1
|
Tang T, Sun J, Li C. The role of Phafin proteins in cell signaling pathways and diseases. Open Life Sci 2024; 19:20220896. [PMID: 38947768 PMCID: PMC11211877 DOI: 10.1515/biol-2022-0896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 05/14/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024] Open
Abstract
Membrane-associated proteins are important membrane readers that mediate and facilitate the signaling and trafficking pathways in eukaryotic membrane-bound compartments. The protein members in the Phafin family are membrane readers containing two phosphoinositide recognition domains: the Pleckstrin Homology domain and the FYVE (Fab1, YOTB, Vac1, and early endosome antigen 1) domain. Phafin proteins, categorized into two subfamilies, Phafin1 and Phafin2, associate with cellular membranes through interactions involving membrane-embedded phosphoinositides and phosphoinositide-binding domains. These membrane-associated Phafin proteins play pivotal roles by recruiting binding partners and forming complexes, which contribute significantly to apoptotic, autophagic, and macropinocytotic pathways. Elevated expression levels of Phafin1 and Phafin2 are observed in various cancers. A recent study highlights a significant increase in Phafin1 protein levels in the lungs of idiopathic pulmonary fibrosis patients compared to normal subjects, suggesting a crucial role for Phafin1 in the pathogenesis of pulmonary fibrosis. Additionally, phosphatidylinositol-3-phosphate-binding 2 (Pib2), a close relative of the Phafin1 protein, functions as an amino acid sensor activating the TOCR1 pathway in yeasts. This review focuses on delineating the involvement of Phafin proteins in cellular signaling and their implications in diseases and briefly discusses the latest research findings concerning Pib2.
Collapse
Affiliation(s)
- Tuoxian Tang
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jing Sun
- Department of Biostatistics and Epidemiology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Chen Li
- Department of Biology, Chemistry, Pharmacy, Free University of Berlin, Berlin, Germany
| |
Collapse
|
2
|
Pierce M, Ji J, Novak SX, Sieburg MA, Nangia S, Nangia S, Hougland JL. Combined Computational-Biochemical Approach Offers an Accelerated Path to Membrane Protein Solubilization. J Chem Inf Model 2023; 63:7159-7170. [PMID: 37939203 PMCID: PMC10685452 DOI: 10.1021/acs.jcim.3c00917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 10/25/2023] [Accepted: 10/25/2023] [Indexed: 11/10/2023]
Abstract
Membrane proteins are difficult to isolate and purify due to their dependence on the surrounding lipid membrane for structural stability. Detergents are often used to solubilize these proteins, with this approach requiring a careful balance between protein solubilization and denaturation. Determining which detergent is most appropriate for a given protein has largely been done empirically through screening, which requires large amounts of membrane protein and associated resources. Here, we describe an alternative to conventional detergent screening using a computational modeling approach to identify the most likely candidate detergents for solubilizing a protein of interest. We demonstrate our approach using ghrelin O-acyltransferase (GOAT), a member of the membrane-bound O-acyltransferase family of integral membrane enzymes that has not been solubilized or purified in active form. A computationally derived GOAT structural model provides the only structural information required for this approach. Using computational analysis of detergent ability to penetrate phospholipid bilayers and stabilize the GOAT structure, a panel of common detergents were rank-ordered for their proposed ability to solubilize GOAT. The simulations were performed at all-atom resolution for a combined simulation time of 24 μs. Independently, we biologically screened these detergents for their solubilization of fluorescently tagged GOAT constructs. We found computational prediction of protein structural stabilization was the better predictor of detergent solubilization ability, but neither approach was effective for predicting detergents that would support GOAT enzymatic function. The current rapid expansion of membrane protein computational models lacking experimental structural information and our computational detergent screening approach can greatly improve the efficiency of membrane protein detergent solubilization, supporting downstream functional and structural studies.
Collapse
Affiliation(s)
- Mariah
R. Pierce
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Jingjing Ji
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Sadie X. Novak
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Michelle A. Sieburg
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Shivangi Nangia
- Department
of Chemistry, University of Hartford, West Hartford, Connecticut 06117, United States
| | - Shikha Nangia
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
- BioInspired
Syracuse, Syracuse, New York 13244, United States
| | - James L. Hougland
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
- BioInspired
Syracuse, Syracuse, New York 13244, United States
- Department
of Biology, Syracuse University, Syracuse, New York 13244, United States
| |
Collapse
|
3
|
Larsen A, John L, Sansom M, Corey R. Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us? Biosci Rep 2022; 42:BSR20211406. [PMID: 35297484 PMCID: PMC9008707 DOI: 10.1042/bsr20211406] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 12/04/2022] Open
Abstract
Peripheral membrane proteins (PMPs) can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding domains are typically solved in a soluble form, sometimes with a lipid or lipid headgroup at the binding site. To provide a detailed molecular view of PMP interactions with the membrane, computational methods such as molecular dynamics (MD) simulations can be applied. Here, we outline recent attempts to characterise these binding interactions, focusing on both intracellular proteins, such as phosphatidylinositol phosphate (PIP)-binding domains, and extracellular proteins such as glycolipid-binding bacterial exotoxins. We compare methods used to identify and analyse lipid-binding sites from simulation data and highlight recent work characterising the energetics of these interactions using free energy calculations. We describe how improvements in methodologies and computing power will help MD simulations to continue to contribute to this field in the future.
Collapse
Affiliation(s)
| | - Laura H. John
- Department of Biochemistry, University of Oxford, Oxford, U.K
| | | | - Robin A. Corey
- Department of Biochemistry, University of Oxford, Oxford, U.K
| |
Collapse
|
4
|
Guo C, Cheng M, Li W, Gross ML. Diethylpyrocarbonate Footprints a Membrane Protein in Micelles. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2636-2643. [PMID: 34664961 PMCID: PMC8903028 DOI: 10.1021/jasms.1c00172] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Membrane proteins play crucial roles in cell signaling and transport and, thus, are the targets of many small molecule drugs. The characterization of membrane protein structures poses challenges for the high-resolution biophysical tools because the transmembrane (TM) domain is hydrophobic, opening an opportunity for mass spectrometry (MS)-based footprinting. The hydrophobic reagent diethylpyrocarbonate (DEPC), a heavily studied footprinter for water-soluble proteins, can label up to 30% of surface residues via a straightforward protocol, streamlining the MS-based footprinting workflow. To test its applicability to membrane proteins, we footprinted vitamin K epoxide reductase (VKOR) membrane protein with DEPC. The results demonstrate that besides labeling the hydrophilic extracellular (extramembrane (EM)) domain, DEPC can also diffuse into the hydrophobic TM domain and subsequently label that region. The labeling process was facilitated by tip sonication to enhance reagent diffusion into micelles. We then analyzed the correlation between the residue modification extent and the theoretical accessible surface area percentage (%ASA); the data generally show good correlation with the residue location. Compared with conventional hydrophilic footprinters, the relatively hydrophobic DEPC can map a membrane protein's TM domain, suggesting that the reagent's hydrophobicity can be exploited to obtain structural information on the membrane-spanning region. This encouraging result should assist in the development of more efficient footprinters for membrane protein TM domain footprinting, enabled by further understanding the relationship between a reagent's hydrophobicity and its preferred labeling sites.
