1
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Mimura H, Osaki T, Takamori S, Nakao K, Takeuchi S. Lipid Bilayer Reformation Using the Wiping Blade for Improved Ion Channel Analysis. Anal Chem 2023; 95:17354-17361. [PMID: 37968939 DOI: 10.1021/acs.analchem.3c03707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
The measurement of ion permeation activity across planar lipid bilayers is a useful technique for the functional analysis and drug evaluation of ion channels at the single-molecule level. To enhance the data throughput, parallelization of lipid bilayers is desirable. However, existing parallelized approaches face challenges in simultaneously and efficiently measuring ion channel activities under various conditions on one chip. In this study, we propose an approach to overcome these limitations by developing a device capable of repeated measurements of ion channels incorporated into individually arrayed lipid bilayers. Our device forms an array of a lipid bilayer at a micropore on a separator by merging two lipid monolayers assembled on the surface of aqueous droplets. We introduce a vertically moving, blade-shaped module─referred to as a "wiping blade"─which enables controlled disruption and reformation of the bilayer at the micropore. By optimizing the surface properties and clearance of the wiping blade, we successfully achieved repeated bilayer formation. The arrayed lipid bilayer device with the integrated wiping blade module demonstrates a 5-fold improvement in data throughput during ion channel activity measurements. Finally, we validate the practical utility of our device by evaluating the effects of an ion channel inhibitor. The developed device opens new avenues for high-throughput analysis and screening of ion channels, leading to significant advancements in drug discovery and functional studies of membrane proteins. It offers a powerful tool for researchers in the field and holds promise for accelerating drug development by targeting ion channels.
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Affiliation(s)
- Hisatoshi Mimura
- Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan
| | - Toshihisa Osaki
- Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan
- MAQsys Inc., 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan
| | - Sho Takamori
- Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan
| | - Kenji Nakao
- MAQsys Inc., 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan
| | - Shoji Takeuchi
- Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan
- Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
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2
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Ogishi K, Osaki T, Mimura H, Hashimoto I, Morimoto Y, Miki N, Takeuchi S. Real-time quantitative characterization of ion channel activities for automated control of a lipid bilayer system. Biosens Bioelectron 2023; 237:115490. [PMID: 37393766 DOI: 10.1016/j.bios.2023.115490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/16/2023] [Accepted: 06/19/2023] [Indexed: 07/04/2023]
Abstract
This paper describes a novel signal processing method to characterize the activity of ion channels on a lipid bilayer system in a real-time and quantitative manner. Lipid bilayer systems, which enable single-channel level recordings of ion channel activities against physiological stimuli in vitro, are gaining attention in various research fields. However, the characterization of ion channel activities has heavily relied on time-consuming analyses after recording, and the inability to return the quantitative results in real time has long been a bottleneck to incorporating the system into practical products. Herein, we report a lipid bilayer system that integrates real-time characterization of ion channel activities and real-time response based on the characterization result. Unlike conventional batch processing, an ion channel signal is divided into short segments and processed during the recording. After optimizing the system to maintain the same characterization accuracy as conventional operation, we demonstrated the usability of the system with two applications. One is quantitative control of a robot based on ion channel signals. The velocity of the robot was controlled every second, which was around tens of times faster than the conventional operation, in proportion to the stimulus intensity estimated from changes in ion channel activities. The other is the automation of data collection and characterization of ion channels. By constantly monitoring and maintaining the functionality of a lipid bilayer, our system enabled continuous recording of ion channels over 2 h without human intervention, and the time of manual labor has been reduced from conventional 3 h to 1 min at a minimum. We believe the accelerated characterization and response in the lipid bilayer systems presented in this work will facilitate the transformation of lipid bilayer technology toward a practical level, finally leading to its industrialization.
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Affiliation(s)
- Kazuto Ogishi
- Department of Mechano-Informatics, Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Toshihisa Osaki
- Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki-shi, Kanagawa, 213-0012, Japan
| | - Hisatoshi Mimura
- Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki-shi, Kanagawa, 213-0012, Japan
| | - Izumi Hashimoto
- Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki-shi, Kanagawa, 213-0012, Japan; Department of Mechanical Engineering, Faculty of Science and Technology, Keio University, 3-14-1, Hiyoshi, Kohoku-ku, Yokohama-shi, Kanagawa, 223-8522, Japan
| | - Yuya Morimoto
- Department of Mechano-Informatics, Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Norihisa Miki
- Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki-shi, Kanagawa, 213-0012, Japan; Department of Mechanical Engineering, Faculty of Science and Technology, Keio University, 3-14-1, Hiyoshi, Kohoku-ku, Yokohama-shi, Kanagawa, 223-8522, Japan
| | - Shoji Takeuchi
- Department of Mechano-Informatics, Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki-shi, Kanagawa, 213-0012, Japan; Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan.
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3
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Schloßhauer JL, Zemella A, Dondapati SK, Thoring L, Meyer M, Kubick S. Enhancing the performance of a mutant pyrrolysyl-tRNA synthetase to create a highly versatile eukaryotic cell-free protein synthesis tool. Sci Rep 2023; 13:15236. [PMID: 37709815 PMCID: PMC10502014 DOI: 10.1038/s41598-023-42198-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023] Open
Abstract
Modification of proteins with a broad range of chemical functionalities enables the investigation of protein structure and activity by manipulating polypeptides at single amino acid resolution. Indeed, various functional groups including bulky non-canonical amino acids like strained cyclooctenes could be introduced by the unique features of the binding pocket of the double mutant pyrrolysyl-tRNA synthetase (Y306A, Y384F), but the instable nature of the enzyme limits its application in vivo. Here, we constructed a cell-free protein production system, which increased the overall enzyme stability by combining different reaction compartments. Moreover, a co-expression approach in a one-pot reaction allowed straightforward site-specific fluorescent labeling of the functional complex membrane protein cystic fibrosis transmembrane conductance regulator. Our work provides a versatile platform for introducing various non-canonical amino acids into difficult-to-express proteins for structural and fluorescence based investigation of proteins activity.
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Affiliation(s)
- Jeffrey L Schloßhauer
- Fraunhofer Project Group PZ-Syn of the Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Institute of Biotechnology,, Brandenburg University of Technology Cottbus-Senftenberg, Am Mühlenberg, Potsdam, Germany
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany.
| | - Srujan K Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
| | - Lena Thoring
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
| | - Manpreet Meyer
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus -Senftenberg, The Brandenburg Medical School Theodor Fontane, University of Potsdam, Potsdam, Germany
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
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4
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Ahmad M, Ha JH, Mayse LA, Presti MF, Wolfe AJ, Moody KJ, Loh SN, Movileanu L. A generalizable nanopore sensor for highly specific protein detection at single-molecule precision. Nat Commun 2023; 14:1374. [PMID: 36941245 PMCID: PMC10027671 DOI: 10.1038/s41467-023-36944-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 02/23/2023] [Indexed: 03/23/2023] Open
Abstract
Protein detection has wide-ranging implications in molecular diagnostics. Substantial progress has been made in protein analytics using nanopores and the resistive-pulse technique. Yet, a long-standing challenge is implementing specific interfaces for detecting proteins without the steric hindrance of the pore interior. Here, we formulate a class of sensing elements made of a programmable antibody-mimetic binder fused to a monomeric protein nanopore. This way, such a modular design significantly expands the utility of nanopore sensors to numerous proteins while preserving their architecture, specificity, and sensitivity. We prove the power of this approach by developing and validating nanopore sensors for protein analytes that drastically vary in size, charge, and structural complexity. These analytes produce unique electrical signatures that depend on their identity and quantity and the binder-analyte assembly at the nanopore tip. The outcomes of this work could impact biomedical diagnostics by providing a fundamental basis for biomarker detection in biofluids.
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Affiliation(s)
- Mohammad Ahmad
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA
| | - Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, State University of New York-Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, NY, 13210, USA
| | - Lauren A Mayse
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, NY, 13244, USA
| | - Maria F Presti
- Department of Biochemistry and Molecular Biology, State University of New York-Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, NY, 13210, USA
| | - Aaron J Wolfe
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA
- Ichor Life Sciences, Inc., 2561 US Route 11, LaFayette, NY, 13084, USA
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699, USA
- Department of Chemistry, College of Environmental Science and Forestry, State University of New York, 1 Forestry Drive, Syracuse, NY, 13210, USA
| | - Kelsey J Moody
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA
- Ichor Life Sciences, Inc., 2561 US Route 11, LaFayette, NY, 13084, USA
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699, USA
- Department of Chemistry, College of Environmental Science and Forestry, State University of New York, 1 Forestry Drive, Syracuse, NY, 13210, USA
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, State University of New York-Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, NY, 13210, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY, 13244-1130, USA.
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, NY, 13244, USA.
- The BioInspired Institute, Syracuse University, Syracuse, NY, 13244, USA.
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5
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Ensslen T, Sarthak K, Aksimentiev A, Behrends JC. Resolving Isomeric Posttranslational Modifications Using a Biological Nanopore as a Sensor of Molecular Shape. J Am Chem Soc 2022; 144:16060-16068. [PMID: 36007197 DOI: 10.1021/jacs.2c06211] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The chemical nature and precise position of posttranslational modifications (PTMs) in proteins or peptides are crucial for various severe diseases, such as cancer. State-of-the-art PTM diagnosis is based on elaborate and costly mass-spectrometry or immunoassay-based approaches, which are limited in selectivity and specificity. Here, we demonstrate the use of a protein nanopore to differentiate peptides─derived from human histone H4 protein─of identical mass according to the positions of acetylated and methylated lysine residues. Unlike sequencing by stepwise threading, our method detects PTMs and their positions by sensing the shape of a fully entrapped peptide, thus eliminating the need for controlled translocation. Molecular dynamics simulations show that the sensitivity to molecular shape derives from a highly nonuniform electric field along the pore. This molecular shape-sensing principle offers a path to versatile, label-free, and high-throughput characterizations of protein isoforms.
