1
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Le Brun AP, Gilbert EP. Advances in sample environments for neutron scattering for colloid and interface science. Adv Colloid Interface Sci 2024; 327:103141. [PMID: 38631095 DOI: 10.1016/j.cis.2024.103141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/19/2024]
Abstract
This review describes recent advances in sample environments across the full complement of applicable neutron scattering techniques to colloid and interface science. Temperature, pressure, flow, tensile testing, ultrasound, chemical reactions, IR/visible/UV light, confinement, humidity and electric and magnetic field application, as well as tandem X-ray methods, are all addressed. Consideration for material choices in sample environments and data acquisition methods are also covered as well as discussion of current and potential future use of machine learning and artificial intelligence.
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Affiliation(s)
- Anton P Le Brun
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - Elliot Paul Gilbert
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Road, Lucas Heights, NSW 2234, Australia.
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2
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Robson T, Shah DSH, Welbourn RJL, Phillips SR, Clifton LA, Lakey JH. Fully Aqueous Self-Assembly of a Gold-Nanoparticle-Based Pathogen Sensor. Int J Mol Sci 2023; 24:ijms24087599. [PMID: 37108766 PMCID: PMC10145400 DOI: 10.3390/ijms24087599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/11/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Surface plasmon resonance (SPR) is a very sensitive measure of biomolecular interactions but is generally too expensive for routine analysis of clinical samples. Here we demonstrate the simplified formation of virus-detecting gold nanoparticle (AuNP) assemblies on glass using only aqueous buffers at room temperature. The AuNP assembled on silanized glass and displayed a distinctive absorbance peak due to the localized SPR (LSPR) response of the AuNPs. Next, assembly of a protein engineering scaffold was followed using LSPR and a sensitive neutron reflectometry approach, which measured the formation and structure of the biological layer on the spherical AuNP. Finally, the assembly and function of an artificial flu sensor layer consisting of an in vitro-selected single-chain antibody (scFv)-membrane protein fusion was followed using the LSPR response of AuNPs within glass capillaries. In vitro selection avoids the need for separate animal-derived antibodies and allows for the rapid production of low-cost sensor proteins. This work demonstrates a simple approach to forming oriented arrays of protein sensors on nanostructured surfaces that uses (i) an easily assembled AuNP silane layer, (ii) self-assembly of an oriented protein layer on AuNPs, and (iii) simple highly specific artificial receptor proteins.
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Affiliation(s)
- Timothy Robson
- Biosciences Institute, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Deepan S H Shah
- Orla Protein Technologies Ltd., Biosciences Centre, International Centre for Life, Times Square, Newcastle upon Tyne NE1 4EP, UK
| | - Rebecca J L Welbourn
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 OQX, UK
| | - Sion R Phillips
- Orla Protein Technologies Ltd., Biosciences Centre, International Centre for Life, Times Square, Newcastle upon Tyne NE1 4EP, UK
| | - Luke A Clifton
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 OQX, UK
| | - Jeremy H Lakey
- Biosciences Institute, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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3
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Majkrzak CF. The development of neutron reflectometry as a probe of the nanoscale structure of polymer thin film systems - founded on the pioneering work of Professor Thomas P. Russell. NANOSCALE 2023; 15:4725-4737. [PMID: 36799457 DOI: 10.1039/d2nr06756k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Among Professor Russell's numerous, original, and significant contributions to polymer science are those in which he helped pioneer the application of neutron reflectometry to the study of thin film systems. For this groundbreaking work, along with his support of neutron scattering methods in general, he was awarded the 2020 Clifford G. Shull Prize by the Neutron Scattering Society of America, named after and in honor of the Nobel Prize laureate. This article highlights some of the first applications of neutron reflectometry to probe the nanoscale structure of polymer thin film systems that Professor Russell and his colleagues pioneered. A concise account of the subsequent evolution of even more powerful phase-sensitive reflectometry techniques, following the success of their early work, is then presented. In addition to a general description of this current methodology, several particularly relevant and illustrative examples are given.
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Affiliation(s)
- C F Majkrzak
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD, USA.
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4
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Andersson J, Bilotto P, Mears LLE, Fossati S, Ramach U, Köper I, Valtiner M, Knoll W. Solid-supported lipid bilayers - A versatile tool for the structural and functional characterization of membrane proteins. Methods 2020; 180:56-68. [PMID: 32920130 DOI: 10.1016/j.ymeth.2020.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023] Open
Abstract
The cellular membrane is central to the development of single-and multicellular life, as it separates the delicate cellular interior from the hostile environment. It exerts tight control over entry and exit of substances, is responsible for signaling with other cells in multicellular organisms and prevents pathogens from entering the cell. In the case of bacteria and viruses, the cellular membrane also hosts the proteins enabling invasion of the host organism. In a very real sense therefore, the cellular membrane is central to all life. The study of the cell membrane and membrane proteins in particular has therefore attracted significant attention. Due to the enormous variety of tasks performed by the membrane, it is a highly complex and challenging structure to study. Ideally, membrane components would be studied in isolation from this environment, but unlike water soluble proteins, the amphiphilic environment provided by the cellular membrane is key to the structure and function of the cell membrane. Therefore, model membranes have been developed to provide an environment in which a membrane protein can be studied. This review presents a set of tools that enable the comprehensive characterization of membrane proteins: electrochemical tools, surface plasmon resonance, neutron scattering, the surface forces apparatus and atomic force microscopy are discussed, with a particular focus on experimental technique and data evaluation.