Collapse
Affiliation(s)
- Chunyang Guo
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United States
| | - Ming Cheng
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United States
| | - Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Michael L Gross
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United States
| |
Collapse
|
5
|
Novikova OD, Naberezhnykh GA, Sergeev AA. Nanostructured Biosensors Based on Components of Bacterial Membranes. Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s0006350921040187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
|
6
|
Missel JW, Salustros N, Becares ER, Steffen JH, Laursen AG, Garcia AS, Garcia-Alai MM, Kolar Č, Gourdon P, Gotfryd K. Cyclohexyl-α maltoside as a highly efficient tool for membrane protein studies. Curr Res Struct Biol 2021; 3:85-94. [PMID: 34235488 PMCID: PMC8244287 DOI: 10.1016/j.crstbi.2021.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/09/2021] [Accepted: 03/05/2021] [Indexed: 01/06/2023] Open
Abstract
Membrane proteins (MPs) constitute a large fraction of the proteome, but exhibit physicochemical characteristics that impose challenges for successful sample production crucial for subsequent biophysical studies. In particular, MPs have to be extracted from the membranes in a stable form. Reconstitution into detergent micelles represents the most common procedure in recovering MPs for subsequent analysis. n-dodecyl-β-D-maltoside (DDM) remains one of the most popular conventional detergents used in production of MPs. Here we characterize the novel DDM analogue 4-trans-(4-trans-propylcyclohexyl)-cyclohexyl α-maltoside (t-PCCαM), possessing a substantially lower critical micelle concentration (CMC) than the parental compound that represents an attractive feature when handling MPs. Using three different types of MPs of human and prokaryotic origin, i.e., a channel, a primary and a secondary active transporter, expressed in yeast and bacterial host systems, respectively, we investigate the performance of t-PCCαM in solubilization and affinity purification together with its capacity to preserve native fold and activity. Strikingly, t-PCCαM displays favorable behavior in extracting and stabilizing the three selected targets. Importantly, t-PCCαM promoted extraction of properly folded protein, enhanced thermostability and provided negatively-stained electron microscopy samples of promising quality. All-in-all, t-PCCαM emerges as competitive surfactant applicable to a broad portfolio of challenging MPs for downstream structure-function analysis.
Collapse
Affiliation(s)
- Julie Winkel Missel
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark
| | - Nina Salustros
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark
| | - Eva Ramos Becares
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark
| | - Jonas Hyld Steffen
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark
| | - Amalie Gerdt Laursen
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark
| | - Angelica Struve Garcia
- European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607, Hamburg, Germany
| | - Maria M Garcia-Alai
- European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607, Hamburg, Germany.,Centre for Structural Systems Biology, Notkestrasse 85, D-22607, Hamburg, Germany
| | - Čeněk Kolar
- Glycon Biochemicals GmbH, Im Biotechnologie Park TGZ 1, D-14943, Luckenwalde, Germany
| | - Pontus Gourdon
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark.,Department of Experimental Medical Science, Lund University, Sölvegatan 19, SE-221 84, Lund, Sweden
| | - Kamil Gotfryd
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark
| |
Collapse
|
7
|
Scratching the surface: native mass spectrometry of peripheral membrane protein complexes. Biochem Soc Trans 2021; 48:547-558. [PMID: 32129823 PMCID: PMC7192793 DOI: 10.1042/bst20190787] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/09/2020] [Accepted: 02/11/2020] [Indexed: 02/06/2023]
Abstract
A growing number of integral membrane proteins have been shown to tune their activity by selectively interacting with specific lipids. The ability to regulate biological functions via lipid interactions extends to the diverse group of proteins that associate only peripherally with the lipid bilayer. However, the structural basis of these interactions remains challenging to study due to their transient and promiscuous nature. Recently, native mass spectrometry has come into focus as a new tool to investigate lipid interactions in membrane proteins. Here, we outline how the native MS strategies developed for integral membrane proteins can be applied to generate insights into the structure and function of peripheral membrane proteins. Specifically, native MS studies of proteins in complex with detergent-solubilized lipids, bound to lipid nanodiscs, and released from native-like lipid vesicles all shed new light on the role of lipid interactions. The unique ability of native MS to capture and interrogate protein–protein, protein–ligand, and protein–lipid interactions opens exciting new avenues for the study of peripheral membrane protein biology.
Collapse
|
8
|
Parallel Recordings of Transmembrane hERG Channel Currents Based on Solvent-Free Lipid Bilayer Microarray. MICROMACHINES 2021; 12:mi12010098. [PMID: 33478052 PMCID: PMC7835820 DOI: 10.3390/mi12010098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/23/2022]
Abstract
The reconstitution of ion-channel proteins in artificially formed bilayer lipid membranes (BLMs) forms a well-defined system for the functional analysis of ion channels and screening of the effects of drugs that act on these proteins. To improve the efficiency of the BLM reconstitution system, we report on a microarray of stable solvent-free BLMs formed in microfabricated silicon (Si) chips, where micro-apertures with well-defined nano- and micro-tapered edges were fabricated. Sixteen micro-wells were manufactured in a chamber made of Teflon®, and the Si chips were individually embedded in the respective wells as a recording site. Typically, 11 to 16 BLMs were simultaneously formed with an average BLM number of 13.1, which corresponded to a formation probability of 82%. Parallel recordings of ion-channel activities from multiple BLMs were successfully demonstrated using the human ether-a-go-go-related gene (hERG) potassium channel, of which the relation to arrhythmic side effects following drug treatment is well recognized.