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Affiliation(s)
- Tobias Ensslen
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Kumar Sarthak
- Center for the Physics of Living Cells, Beckman Institute for Advanced Science and Technology and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Aleksei Aksimentiev
- Center for the Physics of Living Cells, Beckman Institute for Advanced Science and Technology and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jan C Behrends
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
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6
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Ensslen T, Behrends JC. A chip-based array for high-resolution fluorescence characterization of free-standing horizontal lipid membranes under voltage clamp. LAB ON A CHIP 2022; 22:2902-2910. [PMID: 35839072 DOI: 10.1039/d2lc00357k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Optical techniques, such as fluorescence microscopy, are of great value in characterizing the structural dynamics of membranes and membrane proteins. A particular challenge is to combine high-resolution optical measurements with high-resolution voltage clamp electrical recordings providing direct information on e.g. single ion channel gating and/or membrane capacitance. Here, we report on a novel chip-based array device which facilitates optical access with water or oil-immersion objectives of high numerical aperture to horizontal free-standing lipid membranes while controlling membrane voltage and recording currents using individual micropatterned Ag/AgCl-electrodes. Wide-field and confocal imaging, as well as time-resolved single photon counting on free-standing membranes spanning sub-nanoliter cavities are demonstrated while electrical signals, including single channel activity, are simultaneously acquired. This optically addressable microelectrode cavity array will allow combined electrical-optical studies of membranes and membrane proteins to be performed as a routine experiment.
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Affiliation(s)
- Tobias Ensslen
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Hermann-Herder-Str. 7, 79104 Freiburg, Germany.
| | - Jan C Behrends
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Hermann-Herder-Str. 7, 79104 Freiburg, Germany.
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7
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Baxani DK, Jamieson WD, Barrow DA, Castell OK. Encapsulated droplet interface bilayers as a platform for high-throughput membrane studies. SOFT MATTER 2022; 18:5089-5096. [PMID: 35766018 PMCID: PMC9277618 DOI: 10.1039/d1sm01111a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Whilst it is highly desirable to produce artificial lipid bilayer arrays allowing for systematic high-content screening of membrane conditions, it remains a challenge due to the combined requirements of scaled membrane production, simple measurement access, and independent control over individual bilayer experimental conditions. Here, droplet bilayers encapsulated within a hydrogel shell are output individually into multi-well plates for simple, arrayed quantitative measurements. The afforded experimental throughput is used to conduct a 2D concentration screen characterising the synergistic pore-forming peptides Magainin2 and PGLa. Maximal enhanced activity is revealed at equimolar peptide concentrations via a membrane dye leakage assay, a finding consistent with models proposed from NMR data. The versatility of the platform is demonstrated by performing in situ electrophysiology, revealing low conductance pore activity (∼15 to 20 pA with 4.5 pA sub-states). In conclusion, this array platform addresses the aforementioned challenges and provides new and flexible opportunities for high-throughput membrane studies. Furthermore, the ability to engineer droplet networks within each construct paves the way for "lab-in-a-capsule" approaches accommodating multiple assays per construct and allowing for communicative reaction pathways.
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Affiliation(s)
- D K Baxani
- College of Biomedical and Life Sciences, School of Pharmacy and Pharmaceutical Sciences, Cardiff University Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, UK.
| | - W D Jamieson
- College of Biomedical and Life Sciences, School of Pharmacy and Pharmaceutical Sciences, Cardiff University Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, UK.
| | - D A Barrow
- School of Engineering, Cardiff University, 14-17 The Parade, CF4 3AA Cardiff, UK
| | - O K Castell
- College of Biomedical and Life Sciences, School of Pharmacy and Pharmaceutical Sciences, Cardiff University Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, UK.
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8
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Hasegawa N, Shoji K. Microcavity volume control on a tip of Ag/AgCl electrodes for stable channel current measurements of biological nanopores. Analyst 2022; 147:1191-1198. [PMID: 35195650 DOI: 10.1039/d2an00014h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A probe-type channel current measurement system with a planer bilayer lipid membrane (pBLM) at the tip of a probe provided several advantages for pBLM formation and channel current measurements. The procedure for preparing pBLMs was simple (i.e., the probe was submerged into a bath solution layered by an oil/lipid mixture and buffer solution). The probe systems offered local detection of analytes by nanopore sensing. Nevertheless, the current decay caused by changing the ion concentration in the electrolyte held on the tip of the probes influenced the sensing accuracy. Here we applied a cavity microelectrode (CME) technique to fabricate pBLM probes with larger electrolyte volume on the tip. We fabricated silver CMEs with different cavity volumes and measured channel currents of biological nanopores. Furthermore, we evaluated the channel current decay as a function of cavity volume by analyzing the step signals of α-hemolysin nanopores. Consequently, the channel current decay was extended by increasing the cavity volume, indicating that the volume of the electrolyte solution was important for channel current measurements of nanopores. We concluded that the pBLM system using CMEs is useful for channel current measurements of biological nanopores. Additionally, the fundamental evaluation of the relationship between the electrolyte volume and channel current decay will be helpful in the design of pBLM systems made by microfabrication and microfluidic techniques.
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Affiliation(s)
- Naru Hasegawa
- Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan.
| | - Kan Shoji
- Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan.
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9
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Diederichs T, Ahmad K, Burns JR, Nguyen QH, Siwy ZS, Tornow M, Coveney PV, Tampé R, Howorka S. Principles of Small-Molecule Transport through Synthetic Nanopores. ACS NANO 2021; 15:16194-16206. [PMID: 34596387 DOI: 10.1021/acsnano.1c05139] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Synthetic nanopores made from DNA replicate the key biological processes of transporting molecular cargo across lipid bilayers. Understanding transport across the confined lumen of the nanopores is of fundamental interest and of relevance to their rational design for biotechnological applications. Here we reveal the transport principles of organic molecules through DNA nanopores by synergistically combining experiments and computer simulations. Using a highly parallel nanostructured platform, we synchronously measure the kinetic flux across hundreds of individual pores to obtain rate constants. The single-channel transport kinetics are close to the theoretical maximum, while selectivity is determined by the interplay of cargo charge and size, the pores' sterics and electrostatics, and the composition of the surrounding lipid bilayer. The narrow distribution of transport rates implies a high structural homogeneity of DNA nanopores. The molecular passageway through the nanopore is elucidated via coarse-grained constant-velocity steered molecular dynamics simulations. The ensemble simulations pinpoint with high resolution and statistical validity the selectivity filter within the channel lumen and determine the energetic factors governing transport. Our findings on these synthetic pores' structure-function relationship will serve to guide their rational engineering to tailor transport selectivity for cell biological research, sensing, and drug delivery.
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Affiliation(s)
- Tim Diederichs
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/M., 60438, Germany
| | - Katya Ahmad
- Centre for Computational Science, University College London, London, WC1H0AJ, England, U.K
| | - Jonathan R Burns
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H0AJ, England, U.K
| | - Quoc Hung Nguyen
- Molecular Electronics, Technical University of Munich, Munich, 80333, Germany
| | - Zuzanna S Siwy
- School of Physical Sciences, University of California, Irvine, California 92697, United States
| | - Marc Tornow
- Molecular Electronics, Technical University of Munich, Munich, 80333, Germany
- Fraunhofer Research Institution for Microsystems and Solid State Technologies (EMFT), Munich, 80686, Germany
- Center of NanoScience (CeNS), Ludwig-Maximilian-University, Munich, 80539, Germany
| | - Peter V Coveney
- Centre for Computational Science, University College London, London, WC1H0AJ, England, U.K
- Informatics Institute, University of Amsterdam, Amsterdam, 1090 GH, The Netherlands
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/M., 60438, Germany
| | - Stefan Howorka
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H0AJ, England, U.K
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10
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Du X, Wang Y, Zhang S, Fan P, Yan S, Zhang P, Chen HY, Huang S. Microscopic Screening of Cyclodextrin Channel Blockers by DiffusiOptoPhysiology. Anal Chem 2021; 93:14161-14168. [PMID: 34641671 DOI: 10.1021/acs.analchem.1c02775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Blockers of pore-forming toxins (PFTs) limit bacterial virulence by blocking relevant channel proteins. However, screening of desired blockers from a large pool of candidate molecules is not a trivial task. Acknowledging its advantages of low cost, high throughput, and multiplicity, DiffusiOptoPhysiology (DOP), an emerging nanopore technique that visually monitors the states of individual channel proteins without using any electrodes, has shown its potential use in the screening of channel blockers. By taking different α-hemolysin (α-HL) mutants as model PFTs and different cyclodextrins as model blockers, we report direct screening of pore blockers solely by using fluorescence microscopy. Different combinations of pores and blockers were simultaneously evaluated on the same DOP chip and a single-molecule resolution is directly achieved. The entire chip is composed of low-cost and biocompatible materials, which is fully disposable after each use. Though only demonstrated with cyclodextrin derivatives and α-HL mutants, this proof of concept has also suggested its generality to investigate other pore-forming proteins.
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Affiliation(s)
- Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Pingping Fan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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11
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Jayaram AK, Pappa AM, Ghosh S, Manzer ZA, Traberg WC, Knowles TPJ, Daniel S, Owens RM. Biomembranes in bioelectronic sensing. Trends Biotechnol 2021; 40:107-123. [PMID: 34229865 DOI: 10.1016/j.tibtech.2021.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/01/2021] [Accepted: 06/03/2021] [Indexed: 12/14/2022]
Abstract
Cell membranes are integral to the functioning of the cell and are therefore key to drive fundamental understanding of biological processes for downstream applications. Here, we review the current state-of-the-art with respect to biomembrane systems and electronic substrates, with a view of how the field has evolved towards creating biomimetic conditions and improving detection sensitivity. Of particular interest are conducting polymers, a class of electroactive polymers, which have the potential to create the next step-change for bioelectronics devices. Lastly, we discuss the impact these types of devices could have for biomedical applications.
