural changes in P2X4 receptors using fast-scanning atomic force microscopy (AFM). AFM images of the membrane-dissociated and membrane-inserted forms of P2X4 receptors and a functional analysis revealed that P2X4 receptors have an upward orientation on mica but lean to one side. Time-lapse imaging of the ATP-induced structural changes in P2X4 receptors revealed two different forms of activated structures under 0 Ca2+ conditions, namely a trimer structure and a pore dilation-like tripartite structure. A dye uptake measurement demonstrated that ATP-activated P2X4 receptors display pore dilation in the absence of Ca2+. With Ca2+, the P2X4 receptors exhibited only a disengaged trimer and no dye uptake was observed. Thus our data provide a new insight into ATP-induced structural changes in P2X4 receptors that correlate with pore dynamics. ATP is not only a source of intracellular energy but can act as an intercellular signal by binding membrane receptors. Purinergic receptors, which bind with nucleotides including ATP are known as P2 receptors and are divided into two types: ion channel-type P2X receptors and metabotropic-type P2Y receptors. P2X receptors are thought to undergo conformational changes in response to ATP binding, leading to the opening of transmembrane channels, through which cations enter the cells. A growing body of evidence shows that P2X receptors control various physiological and pathophysiological cellular responses. However, the receptor structure and the conformational changes it experiences upon stimulation remained to be clarified. Here, we employed an atomic force microscope (AFM) to observe P2X receptor behavior at the single channel level. We chose to analyze the P2X4 receptor, because it is known to increase the transmembrane pore size (i.e., pore dilation) in the absence of extracellular calcium. Activated P2X4 receptor exhibited a trimeric topology with a pore-like structure in the center. When calcium was present the receptor exhibited a trimer without a pore structure at its center. These structural changes corresponded well with the changes of ion permeability of P2X4 receptor. Fast-scanning atomic force microscopy reveals the topology, ATP-induced conformational changes, and Ca2+ regulation of the pore-opening in P2X4 receptors.
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19
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Atomic force microscopy of biological membranes. Biophys J 2009; 96:329-38. [PMID: 19167286 DOI: 10.1016/j.bpj.2008.09.046] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Accepted: 09/15/2008] [Indexed: 11/21/2022] Open
Abstract
Atomic force microscopy (AFM) is an ideal method to study the surface topography of biological membranes. It allows membranes that are adsorbed to flat solid supports to be raster-scanned in physiological solutions with an atomically sharp tip. Therefore, AFM is capable of observing biological molecular machines at work. In addition, the tip can be tethered to the end of a single membrane protein, and forces acting on the tip upon its retraction indicate barriers that occur during the process of protein unfolding. Here we discuss the fundamental limitations of AFM determined by the properties of cantilevers, present aspects of sample preparation, and review results achieved on reconstituted and native biological membranes.
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20
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Strategies to prepare and characterize native membrane proteins and protein membranes by AFM. Curr Opin Colloid Interface Sci 2008. [DOI: 10.1016/j.cocis.2007.09.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Monitoring the assembly of antibody-binding membrane protein arrays using polarised neutron reflection. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 37:639-45. [DOI: 10.1007/s00249-008-0291-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2007] [Revised: 02/01/2008] [Accepted: 02/11/2008] [Indexed: 10/22/2022]
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22
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Chaffey BT, Mitchell E, Birch MA, Lakey JH. A generic expression system to produce proteins that co-assemble with alkane thiol SAM. Int J Nanomedicine 2008; 3:287-93. [PMID: 18990938 PMCID: PMC2626940 DOI: 10.2147/ijn.s2655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Surface biology aims to observe and control biological processes by combining bio-, surface, and physical chemistry. Self-assembled monolayers (SAM) on gold surfaces have provided excellent methods for nanoscale surface preparation for such studies. However, extension of this work requires the specific immobilization of whole protein domains and the direct incorporation of recombinant proteins into SAM is still problematic. In this study a short random coil peptide has been designed to insert into thioalkane layers by formation of a hydrophobic helix. Surface plasmon resonance (SPR) studies show that specific immobilization via the internal cysteine is achieved. Addition of the peptide sequence to the terminus of a protein at the genetic level enables the production of a range of recombinant fusion-proteins with good yield. SPR shows that the proteins display the same gold-binding behavior as the peptide. It is shown that cell growth control can be achieved by printing the proteins using soft lithography with subsequent infilling with thio-alkanes The expression plasmid is constructed so that any stable protein domain can be easily cloned, expressed, purified and immobilized.
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Affiliation(s)
| | | | - Mark A Birch
- The School of Surgical and Reproductive Sciences, The Medical School, Framlington Place, The University of Newcastle-upon-Tyne, Newcastle-upon-Tyne, Great Britain
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Shah DS, Thomas MB, Phillips S, Cisneros DA, Le Brun AP, Holt SA, Lakey JH. Self-assembling layers created by membrane proteins on gold. Biochem Soc Trans 2007; 35:522-6. [PMID: 17511643 DOI: 10.1042/bst0350522] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Membrane systems are based on several types of organization. First, amphiphilic lipids are able to create monolayer and bilayer structures which may be flat, vesicular or micellar. Into these structures membrane proteins can be inserted which use the membrane to provide signals for lateral and orientational organization. Furthermore, the proteins are the product of highly specific self-assembly otherwise known as folding, which mostly places individual atoms at precise places in three dimensions. These structures all have dimensions in the nanoscale, except for the size of membrane planes which may extend for millimetres in large liposomes or centimetres on planar surfaces such as monolayers at the air/water interface. Membrane systems can be assembled on to surfaces to create supported bilayers and these have uses in biosensors and in electrical measurements using modified ion channels. The supported systems also allow for measurements using spectroscopy, surface plasmon resonance and atomic force microscopy. By combining the roles of lipids and proteins, highly ordered and specific structures can be self-assembled in aqueous solution at the nanoscale.
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Affiliation(s)
- D S Shah
- Orla Protein Technologies Ltd, Nanotechnology Centre, Newcastle upon Tyne NE1 7RU, UK
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