Collapse
|
9
|
Fuel Cell Using Squid Axon Electrolyte and Its Proton Conductivity. J Funct Biomater 2020; 11:jfb11040086. [PMID: 33287321 PMCID: PMC7768438 DOI: 10.3390/jfb11040086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/25/2020] [Accepted: 12/01/2020] [Indexed: 11/16/2022] Open
Abstract
Fuel cells using biomaterials have the potential for environmentally friendly clean energy and have attracted a lot of interest. Moreover, biomaterials are expected to develop into in vivo electrical devices such as pacemakers with no side effects. Ion channels, which are membrane proteins, are known to have a fast ion transport capacity. Therefore, by using ion channels, the realization of fuel cell electrolytes with high-proton conductivity can be expected. In this study, we have fabricated a fuel cell using an ion channel electrolyte for the first time and investigated the electrical properties of the ion channel electrolyte. It was found that the fuel cell using the ion channel membrane shows a power density of 0.78 W/cm2 in the humidified condition. On the other hand, the power density of the fuel cell blocking the ion channel with the channel blocker drastically decreased. These results indicate that the fuel cell using the ion channel electrolyte operates through the existence of the ion channel and that the ion channel membrane can be used as the electrolyte of the fuel cell in humidified conditions. Furthermore, the proton conductivity of the ion channel electrolyte drastically increases above 85% relative humidity (RH) and becomes 2 × 10-2 S/m at 96% RH. This result indicates that the ion channel becomes active above 96%RH. In addition, it was deduced from the impedance analysis that the high proton conductivity of the ion channel electrolyte above 96% RH is caused by the activation of ion channels, which are closely related to the fractionalization of water molecule clusters. From these results, it was found that a fuel cell using the squid axon becomes a new fuel cell using the function of the ion channel above 96% RH.
Collapse
|
10
|
Abstract
Proteins are the main source of drug targets and some of them possess therapeutic potential themselves. Among them, membrane proteins constitute approximately 50% of the major drug targets. In the drug discovery pipeline, rapid methods for producing different classes of proteins in a simple manner with high quality are important for structural and functional analysis. Cell-free systems are emerging as an attractive alternative for the production of proteins due to their flexible nature without any cell membrane constraints. In a bioproduction context, open systems based on cell lysates derived from different sources, and with batch-to-batch consistency, have acted as a catalyst for cell-free synthesis of target proteins. Most importantly, proteins can be processed for downstream applications like purification and functional analysis without the necessity of transfection, selection, and expansion of clones. In the last 5 years, there has been an increased availability of new cell-free lysates derived from multiple organisms, and their use for the synthesis of a diverse range of proteins. Despite this progress, major challenges still exist in terms of scalability, cost effectiveness, protein folding, and functionality. In this review, we present an overview of different cell-free systems derived from diverse sources and their application in the production of a wide spectrum of proteins. Further, this article discusses some recent progress in cell-free systems derived from Chinese hamster ovary and Sf21 lysates containing endogenous translocationally active microsomes for the synthesis of membrane proteins. We particularly highlight the usage of internal ribosomal entry site sequences for more efficient protein production, and also the significance of site-specific incorporation of non-canonical amino acids for labeling applications and creation of antibody drug conjugates using cell-free systems. We also discuss strategies to overcome the major challenges involved in commercializing cell-free platforms from a laboratory level for future drug development.
Collapse
Affiliation(s)
- Srujan Kumar Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany.
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus-Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany.
| |
Collapse
|
11
|
Damiati S, Schuster B. Electrochemical Biosensors Based on S-Layer Proteins. SENSORS (BASEL, SWITZERLAND) 2020; 20:E1721. [PMID: 32204503 PMCID: PMC7147708 DOI: 10.3390/s20061721] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/05/2020] [Accepted: 03/17/2020] [Indexed: 01/29/2023]
Abstract
Designing and development of electrochemical biosensors enable molecule sensing and quantification of biochemical compositions with multitudinous benefits such as monitoring, detection, and feedback for medical and biotechnological applications. Integrating bioinspired materials and electrochemical techniques promote specific, rapid, sensitive, and inexpensive biosensing platforms for (e.g., point-of-care testing). The selection of biomaterials to decorate a biosensor surface is a critical issue as it strongly affects selectivity and sensitivity. In this context, smart biomaterials with the intrinsic self-assemble capability like bacterial surface (S-) layer proteins are of paramount importance. Indeed, by forming a crystalline two-dimensional protein lattice on many sensors surfaces and interfaces, the S-layer lattice constitutes an immobilization matrix for small biomolecules and lipid membranes and a patterning structure with unsurpassed spatial distribution for sensing elements and bioreceptors. This review aims to highlight on exploiting S-layer proteins in biosensor technology for various applications ranging from detection of metal ions over small organic compounds to cells. Furthermore, enzymes immobilized on the S-layer proteins allow specific detection of several vital biomolecules. The special features of the S-layer protein lattice as part of the sensor architecture enhances surface functionalization and thus may feature an innovative class of electrochemical biosensors.
Collapse
Affiliation(s)
- Samar Damiati
- Department of Biochemistry, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia;
- Institute for Synthetic Bioarchitectures, Department of NanoBiotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190 Vienna, Austria
- Current address: Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 171 21 Solna, Stockholm, Sweden
| | - Bernhard Schuster
- Institute for Synthetic Bioarchitectures, Department of NanoBiotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190 Vienna, Austria
| |
Collapse
|
12
|
Enhancement of membrane protein reconstitution on 3D free-standing lipid bilayer array in a microfluidic channel. Biosens Bioelectron 2019; 141:111404. [DOI: 10.1016/j.bios.2019.111404] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/24/2019] [Accepted: 06/01/2019] [Indexed: 12/11/2022]
|
13
|
Shelby ML, He W, Dang AT, Kuhl TL, Coleman MA. Cell-Free Co-Translational Approaches for Producing Mammalian Receptors: Expanding the Cell-Free Expression Toolbox Using Nanolipoproteins. Front Pharmacol 2019; 10:744. [PMID: 31333463 PMCID: PMC6616253 DOI: 10.3389/fphar.2019.00744] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/07/2019] [Indexed: 12/28/2022] Open
Abstract
Membranes proteins make up more than 60% of current drug targets and account for approximately 30% or more of the cellular proteome. Access to this important class of proteins has been difficult due to their inherent insolubility and tendency to aggregate in aqueous solutions. Understanding membrane protein structure and function demands novel means of membrane protein production that preserve both their native conformational state as well as function. Over the last decade, cell-free expression systems have emerged as an important complement to cell-based expression of membrane proteins due to their simple and customizable experimental parameters. One approach to overcome the solubility and stability limitations of purified membrane proteins is to support them in stable, native-like states within nanolipoprotein particles (NLPs), aka nanodiscs. This has become common practice to facilitate biochemical and biophysical characterization of proteins of interest. NLP technology can be easily coupled with cell-free systems to achieve functional membrane protein production for this purpose. Our approach involves utilizing cell-free expression systems in the presence of NLPs or using co-translation techniques to perform one-pot expression and self-assembly of membrane protein/NLP complexes. We describe how cell-free reactions can be modified to render control over nanoparticle size and monodispersity in support of membrane protein production. These modifications have been exploited to facilitate co-expression of full-length functional membrane proteins such as G-protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs). In particular, we summarize the state of the art in NLP-assisted cell-free coexpression of these important classes of membrane proteins as well as evaluate the advances in and prospects for this technology that will drive drug discovery against these targets. We conclude with a prospective on the use of NLPs to produce as well as deliver functional mammalian membrane-bound proteins for a range of applications.