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Affiliation(s)
- A K Jayaram
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK; Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0JH, UK
| | - A M Pappa
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, CB30AS Cambridge, UK
| | - S Ghosh
- RF Smith School of Chemical and Biomolecular Engineering, Cornell University, Olin Hall, Ithaca, NY 14850, USA
| | - Z A Manzer
- RF Smith School of Chemical and Biomolecular Engineering, Cornell University, Olin Hall, Ithaca, NY 14850, USA
| | - W C Traberg
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, CB30AS Cambridge, UK
| | - T P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK; Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0JH, UK
| | - S Daniel
- RF Smith School of Chemical and Biomolecular Engineering, Cornell University, Olin Hall, Ithaca, NY 14850, USA
| | - R M Owens
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, CB30AS Cambridge, UK.
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12
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Zaitseva E, Obergrussberger A, Weichbrodt C, Boukhet M, Bernhard F, Hein C, Baaken G, Fertig N, Behrends JC. Electrophysiology on Channel-Forming Proteins in Artificial Lipid Bilayers: Next-Generation Instrumentation for Multiple Recordings in Parallel. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2188:67-92. [PMID: 33119847 DOI: 10.1007/978-1-0716-0818-0_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Artificial lipid bilayers have been used for several decades to study channel-forming pores and ion channels in membranes. Until recently, the classical two-chamber setups have been primarily used for studying the biophysical properties of pore forming proteins. Within the last 10 years, instruments for automated lipid bilayer measurements have been developed and are now commercially available. This chapter focuses on protein purification and reconstitution of channel-forming proteins into lipid bilayers using a classic setup and on the commercially available systems, the Orbit mini and Orbit 16.
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Affiliation(s)
| | | | | | | | - Frank Bernhard
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Christopher Hein
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | | | - Jan C Behrends
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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13
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Piguet F, Ensslen T, Bakshloo MA, Talarimoghari M, Ouldali H, Baaken G, Zaitseva E, Pastoriza-Gallego M, Behrends JC, Oukhaled A. Pore-forming toxins as tools for polymer analytics: From sizing to sequencing. Methods Enzymol 2021; 649:587-634. [PMID: 33712201 DOI: 10.1016/bs.mie.2021.01.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
We report here on the nanopore resistive pulse sensing (Np-RPS) method, involving pore-forming toxins as tools for polymer analytics at single molecule level. Np-RPS is an electrical method for the label-free detection of single molecules. A molecule interacting with the pore causes a change of the electrical resistance of the pore, called a resistive pulse, associated with a measurable transient current blockade. The features of the blockades, in particular their depth and duration, contain information on the molecular properties of the analyte. We first revisit the history of Np-RPS, then we discuss the effect of the configuration of the molecule/nanopore interaction on the molecular information that can be extracted from the signal, illustrated in two different regimes that either favor molecular sequencing or molecular sizing. Specifically, we focus on the sizing regime and on the use of two different pore-forming toxins, staphylococcal α-hemolysin (αHL) and aerolysin (AeL) nanopores, for the characterization of water-soluble polymers (poly-(ethylene glycol), (PEG)), homopeptides, and heteropeptides. We discuss how nanopore sizing of polymers could be envisioned as a new approach for peptide/protein sequencing.
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Affiliation(s)
- Fabien Piguet
- CY Cergy Paris Université, CNRS, LAMBE, Cergy, France; Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France
| | - Tobias Ensslen
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Mazdak A Bakshloo
- CY Cergy Paris Université, CNRS, LAMBE, Cergy, France; Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France
| | - Monasadat Talarimoghari
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hadjer Ouldali
- CY Cergy Paris Université, CNRS, LAMBE, Cergy, France; Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France
| | | | | | - Manuela Pastoriza-Gallego
- CY Cergy Paris Université, CNRS, LAMBE, Cergy, France; Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France
| | - Jan C Behrends
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Freiburg Centre for Interactive Materials and Bioinspired Technologies (FIT), Freiburg, Germany; Freiburg Centre for Materials Research, Freiburg, Germany.
| | - Abdelghani Oukhaled
- CY Cergy Paris Université, CNRS, LAMBE, Cergy, France; Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France.
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14
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Multilayered film for the controlled formation of freestanding lipid bilayers. Colloids Surf B Biointerfaces 2020; 199:111552. [PMID: 33421926 DOI: 10.1016/j.colsurfb.2020.111552] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/05/2020] [Accepted: 12/19/2020] [Indexed: 11/23/2022]
Abstract
A freestanding lipid bilayer or black lipid membrane is a powerful tool for studying ion channels and for biophysical studies of other membrane proteins under controlled chemical and physical conditions. Even though the lipid bilayer has been considered an excellent sensing platform to detect diverse single molecules from nucleotides to cells, it is not yet widely used, mainly due to its low stability and the expertise needed for membrane formation. To ameliorate the issues of conventional membrane formation techniques, we report a novel layered film that consists of a nonporous layer sandwiched between two porous layers to facilitate bilayer formation. Moreover, the absorption of excess solvent present in the membrane precursor solution can be achieved by the film, enabling control over the membrane formation process. Through this layered design, we could obtain an ideal film that has a reduced and controlled membrane formation time (<30 min) and a sufficient bilayer lifetime (3 h) for ion channel studies and biosensing.
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15
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Ito Y, Osaki T, Kamiya K, Yamada T, Miki N, Takeuchi S. Rapid and Resilient Detection of Toxin Pore Formation Using a Lipid Bilayer Array. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2005550. [PMID: 33191570 DOI: 10.1002/smll.202005550] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/14/2020] [Indexed: 06/11/2023]
Abstract
An artificial cell membrane is applied to study the pore formation mechanisms of bacterial pore-forming toxins for therapeutic applications. Electrical monitoring of ionic current across the membrane provides information on the pore formation process of toxins at the single pore level, as well as the pore characteristics such as dimensions and ionic selectivity. However, the efficiency of pore formation detection largely depends on the encounter probability of toxin to the membrane and the fragility of the membrane. This study presents a bilayer lipid membrane array that parallelizes 4 or 16 sets of sensing elements composed of pairs of a membrane and a series electrical resistor. The series resistor prevents current overflow attributed to membrane rupture, and enables current monitoring of the parallelized membranes with a single detector. The array system shortens detection time of a pore-forming protein and improves temporal stability. The current signature represents the states of pore formation and rupture at respective membranes. The developed system will help in understanding the toxic activity of pore-forming toxins.
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Affiliation(s)
- Yoshihisa Ito
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
- Center for Multidisciplinary and Design Science, School of Integrated Design Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Toshihisa Osaki
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
| | - Koki Kamiya
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
| | - Tetsuya Yamada
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
| | - Norihisa Miki
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
- Department of Mechanical Engineering, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Shoji Takeuchi
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
- Department of Mechano-Informatics, Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
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16
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Lee HR, Lee Y, Oh SS, Choi SQ. Ultra-Stable Freestanding Lipid Membrane Array: Direct Visualization of Dynamic Membrane Remodeling with Cholesterol Transport and Enzymatic Reactions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2002541. [PMID: 32924281 DOI: 10.1002/smll.202002541] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/09/2020] [Indexed: 06/11/2023]
Abstract
Cell membranes actively change their local compositions, serving essential biological processes such as cellular signaling and endocytosis. Although membrane dynamics is vital in the cellular functions, the complexity of natural membranes has made its fundamental understanding and systematic assessment difficult. Here, a powerful artificial membrane system is developed for real-time visualization of the spatiotemporal dynamics of membrane remodeling. Through well-defined air/oil/water interfaces on grid holes, tens of planar lipid bilayer membranes are easily created, and their reproducibility, controllability, and generality are highlighted. The freestanding membranes are large but also highly stable, facilitating direct long-term monitoring of dynamic membrane reconstitution caused by external stimuli. As an example to demonstrate the superiority of this membrane system, the effect of cholesterol trafficking, which significantly affects biophysical properties of cell membranes, is investigated at different membrane compositions. Cholesterol transport into and out of the membranes at different rates causes anomalous lipid arrangements through cholesterol-mediated phase transitions and decomposition, which have never been witnessed before. Furthermore, enzyme-induced membrane dynamics is successfully shown in this platform; sphingomyelinases locally generate asymmetry between two membrane leaflets. This technique is broadly applicable for exploring the membrane heterogeneity under various membrane-based reactions, providing valuable insight into the membrane dynamics.
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Affiliation(s)
- Hyun-Ro Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Yohan Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Seung Soo Oh
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Siyoung Q Choi
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
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17
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Fu J, Wu L, Qiao Y, Tu J, Lu Z. Microfluidic Systems Applied in Solid-State Nanopore Sensors. MICROMACHINES 2020; 11:mi11030332. [PMID: 32210148 PMCID: PMC7142662 DOI: 10.3390/mi11030332] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/08/2020] [Accepted: 03/20/2020] [Indexed: 01/04/2023]
Abstract
Microfluidic system, as a kind of miniature integrated operating platform, has been applied to solid-state nanopore sensors after many years of experimental study. In the process of introducing microfluidic into solid-state nanopore sensors, many novel device structures are designed due to the abundance of analytes and the diversity of detection methods. Here we review the fundamental setup of nanopore-based microfluidic systems and the developments and advancements that have been taking place in the field. The microfluidic systems with a multichannel strategy to elevate the throughput and efficiency of nanopore sensors are then presented. Multifunctional detection represented by optical-electrical detection, which is realized by microfluidic integration, is also described. A high integration microfluidic system with nanopore is further discussed, which shows the prototype of commercialization.