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Affiliation(s)
| | - Pierluigi Bilotto
- Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria
| | - Laura L E Mears
- Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria
| | - Stefan Fossati
- AIT Austrian Institute of Technology, 1210 Vienna, Austria; Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria
| | - Ulrich Ramach
- Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria; CEST Kompetenzzentrum für elektrochemische Oberflächentechnologie, Wiener Neustadt 2700, Austria
| | - Ingo Köper
- Flinders Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Markus Valtiner
- Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria; CEST Kompetenzzentrum für elektrochemische Oberflächentechnologie, Wiener Neustadt 2700, Austria
| | - Wolfgang Knoll
- AIT Austrian Institute of Technology, 1210 Vienna, Austria; CEST Kompetenzzentrum für elektrochemische Oberflächentechnologie, Wiener Neustadt 2700, Austria
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5
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Zhang W, Besford QA, Christofferson AJ, Charchar P, Richardson JJ, Elbourne A, Kempe K, Hagemeyer CE, Field MR, McConville CF, Yarovsky I, Caruso F. Cobalt-Directed Assembly of Antibodies onto Metal-Phenolic Networks for Enhanced Particle Targeting. NANO LETTERS 2020; 20:2660-2666. [PMID: 32155075 DOI: 10.1021/acs.nanolett.0c00295] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The orientation-specific immobilization of antibodies onto nanoparticles, to preserve antibody-antigen recognition, is a key challenge in developing targeted nanomedicines. Herein, we report the targeting ability of metal-phenolic network (MPN)-coated gold nanoparticles with surface-physisorbed antibodies against respective antigens. The MPN coatings were self-assembled from metal ions (FeIII, CoII, CuII, NiII, or ZnII) cross-linked with tannic acid. Upon physisorption of antibodies, all particle systems exhibited enhanced association with target antigens, with CoII systems demonstrating more than 2-fold greater association. These systems contained more metal atoms distributed in a way to specifically interact with antibodies, which were investigated by molecular dynamics simulations. A model antibody fragment crystallizable (Fc) region in solution with CoII-tannic acid complexes revealed that the solvent-exposed CoII can directly coordinate to the histidine-rich portion of the Fc region. This one-pot interaction suggests anchoring of the antibody Fc region to the MPN on nanoparticles, allowing for enhanced targeting.
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Affiliation(s)
- Wenjie Zhang
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Quinn A Besford
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | | | - Patrick Charchar
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Joseph J Richardson
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Aaron Elbourne
- Nanobiotechnology Laboratory, School of Science, RMIT University, Melbourne Victoria 3001, Australia
| | - Kristian Kempe
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Christoph E Hagemeyer
- NanoBiotechnology Laboratory, Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia
| | - Matthew R Field
- RMIT Microscopy & Microanalysis Facility, RMIT University, Melbourne, Victoria 3001, Australia
| | - Chris F McConville
- College of Science, Engineering and Health, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Frank Caruso
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
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6
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Iijima M, Nakayama T, Kuroda S. Two-dimensional membrane scaffold for the oriented immobilization of biosensing molecules. Biosens Bioelectron 2020; 150:111860. [PMID: 31735623 DOI: 10.1016/j.bios.2019.111860] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/21/2019] [Accepted: 11/07/2019] [Indexed: 11/28/2022]
Abstract
The orientation and density of biosensing molecules on sensor chip should be precisely controlled to improve sensitivity and ligand-binding capacity. We previously developed a ~30-nm bio-nanocapsule (ZZ-BNC), consisting of the hepatitis B virus envelope L protein fused with the tandem form of protein A-derived IgG Fc-binding Z domain (ZZ-L protein). This is used as a robust nanoparticle scaffold to enhance the sensitivity and ligand-binding capacity of IgGs and Fc-fused sensing molecules (Fc-fused receptors). However, due to their rigid particle structure, the surface density of ZZ-L proteins could not be optimized for biosensor functions, and useless ZZ-L proteins become stuck between ZZ-BNC and the sensor chip. Here, we have developed a planar lipid membrane embedded with ZZ-L micelles (ZZ-L membrane), which could modify the surface of any biosensor chip with a controlled density of ZZ-L proteins. Compared with ZZ-BNC, the sensitivity and ligand-binding capacity of IgGs were enhanced about 10-fold with the ZZ-L membrane. Furthermore, the immobilized IgGs could capture their respective antigens almost stoichiometrically, indicating that ZZ-L membrane is the most ideal scaffold for Fc-fused sensing molecules in terms of both clustering and oriented immobilization.
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Affiliation(s)
- Masumi Iijima
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, 567-0047, Japan; Department of Nutritional Science and Food Safety, Faculty of Applied Bioscience, Tokyo University of Agriculture, Setagaya, Tokyo, 156-8502, Japan
| | - Tsutomu Nakayama
- Department of Nutritional Science and Food Safety, Faculty of Applied Bioscience, Tokyo University of Agriculture, Setagaya, Tokyo, 156-8502, Japan
| | - Shun'ichi Kuroda
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, 567-0047, Japan.
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7
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Shen M, Jiang D, De Silva PIT, Song B, Rusling JF. Restricted Proteolysis and LC-MS/MS To Evaluate the Orientation of Surface-Immobilized Antibodies. Anal Chem 2019; 91:4913-4919. [PMID: 30840436 DOI: 10.1021/acs.analchem.9b01155] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The molecular orientation of antibodies immobilized on solid surfaces plays a significant role in the sensitivity of immunoassays and efficiency of protein isolation using antibody-decorated nanoparticles. Optimally, nearly all antibody binding sites should be available to bind. Here we report for the first time an LC-MS/MS approach to probe antibody orientation directly, utilizing sterically restricted proteolysis. Trypsin-decorated magnetic beads (MBs, 1.5 μm) were much larger than average antibody-free areas (55 × 55 nm) of oriented antibodies on MBs, restricting proteolysis to mainly Fab regions. Randomly attached antibodies on MB surfaces served as controls. The tryptic-hydrolyzed peptides were quantified using LC-MS/MS peptide analysis as markers for average positions of Fc and Fab of antibodies on the beads. Different patterns of digestion rates were found due to proteolysis of the oriented and nonoriented antibodies on MBs. For oriented antibodies, the peptides from outer Fab regions gave a much higher digestion rate than those from Fc regions, while for randomly immobilized antibodies digestion rates for Fab and Fc peptides were similar. This novel approach is a useful and convenient tool to characterize antibody orientation for immunoassays and other applications. The relative degree of orientation can be assessed using a metric Ro denoting amount of Fab marker peptides found divided by Fc + Fab marker peptides × 100%. Oriented antibodies on the MBs also provided more efficient antigen capture compared to randomly immobilized antibodies.