Collapse
Affiliation(s)
- Megan L Shelby
- Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Wei He
- Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Amanda T Dang
- University of California at Davis, Davis, CA, United States
| | - Tonya L Kuhl
- University of California at Davis, Davis, CA, United States
| | - Matthew A Coleman
- Lawrence Livermore National Laboratory, Livermore, CA, United States.,University of California at Davis, Davis, CA, United States
| |
Collapse
|
14
|
Getz RA, Kwak G, Cornell S, Mbugua S, Eberhard J, Huang SX, Abbasi Z, de Medeiros AS, Thomas R, Bukowski B, Dranchak PK, Inglese J, Hoffman CS. A fission yeast platform for heterologous expression of mammalian adenylyl cyclases and high throughput screening. Cell Signal 2019; 60:114-121. [PMID: 31026495 DOI: 10.1016/j.cellsig.2019.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/12/2019] [Accepted: 04/22/2019] [Indexed: 01/18/2023]
Abstract
The fission yeast Schizosaccharomyces pombe uses a cAMP signaling pathway to link glucose-sensing to Protein Kinase A activity in order to regulate cell growth, sexual development, gluconeogenesis, and exit from stationary phase. We previously used a PKA-repressed fbp1-ura4 reporter to conduct high throughput screens (HTSs) for inhibitors of heterologously-expressed mammalian cyclic nucleotide phosphodiesterases (PDEs). Here, we describe the successful expression of all ten mammalian adenylyl cyclase (AC) genes, along with the human GNAS Gαs gene. By measuring expression of an fbp1-GFP reporter together with direct measurements of intracellular cAMP levels, we can detect both basal AC activity from all ten AC genes as well as GNAS-stimulated activity from eight of the nine transmembrane ACs (tmACs; AC2-AC9). The ability to use this platform to conduct HTS for novel chemical probes that reduce PKA activity was demonstrated by a pilot screen of the LOPAC®1280 library, leading to the identification of diphenyleneiodonium chloride (DPI) as an inhibitor of basal AC activity. This screening technology could open the door to the development of therapeutic compounds that target GNAS or the ACs, an area in which there is significant unmet need.
Collapse
Affiliation(s)
- Rachel A Getz
- Biology Department, Boston College, 140 Commonwealth Ave., Chestnut Hill, MA 02467, USA
| | - Grace Kwak
- Biology Department, Boston College, 140 Commonwealth Ave., Chestnut Hill, MA 02467, USA
| | - Stacie Cornell
- Biology Department, Boston College, 140 Commonwealth Ave., Chestnut Hill, MA 02467, USA
| | - Samuel Mbugua
- Biology Department, Boston College, 140 Commonwealth Ave., Chestnut Hill, MA 02467, USA.
| | - Jeremy Eberhard
- Biology Department, Boston College, 140 Commonwealth Ave., Chestnut Hill, MA 02467, USA.
| | - Sheng Xiang Huang
- Biology Department, Boston College, 140 Commonwealth Ave., Chestnut Hill, MA 02467, USA.
| | - Zainab Abbasi
- Biology Department, Boston College, 140 Commonwealth Ave., Chestnut Hill, MA 02467, USA.
| | | | - Rony Thomas
- Biology Department, Boston College, 140 Commonwealth Ave., Chestnut Hill, MA 02467, USA.
| | - Brett Bukowski
- Biology Department, Boston College, 140 Commonwealth Ave., Chestnut Hill, MA 02467, USA.
| | - Patricia K Dranchak
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA.
| | - James Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA.
| | - Charles S Hoffman
- Biology Department, Boston College, 140 Commonwealth Ave., Chestnut Hill, MA 02467, USA.
| |
Collapse
|
15
|
Yamaura D, Tadaki D, Araki S, Yoshida M, Arata K, Ohori T, Ishibashi KI, Kato M, Ma T, Miyata R, Yamamoto H, Tero R, Sakuraba M, Ogino T, Niwano M, Hirano-Iwata A. Amphiphobic Septa Enhance the Mechanical Stability of Free-Standing Bilayer Lipid Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:5615-5622. [PMID: 29664647 DOI: 10.1021/acs.langmuir.8b00747] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Artificial bilayer lipid membranes (BLMs) provide well-defined systems for investigating the fundamental properties of membrane proteins, including ion channels, and for screening the effect of drugs that act on them. However, the application of this technique is limited due to the low stability and low reconstitution efficiency of the process. We previously reported on improving the stability of BLM based on the fabrication of microapertures having a tapered edge in SiO2/Si3N4 septa and efficient ion channel incorporation based on vesicle fusion accelerated by a centrifugal force. Although the BLM stability and incorporation probability were dramatically improved when these approaches were used, some BLMs were ruptured when subjected to a centrifugal force. To further improve the BLM stability, we investigated the effect of modifying the surface of the SiO2/Si3N4 septa on the stability of BLM suspended in the septa. The modified surfaces were characterized in terms of hydrophobicity, lipophobicity, and surface roughness. Diffusion coefficients of the lipid monolayers formed on the modified surfaces were also determined. Highly fluidic lipid monolayers were formed on the amphiphobic substrates that had been modified with long-chain perfluorocarbons. Free-standing BLMs formed in amphiphobic septa showed a much higher mechanical stability, including tolerance to water movement and applied centrifugal forces with and without proteoliposomes, than those formed in the septa that had been modified with a short alkyl chain. These results demonstrate that highly stable BLMs are formed when the surface of the septa has amphiphobic properties. Because highly fluidic lipid monolayers that are formed on the septa seamlessly connect with BLMs in a free-standing region, the high fluidity of the lipids contributes to decreasing potential damage to BLMs when mechanical stresses are applied. This approach to improve the BLM stability increases the experimental efficiency of the BLM systems and will contribute to the development of high-throughput platforms for functional assays of ion channel proteins.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Ken-Ichi Ishibashi
- Hang-Ichi Corporation , 1-7-315 Honcho , Naka-ku, Yokohama , Kanagawa 231-0005 , Japan