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Affiliation(s)
| | | | | | - Jing Tu
- Correspondence: (J.T.); (Z.L.); Tel.: +86-25-8379-2396 (J.T.); +86-25-8379-3779 (Z.L.)
| | - Zuhong Lu
- Correspondence: (J.T.); (Z.L.); Tel.: +86-25-8379-2396 (J.T.); +86-25-8379-3779 (Z.L.)
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18
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Ouldali H, Sarthak K, Ensslen T, Piguet F, Manivet P, Pelta J, Behrends JC, Aksimentiev A, Oukhaled A. Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore. Nat Biotechnol 2020; 38:176-181. [PMID: 31844293 PMCID: PMC7008938 DOI: 10.1038/s41587-019-0345-2] [Citation(s) in RCA: 240] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 10/18/2019] [Accepted: 11/06/2019] [Indexed: 02/04/2023]
Abstract
Efforts to sequence single protein molecules in nanopores1-5 have been hampered by the lack of techniques with sufficient sensitivity to discern the subtle molecular differences among all twenty amino acids. Here we report ionic current detection of all twenty proteinogenic amino acids in an aerolysin nanopore with the help of a short polycationic carrier. Application of molecular dynamics simulations revealed that the aerolysin nanopore has a built-in single-molecule trap that fully confines a polycationic carrier-bound amino acid inside the sensing region of the aerolysin. This structural feature means that each amino acid spends sufficient time in the pore for sensitive measurement of the excluded volume of the amino acid. We show that distinct current blockades in wild-type aerolysin can be used to identify 13 of the 20 natural amino acids. Furthermore, we show that chemical modifications, instrumentation advances and nanopore engineering offer a route toward identification of the remaining seven amino acids. These findings may pave the way to nanopore protein sequencing.
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Affiliation(s)
- Hadjer Ouldali
- LAMBE UMR 8587, Université de Cergy-Pontoise, CNRS, CEA, Université Paris-Seine, Cergy-Pontoise, France
| | - Kumar Sarthak
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Tobias Ensslen
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Fabien Piguet
- LAMBE UMR 8587, Université de Cergy-Pontoise, CNRS, CEA, Université Paris-Seine, Cergy-Pontoise, France
- DreamPore S.A.S., 33 Boulevard du Port 95000, Cergy, France
| | - Philippe Manivet
- APHP, GHU APHP.Nord, DMU BioGem, Hôpital Lariboisière, BIOBANK Lariboisière Department BB-0033-00064, Plateforme de BioPathologie et de Technologies Innovantes en Santé, Paris, France
- INSERM UMR 1141 "NeuroDiderot", Université de Paris, Paris, France
| | - Juan Pelta
- LAMBE UMR 8587, Université d'Evry-Val-d'Essonne, CNRS, CEA, Université Paris-Saclay, Evry, France
| | - Jan C Behrends
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Freiburg Materials Research Centre (FMF), University of Freiburg, Freiburg, Germany
- Freiburg Centre for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Freiburg, Germany
| | - Aleksei Aksimentiev
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Abdelghani Oukhaled
- LAMBE UMR 8587, Université de Cergy-Pontoise, CNRS, CEA, Université Paris-Seine, Cergy-Pontoise, France.
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19
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Lenhart B, Wei X, Zhang Z, Wang X, Wang Q, Liu C. Nanopore Fabrication and Application as Biosensors in Neurodegenerative Diseases. Crit Rev Biomed Eng 2020; 48:29-62. [PMID: 32749118 PMCID: PMC8020784 DOI: 10.1615/critrevbiomedeng.2020033151] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Since its conception as an applied biomedical technology nearly 30 years ago, nanopore is emerging as a promising, high-throughput, biomarker-targeted diagnostic tool for clinicians. The attraction of a nanopore-based detection system is its simple, inexpensive, robust, user-friendly, high-throughput blueprint with minimal sample preparation needed prior to analysis. The goal of clinical-based nanopore biosensing is to go from sample acquisition to a meaningful readout quickly. The most extensive work in nanopore applications has been targeted at DNA, RNA, and peptide identification. Although, biosensing of pathological biomarkers, which is covered in this review, is on the rise. This review is broken into two major sections: (i) the current state of existing biological, solid state, and hybrid nanopore systems and (ii) the applications of nanopore biosensors toward detecting neurodegenerative biomarkers.
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Affiliation(s)
- Brian Lenhart
- Department of Chemical Engineering, University of South Carolina, Columbia, SC
| | - Xiaojun Wei
- Department of Chemical Engineering, University of South Carolina, Columbia, SC
- Biomedical Engineering Program, University of South Carolina, Columbia, SC
| | - Zehui Zhang
- Biomedical Engineering Program, University of South Carolina, Columbia, SC
| | - Xiaoqin Wang
- Department of Chemical Engineering, University of South Carolina, Columbia, SC
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC
| | - Chang Liu
- Department of Chemical Engineering, University of South Carolina, Columbia, SC
- Biomedical Engineering Program, University of South Carolina, Columbia, SC
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20
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Zheng T, Baaken G, Behrends JC, Rühe J. Microelectrochemical cell arrays for whole-cell currents recording through ion channel proteins based on trans-electroporation approach. Analyst 2019; 145:197-205. [PMID: 31730143 DOI: 10.1039/c9an01737b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
High electrostability and long life-time of planar chip technology are crucial for electrophysiological measurements such as ionic current recording through ion channel proteins embedded in biological cell membrane. In this paper, we propose a novel planar microchip integrated with microelectrochemical cell array toward to a feasible solution for ion channel screening with high resolution and long life-time. In order to reduce the interference from the leakage currents, a synthetic lipid bilayer is applied to form a high sealing resistance. The whole-cell electrical access can be constructed via electroporating the lipid bilayer in close proximity to the cell membrane. Parameters of electroporation including amplitude and time scale are firstly optimized by using parallel electroporation to the lipid bilayers. In this approach, individual cells can be trapped to the target positions by applying dielectrophoresis (DEP) manipulation. Poly(ethylene glycol) (PEG) is employed with low concentration to facilitate the closed contact between the cells and the lipid bilayer to increase the efficiency of the whole-cell mode construction. Through this chip based method, stable current recordings through inward rectifier potassium (Kir) ion channels embedded in rat basophilic leukemia (RBL-1) cell membrane are achieved with high electrical sealing resistance (over 1 GΩ). In addition, without need for complex fluidic connections, this method allows for an easy operation and further miniaturization of the measuring system.
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Affiliation(s)
- Tianyang Zheng
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, 100084, Beijing, China.
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21
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Reiter R, Zaitseva E, Baaken G, Halimeh I, Behrends JC, Zumbuehl A. Activity of the Gramicidin A Ion Channel in a Lipid Membrane with Switchable Physical Properties. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:14959-14966. [PMID: 31645105 DOI: 10.1021/acs.langmuir.9b02752] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Lipid bilayer membranes formed from the artificial 1,3-diamidophospholipid Pad-PC-Pad have the remarkable property that their hydrophobic thickness can be modified in situ: the particular arrangement of the fatty acid chains in Pad-PC-Pad allows them to fully interdigitate below 37 °C, substantially thinning the membrane with respect to the noninterdigitated state. Two stimuli, traversing the main phase transition temperature of the lipid or addition of cholesterol, have previously been shown to disable the interdigitated state. Both manipulations cause an increase in hydrophobic thickness of about 25 Å due to enhanced conformational entropy of the lipids. Here, we characterize the interdigitated state using electrophysiological recordings from free-standing lipid-membranes formed on micro structured electrode cavity arrays. Compared to standard membranes made from 1,2-diphytanoyl-sn-glycero-3-phosphocholin (DPhPC), pure Pad-PC-Pad membranes at room temperature had lowered electroporation threshold and higher capacitance. Ion channel formation by the peptide Gramicidin A was clearly facilitated in pure Pad-PC-Pad membranes at room temperature, with activity occurring at significantly lower peptide concentrations and channel dwell times increased by 2 orders of magnitude with respect to DPhPC-membranes. Both elevation of temperature beyond the phase transition and addition of cholesterol reduced channel dwell times, as expected if the reduced membrane thickness stabilized channel formation due to decreased hydrophobic mismatch.
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Affiliation(s)
- Renate Reiter
- Institute of Physics , University of Freiburg , Hermann-Herder-Strasse 3 , 79104 , Freiburg , Germany
- Freiburg Centre for Interactive Materials and Bioinspired Technologies (FIT) , 79110 , Freiburg , Germany
| | - Ekaterina Zaitseva
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine , University of Freiburg , Hermann-Herder-Strasse 7 , 79104 , Freiburg , Germany
- Ionera Technologies GmbH , Hermann-Herder-Strasse 7 , 79104 , Freiburg , Germany
| | - Gerhard Baaken
- Ionera Technologies GmbH , Hermann-Herder-Strasse 7 , 79104 , Freiburg , Germany
| | - Ibrahim Halimeh
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine , University of Freiburg , Hermann-Herder-Strasse 7 , 79104 , Freiburg , Germany
- Ionera Technologies GmbH , Hermann-Herder-Strasse 7 , 79104 , Freiburg , Germany
| | - Jan C Behrends
- Freiburg Centre for Interactive Materials and Bioinspired Technologies (FIT) , 79110 , Freiburg , Germany
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine , University of Freiburg , Hermann-Herder-Strasse 7 , 79104 , Freiburg , Germany
- Freiburg Centre for Materials Research , (FMF) Stefan Meier Strasse 21 , 79104 , Freiburg , Germany
| | - Andreas Zumbuehl
- National Center of Competence in Research in Chemical Biology , Geneva CH-1211 , Switzerland
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22
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Synthetic protein-conductive membrane nanopores built with DNA. Nat Commun 2019; 10:5018. [PMID: 31685824 PMCID: PMC6828756 DOI: 10.1038/s41467-019-12639-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 09/23/2019] [Indexed: 11/08/2022] Open
Abstract
AbstractNanopores are key in portable sequencing and research given their ability to transport elongated DNA or small bioactive molecules through narrow transmembrane channels. Transport of folded proteins could lead to similar scientific and technological benefits. Yet this has not been realised due to the shortage of wide and structurally defined natural pores. Here we report that a synthetic nanopore designed via DNA nanotechnology can accommodate folded proteins. Transport of fluorescent proteins through single pores is kinetically analysed using massively parallel optical readout with transparent silicon-on-insulator cavity chips vs. electrical recordings to reveal an at least 20-fold higher speed for the electrically driven movement. Pores nevertheless allow a high diffusive flux of more than 66 molecules per second that can also be directed beyond equillibria. The pores may be exploited to sense diagnostically relevant proteins with portable analysis technology, to create molecular gates for drug delivery, or to build synthetic cells.