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Affiliation(s)
| | | | | | | | - James F Rusling
- Department of Surgery and Neag Cancer Center , UConn Health , Farmington , Connecticut 06032 , United States.,School of Chemistry , National University of Ireland at Galway , Galway , Ireland
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8
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Orientation Control of the Molecular Recognition Layer for Improved Sensitivity: a Review. BIOCHIP JOURNAL 2019. [DOI: 10.1007/s13206-019-3103-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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9
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Robson T, Shah DSH, Solovyova AS, Lakey JH. Modular Protein Engineering Approach to the Functionalization of Gold Nanoparticles for Use in Clinical Diagnostics. ACS APPLIED NANO MATERIALS 2018; 1:3590-3599. [PMID: 30101217 PMCID: PMC6083416 DOI: 10.1021/acsanm.8b00737] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 06/28/2018] [Indexed: 05/21/2023]
Abstract
Functional protein-gold nanoparticle (AuNP) conjugates have a wide variety of applications including biosensing and drug delivery. Correct protein orientation, which is important to maintain functionality on the nanoparticle surface, can be difficult to achieve in practice, and dedicated protein scaffolds have been used on planar gold surfaces to drive the self-assembly of oriented protein arrays. Here we use the transmembrane domain of Escherichia coli outer membrane protein A (OmpATM) to create protein-AuNP conjugates. The addition of a single cysteine residue into a periplasmic loop, to create cysOmpATM, drives oriented assembly and increased equilibrium binding. As the protein surface concentration increases, the sulfur-gold bond in cysOmpATM creates a more densely populated AuNP surface than the poorly organized wtOmpATM layer. The functionalization of AuNP improved both their stability and homogeneity. This was further exploited using multidomain protein chimeras, based on cysOmpATM, which were shown to form ordered protein arrays with their functional domains displayed away from the AuNP surface. A fusion with protein G was shown to specifically bind antibodies via their Fc region. Next, an in vitro selected single chain antibody (scFv)-cysOmpATM fusion protein, bound to AuNP, detected influenza A nucleoprotein, a widely used antigen in diagnostic assays. Finally, using the same scFv-cysOmpATM-AuNP conjugates, a prototype lateral flow assay for influenza demonstrated the utility of fully recombinant self-assembling sensor layers. By simultaneously removing the need for both animal antibodies and a separate immobilization procedure, this technology could greatly simplify the development of a range of in vitro diagnostics.
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Affiliation(s)
- Timothy Robson
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle
upon Tyne NE2 4HH, U.K.
| | - Deepan S. H. Shah
- Orla
Protein Technologies Ltd., Biosciences Centre, International Centre for Life, Times Square, Newcastle upon Tyne NE1 4EP, U.K.
| | - Alexandra S. Solovyova
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle
upon Tyne NE2 4HH, U.K.
| | - Jeremy H. Lakey
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle
upon Tyne NE2 4HH, U.K.
- E-mail:
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10
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Yang F, Zuo X, Fan C, Zhang XE. Biomacromolecular nanostructures-based interfacial engineering: from precise assembly to precision biosensing. Natl Sci Rev 2018. [DOI: 10.1093/nsr/nwx134] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Abstract
Biosensors are a type of important biodevice that integrate biological recognition elements, such as enzyme, antibody and DNA, and physical or chemical transducers, which have revolutionized clinical diagnosis especially under the context of point-of-care tests. Since the performance of a biosensor depends largely on the bio–solid interface, design and engineering of the interface play a pivotal role in developing quality biosensors. Along this line, a number of strategies have been developed to improve the homogeneity of the interface or the precision in regulating the interactions between biomolecules and the interface. Especially, intense efforts have been devoted to controlling the surface chemistry, orientation of immobilization, molecular conformation and packing density of surface-confined biomolecular probes (proteins and nucleic acids). By finely tuning these surface properties, through either gene manipulation or self-assembly, one may reduce the heterogeneity of self-assembled monolayers, increase the accessibility of target molecules and decrease the binding energy barrier to realize high sensitivity and specificity. In this review, we summarize recent progress in interfacial engineering of biosensors with particular focus on the use of protein and DNA nanostructures. These biomacromolecular nanostructures with atomistic precision lead to highly regulated interfacial assemblies at the nanoscale. We further describe the potential use of the high-performance biosensors for precision diagnostics.
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Affiliation(s)
- Fan Yang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Xiaolei Zuo
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xian-En Zhang
- National Key Laboratory of Biomacromolecules, CAS Excellence Center for Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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11
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Lou Z, Han H, Zhou M, Wan J, Sun Q, Zhou X, Gu N. Fabrication of Magnetic Conjugation Clusters via Intermolecular Assembling for Ultrasensitive Surface Plasmon Resonance (SPR) Detection in a Wide Range of Concentrations. Anal Chem 2017; 89:13472-13479. [PMID: 29164862 DOI: 10.1021/acs.analchem.7b03768] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Herein, a novel sandwich surface plasmon resonance (SPR) detection assay, which utilizes prion disease-associated isoform (PrPSc) conjugating magnetic nanoparticle clusters (nanoparticle-organic clusters, NOCs) as signal amplification reagents, is constructed for the ultrasensitive detection of PrPSc. Due to the highly specific affinity of aptamer-Fe3O4 nanoparticles (AMNPs) toward PrPSc and the intermolecular assembly behaviors among PrPSc, PrPSc conjugating magnetic nanoparticle clusters were obtained after the incubation of AMNPs and PrPSc and the subsequent concentration processes in an external magnetic field. The conjugation clusters were further injected into the SPR cuvette and captured by the gold sensing film via the Au-S bonding interaction, inducing intense SPR responses. Meanwhile, a traditional sandwich SPR detection format using a gold/PrPSc/AMNPs amplification mode was conducted for the detection of PrPSc as comparison. The results reveal that the synthesized NOCs permitted a 215-fold increase of the SPR signal, while the sandwich format permitted only a 65-fold increase. Moreover, a lower detection limit (1 × 10-4 ng/mL) and a wider quantitation range (1 × 10-4-1 × 105 ng/mL) were demonstrated. The formation of the conjugation clusters and the capture of these clusters were confirmed by high-resolution AFM imaging and molecular simulations. This conjugation-cluster-induced signal amplification strategy has great potential for the detection of small analytes with similar structural characteristics in trace level concentrations with high selectivity and sensitivity by altering the corresponding aptamer labeled to magnetic particles.