| | | | | | | | - Hideaki Yamamoto
- Frontier Research Institute for Interdisciplinary Sciences , Tohoku University , 6-3 Aramaki-Aza-Aoba , Aoba-ku, Sendai , Miyagi 980-8578 , Japan
| | - Ryugo Tero
- Department of Environmental and Life Sciences , Toyohashi University of Technology , Toyohashi , Aichi 441-8580 , Japan
| | | | - Toshio Ogino
- The Instrumental Analysis Center , Yokohama National University , Tokiwadai 79-5 , Hodogaya-ku, Yokohama , Kanagawa 240-8501 , Japan
| | - Michio Niwano
- Kansei Fukushi Research Institute , Tohoku Fukushi University , 6-149-1 Kunimi-ga-oka , Aoba-ku, Sendai , Miyagi 989-3201 , Japan
| | | |
Collapse
|
16
|
Oshima A, Sumitomo K. Vesicle fusion with bilayer lipid membrane controlled by electrostatic interaction. Biochem Biophys Rep 2017; 11:58-63. [PMID: 28955768 PMCID: PMC5614691 DOI: 10.1016/j.bbrep.2017.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/16/2017] [Accepted: 06/16/2017] [Indexed: 11/07/2022] Open
Abstract
The fusion of proteoliposomes is a promising approach for incorporating membrane proteins in artificial lipid membranes. In this study, we employed an electrostatic interaction between vesicles and supported bilayer lipid membranes (s-BLMs) to control the fusion process. We combined large unilamellar vesicles (LUVs) containing anionic lipids, which we used instead of proteoliposomes, and s-BLMs containing cationic lipids to control electrostatic interaction. Anionic LUVs were never adsorbed or ruptured on the SiO2 substrate with a slight negative charge, and selectively fused with cationic s-BLMs. The LUVs can be fused effectively to the target position. Furthermore, as the vesicle fusion proceeds and some of the positive charges are neutralized, the attractive interaction weakens and finally the vesicle fusion saturates. In other words, we can control the number of LUVs fused with s-BLMs by controlling the concentration of the cationic lipids in the s-BLMs. The fluidity of the s-BLMs after vesicle fusion was confirmed to be sufficiently high. This indicates that the LUVs attached to the s-BLMs were almost completely fused, and there were few intermediate state vesicles in the fusion process. We could control the position and amount of vesicle fusion with the s-BLMs by employing an electrostatic interaction.
Collapse
Affiliation(s)
- Azusa Oshima
- NTT Basic Research Laboratories, NTT Corporation, 3-1 Morinosato Wakamiya, Atsugi, Kanagawa 243-0198, Japan
| | | |
Collapse
|
17
|
Fernandez Oropeza N, Zurek NA, Galvan-De La Cruz M, Fabry-Wood A, Fetzer JM, Graves SW, Shreve AP. Multiplexed Lipid Bilayers on Silica Microspheres for Analytical Screening Applications. Anal Chem 2017; 89:6440-6447. [PMID: 28558200 PMCID: PMC6342469 DOI: 10.1021/acs.analchem.7b00296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Most druggable targets are membrane components, including membrane proteins and soluble proteins that interact with ligands or receptors embedded in membranes. Current target-based screening and intermolecular interaction assays generally do not include the lipid membrane environment in presenting these targets, possibly altering their native structure and leading to misleading or incorrect results. To address this issue, an ideal assay involving membrane components would (1) mimic the natural membrane environment, (2) be amenable to high-throughput implementation, and (3) be easily multiplexed. In a step toward developing such an ideal target-based analytical assay for membrane components, we present fluorescently indexed multiplexed biomimetic membrane assays amenable to high-throughput flow cytometric detection. We build fluorescently multiplexed biomimetic membrane assays by using varying amounts of a fluorescently labeled lipid, NBD-DOPE [1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-(7-nitro-2-1,3-benzoxadiazol-4-yl)], incorporated into a phospholipid membrane bilayer supported on 3 μm silica microspheres. Using flow cytometry, we demonstrate this multiplexed approach by measuring specific affinity of two well-characterized systems, the fluorescently labeled soluble proteins cholera toxin B subunit-Alexa 647 and streptavidin-PE/Cy5, to membranes containing different amounts of ligand targets of these proteins, GM1 and biotin-DOPE, respectively. This work will enable future efforts in developing highly efficient biomimetic assays for interaction analysis and drug screening involving membrane components.
Collapse
Affiliation(s)
| | | | | | | | | | - Steven W. Graves
- Center for Biomedical Engineering
- Department of Chemical and Biological Engineering University of New Mexico Albuquerque, NM 87131
| | - Andrew P. Shreve
- Center for Biomedical Engineering
- Department of Chemical and Biological Engineering University of New Mexico Albuquerque, NM 87131
| |
Collapse
|
18
|
Bruzas I, Unser S, Yazdi S, Ringe E, Sagle L. Ultrasensitive Plasmonic Platform for Label-Free Detection of Membrane-Associated Species. Anal Chem 2016; 88:7968-74. [PMID: 27436204 DOI: 10.1021/acs.analchem.6b00801] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Lipid membranes and membrane proteins are important biosensing targets, motivating the development of label-free methods with improved sensitivity. Silica-coated metal nanoparticles allow these systems to be combined with supported lipid bilayers for sensing membrane proteins through localized surface plasmon resonance (LSPR). However, the small sensing volume of LSPR makes the thickness of the silica layer critical for performance. Here, we develop a simple, inexpensive, and rapid sol-gel method for preparing thin conformal, continuous silica films and demonstrate its applicability using gold nanodisk arrays with LSPRs in the near-infrared range. Silica layers as thin as ∼5 nm are observed using cross-sectional scanning transmission electron microscopy. The loss in sensitivity due to the thin silica coating was found to be only 16%, and the biosensing capabilities of the substrates were assessed through the binding of cholera toxin B to GM1 lipids. This sensor platform should prove useful in the rapid, multiplexed detection and screening of membrane-associated biological targets.