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23
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Misawa N, Osaki T, Takeuchi S. Membrane protein-based biosensors. J R Soc Interface 2019; 15:rsif.2017.0952. [PMID: 29669891 DOI: 10.1098/rsif.2017.0952] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/19/2018] [Indexed: 01/09/2023] Open
Abstract
This review highlights recent development of biosensors that use the functions of membrane proteins. Membrane proteins are essential components of biological membranes and have a central role in detection of various environmental stimuli such as olfaction and gustation. A number of studies have attempted for development of biosensors using the sensing property of these membrane proteins. Their specificity to target molecules is particularly attractive as it is significantly superior to that of traditional human-made sensors. In this review, we classified the membrane protein-based biosensors into two platforms: the lipid bilayer-based platform and the cell-based platform. On lipid bilayer platforms, the membrane proteins are embedded in a lipid bilayer that bridges between the protein and a sensor device. On cell-based platforms, the membrane proteins are expressed in a cultured cell, which is then integrated in a sensor device. For both platforms we introduce the fundamental information and the recent progress in the development of the biosensors, and remark on the outlook for practical biosensing applications.
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Affiliation(s)
- Nobuo Misawa
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu, Kawasaki 213-0012, Japan
| | - Toshihisa Osaki
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu, Kawasaki 213-0012, Japan.,Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan
| | - Shoji Takeuchi
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu, Kawasaki 213-0012, Japan .,Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan
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24
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Dondapati SK, Lübberding H, Zemella A, Thoring L, Wüstenhagen DA, Kubick S. Functional Reconstitution of Membrane Proteins Derived From Eukaryotic Cell-Free Systems. Front Pharmacol 2019; 10:917. [PMID: 31543813 PMCID: PMC6728924 DOI: 10.3389/fphar.2019.00917] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/22/2019] [Indexed: 11/23/2022] Open
Abstract
Cell-free protein synthesis (CFPS) based on eukaryotic Sf21 lysate is gaining interest among researchers due to its ability to handle the synthesis of complex human membrane proteins (MPs). Additionally Sf21 cell-free systems contain endogenous microsomal vesicles originally derived from the endoplasmic reticulum (ER). After CFPS, MPs will be translocated into the microsomal vesicles membranes present in the lysates. Thus microsomal membranes offer a natural environment for de novo synthesized MPs. Despite the advantage of synthesizing complex MPs with post translational modifications directly into the microsomal membranes without any additional solubilization supplements, batch based Sf21 cell-free synthesis suffers from low yields. The bottleneck for MPs in particular after the synthesis and incorporation into the microsomal membranes is to analyze their functionality. Apart from low yields of the synthesized MPs with batch based cell-free synthesis, the challenges arise in the form of cytoskeleton elements and peripheral endogenous proteins surrounding the microsomes which may impede the functional analysis of the synthesized proteins. So careful sample processing after the synthesis is particularly important for developing the appropriate functional assays. Here we demonstrate how MPs (native and batch synthesized) from ER derived microsomes can be processed for functional analysis by electrophysiology and radioactive uptake assay methods. Treatment of the microsomal membranes either with a sucrose washing step in the case of human serotonin transporter (hSERT) and sarco/endoplasmic reticulum Ca2+/ATPase (SERCA) pump or with mild detergents followed by the preparation of proteoliposomes in the case of the human voltage dependent anionic channel (hVDAC1) helps to analyze the functional properties of MPs.
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Affiliation(s)
- Srujan Kumar Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
| | - Henning Lübberding
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
| | - Lena Thoring
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
| | - Doreen A Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, Potsdam, Germany.,Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, The Brandenburg Medical School Theodor Fontane, University of Potsdam, Potsdam, Germany
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25
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Wang H, Kasianowicz JJ, Robertson JWF, Poster DL, Ettedgui J. A comparison of ion channel current blockades caused by individual poly(ethylene glycol) molecules and polyoxometalate nanoclusters. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2019; 42:83. [PMID: 31250227 DOI: 10.1140/epje/i2019-11838-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
Proteinaceous nanometer-scale pores have been used to detect and physically characterize many different types of analytes at the single-molecule limit. The method is based on the ability to measure the transient reduction in the ionic channel conductance caused by molecules that partition into the pore. The distribution of blockade depth amplitudes and residence times of the analytes in the pore are used to physically and chemically characterize them. Here we compare the current blockade events caused by flexible linear polymers of ethylene glycol (PEGs) and structurally well-defined tungsten polyoxymetallate nanoparticles in the nanopores formed by Staphylococcus aureusα-hemolysin and Aeromonas hydrophila aerolysin. Surprisingly, the variance in the ionic current blockade depth values for the relatively rigid metallic nanoparticles is much greater than that for the flexible PEGs, possibly because of multiple charged states of the polyoxymetallate clusters.
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Affiliation(s)
- Haiyan Wang
- National Institute of Standards and Technology, Physical Measurement Laboratory, 20899, Gaithersburg, MD, USA
- Shenzhen Key Laboratory of Biomedical Engineering, School of Medicine, Shenzhen University, 3688 Nanhai Road, 508060, Shenzhen, China
| | - John J Kasianowicz
- National Institute of Standards and Technology, Physical Measurement Laboratory, 20899, Gaithersburg, MD, USA.
- Columbia University, Department of Applied Physics Applied Mathematics, 10027, New York, NY, USA.
| | - Joseph W F Robertson
- National Institute of Standards and Technology, Physical Measurement Laboratory, 20899, Gaithersburg, MD, USA
| | - Dianne L Poster
- National Institute of Standards and Technology, Material Measurement Laboratory, 20899, Gaithersburg, MD, USA
| | - Jessica Ettedgui
- National Institute of Standards and Technology, Physical Measurement Laboratory, 20899, Gaithersburg, MD, USA
- Columbia University, Department of Chemical Engineering, 10027, New York, NY, USA
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26
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Aisenbrey C, Marquette A, Bechinger B. The Mechanisms of Action of Cationic Antimicrobial Peptides Refined by Novel Concepts from Biophysical Investigations. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1117:33-64. [PMID: 30980352 DOI: 10.1007/978-981-13-3588-4_4] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Even 30 years after the discovery of magainins, biophysical and structural investigations on how these peptides interact with membranes can still bear surprises and add new interesting detail to how these peptides exert their antimicrobial action. Early on, using oriented solid-state NMR spectroscopy, it was found that the amphipathic helices formed by magainins are active when being oriented parallel to the membrane surface. More recent investigations indicate that this in-planar alignment is also found when PGLa and magainin in combination exert synergistic pore-forming activities, where studies on the mechanism of synergistic interaction are ongoing. In a related manner, the investigation of dimeric antimicrobial peptide sequences has become an interesting topic of research which bears promise to refine our views how antimicrobial action occurs. The molecular shape concept has been introduced to explain the effects of lipids and peptides on membrane morphology, locally and globally, and in particular of cationic amphipathic helices that partition into the membrane interface. This concept has been extended in this review to include more recent ideas on soft membranes that can adapt to external stimuli including membrane-disruptive molecules. In this manner, the lipids can change their shape in the presence of low peptide concentrations, thereby maintaining the bilayer properties. At higher peptide concentrations, phase transitions occur which lead to the formation of pores and membrane lytic processes. In the context of the molecular shape concept, the properties of lipopeptides, including surfactins, are shortly presented, and comparisons with the hydrophobic alamethicin sequence are made.
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Affiliation(s)
| | - Arnaud Marquette
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, Strasbourg, France
| | - Burkhard Bechinger
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, Strasbourg, France. .,Faculté de chimie, Institut le Bel, Strasbourg, France.
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27
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Kamiya K, Osaki T, Nakao K, Kawano R, Fujii S, Misawa N, Hayakawa M, Takeuchi S. Electrophysiological measurement of ion channels on plasma/organelle membranes using an on-chip lipid bilayer system. Sci Rep 2018; 8:17498. [PMID: 30504856 PMCID: PMC6269590 DOI: 10.1038/s41598-018-35316-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 11/05/2018] [Indexed: 01/08/2023] Open
Abstract
Ion channels are located in plasma membranes as well as on mitochondrial, lysosomal, and endoplasmic reticulum membranes. They play a critical role in physiology and drug targeting. It is particularly challenging to measure the current mediated by ion channels in the lysosomal and the endoplasmic reticulum membranes using the conventional patch clamp method. In this study, we show that our proposed device is applicable for an electrophysiological measurement of various types of ion channel in plasma and organelle membranes. We designed an on-chip device that can form multiple electrical contacts with a measurement system when placed on a mount system. Using crude cell membranes containing ion channels extracted from cultured cells without detergents, we detected open/close signals of the hERG, TRPV1, and NMDA channels on plasma membranes, those of the TRPML1 channels on lysosomal membranes, and open/close signals of the RyR channels on SR membranes. This method will provide a highly versatile drug screening system for ion channels expressed by various cell membranes, including plasma, SR, mitochondrial, Golgi, and lysosomal membranes.