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Affiliation(s)
- Zhichao Lou
- College of Materials Science and Engineering, Nanjing Forestry University , Nanjing 210037, China.,State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University , Nanjing 210096, China
| | - He Han
- College of Materials Science and Engineering, Nanjing Forestry University , Nanjing 210037, China
| | - Ming Zhou
- College of Materials Science and Engineering, Nanjing Forestry University , Nanjing 210037, China
| | - Jinfeng Wan
- College of Materials Science and Engineering, Nanjing Forestry University , Nanjing 210037, China
| | - Qian Sun
- College of Materials Science and Engineering, Nanjing Forestry University , Nanjing 210037, China
| | - Xiaoyan Zhou
- College of Materials Science and Engineering, Nanjing Forestry University , Nanjing 210037, China
| | - Ning Gu
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University , Nanjing 210096, China
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12
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Zhang S, Geryak R, Geldmeier J, Kim S, Tsukruk VV. Synthesis, Assembly, and Applications of Hybrid Nanostructures for Biosensing. Chem Rev 2017; 117:12942-13038. [DOI: 10.1021/acs.chemrev.7b00088] [Citation(s) in RCA: 206] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Shuaidi Zhang
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Ren Geryak
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Jeffrey Geldmeier
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Sunghan Kim
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Vladimir V. Tsukruk
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
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13
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Lou Z, Wan J, Zhang X, Zhang H, Zhou X, Cheng S, Gu N. Quick and sensitive SPR detection of prion disease-associated isoform (PrP Sc) based on its self-assembling behavior on bare gold film and specific interactions with aptamer-graphene oxide (AGO). Colloids Surf B Biointerfaces 2017; 157:31-39. [PMID: 28570989 DOI: 10.1016/j.colsurfb.2017.05.058] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/18/2017] [Accepted: 05/23/2017] [Indexed: 01/31/2023]
Abstract
Herein, we constructed a novel sandwich surface plasmon resonance (SPR) detection assay for sensitive prion disease-associated isoform (PrPSc) detection, utilizing bare gold film and apatamer-graphene oxide (AGO). Due to the self-assembling behavior of PrPSc on gold surface, the non-modified gold surface can be directly used as sensing surface for the quick detection, for the purpose to avoid the interference from the traditional, complex and changeable probe-modified sensing surface. And due to the highly specific affinity of AGO towards PrPSc, the sandwich type SPR sensor exhibits excellent analytical performance towards the discrimination and quantitation of PrPSc. A good linear relationship was obtained between SPR responses and the logarithm of PrPSc concentrations over a range of 0.001-1ng/mL. The detection sensitivity for PrPSc was improved by ∼156 orders of AGO compared with SPR direct detection format. Besides, morphological changes of the sensing film surfaces were investigated by high resolution AFM imaging, confirming the capture of PrPSc molecules and their further specific recognition by AGO. The specificity of the present biosensor was also investigated by PrPC and other regents as controls. By compared with other reported methods, the AGO enhanced sandwich SPR assay was confirmed to be efficient, sensitive, and with wide working range.
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Affiliation(s)
- Zhichao Lou
- College of Materials Science and Engineering, Nanjing Forestry University, Nanjing 210037, China; State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Jinfeng Wan
- College of Materials Science and Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Xiaohong Zhang
- College of Materials Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Haiqian Zhang
- College of Materials Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Xiaoyan Zhou
- College of Materials Science and Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Su Cheng
- Zhongda Hospital, Southeast University, Nanjing 210009, China
| | - Ning Gu
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
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14
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Mazzer AR, Clifton LA, Perevozchikova T, Butler PD, Roberts CJ, Bracewell DG. Neutron reflectivity measurement of protein A-antibody complex at the solid-liquid interface. J Chromatogr A 2017; 1499:118-131. [PMID: 28410804 PMCID: PMC5408906 DOI: 10.1016/j.chroma.2017.03.084] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/15/2017] [Accepted: 03/30/2017] [Indexed: 01/05/2023]
Abstract
The orientation of IgG4 adsorbed at the solid-liquid interface was probed. A chromatography resin was mimicked by attaching protein A to a silica surface. Neutron reflectivity was used to measure protein A and adsorbed IgG structures. Protein A-modified silica was blocked with either BSA or PEG before IgG adsorption. Adsorbed IgG extended up to 230 Å from the surface, depending on blocking strategy.
Chromatography is a ubiquitous unit operation in the purification of biopharmaceuticals yet few studies have addressed the biophysical characterisation of proteins at the solution-resin interface. Chromatography and other adsorption and desorption processes have been shown to induce protein aggregation which is undesirable in biopharmaceutical products. In order to advance understanding of how adsorption processes might impact protein stability, neutron reflectivity was used to characterise the structure of adsorbed immunoglobulin G (IgG) on model surfaces. In the first model system, IgG was adsorbed directly to silica and demonstrated a side-on orientation with high surface contact. A maximum dimension of 60 Å in the surface normal direction and high density surface coverage were observed under pH 4.1 conditions. In chromatography buffers, pH was found to influence IgG packing density and orientation at the solid-liquid interface. In the second model system, which was designed to mimic an affinity chromatography surface, protein A was attached to a silica surface to produce a configuration representative of a porous glass chromatography resin. Interfacial structure was probed during sequential stages from ligand attachment, through to IgG binding and elution. Adsorbed IgG structures extended up to 250 Å away from the surface and showed dependence on surface blocking strategies. The data was suggestive of two IgG molecules bound to protein A with a somewhat skewed orientation and close proximity to the silica surface. The findings provide insight into the orientation of adsorbed antibody structures under conditions encountered during chromatographic separations.
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Affiliation(s)
- Alice R Mazzer
- Dept. Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, UK
| | - Luke A Clifton
- ISIS, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxon, OX11 0QX, UK
| | - Tatiana Perevozchikova
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Paul D Butler
- National Institute of Standards and Technology, 100 Bureau Drive, Bldg. 235, Gaithersburg, MD 20899-8562, USA
| | - Christopher J Roberts
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Daniel G Bracewell
- Dept. Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, UK.
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15
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Shen M, Rusling J, Dixit CK. Site-selective orientated immobilization of antibodies and conjugates for immunodiagnostics development. Methods 2017; 116:95-111. [PMID: 27876681 PMCID: PMC5374010 DOI: 10.1016/j.ymeth.2016.11.010] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 01/11/2023] Open
Abstract
Immobilized antibody systems are the key to develop efficient diagnostics and separations tools. In the last decade, developments in the field of biomolecular engineering and crosslinker chemistry have greatly influenced the development of this field. With all these new approaches at our disposal, several new immobilization methods have been created to address the main challenges associated with immobilized antibodies. Few of these challenges that we have discussed in this review are mainly associated to the site-specific immobilization, appropriate orientation, and activity retention. We have discussed the effect of antibody immobilization approaches on the parameters on the performance of an immunoassay.