Collapse
Affiliation(s)
- Ian Bruzas
- Department of Chemistry, College of Arts and Sciences, University of Cincinnati , 301 West Clifton Court, Cincinnati, Ohio 45221-0172, United States
| | - Sarah Unser
- Department of Chemistry, College of Arts and Sciences, University of Cincinnati , 301 West Clifton Court, Cincinnati, Ohio 45221-0172, United States
| | - Sadegh Yazdi
- Department of Materials Science and NanoEngineering, Rice University , 6100 Main Street, MS-325, Houston, Texas 77005, United States
| | - Emilie Ringe
- Department of Materials Science and NanoEngineering, Rice University , 6100 Main Street, MS-325, Houston, Texas 77005, United States
| | - Laura Sagle
- Department of Chemistry, College of Arts and Sciences, University of Cincinnati , 301 West Clifton Court, Cincinnati, Ohio 45221-0172, United States
| |
Collapse
|
19
|
Streamlined Membrane Proteome Preparation for Shotgun Proteomics Analysis with Triton X-100 Cloud Point Extraction and Nanodiamond Solid Phase Extraction. MATERIALS 2016; 9:ma9050385. [PMID: 28773508 PMCID: PMC5503057 DOI: 10.3390/ma9050385] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 04/28/2016] [Accepted: 05/11/2016] [Indexed: 12/19/2022]
Abstract
While mass spectrometry (MS) plays a key role in proteomics research, characterization of membrane proteins (MP) by MS has been a challenging task because of the presence of a host of interfering chemicals in the hydrophobic protein extraction process, and the low protease digestion efficiency. We report a sample preparation protocol, two-phase separation with Triton X-100, induced by NaCl, with coomassie blue added for visualizing the detergent-rich phase, which streamlines MP preparation for SDS-PAGE analysis of intact MP and shot-gun proteomic analyses. MP solubilized in the detergent-rich milieu were then sequentially extracted and fractionated by surface-oxidized nanodiamond (ND) at three pHs. The high MP affinity of ND enabled extensive washes for removal of salts, detergents, lipids, and other impurities to ensure uncompromised ensuing purposes, notably enhanced proteolytic digestion and down-stream mass spectrometric (MS) analyses. Starting with a typical membranous cellular lysate fraction harvested with centrifugation/ultracentrifugation, MP purities of 70%, based on number (not weight) of proteins identified by MS, was achieved; the weight-based purity can be expected to be much higher.
Collapse
|
20
|
Orosz KS, Jones IW, Keogh JP, Smith CM, Griffin KR, Xu J, Comi TJ, Hall HK, Saavedra SS. Photopolymerization of Dienoyl Lipids Creates Planar Supported Poly(lipid) Membranes with Retained Fluidity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:1577-84. [PMID: 26794208 PMCID: PMC4755918 DOI: 10.1021/acs.langmuir.5b03437] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Polymerization of substrate-supported bilayers composed of dienoylphosphatidylcholine (PC) lipids is known to greatly enhance their chemical and mechanical stability; however, the effects of polymerization on membrane fluidity have not been investigated. Here planar supported lipid bilayers (PSLBs) composed of dienoyl PCs on glass substrates were examined to assess the degree to which UV-initiated polymerization affects lateral lipid mobility. Fluorescence recovery after photobleaching (FRAP) was used to measure the diffusion coefficients (D) and mobile fractions of rhodamine-DOPE in unpolymerized and polymerized PSLBs composed of bis-sorbyl phosphatidylcholine (bis-SorbPC), mono-sorbyl-phosphatidylcholine (mono-SorbPC), bis-dienoyl-phosphatidylcholine (bis-DenPC), and mono-dienoyl phosphatidylcholine (mono-DenPC). Polymerization was performed in both the Lα and Lβ phase for each lipid. In all cases, polymerization reduced membrane fluidity; however, measurable lateral diffusion was retained which is attributed to a low degree of polymerization. The D values for sorbyl lipids were less than those of the denoyl lipids; this may be a consequence of the distal location of polymerizable group in the sorbyl lipids which may facilitate interleaflet bonding. The D values measured after polymerization were 0.1-0.8 of those measured before polymerization, a range that corresponds to fluidity intermediate between that of a Lα phase and a Lβ phase. This D range is comparable to ratios of D values reported for liquid-disordered (Ld) and liquid-ordered (Lo) lipid phases and indicates that the effect of UV polymerization on lateral diffusion in a dienoyl PSLB is similar to the transition from a Ld phase to a Lo phase. The partial retention of fluidity in UV-polymerized PSLBs, their enhanced stability, and the activity of incorporated transmembrane proteins and peptides is discussed.
Collapse
Affiliation(s)
- Kristina S. Orosz
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721
| | - Ian W. Jones
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721
| | - John P. Keogh
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721
| | - Christopher M. Smith
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721
| | - Kaitlyn R. Griffin
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721
| | - Juhua Xu
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721
| | - Troy J. Comi
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721
| | - H. K. Hall
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721
| | - S. Scott Saavedra
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721
- BIO5 Institute, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721
| |
Collapse
|
21
|
Hirano-Iwata A, Ishinari Y, Yamamoto H, Niwano M. Micro- and Nano-Technologies for Lipid Bilayer-Based Ion-Channel Functional Assays. Chem Asian J 2015; 10:1266-74. [DOI: 10.1002/asia.201403391] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Ayumi Hirano-Iwata
- CREST (Japan) Science and Technology Agency (JST); 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
- Graduate School of Biomedical Engineering; Tohoku University; 6-6 Aoba Aramaki, Aoba-ku Sendai 980-8579 Japan
| | - Yutaka Ishinari
- CREST (Japan) Science and Technology Agency (JST); 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
- Graduate School of Biomedical Engineering; Tohoku University; 6-6 Aoba Aramaki, Aoba-ku Sendai 980-8579 Japan
| | - Hideaki Yamamoto
- Graduate School of Biomedical Engineering; Tohoku University; 6-6 Aoba Aramaki, Aoba-ku Sendai 980-8579 Japan
- Frontier Research Institute for Interdisciplinary Sciences; Tohoku University; 6-3 Aoba Aramaki, Aoba-ku Sendai 980-8578 Japan
| | - Michio Niwano
- Graduate School of Biomedical Engineering; Tohoku University; 6-6 Aoba Aramaki, Aoba-ku Sendai 980-8579 Japan
- Laboratory for Nanoelectronics and Spintronics; Research Institute of Electrical Communication; Tohoku University; 6-6 Aoba Aramaki, Aoba-ku Sendai 980-8579 Japan
| |
Collapse
|
22
|
del Rio Martinez JM, Zaitseva E, Petersen S, Baaken G, Behrends JC. Automated formation of lipid membrane microarrays for ionic single-molecule sensing with protein nanopores. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:119-125. [PMID: 25115837 DOI: 10.1002/smll.201402016] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Indexed: 06/03/2023]
Abstract
Efficient use of membrane protein nanopores in ionic single-molecule sensing requires technology for the reliable formation of suspended molecular membranes densely arrayed in formats that allow high-resolution electrical recording. Here, automated formation of bimolecular lipid layers is shown using a simple process where a poly(tetrafluoroethylene)-coated magnetic bar is remotely actuated to perform a turning motion, thereby spreading phospholipid in organic solvent on a nonpolar surface containing a <1 mm(2) 4 × 4 array of apertures with embedded microelectrodes (microelectrode cavity array). Parallel and high-resolution single-molecule detection by single nanopores is demonstrated on the resulting bilayer arrays, which are shown to form by a classical but very rapid self-assembly process. The technique provides a robust and scalable solution for the problem of reliable, automated formation of multiple independent lipid bilayers in a dense microarray format, while preserving the favorable electrical properties of the microelectrode cavity array.