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Affiliation(s)
- Koki Kamiya
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
| | - Toshihisa Osaki
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan.,Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
| | - Kenji Nakao
- Biomolecular Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., 2-26-1 Muraokahigashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Ryuji Kawano
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
| | - Satoshi Fujii
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
| | - Nobuo Misawa
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
| | - Masatoshi Hayakawa
- Research and Development Department, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kanagawa, 213-0012, Japan
| | - Shoji Takeuchi
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan. .,Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan.
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28
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Talarimoghari M, Baaken G, Hanselmann R, Behrends JC. Size-dependent interaction of a 3-arm star poly(ethylene glycol) with two biological nanopores. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:77. [PMID: 29926213 DOI: 10.1140/epje/i2018-11687-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/31/2018] [Indexed: 06/08/2023]
Abstract
We use two pore-forming proteins, alpha-hemolysin and aerolysin, to compare the polymer size-dependence of ionic current block by two types of ethyleneglycol polymers: 1) linear and 2) 3-arm star poly(ethylene glycol), both applied as a polydisperse mixture of average mass 1kDa under high salt conditions. The results demonstrate that monomer size sensitivity, as known for linear PEGs, is conserved for the star polymers with only subtle differences in the dependence of the residual conductance on monomer number. To explain this absence of a dominant effect of polymer architecture, we propose that PEG adsorbs to the inner pore wall in a collapsed, salted-out state, likely due to the effect of hydrophobic residues in the pore wall on the availability of water for hydration.
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Affiliation(s)
- Monasadat Talarimoghari
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Hermann-Herder-Str. 7, 79104, Freiburg, Germany
| | - Gerhard Baaken
- Ionera Technologies GmbH, Hermann-Herder-Str. 7, 79104, Freiburg, Germany
| | - Ralf Hanselmann
- Institute for Macromolecular Chemistry, Stefan-Meier-Str. 31, 79104, Freiburg, Germany
- Freiburg Materials Research Centre, University of Freiburg, Stefan-Meier-Str. 19, 79104, Freiburg, Germany
| | - Jan C Behrends
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Hermann-Herder-Str. 7, 79104, Freiburg, Germany.
- Freiburg Materials Research Centre, University of Freiburg, Stefan-Meier-Str. 19, 79104, Freiburg, Germany.
- Freiburg Centre for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110, Freiburg, Germany.
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29
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Abstract
Cell-free production is a valuable and alternative method for the synthesis of membrane proteins. This system offers openness allowing the researchers to modify the reaction conditions without any boundaries. Additionally, the cell-free reactions are scalable from 20 μL up to several mL, faster and suitable for the high-throughput protein production. Here, we present two cell-free systems derived from Escherichia coli (E. coli) and Spodoptera frugiperda (Sf21) lysates. In the case of the E. coli cell-free system, nanodiscs are used for the solubilization and purification of membrane proteins. In the case of the Sf21 system, endogenous microsomes with an active translocon complex are present within the lysates which facilitate the incorporation of the bacterial potassium channel KcsA within the microsomal membranes. Following cell-free synthesis, these microsomes are directly used for the functional analysis of membrane proteins.
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30
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Burns JR, Howorka S. Defined Bilayer Interactions of DNA Nanopores Revealed with a Nuclease-Based Nanoprobe Strategy. ACS NANO 2018; 12:3263-3271. [PMID: 29493216 DOI: 10.1021/acsnano.7b07835] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
DNA nanopores are a recent class of bilayer-puncturing nanodevices that can help advance biosensing, synthetic biology, and nanofluidics. Here, we create archetypal lipid-anchored DNA nanopores and characterize them with a nanoprobe-based approach to gain essential information about their interactions with bilayers. The strategy determines the molecular accessibility of DNA pores with a nuclease and can thus distinguish between the nanopores' membrane-adhering and membrane-spanning states. The analysis reveals, for example, that pores interact with bilayers in two steps whereby fast initial membrane tethering is followed by slower reorientation to the puncturing state. Tethering occurs for pores with one anchor, while puncturing requires multiple anchors. Both low and high-curvature membranes are good substrates for tethering, but efficient insertion proceeds only for high-curvature bilayers of the examined lipid composition. This is likely due to the localized lipid misalignments and the associated lower energetic barrier for pore permeation. Our study advances the fields of DNA nanotechnology and nanopores by overcoming the considerable experimental hurdle of efficient membrane insertion. It also provides mechanistic insights to aid the design of advanced nanopores, and offers a useful route to probe bilayer orientation of DNA nanostructures.
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Affiliation(s)
- Jonathan R Burns
- Department of Chemistry, Institute of Structural Molecular Biology , University College London , London WC1H 0AJ , United Kingdom
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology , University College London , London WC1H 0AJ , United Kingdom
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31
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Kim YH, Hang L, Cifelli JL, Sept D, Mayer M, Yang J. Frequency-Based Analysis of Gramicidin A Nanopores Enabling Detection of Small Molecules with Picomolar Sensitivity. Anal Chem 2018; 90:1635-1642. [DOI: 10.1021/acs.analchem.7b02961] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
| | | | | | - David Sept
- Department
of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109-2110, United States
| | - Michael Mayer
- Adolphe
Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
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32
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Dondapati SK, Wüstenhagen DA, Strauch E, Kubick S. Cell-free production of pore forming toxins: Functional analysis of thermostable direct hemolysin from Vibrio parahaemolyticus. Eng Life Sci 2017; 18:140-148. [PMID: 29497355 PMCID: PMC5814925 DOI: 10.1002/elsc.201600259] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 09/19/2017] [Accepted: 11/02/2017] [Indexed: 01/21/2023] Open
Abstract
The pore forming characteristic of TDH1 and TDH2 variants of thermostable direct hemolysin (TDH), a major toxin involved in the pathogenesis of Vibrio parahaemolyticus, was studied on a planar lipid bilayer painted over individual picoliter cavities containing microelectrodes assembled in a multiarray. Both proteins formed pores upon insertion into the lipid bilayer which was shown as a shift in the conductance from the baseline current. TDH2 protein was able to produce stable currents and the currents were influenced by external factors like concentration, type of salt and voltage. The pore currents were influenced and showed a detectable response in the presence of polymers which makes them suitable for biotechnology applications.
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Affiliation(s)
- Srujan Kumar Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI) Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB) Potsdam Germany
| | - Doreen A Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI) Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB) Potsdam Germany
| | - Eckhard Strauch
- Federal Institute for Risk Assessment Department of Biological Safety National Reference Laboratory for Monitoring Bacteriological Contamination of Bivalve Molluscs Berlin Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI) Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB) Potsdam Germany
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33
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Thoring L, Dondapati SK, Stech M, Wüstenhagen DA, Kubick S. High-yield production of "difficult-to-express" proteins in a continuous exchange cell-free system based on CHO cell lysates. Sci Rep 2017; 7:11710. [PMID: 28916746 PMCID: PMC5601898 DOI: 10.1038/s41598-017-12188-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 09/06/2017] [Indexed: 11/10/2022] Open
Abstract
Cell-free protein synthesis (CFPS) represents a promising technology for efficient protein production targeting especially so called "difficult-to-express" proteins whose synthesis is challenging in conventional in vivo protein production platforms. Chinese hamster ovary (CHO) cells are one of the most prominent and safety approved cell lines for industrial protein production. In this study we demonstrated the ability to produce high yields of various protein types including membrane proteins and single chain variable fragments (scFv) in a continuous exchange cell-free (CECF) system based on CHO cell lysate that contains endogenous microsomal structures. We showed significant improvement of protein yield compared to batch formatted reactions and proved biological activity of synthesized proteins using various analysis technologies. Optimized CECF reaction conditions led to membrane protein yields up to 980 µg/ml, which is the highest protein yield reached in a microsome containing eukaryotic cell-free system presented so far.
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Affiliation(s)
- Lena Thoring
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476, Potsdam, Germany
- Institute for Biotechnology, Technical University of Berlin (TUB), Gustav-Meyer-Allee 25, 13355, Berlin, Germany
| | - Srujan K Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476, Potsdam, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476, Potsdam, Germany
| | - Doreen A Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476, Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476, Potsdam, Germany.
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34
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Thoring L, Dondapati SK, Stech M, Wüstenhagen DA, Kubick S. High-yield production of "difficult-to-express" proteins in a continuous exchange cell-free system based on CHO cell lysates. Sci Rep 2017; 7:11710. [PMID: 28916746 DOI: 10.1038/s41598-017-12188-12188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 09/06/2017] [Indexed: 05/28/2023] Open
Abstract
Cell-free protein synthesis (CFPS) represents a promising technology for efficient protein production targeting especially so called "difficult-to-express" proteins whose synthesis is challenging in conventional in vivo protein production platforms. Chinese hamster ovary (CHO) cells are one of the most prominent and safety approved cell lines for industrial protein production. In this study we demonstrated the ability to produce high yields of various protein types including membrane proteins and single chain variable fragments (scFv) in a continuous exchange cell-free (CECF) system based on CHO cell lysate that contains endogenous microsomal structures. We showed significant improvement of protein yield compared to batch formatted reactions and proved biological activity of synthesized proteins using various analysis technologies. Optimized CECF reaction conditions led to membrane protein yields up to 980 µg/ml, which is the highest protein yield reached in a microsome containing eukaryotic cell-free system presented so far.