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Affiliation(s)
- Min Shen
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060
| | - James Rusling
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269-3136
- Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut 060
- School of Chemistry, National University of Ireland at Galway, Galway, Ireland
| | - Chandra K Dixit
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060
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16
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Scaffolds for oriented and close-packed immobilization of immunoglobulins. Biosens Bioelectron 2017; 89:810-821. [DOI: 10.1016/j.bios.2016.10.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/27/2016] [Accepted: 10/03/2016] [Indexed: 02/07/2023]
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17
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Chen J, Li Q, Li J, Maitz MF. The effect of anti-CD34 antibody orientation control on endothelial progenitor cell capturing cardiovascular devices. J BIOACT COMPAT POL 2016. [DOI: 10.1177/0883911516637376] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Efficient immobilization of the antibody to the substrate is of crucial importance in the development of anti-CD34-based endothelial progenitor cells capturing cardiovascular devices. This should go along with precise control of the antibody orientation by appropriate immobilization technology for retaining antibody activity, like in immunosensors. Recently, great attention was paid to immobilization of anti-CD34 antibody onto substrates by covalent binding, but at random orientation. Here, to investigate the biological effect of antibody orientation, we have prepared two kinds of anti-CD34 antibody coated surfaces, with random immobilization and oriented immobilization. The immunological binding activity (IBA) of the antibody at oriented immobilization was 3.48 times higher than at random immobilization, indicating that the two different surfaces were successfully prepared. The endothelial progenitor cell-capturing capability of oriented antibody-immobilized surface was 1.35 and 1.64 times higher than for the random immobilized surface after seeding for 2 and 12 h under flow condition, respectively. The endothelial progenitor cell-capturing efficiency per antibody by oriented immobilization was 5.16 and 6.26 times higher than for the random after seeding for 2 and 12 h under flow condition, respectively. In addition, the oriented antibody-immobilized surface possessed better blood-compatibility. These results clearly revealed the significance of antibody orientation which could retain its biological effect and may revolutionize the antibody-immobilization protocols used in cardiovascular and other blood-contacting biomedical devices.
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Affiliation(s)
- Jialong Chen
- Stomatologic Hospital & College, Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province, Hefei, China
- College of Pharmacy, Anhui Medical University, Hefei, China
- Faculty of Dentistry, The University of Hong Kong, Hong Kong, China
| | - Quanli Li
- Stomatologic Hospital & College, Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province, Hefei, China
| | - Jun Li
- College of Pharmacy, Anhui Medical University, Hefei, China
| | - Manfred F Maitz
- Leibniz Institute of Polymer Research Dresden, Max Bergmann Center of Biomaterials Dresden, Dresden, Germany
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18
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19
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Toma K, Miki D, Kishikawa C, Yoshimura N, Miyajima K, Arakawa T, Yatsuda H, Mitsubayashi K. Repetitive Immunoassay with a Surface Acoustic Wave Device and a Highly Stable Protein Monolayer for On-Site Monitoring of Airborne Dust Mite Allergens. Anal Chem 2015; 87:10470-4. [DOI: 10.1021/acs.analchem.5b02594] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Koji Toma
- Department
of Biomedical Devices and Instrumentation, Institute of Biomaterials
and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Daisuke Miki
- Graduate
School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
| | - Chisato Kishikawa
- Graduate
School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
| | | | - Kumiko Miyajima
- Department
of Biomedical Devices and Instrumentation, Institute of Biomaterials
and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
- Japan Society for the Promotion of Science, Tokyo 102-0083, Japan
| | - Takahiro Arakawa
- Department
of Biomedical Devices and Instrumentation, Institute of Biomaterials
and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Hiromi Yatsuda
- Japan Radio Co. Ltd., Saitama 356-8510, Japan
- OJ-Bio Ltd., NE1 4EP Newcastle upon Tyne, United Kingdom
| | - Kohji Mitsubayashi
- Department
of Biomedical Devices and Instrumentation, Institute of Biomaterials
and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
- Graduate
School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
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20
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Liu Y, Yu J. Oriented immobilization of proteins on solid supports for use in biosensors and biochips: a review. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1623-4] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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21
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Chen J, Li Q, Xu J, Zhang L, Maitz MF, Li J. Thromboresistant and rapid-endothelialization effects of dopamine and staphylococcal protein A mediated anti-CD34 coating on 316L stainless steel for cardiovascular devices. J Mater Chem B 2015; 3:2615-2623. [PMID: 32262909 DOI: 10.1039/c4tb01825g] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The oriented immobilization surface of anti-CD34 antibodies displayed excellent affinity for EPCs and good anticoagulation performance.
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Affiliation(s)
- Jialong Chen
- Stomatologic Hospital & College
- Anhui Medical University
- Key Lab. of Oral Diseases Research of Anhui Province
- Hefei 230032
- China
| | - Quanli Li
- Stomatologic Hospital & College
- Anhui Medical University
- Key Lab. of Oral Diseases Research of Anhui Province
- Hefei 230032
- China
| | - Jianguang Xu
- Stomatologic Hospital & College
- Anhui Medical University
- Key Lab. of Oral Diseases Research of Anhui Province
- Hefei 230032
- China
| | - Le Zhang
- Stomatologic Hospital & College
- Anhui Medical University
- Key Lab. of Oral Diseases Research of Anhui Province
- Hefei 230032
- China
| | - Manfred F. Maitz
- Leibniz Institute of Polymer Research Dresden
- Max Bergmann Center of Biomaterials Dresden
- Dresden 01069
- Germany
| | - Jun Li
- College of Pharmacy
- Anhui Medical University
- Hefei 230032
- China
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22
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Le Brun AP, Soliakov A, Shah DSH, Holt SA, McGill A, Lakey JH. Engineered self-assembling monolayers for label free detection of influenza nucleoprotein. Biomed Microdevices 2015; 17:9951. [PMID: 25860669 PMCID: PMC4392172 DOI: 10.1007/s10544-015-9951-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Integrating nanotechnology into useable devices requires a combination of bottom up and top down methodology. Often the techniques to measure and control these different components are entirely different, so methods that can analyse the nanoscale component in situ are of increasing importance. Here we describe a strategy that employs a self-assembling monolayer of engineered protein chimeras to display an array of oriented antibodies (IgG) on a microelectronic device for the label free detection of influenza nucleoprotein. The structural and functional properties of the bio-interface were characterised by a range of physical techniques including surface plasmon resonance, quartz-crystal microbalance and neutron reflectometry. This combination of methods reveals a 13.5 nm thick engineered-monolayer that (i) self-assembles on gold surfaces, (ii) captures IgG with high affinity in a defined orientation and (iii) specifically recognises the influenza A nucleoprotein. Furthermore we also show that this non-covalent self-assembled structure can render the dissociation of bound IgG irreversible by chemical crosslinking in situ without affecting the IgG function. The methods can thus describe in detail the transition from soluble engineered molecules with nanometre dimensions to an array that demonstrates the principles of a working influenza sensor.