Collapse
Affiliation(s)
- Juan M del Rio Martinez
- Laboratory for Membrane Physiology and -Technology, Department of Physiology, University of Freiburg, Hermann-Herder-Str. 7, 79104, Freiburg, Germany
| | | | | | | | | |
Collapse
|
23
|
Spycher PR, Hall H, Vogel V, Reimhult E. Patterning of supported lipid bilayers and proteins using material selective nitrodopamine-mPEG. Biomater Sci 2015. [DOI: 10.1039/c4bm00090k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We present a generic patterning process by which biomolecules in a passivated background are patterned directly from physiological buffer to microfabricated surfaces without the need for further processing.
Collapse
Affiliation(s)
- Philipp R. Spycher
- Laboratory of Applied Mechanobiology
- Department of Health Sciences and Technology
- ETH Zurich
- Switzerland
| | - Heike Hall
- Laboratory of Applied Mechanobiology
- Department of Health Sciences and Technology
- ETH Zurich
- Switzerland
| | - Viola Vogel
- Laboratory of Applied Mechanobiology
- Department of Health Sciences and Technology
- ETH Zurich
- Switzerland
| | - Erik Reimhult
- Laboratory for Surface Science and Technology
- Department of Materials
- ETH Zurich
- Switzerland
- Institute for Biologically Inspired Materials
| |
Collapse
|
24
|
Horger KS, Liu H, Rao DK, Shukla S, Sept D, Ambudkar SV, Mayer M. Hydrogel-assisted functional reconstitution of human P-glycoprotein (ABCB1) in giant liposomes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:643-53. [PMID: 25450342 DOI: 10.1016/j.bbamem.2014.10.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 09/17/2014] [Accepted: 10/20/2014] [Indexed: 11/24/2022]
Abstract
This paper describes the formation of giant proteoliposomes containing P-glycoprotein (P-gp) from a solution of small proteoliposomes that had been deposited and partially dried on a film of agarose. This preparation method generated a significant fraction of giant proteoliposomes that were free of internalized vesicles, making it possible to determine the accessible liposome volume. Measuring the intensity of the fluorescent substrate rhodamine 123 (Rho123) inside and outside these giant proteoliposomes determined the concentration of transported substrates of P-gp. Fitting a kinetic model to the fluorescence data revealed the rate of passive diffusion as well as active transport by reconstituted P-gp in the membrane. This approach determined estimates for the membrane permeability coefficient (Ps) of passive diffusion and rate constants of active transport (kT) by P-gp as a result of different experimental conditions. The Ps value for Rho123 was larger in membranes containing P-gp under all assay conditions than in membranes without P-gp indicating increased leakiness in the presence of reconstituted transmembrane proteins. For P-gp liposomes, the kT value was significantly higher in the presence of ATP than in its absence or in the presence of ATP and the competitive inhibitor verapamil. This difference in kT values verified that P-gp was functionally active after reconstitution and quantified the rate of active transport. Lastly, patch clamp experiments on giant proteoliposomes showed ion channel activity consistent with a chloride ion channel protein that co-purified with P-gp. Together, these results demonstrate several advantages of using giant rather than small proteoliposomes to characterize transport properties of transport proteins and ion channels.
Collapse
Affiliation(s)
- Kim S Horger
- Department of Chemical Engineering, University of Michigan, 2300 Hayward Street, Ann Arbor, MI 48109, USA
| | - Haiyan Liu
- Department of Biomedical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, MI 48109, USA
| | - Divya K Rao
- Department of Biomedical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, MI 48109, USA
| | - Suneet Shukla
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20814, USA
| | - David Sept
- Department of Biomedical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, MI 48109, USA; Center for Computational Medicine and Bioinformatics, University of Michigan, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - Suresh V Ambudkar
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20814, USA
| | - Michael Mayer
- Department of Chemical Engineering, University of Michigan, 2300 Hayward Street, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, MI 48109, USA.
| |
Collapse
|
25
|
Sleytr UB, Schuster B, Egelseer E, Pum D. S-layers: principles and applications. FEMS Microbiol Rev 2014; 38:823-64. [PMID: 24483139 PMCID: PMC4232325 DOI: 10.1111/1574-6976.12063] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 01/10/2014] [Accepted: 01/13/2014] [Indexed: 01/12/2023] Open
Abstract
Monomolecular arrays of protein or glycoprotein subunits forming surface layers (S-layers) are one of the most commonly observed prokaryotic cell envelope components. S-layers are generally the most abundantly expressed proteins, have been observed in species of nearly every taxonomical group of walled bacteria, and represent an almost universal feature of archaeal envelopes. The isoporous lattices completely covering the cell surface provide organisms with various selection advantages including functioning as protective coats, molecular sieves and ion traps, as structures involved in surface recognition and cell adhesion, and as antifouling layers. S-layers are also identified to contribute to virulence when present as a structural component of pathogens. In Archaea, most of which possess S-layers as exclusive wall component, they are involved in determining cell shape and cell division. Studies on structure, chemistry, genetics, assembly, function, and evolutionary relationship of S-layers revealed considerable application potential in (nano)biotechnology, biomimetics, biomedicine, and synthetic biology.