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Affiliation(s)
- Lena Thoring
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476, Potsdam, Germany
- Institute for Biotechnology, Technical University of Berlin (TUB), Gustav-Meyer-Allee 25, 13355, Berlin, Germany
| | - Srujan K Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476, Potsdam, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476, Potsdam, Germany
| | - Doreen A Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476, Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476, Potsdam, Germany.
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35
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Salnikov ES, Raya J, De Zotti M, Zaitseva E, Peggion C, Ballano G, Toniolo C, Raap J, Bechinger B. Alamethicin Supramolecular Organization in Lipid Membranes from 19F Solid-State NMR. Biophys J 2017; 111:2450-2459. [PMID: 27926846 DOI: 10.1016/j.bpj.2016.09.048] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 09/10/2016] [Accepted: 09/29/2016] [Indexed: 11/24/2022] Open
Abstract
Alamethicins (ALMs) are antimicrobial peptides of fungal origin. Their sequences are rich in hydrophobic amino acids and strongly interact with lipid membranes, where they cause a well-defined increase in conductivity. Therefore, the peptides are thought to form transmembrane helical bundles in which the more hydrophilic residues line a water-filled pore. Whereas the peptide has been well characterized in terms of secondary structure, membrane topology, and interactions, much fewer data are available regarding the quaternary arrangement of the helices within lipid bilayers. A new, to our knowledge, fluorine-labeled ALM derivative was prepared and characterized when reconstituted into phospholipid bilayers. As a part of these studies, C19F3-labeled compounds were characterized and calibrated for the first time, to our knowledge, for 19F solid-state NMR distance and oligomerization measurements by centerband-only detection of exchange (CODEX) experiments, which opens up a large range of potential labeling schemes. The 19F-19F CODEX solid-state NMR experiments performed with ALM in POPC lipid bilayers and at peptide/lipid ratios of 1:13 are in excellent agreement with molecular-dynamics calculations of dynamic pentameric assemblies. When the peptide/lipid ratio was lowered to 1:30, ALM was found in the dimeric form, indicating that the supramolecular organization is tuned by equilibria that can be shifted by changes in environmental conditions.
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Affiliation(s)
- Evgeniy S Salnikov
- Institute of Chemistry, University of Strasbourg/CNRS, UMR7177, Strasbourg, France
| | - Jesus Raya
- Institute of Chemistry, University of Strasbourg/CNRS, UMR7177, Strasbourg, France
| | - Marta De Zotti
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, Padova, Italy
| | - Ekaterina Zaitseva
- Department of Membrane Physiology and Technology, Institute of Physiology, University of Freiburg, Freiburg, Germany
| | - Cristina Peggion
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, Padova, Italy
| | - Gema Ballano
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, Padova, Italy
| | - Claudio Toniolo
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, Padova, Italy
| | - Jan Raap
- Leiden Institute of Chemistry, Gorlaeus Laboratories, University of Leiden, Leiden, the Netherlands
| | - Burkhard Bechinger
- Institute of Chemistry, University of Strasbourg/CNRS, UMR7177, Strasbourg, France.
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36
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Ruiz-Arroyo VM, García-Robles I, Ochoa-Campuzano C, Goig GA, Zaitseva E, Baaken G, Martínez-Ramírez AC, Rausell C, Real MD. Validation of ADAM10 metalloprotease as a Bacillus thuringiensis Cry3Aa toxin functional receptor in Colorado potato beetle (Leptinotarsa decemlineata). INSECT MOLECULAR BIOLOGY 2017; 26:204-214. [PMID: 27918112 DOI: 10.1111/imb.12285] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Bacillus thuringiensis parasporal crystal proteins (Cry proteins) are insecticidal pore-forming toxins that bind to specific receptor molecules on the brush border membrane of susceptible insect midgut cells to exert their toxic action. In the Colorado potato beetle (CPB), a coleopteran pest, we previously proposed that interaction of Cry3Aa toxin with a CPB ADAM10 metalloprotease is an essential part of the mode of action of this toxin. Here, we annotated the gene sequence encoding an ADAM10 metalloprotease protein (CPB-ADAM10) in the CPB genome sequencing project, and using RNA interference gene silencing we demonstrated that CPB-ADAM10 is a Cry3Aa toxin functional receptor in CPB. Cry3Aa toxicity was significantly lower in CPB-ADAM10 silenced larvae and in vitro toxin pore-forming ability was greatly diminished in lipid planar bilayers fused with CPB brush border membrane vesicles (BBMVs) prepared from CPB-ADAM10 silenced larvae. In accordance with our previous data that indicated this toxin was a substrate of ADAM10 in CPB, Cry3Aa toxin membrane-associated proteolysis was altered when CPB BBMVs lacked ADAM10. The functional validation of CPB-ADAM10 as a Cry3Aa toxin receptor in CPB expands the already recognized role of ADAM10 as a pathogenicity determinant of pore-forming toxins in humans to an invertebrate species.
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Affiliation(s)
- V M Ruiz-Arroyo
- Department of Genetics, University of Valencia, Burjassot, Valencia, Spain
| | - I García-Robles
- Department of Genetics, University of Valencia, Burjassot, Valencia, Spain
| | - C Ochoa-Campuzano
- Department of Genetics, University of Valencia, Burjassot, Valencia, Spain
| | - G A Goig
- Department of Genetics, University of Valencia, Burjassot, Valencia, Spain
| | - E Zaitseva
- Department of Physiology, University of Freiburg, Freiburg, Germany
- Ionera Technologies GmbH, Freiburg, Germany
| | - G Baaken
- Ionera Technologies GmbH, Freiburg, Germany
| | - A C Martínez-Ramírez
- Servicios Centrales de Soporte a la Investigación Experimental (SCSIE), University of Valencia, Burjassot, Valencia, Spain
| | - C Rausell
- Department of Genetics, University of Valencia, Burjassot, Valencia, Spain
| | - M D Real
- Department of Genetics, University of Valencia, Burjassot, Valencia, Spain
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37
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Affiliation(s)
- Toshihisa Osaki
- Artificial Cell
Membrane
Systems Group, Kanagawa Academy of Science and Technology, 3-2-1
Sakado, Takatsu, 213-0012 Kawasaki, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, 153-8505 Tokyo, Japan
| | - Shoji Takeuchi
- Artificial Cell
Membrane
Systems Group, Kanagawa Academy of Science and Technology, 3-2-1
Sakado, Takatsu, 213-0012 Kawasaki, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, 153-8505 Tokyo, Japan
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38
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Piguet F, Ouldali H, Discala F, Breton MF, Behrends JC, Pelta J, Oukhaled A. High Temperature Extends the Range of Size Discrimination of Nonionic Polymers by a Biological Nanopore. Sci Rep 2016; 6:38675. [PMID: 27924860 PMCID: PMC5141499 DOI: 10.1038/srep38675] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/11/2016] [Indexed: 01/29/2023] Open
Abstract
We explore the effect of temperature on the interaction of polydisperse mixtures of nonionic poly(ethylene glycol) (PEG) polymers of different average molar masses with the biological nanopore α-hemolysin. In contrast with what has been previously observed with various nanopores and analytes, we find that, for PEGs larger than a threshold molar mass (2000 g/mol, PEG 2000), increasing temperature increases the duration of the PEG/nanopore interaction. In the case of PEG 3400 the duration increases by up to a factor of 100 when the temperature increases from 5 °C to 45 °C. Importantly, we find that increasing temperature extends the polymer size range of application of nanopore-based single-molecule mass spectrometry (Np-SMMS)-type size discrimination. Indeed, in the case of PEG 3400, discrimination of individual molecular species of different monomer number is impossible at room temperature but is achieved when the temperature is raised to 45 °C. We interpret our observations as the consequence of a decrease of PEG solubility and a collapse of PEG molecules with higher temperatures. In addition to expanding the range of application of Np-SMMS to larger nonionic polymers, our findings highlight the crucial role of the polymer solubility for the nanopore detection.
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Affiliation(s)
- Fabien Piguet
- LAMBE UMR 8587 CNRS, Cergy and Évry Universities, France.,LPTM UMR 8089 CNRS, Cergy University, France
| | - Hadjer Ouldali
- LAMBE UMR 8587 CNRS, Cergy and Évry Universities, France
| | | | | | - Jan C Behrends
- Laboratory for Membrane Physiology and Technology, Faculty of Medicine, Department of Physiology, University of Freiburg, Germany.,Freiburg Materials Research Centre, University of Freiburg, Germany.,Centre for Interactive Materials and Bioinspired Technologies, University of Freiburg, Germany
| | - Juan Pelta
- LAMBE UMR 8587 CNRS, Cergy and Évry Universities, France
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39
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Boukhet M, Piguet F, Ouldali H, Pastoriza-Gallego M, Pelta J, Oukhaled A. Probing driving forces in aerolysin and α-hemolysin biological nanopores: electrophoresis versus electroosmosis. NANOSCALE 2016; 8:18352-18359. [PMID: 27762420 DOI: 10.1039/c6nr06936c] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The transport of macromolecules through nanopores is involved in many biological functions and is today at the basis of promising technological applications. Nevertheless the interpretation of the dynamics of the macromolecule/nanopore interaction is still misunderstood and under debate. At the nanoscale, inside biomimetic channels under an external applied voltage, electrophoresis, which is the electric force acting on electrically charged molecules, and electroosmotic flow (EOF), which is the fluid transport associated with ions, contribute to the direction and magnitude of the molecular transport. In order to decipher the contribution of the electrophoresis and electroosmotic flow, we explored the interaction of small, rigid, neutral molecules (cyclodextrins) and flexible, non-ionic polymers (poly(ethylene glycol), PEG) that can coordinate cations under appropriate experimental conditions, with two biological nanopores: aerolysin (AeL) and α-hemolysin (aHL). We performed experiments using two electrolytes with different ionic hydration (KCl and LiCl). Regardless of the nature of the nanopore and of the electrolyte, cyclodextrins behaved as neutral analytes. The dominant driving force was attributed to EOF, acting in the direction of the anion flow and stronger in LiCl than in KCl. The same qualitative behaviour was observed for PEGs in LiCl. In contrast, in KCl, PEGs behaved as positively charged polyelectrolytes through both AeL and aHL. Our results are in agreement with theoretical predictions about the injection of polymers inside a confined geometry (ESI). We believe our results to be of significant importance for better control of the dynamics of analytes of different nature through biological nanopores.