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Affiliation(s)
- Anton P. Le Brun
- />Bragg Institute, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232 Australia
| | - Andrei Soliakov
- />Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH UK
- />Fujifilm Diosynth, Belasis Avenue, Billingham, Cleveland TS23 1LH UK
| | - Deepan S. H. Shah
- />Orla Protein Technologies Ltd, Biosciences Centre, International Centre for Life, Times Square, Newcastle upon Tyne, NE1 4EP UK
| | - Stephen A. Holt
- />Bragg Institute, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC, NSW 2232 Australia
| | - Alison McGill
- />Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH UK
- />Fujifilm Diosynth, Belasis Avenue, Billingham, Cleveland TS23 1LH UK
| | - Jeremy H. Lakey
- />Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH UK
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23
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Hosseinidoust Z, Olsson AL, Tufenkji N. Going viral: Designing bioactive surfaces with bacteriophage. Colloids Surf B Biointerfaces 2014; 124:2-16. [DOI: 10.1016/j.colsurfb.2014.05.036] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/25/2014] [Accepted: 05/26/2014] [Indexed: 12/22/2022]
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24
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Reconstitution of a nanomachine driving the assembly of proteins into bacterial outer membranes. Nat Commun 2014; 5:5078. [PMID: 25341963 DOI: 10.1038/ncomms6078] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 08/27/2014] [Indexed: 12/25/2022] Open
Abstract
In biological membranes, various protein secretion devices function as nanomachines, and measuring the internal movements of their component parts is a major technological challenge. The translocation and assembly module (TAM) is a nanomachine required for virulence of bacterial pathogens. We have reconstituted a membrane containing the TAM onto a gold surface for characterization by quartz crystal microbalance with dissipation (QCM-D) and magnetic contrast neutron reflectrometry (MCNR). The MCNR studies provided structural resolution down to 1 Å, enabling accurate measurement of protein domains projecting from the membrane layer. Here we show that dynamic movements within the TamA component of the TAM are initiated in the presence of a substrate protein, Ag43, and that these movements recapitulate an initial stage in membrane protein assembly. The reconstituted system provides a powerful new means to study molecular movements in biological membranes, and the technology is widely applicable to studying the dynamics of diverse cellular nanomachines.
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25
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Heinrich F, Lösche M. Zooming in on disordered systems: neutron reflection studies of proteins associated with fluid membranes. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1838:2341-9. [PMID: 24674984 PMCID: PMC4082750 DOI: 10.1016/j.bbamem.2014.03.007] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 03/13/2014] [Accepted: 03/17/2014] [Indexed: 11/23/2022]
Abstract
Neutron reflectometry (NR) is an emerging experimental technique for the structural characterization of proteins interacting with fluid bilayer membranes under conditions that mimic closely the cellular environment. Thus, cellular processes can be emulated in artificial systems and their molecular basis studied by adding cellular components one at a time in a well-controlled environment while the resulting structures, or structural changes in response to external cues, are monitored with neutron reflection. In recent years, sample environments, data collection strategies and data analysis were continuously refined. The combination of these improvements increases the information which can be obtained from NR to an extent that enables structural characterization of protein-membrane complexes at a length scale that exceeds the resolution of the measurement by far. Ultimately, the combination of NR with molecular dynamics (MD) simulations can be used to cross-validate the results of the two techniques and provide atomic-scale structural models. This review discusses these developments in detail and demonstrates how they provide new windows into relevant biomedical problems. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova.
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Affiliation(s)
- Frank Heinrich
- Physics Department, Carnegie Mellon University, Pittsburgh, PA, U.S.A.; NIST Center for Neutron Research, Gaithersburg, MD, U.S.A
| | - Mathias Lösche
- Physics Department, Carnegie Mellon University, Pittsburgh, PA, U.S.A.; NIST Center for Neutron Research, Gaithersburg, MD, U.S.A..
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26
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The free energy landscape of dimerization of a membrane protein, NanC. PLoS Comput Biol 2014; 10:e1003417. [PMID: 24415929 PMCID: PMC3886892 DOI: 10.1371/journal.pcbi.1003417] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 11/18/2013] [Indexed: 11/19/2022] Open
Abstract
Membrane proteins are frequently present in crowded environments, which favour lateral association and, on occasions, two-dimensional crystallization. To better understand the non-specific lateral association of a membrane protein we have characterized the free energy landscape for the dimerization of a bacterial outer membrane protein, NanC, in a phospholipid bilayer membrane. NanC is a member of the KdgM-family of bacterial outer membrane proteins and is responsible for sialic acid transport in E. coli. Umbrella sampling and coarse-grained molecular dynamics were employed to calculate the potentials of mean force (PMF) for a variety of restrained relative orientations of two NanC proteins as the separation of their centres of mass was varied. We found the free energy of dimerization for NanC to be in the range of to . Differences in the depths of the PMFs for the various orientations are related to the shape of the proteins. This was quantified by calculating the lipid-inaccessible buried surface area of the proteins in the region around the minimum of each PMF. The depth of the potential well of the PMF was shown to depend approximately linearly on the buried surface area. We were able to resolve local minima in the restrained PMFs that would not be revealed using conventional umbrella sampling. In particular, these features reflected the local organization of the intervening lipids between the two interacting proteins. Through a comparison with the distribution of lipids around a single freely-diffusing NanC, we were able to predict the location of these restrained local minima for the orientational configuration in which they were most pronounced. Our ability to make this prediction highlights the important role that lipid organization plays in the association of two NanCs in a bilayer. Cells are surrounded by selectively-permeable bilayer membranes, enabling the cell to control its internal environment. Embedded within these membranes are a variety of membrane proteins, many of which facilitate this environmental control and are integral to numerous metabolic processes. Their location within the membrane and their mutual association are controlled by many factors. We use molecular dynamics simulations to investigate the free energy of association for a pair of relatively simple membrane proteins. By doing so, we are able to characterize the effect that the geometrical properties of the protein have on their mutual association in a bilayer environment, showing that there is a correlation between the buried surface area of two proteins when in contact and the strength of their interaction. We also observe the effect of protein-lipid-protein interactions in this free energy characterization. Such interactions are related to the preferential distribution of lipids around proteins in the membrane.