Collapse
Affiliation(s)
- Uwe B. Sleytr
- Institute of BiophysicsDepartment of NanobiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Bernhard Schuster
- Institute of Synthetic BiologyDepartment of NanobiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Eva‐Maria Egelseer
- Institute of BiophysicsDepartment of NanobiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Dietmar Pum
- Institute of BiophysicsDepartment of NanobiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| |
Collapse
|
26
|
Schuster B, Sleytr UB. Biomimetic interfaces based on S-layer proteins, lipid membranes and functional biomolecules. J R Soc Interface 2014; 11:20140232. [PMID: 24812051 PMCID: PMC4032536 DOI: 10.1098/rsif.2014.0232] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 04/15/2014] [Indexed: 12/20/2022] Open
Abstract
Designing and utilization of biomimetic membrane systems generated by bottom-up processes is a rapidly growing scientific and engineering field. Elucidation of the supramolecular construction principle of archaeal cell envelopes composed of S-layer stabilized lipid membranes led to new strategies for generating highly stable functional lipid membranes at meso- and macroscopic scale. In this review, we provide a state-of-the-art survey of how S-layer proteins, lipids and polymers may be used as basic building blocks for the assembly of S-layer-supported lipid membranes. These biomimetic membrane systems are distinguished by a nanopatterned fluidity, enhanced stability and longevity and, thus, provide a dedicated reconstitution matrix for membrane-active peptides and transmembrane proteins. Exciting areas in the (lab-on-a-) biochip technology are combining composite S-layer membrane systems involving specific membrane functions with the silicon world. Thus, it might become possible to create artificial noses or tongues, where many receptor proteins have to be exposed and read out simultaneously. Moreover, S-layer-coated liposomes and emulsomes copying virus envelopes constitute promising nanoformulations for the production of novel targeting, delivery, encapsulation and imaging systems.
Collapse
Affiliation(s)
- Bernhard Schuster
- Department of NanoBiotechnology, University of Natural Resources and Life Sciences, Institute for Synthetic Bioarchitectures, Muthgasse 11, 1190 Vienna, Austria
| | - Uwe B. Sleytr
- Department of NanoBiotechnology, University of Natural Resources and Life Sciences, Institute for Biophysics, Muthgasse 11, 1190 Vienna, Austria
| |
Collapse
|
27
|
Forsberg EM, Sicard C, Brennan JD. Solid-phase biological assays for drug discovery. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2014; 7:337-359. [PMID: 25000820 DOI: 10.1146/annurev-anchem-071213-020241] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In the past 30 years, there has been a significant growth in the use of solid-phase assays in the area of drug discovery, with a range of new assays being used for both soluble and membrane-bound targets. In this review, we provide some basic background to typical drug targets and immobilization protocols used in solid-phase biological assays (SPBAs) for drug discovery, with emphasis on particularly labile biomolecular targets such as kinases and membrane-bound receptors, and highlight some of the more recent approaches for producing protein microarrays, bioaffinity columns, and other devices that are central to small molecule screening by SPBA. We then discuss key applications of such assays to identify drug leads, with an emphasis on the screening of mixtures. We conclude by highlighting specific advantages and potential disadvantages of SPBAs, particularly as they relate to particular assay formats.
Collapse
Affiliation(s)
- Erica M Forsberg
- Biointerfaces Institute, McMaster University, Hamilton, Ontario L8S 4L8, Canada;
| | | | | |
Collapse
|
28
|
de Groot GW, Demarche S, Santonicola MG, Tiefenauer L, Vancso GJ. Smart polymer brush nanostructures guide the self-assembly of pore-spanning lipid bilayers with integrated membrane proteins. NANOSCALE 2014; 6:2228-37. [PMID: 24425208 DOI: 10.1039/c3nr05356c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Nanopores in arrays on silicon chips are functionalized with pH-responsive poly(methacrylic acid) (PMAA) brushes and used as supports for pore-spanning lipid bilayers with integrated membrane proteins. Robust platforms are created by the covalent grafting of polymer brushes using surface-initiated atom transfer radical polymerization (ATRP), resulting in sensor chips that can be successfully reused over several assays. His-tagged proteins are selectively and reversibly bound to the nitrilotriacetic acid (NTA) functionalization of the PMAA brush, and consequently lipid bilayer membranes are formed. The enhanced membrane resistance as determined by electrochemical impedance spectroscopy and free diffusion of dyed lipids observed as fluorescence recovery after photobleaching confirmed the presence of lipid bilayers. Immobilization of the His-tagged membrane proteins on the NTA-modified PMAA brush near the pore edges is characterized by fluorescence microscopy. This system allows us to adjust the protein density in free-standing bilayers, which are stabilized by the polymer brush underneath. The potential application of the integrated platform for ion channel protein assays is demonstrated.
Collapse
Affiliation(s)
- G Wilhelmina de Groot
- Materials Science and Technology of Polymers, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands.
| | | | | | | | | |
Collapse
|
29
|
Schrems A, Phillips J, Casey D, Wylie D, Novakova M, Sleytr UB, Klug D, Neil MAA, Schuster B, Ces O. The grab-and-drop protocol: a novel strategy for membrane protein isolation and reconstitution from single cells. Analyst 2014; 139:3296-304. [DOI: 10.1039/c4an00059e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Samples of cell membrane were non-destructively removed from individual, live cells using optically trapped beads, and deposited into a supported lipid bilayer mounted on an S-layer protein-coated substrate.
Collapse
Affiliation(s)
- Angelika Schrems
- Department of Nanobiotechnology
- University of Natural Resources and Life Sciences
- Vienna, 1190 Austria
| | - John Phillips
- The Proxomics Group
- Institute of Chemical Biology
- Imperial College London
- London, SW7 2AZ UK
| | - Duncan Casey
- The Proxomics Group
- Institute of Chemical Biology
- Imperial College London
- London, SW7 2AZ UK
| | - Douglas Wylie
- The Proxomics Group
- Institute of Chemical Biology
- Imperial College London
- London, SW7 2AZ UK
| | - Mira Novakova
- The Proxomics Group
- Institute of Chemical Biology
- Imperial College London
- London, SW7 2AZ UK
| | - Uwe B. Sleytr
- Department of Nanobiotechnology
- University of Natural Resources and Life Sciences
- Vienna, 1190 Austria
| | - David Klug
- The Proxomics Group
- Institute of Chemical Biology
- Imperial College London
- London, SW7 2AZ UK
| | - Mark A. A. Neil
- The Proxomics Group
- Institute of Chemical Biology
- Imperial College London
- London, SW7 2AZ UK
| | - Bernhard Schuster
- Department of Nanobiotechnology
- University of Natural Resources and Life Sciences
- Vienna, 1190 Austria
| | - Oscar Ces
- The Proxomics Group
- Institute of Chemical Biology
- Imperial College London
- London, SW7 2AZ UK
| |
Collapse
|
30
|
Simon A, Gounou C, Tan S, Tiefenauer L, Di Berardino M, Brisson AR. Free-standing lipid films stabilized by Annexin-A5. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2739-44. [DOI: 10.1016/j.bbamem.2013.07.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Revised: 07/16/2013] [Accepted: 07/24/2013] [Indexed: 10/26/2022]
|