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Affiliation(s)
- Mordjane Boukhet
- LAMBE UMR 8587 CNRS, Universities of Cergy-Pontoise and Évry, France.
| | - Fabien Piguet
- LAMBE UMR 8587 CNRS, Universities of Cergy-Pontoise and Évry, France.
| | - Hadjer Ouldali
- LAMBE UMR 8587 CNRS, Universities of Cergy-Pontoise and Évry, France.
| | | | - Juan Pelta
- LAMBE UMR 8587 CNRS, Universities of Cergy-Pontoise and Évry, France.
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40
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Kenaan A, Nguyen TD, Dallaporta H, Raimundo JM, Charrier AM. Subpicomolar Iron Sensing Platform Based on Functional Lipid Monolayer Microarrays. Anal Chem 2016; 88:3804-9. [DOI: 10.1021/acs.analchem.5b04834] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ahmad Kenaan
- Aix-Marseille Université, CNRS, CINaM-UMR 7325, Marseille 13288, France
| | - Tuyen D. Nguyen
- Institute
for Microelectronic Technology and Information, NACENTECH, Ha Noi, Vietnam
| | - Hervé Dallaporta
- Aix-Marseille Université, CNRS, CINaM-UMR 7325, Marseille 13288, France
| | | | - Anne M. Charrier
- Aix-Marseille Université, CNRS, CINaM-UMR 7325, Marseille 13288, France
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41
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Burns JR, Seifert A, Fertig N, Howorka S. A biomimetic DNA-based channel for the ligand-controlled transport of charged molecular cargo across a biological membrane. NATURE NANOTECHNOLOGY 2016; 11:152-6. [PMID: 26751170 DOI: 10.1038/nnano.2015.279] [Citation(s) in RCA: 257] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 10/29/2015] [Indexed: 05/21/2023]
Abstract
Biological ion channels are molecular gatekeepers that control transport across cell membranes. Recreating the functional principle of such systems and extending it beyond physiological ionic cargo is both scientifically exciting and technologically relevant to sensing or drug release. However, fabricating synthetic channels with a predictable structure remains a significant challenge. Here, we use DNA as a building material to create an atomistically determined molecular valve that can control when and which cargo is transported across a bilayer. The valve, which is made from seven concatenated DNA strands, can bind a specific ligand and, in response, undergo a nanomechanical change to open up the membrane-spanning channel. It is also able to distinguish with high selectivity the transport of small organic molecules that differ by the presence of a positively or negatively charged group. The DNA device could be used for controlled drug release and the building of synthetic cell-like or logic ionic networks.
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Affiliation(s)
- Jonathan R Burns
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, UK
| | | | | | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, UK
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42
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Baaken G, Halimeh I, Bacri L, Pelta J, Oukhaled A, Behrends JC. High-Resolution Size-Discrimination of Single Nonionic Synthetic Polymers with a Highly Charged Biological Nanopore. ACS NANO 2015; 9:6443-6449. [PMID: 26028280 DOI: 10.1021/acsnano.5b02096] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Electrophysiological studies of the interaction of polymers with pores formed by bacterial toxins (1) provide a window on single molecule interaction with proteins in real time, (2) report on the behavior of macromolecules in confinement, and (3) enable label-free single molecule sensing. Using pores formed by the staphylococcal toxin α-hemolysin (aHL), a particularly pertinent observation was that, under high salt conditions (3-4 M KCl), the current through the pore is blocked for periods of hundreds of microseconds to milliseconds by poly(ethylene glycol) (PEG) oligomers (degree of polymerization approximately 10-60). Notably, this block showed monomeric sensitivity on the degree of polymerization of individual oligomers, allowing the construction of size or mass spectra from the residual current values. Here, we show that the current through the pore formed by aerolysin (AeL) from Aeromonas hydrophila is also blocked by PEG but with drastic differences in the voltage-dependence of the interaction. In contrast to aHL, AeL strongly binds PEG at high transmembrane voltages. This fact, which is likely related to AeL's highly charged pore wall, allows discrimination of polymer sizes with particularly high resolution. Multiple applications are now conceivable with this pore to screen various nonionic or charged polymers.
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Affiliation(s)
- Gerhard Baaken
- ‡Ionera Technologies GmbH, Hermann Herder Strasse 7, 79104 Freiburg, Germany
| | - Ibrahim Halimeh
- ‡Ionera Technologies GmbH, Hermann Herder Strasse 7, 79104 Freiburg, Germany
| | - Laurent Bacri
- §Laboratoire LAMBE, Équipe Polymères aux Interfaces, LAMBE UMR 8587 CNRS, Évry and Cergy University, Cergy-Pontoise 95011 cedex, France
| | - Juan Pelta
- §Laboratoire LAMBE, Équipe Polymères aux Interfaces, LAMBE UMR 8587 CNRS, Évry and Cergy University, Cergy-Pontoise 95011 cedex, France
| | - Abdelghani Oukhaled
- §Laboratoire LAMBE, Équipe Polymères aux Interfaces, LAMBE UMR 8587 CNRS, Évry and Cergy University, Cergy-Pontoise 95011 cedex, France
| | - Jan C Behrends
- ∥Freiburg Materials Research Centre (FMF), University of Freiburg, Stefan-Meier-Strasse 21, 79104 Freiburg, Germany
- ⊥Centre for Interactive Materials and Bioinspired Technologies (FIT), Georges-Köhler-Allee 105, 79110 Freiburg, Germany
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43
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Cell Surface and Membrane Engineering: Emerging Technologies and Applications. J Funct Biomater 2015; 6:454-85. [PMID: 26096148 PMCID: PMC4493524 DOI: 10.3390/jfb6020454] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/08/2015] [Accepted: 06/12/2015] [Indexed: 12/31/2022] Open
Abstract
Membranes constitute the interface between the basic unit of life—a single cell—and the outside environment and thus in many ways comprise the ultimate “functional biomaterial”. To perform the many and often conflicting functions required in this role, for example to partition intracellular contents from the outside environment while maintaining rapid intake of nutrients and efflux of waste products, biological membranes have evolved tremendous complexity and versatility. This article describes how membranes, mainly in the context of living cells, are increasingly being manipulated for practical purposes with drug discovery, biofuels, and biosensors providing specific, illustrative examples. Attention is also given to biology-inspired, but completely synthetic, membrane-based technologies that are being enabled by emerging methods such as bio-3D printers. The diverse set of applications covered in this article are intended to illustrate how these versatile technologies—as they rapidly mature—hold tremendous promise to benefit human health in numerous ways ranging from the development of new medicines to sensitive and cost-effective environmental monitoring for pathogens and pollutants to replacing hydrocarbon-based fossil fuels.
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44
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Weichbrodt C, Bajaj H, Baaken G, Wang J, Guinot S, Kreir M, Behrends JC, Winterhalter M, Fertig N. Antibiotic translocation through porins studied in planar lipid bilayers using parallel platforms. Analyst 2015; 140:4874-81. [DOI: 10.1039/c4an02335h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A comparative study of three different techniques Orbit16, Port-a-Patch and BLM applied for the investigation of antibiotic translocation.
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Affiliation(s)
| | | | | | - Jiajun Wang
- Nanion Technologies GmbH
- 80 636 Munich
- Germany
- Jacobs University Bremen
- 28 759 Bremen
| | | | | | - Jan C. Behrends
- Ionera Technologies GmbH
- 79104 Freiburg
- Germany
- Laboratory for Membrane Physiology and Technology
- Department of Physiology
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45
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Structural and mechanistic insights into the bacterial amyloid secretion channel CsgG. Nature 2014; 516:250-3. [PMID: 25219853 DOI: 10.1038/nature13768] [Citation(s) in RCA: 202] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 08/13/2014] [Indexed: 11/09/2022]
Abstract
Curli are functional amyloid fibres that constitute the major protein component of the extracellular matrix in pellicle biofilms formed by Bacteroidetes and Proteobacteria (predominantly of the α and γ classes). They provide a fitness advantage in pathogenic strains and induce a strong pro-inflammatory response during bacteraemia. Curli formation requires a dedicated protein secretion machinery comprising the outer membrane lipoprotein CsgG and two soluble accessory proteins, CsgE and CsgF. Here we report the X-ray structure of Escherichia coli CsgG in a non-lipidated, soluble form as well as in its native membrane-extracted conformation. CsgG forms an oligomeric transport complex composed of nine anticodon-binding-domain-like units that give rise to a 36-stranded β-barrel that traverses the bilayer and is connected to a cage-like vestibule in the periplasm. The transmembrane and periplasmic domains are separated by a 0.9-nm channel constriction composed of three stacked concentric phenylalanine, asparagine and tyrosine rings that may guide the extended polypeptide substrate through the secretion pore. The specificity factor CsgE forms a nonameric adaptor that binds and closes off the periplasmic face of the secretion channel, creating a 24,000 Å(3) pre-constriction chamber. Our structural, functional and electrophysiological analyses imply that CsgG is an ungated, non-selective protein secretion channel that is expected to employ a diffusion-based, entropy-driven transport mechanism.
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