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27
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Goose JE, Sansom MSP. Reduced lateral mobility of lipids and proteins in crowded membranes. PLoS Comput Biol 2013; 9:e1003033. [PMID: 23592975 PMCID: PMC3623704 DOI: 10.1371/journal.pcbi.1003033] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 02/28/2013] [Indexed: 12/31/2022] Open
Abstract
Coarse-grained molecular dynamics simulations of the E. coli outer membrane proteins FhuA, LamB, NanC, OmpA and OmpF in a POPE/POPG (3∶1) bilayer were performed to characterise the diffusive nature of each component of the membrane. At small observation times (<10 ns) particle vibrations dominate phospholipid diffusion elevating the calculated values from the longer time-scale bulk value (>50 ns) of 8.5×10−7 cm2 s−1. The phospholipid diffusion around each protein was found to vary based on distance from protein. An asymmetry in the diffusion of annular lipids in the inner and outer leaflets was observed and correlated with an asymmetry in charged residues in the vicinity of the inner and outer leaflet head-groups. Protein rotational and translational diffusion were also found to vary with observation time and were inversely correlated with the radius of gyration of the protein in the plane of the bilayer. As the concentration of protein within the bilayer was increased, the overall mobility of the membrane decreased reflected in reduced lipid diffusion coefficients for both lipid and protein components. The increase in protein concentration also resulted in a decrease in the anomalous diffusion exponent α of the lipid. Formation of extended clusters and networks of proteins led to compartmentalisation of lipids in extreme cases. Biological membranes are selective barriers which control the entry/exit of molecules to/from the interior of a cell. They are composed of a lipid bilayer in which are embedded many membrane proteins. Whilst the individual components of membranes are relatively well characterised, the lateral organization and dynamics of the membrane remain less well understood. The lateral mobility of constituent membrane species affects many processes, including how quickly proteins complexes form and protein recruitment occurs, how quickly lipids can be modified/lysed, and the formation of disordered and ordered microdomains. Biological membranes can contain as much as 50% protein. The dynamics of these crowded environments differ greatly from the sparsely populated membranes often studied in silico or in vitro. We use molecular dynamics computer simulations to quantify how mobility within the membrane decreases as the protein concentration increases. We calculate a baseline diffusion of both lipids and selected bacterial outer membrane proteins in the simplest of systems, namely a single protein in a large lipid bilayer patch. In this case diffusion can be correlated with the size of the protein. We observe how proteins affect the mobility of adjacent lipids. As the protein concentration within our systems increases we show that diffusion of both the proteins and lipids is reduced.
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Affiliation(s)
- Joseph E. Goose
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- * E-mail:
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28
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Trilling AK, Harmsen MM, Ruigrok VJ, Zuilhof H, Beekwilder J. The effect of uniform capture molecule orientation on biosensor sensitivity: Dependence on analyte properties. Biosens Bioelectron 2013; 40:219-26. [DOI: 10.1016/j.bios.2012.07.027] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 06/28/2012] [Accepted: 07/13/2012] [Indexed: 01/25/2023]
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29
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Saerbeck T, Cortie D, Brück S, Bertinshaw J, Holt S, Nelson A, James M, Lee W, Klose F. Time-of-Flight Polarized Neutron Reflectometry on PLATYPUS: Status and Future Developments. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.phpro.2013.03.198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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30
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Trilling AK, Beekwilder J, Zuilhof H. Antibody orientation on biosensor surfaces: a minireview. Analyst 2013; 138:1619-27. [DOI: 10.1039/c2an36787d] [Citation(s) in RCA: 301] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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31
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Marshall JL, Flores-Langarica A, Kingsley RA, Hitchcock JR, Ross EA, Lopez-Macias C, Lakey J, Martin LB, Toellner KM, MacLennan CA, MacLennan IC, Henderson IR, Dougan G, Cunningham AF. The capsular polysaccharide Vi from Salmonella typhi is a B1b antigen. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2012; 189:5527-32. [PMID: 23162127 PMCID: PMC3605773 DOI: 10.4049/jimmunol.1103166] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Vaccination with purified capsular polysaccharide Vi Ag from Salmonella typhi can protect against typhoid fever, although the mechanism for its efficacy is not clearly established. In this study, we have characterized the B cell response to this vaccine in wild-type and T cell-deficient mice. We show that immunization with typhoid Vi polysaccharide vaccine rapidly induces proliferation in B1b peritoneal cells, but not in B1a cells or marginal zone B cells. This induction of B1b proliferation is concomitant with the detection of splenic Vi-specific Ab-secreting cells and protective Ab in Rag1-deficient B1b cell chimeras generated by adoptive transfer-induced specific Ab after Vi immunization. Furthermore, Ab derived from peritoneal B cells is sufficient to confer protection against Salmonella that express Vi Ag. Expression of Vi by Salmonella during infection did not inhibit the development of early Ab responses to non-Vi Ags. Despite this, the protection conferred by immunization of mice with porin proteins from Salmonella, which induce Ab-mediated protection, was reduced postinfection with Vi-expressing Salmonella, although protection was not totally abrogated. This work therefore suggests that, in mice, B1b cells contribute to the protection induced by Vi Ag, and targeting non-Vi Ags as subunit vaccines may offer an attractive strategy to augment current Vi-based vaccine strategies.
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Affiliation(s)
- Jennifer L. Marshall
- Medical Research Council Centre for Immune Regulation, School of Immunity and Infection and Institute for Biomedical Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Adriana Flores-Langarica
- Medical Research Council Centre for Immune Regulation, School of Immunity and Infection and Institute for Biomedical Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Robert A. Kingsley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jessica R. Hitchcock
- Medical Research Council Centre for Immune Regulation, School of Immunity and Infection and Institute for Biomedical Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Ewan A. Ross
- Medical Research Council Centre for Immune Regulation, School of Immunity and Infection and Institute for Biomedical Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Constantino Lopez-Macias
- Medical Research Unit on Immunochemistry, Specialties Hospital, National Medical Centre “Siglo XXI” Mexican Institute for Social Security (IMSS), Mexico City, Mexico
| | - Jeremy Lakey
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK
| | - Laura B. Martin
- Novartis Vaccines Institute for Global Health, Via Fiorentina 1, 53100 Siena, Italy
| | - Kai-Michael Toellner
- Medical Research Council Centre for Immune Regulation, School of Immunity and Infection and Institute for Biomedical Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Calman A. MacLennan
- Novartis Vaccines Institute for Global Health, Via Fiorentina 1, 53100 Siena, Italy
| | - Ian C MacLennan
- Medical Research Council Centre for Immune Regulation, School of Immunity and Infection and Institute for Biomedical Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Ian R. Henderson
- Medical Research Council Centre for Immune Regulation, School of Immunity and Infection and Institute for Biomedical Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Adam F. Cunningham
- Medical Research Council Centre for Immune Regulation, School of Immunity and Infection and Institute for Biomedical Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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32
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Couston RG, Skoda MW, Uddin S, van der Walle CF. Adsorption behavior of a human monoclonal antibody at hydrophilic and hydrophobic surfaces. MAbs 2012. [PMID: 23196810 DOI: 10.4161/mabs.22522] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
One aspiration for the formulation of human monoclonal antibodies (mAb) is to reach high solution concentrations without compromising stability. Protein surface activity leading to instability is well known, but our understanding of mAb adsorption to the solid-liquid interface in relevant pH and surfactant conditions is incomplete. To investigate these conditions, we used total internal reflection fluorescence (TIRF) and neutron reflectometry (NR). The mAb tested ("mAb-1") showed highest surface loading to silica at pH 7.4 (~12 mg/m(2)), with lower surface loading at pH 5.5 (~5.5 mg/m(2), further from its pI of 8.99) and to hydrophobized silica (~2 mg/m(2)). The extent of desorption of mAb-1 from silica or hydrophobized silica was related to the relative affinity of polysorbate 20 or 80 for the same surface. mAb-1 adsorbed to silica on co-injection with polysorbate (above its critical micelle concentration) and also to silica pre-coated with polysorbate. A bilayer model was developed from NR data for mAb-1 at concentrations of 50-5000 mg/L, pH 5.5, and 50-2000 mg/L, pH 7.4. The inner mAb-1 layer was adsorbed to the SiO₂ surface at near saturation with an end-on" orientation, while the outer mAb-1 layer was sparse and molecules had a "side-on" orientation. A non-uniform triple layer was observed at 5000 mg/L, pH 7.4, suggesting mAb-1 adsorbed to the SiO₂ surface as oligomers at this concentration and pH. mAb-1 adsorbed as a sparse monolayer to hydrophobized silica, with a layer thickness increasing with bulk concentration - suggesting a near end-on orientation without observable relaxation-unfolding.
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Affiliation(s)
- Ruairidh G Couston
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK
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Onen O, Ahmad AA, Guldiken R, Gallant ND. Surface modification on acoustic wave biosensors for enhanced specificity. SENSORS 2012; 12:12317-28. [PMID: 23112714 PMCID: PMC3478841 DOI: 10.3390/s120912317] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 09/03/2012] [Accepted: 09/04/2012] [Indexed: 02/06/2023]
Abstract
Changes in mass loading on the surface of acoustic biosensors result in output frequency shifts which provide precise measurements of analytes. Therefore, to detect a particular biomarker, the sensor delay path must be judiciously designed to maximize sensitivity and specificity. B-cell lymphoma 2 protein (Bcl-2) found in urine is under investigation as a biomarker for non-invasive early detection of ovarian cancer. In this study, surface chemistry and biofunctionalization approaches were evaluated for their effectiveness in presenting antibodies for Bcl-2 capture while minimizing non-specific protein adsorption. The optimal combination of sequentially adsorbing protein A/G, anti-Bcl-2 IgG and Pluronic F127 onto a hydrophobic surface provided the greatest signal-to-noise ratio and enabled the reliable detection of Bcl-2 concentrations below that previously identified for early stage ovarian cancer as characterized by a modified ELISA method. Finally, the optimal surface modification was applied to a prototype acoustic device and the frequency shift for a range of Bcl-2 concentration was quantified to demonstrate the effectiveness in surface acoustic wave (SAW)-based detection applications. The surface functionalization approaches demonstrated here to specifically and sensitively detect Bcl-2 in a working ultrasonic MEMS biosensor prototype can easily be modified to detect additional biomarkers and enhance other acoustic biosensors.
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Affiliation(s)
- Onursal Onen
- Department of Mechanical Engineering, University of South Florida, 4202 E Fowler Ave, ENB 118, Tampa, FL 33620, USA.
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Saerbeck T, Klose F, Le Brun AP, Füzi J, Brule A, Nelson A, Holt SA, James M. Invited article: polarization "down under": the polarized time-of-flight neutron reflectometer PLATYPUS. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2012; 83:081301. [PMID: 22938267 DOI: 10.1063/1.4738579] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
This review presents the implementation and full characterization of the polarization equipment of the time-of-flight neutron reflectometer PLATYPUS at the Australian Nuclear Science and Technology Organisation (ANSTO). The functionality and efficiency of individual components are evaluated and found to maintain a high neutron beam polarization with a maximum of 99.3% through polarizing Fe/Si supermirrors. Neutron spin-flippers with efficiencies of 99.7% give full control over the incident and scattered neutron spin direction over the whole wavelength spectrum available in the instrument. The first scientific experiments illustrate data correction mechanisms for finite polarizations and reveal an extraordinarily high reproducibility for measuring magnetic thin film samples. The setup is now fully commissioned and available for users through the neutron beam proposal system of the Bragg Institute at ANSTO.
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Affiliation(s)
- T Saerbeck
- School of Physics, University of Western Australia, Crawley WA6009, Australia.
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Kirby B, Kienzle P, Maranville B, Berk N, Krycka J, Heinrich F, Majkrzak C. Phase-sensitive specular neutron reflectometry for imaging the nanometer scale composition depth profile of thin-film materials. Curr Opin Colloid Interface Sci 2012. [DOI: 10.1016/j.cocis.2011.11.001] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Self-assembly of protein monolayers engineered for improved monoclonal immunoglobulin G binding. Int J Mol Sci 2011; 12:5157-67. [PMID: 21954350 PMCID: PMC3179157 DOI: 10.3390/ijms12085157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 07/04/2011] [Accepted: 08/10/2011] [Indexed: 02/04/2023] Open
Abstract
Bacterial outer membrane proteins, along with a filling lipid molecule can be modified to form stable self-assembled monolayers on gold. The transmembrane domain of Escherichia coli outer membrane protein A has been engineered to create a scaffold protein to which functional motifs can be fused. In earlier work we described the assembly and structure of an antibody-binding array where the Z domain of Staphylococcus aureus protein A was fused to the scaffold protein. Whilst the binding of rabbit polyclonal immunoglobulin G (IgG) to the array is very strong, mouse monoclonal IgG dissociates from the array easily. This is a problem since many immunodiagnostic tests rely upon the use of mouse monoclonal antibodies. Here we describe a strategy to develop an antibody-binding array that will bind mouse monoclonal IgG with lowered dissociation from the array. A novel protein consisting of the scaffold protein fused to two pairs of Z domains separated by a long flexible linker was manufactured. Using surface plasmon resonance the self-assembly of the new protein on gold and the improved binding of mouse monoclonal IgG were demonstrated.
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