1
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Su Q, Sun Y, Tang Y, Ni N, Ding N. Measurement of enzyme activity of insoluble substrates based on ordered porous layer interferometry and the application in evaluation of thrombolytic drugs. Analyst 2024; 149:1537-1547. [PMID: 38284466 DOI: 10.1039/d3an02054a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
The development of innovative methods for real-time surveillance of enzymatic activity determination processes is essential, particularly for insoluble substrate enzymatic assessments. In this work, a novel method for enzymatic activity determination was devised by assembling a 190 nm silica colloidal crystal (SCC) film onto a glass slide, coupled with Ordered Porous Layer Interferometry (OPLI) technology. By fixing the substrate of the enzyme on the surface of the silica sphere, a solid-liquid interface can be formed for monitoring enzymatic activity. The enzymatic activity is gauged by the change in the SCC film's thickness caused by the digestion of the loaded substrate. The procedure of chymotrypsin-mediated casein digestion was documented in real time, facilitating the examination of chymotrypsin's activity and kinetics. The newly-developed enzymatic activity determination method demonstrated exceptional sensitivity towards chymotrypsin activity, with a linear range spanning 0.0505-2.02 units per mg. Additionally, the method was extended to the assessment of fibrinolysis enzyme activity and kinetic analysis, yielding promising results. Therefore, this technique can serve as a real-time, user-friendly, cost-effective novel approach for enzymatic activity determination, providing fresh perspectives for enzymatic activity determination studies.
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Affiliation(s)
- Qianqian Su
- Pharmacy School, Jiangsu Ocean University, Lianyungang 222005, China.
- Jiangsu Key Laboratory of Marine Drug Screening, Lianyungang 222005, China
| | - Yu Sun
- Pharmacy School, Jiangsu Ocean University, Lianyungang 222005, China.
- Jiangsu Key Laboratory of Marine Drug Screening, Lianyungang 222005, China
| | - Yanhua Tang
- Pharmacy School, Jiangsu Ocean University, Lianyungang 222005, China.
- Jiangsu Key Laboratory of Marine Drug Screening, Lianyungang 222005, China
| | - Na Ni
- Pharmacy School, Jiangsu Ocean University, Lianyungang 222005, China.
- Jiangsu Key Laboratory of Marine Drug Screening, Lianyungang 222005, China
| | - Nian Ding
- Pharmacy School, Jiangsu Ocean University, Lianyungang 222005, China.
- Jiangsu Key Laboratory of Marine Drug Screening, Lianyungang 222005, China
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2
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Goodman KM, Katsamba PS, Rubinstein R, Ahlsén G, Bahna F, Mannepalli S, Dan H, Sampogna RV, Shapiro L, Honig B. How clustered protocadherin binding specificity is tuned for neuronal self-/nonself-recognition. eLife 2022; 11:e72416. [PMID: 35253643 PMCID: PMC8901172 DOI: 10.7554/elife.72416] [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: 07/22/2021] [Accepted: 01/26/2022] [Indexed: 12/30/2022] Open
Abstract
The stochastic expression of fewer than 60 clustered protocadherin (cPcdh) isoforms provides diverse identities to individual vertebrate neurons and a molecular basis for self-/nonself-discrimination. cPcdhs form chains mediated by alternating cis and trans interactions between apposed membranes, which has been suggested to signal self-recognition. Such a mechanism requires that cPcdh cis dimers form promiscuously to generate diverse recognition units, and that trans interactions have precise specificity so that isoform mismatches terminate chain growth. However, the extent to which cPcdh interactions fulfill these requirements has not been definitively demonstrated. Here, we report biophysical experiments showing that cPcdh cis interactions are promiscuous, but with preferences favoring formation of heterologous cis dimers. Trans homophilic interactions are remarkably precise, with no evidence for heterophilic interactions between different isoforms. A new C-type cPcdh crystal structure and mutagenesis data help to explain these observations. Overall, the interaction characteristics we report for cPcdhs help explain their function in neuronal self-/nonself-discrimination.
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Affiliation(s)
- Kerry Marie Goodman
- Zuckerman Mind, Brain and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Phinikoula S Katsamba
- Zuckerman Mind, Brain and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Rotem Rubinstein
- School of Neurobiology, Biochemistry and Biophysics, Tel Aviv UniversityTel AvivIsrael
- Sagol School of Neuroscience, Tel Aviv UniversityTel AvivIsrael
| | - Göran Ahlsén
- Zuckerman Mind, Brain and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Fabiana Bahna
- Zuckerman Mind, Brain and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Seetha Mannepalli
- Zuckerman Mind, Brain and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Hanbin Dan
- Department of Medicine, Division of Nephrology, Columbia UniversityNew YorkUnited States
| | - Rosemary V Sampogna
- Department of Medicine, Division of Nephrology, Columbia UniversityNew YorkUnited States
| | - Lawrence Shapiro
- Zuckerman Mind, Brain and Behavior Institute, Columbia UniversityNew YorkUnited States
- Department of Biochemistry and Molecular Biophysics, Columbia UniversityNew YorkUnited States
| | - Barry Honig
- Zuckerman Mind, Brain and Behavior Institute, Columbia UniversityNew YorkUnited States
- Department of Medicine, Division of Nephrology, Columbia UniversityNew YorkUnited States
- Department of Biochemistry and Molecular Biophysics, Columbia UniversityNew YorkUnited States
- Department of Systems Biology, Columbia UniversityNew YorkUnited States
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3
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Terao K, Kondo S. AC-Electroosmosis-Assisted Surface Plasmon Resonance Sensing for Enhancing Protein Signals with a Simple Kretschmann Configuration. SENSORS 2022; 22:s22030854. [PMID: 35161603 PMCID: PMC8838944 DOI: 10.3390/s22030854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 11/27/2022]
Abstract
A surface plasmon resonance (SPR) sensor chip fabricated with a comb-shaped microelectrode array to supply alternating current (AC) voltage is reported. The chip induces circulating flow near the surface (i.e., AC electroosmosis). The circulating flow provides a mixing effect, which enhances the binding of the analyte molecules. We evaluated the SPR characteristics of the chip and demonstrated an improvement in protein binding to the chip surface. SPR sensor chips with comb-shaped microelectrodes were fabricated using standard UV lithography. Sensing experiments were conducted using a standard Kretschmann-type SPR measurement system. To demonstrate the mixing effect of AC electroosmosis, we evaluated the binding of immunoglobulin G molecules onto the sensor surface where anti-immunoglobulin G antibodies were covalently immobilized. The result indicates that the amount of binding increases by a factor of 1.7 above that achieved by using a conventional chip, suggesting enhancement of the protein signal.
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4
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Su Q, Jiang C, Gou D, Long Y. Surface Plasmon-Assisted Fluorescence Enhancing and Quenching: From Theory to Application. ACS APPLIED BIO MATERIALS 2021; 4:4684-4705. [PMID: 35007020 DOI: 10.1021/acsabm.1c00320] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The integration of surface plasmon resonance and fluorescence yields a multiaspect improvement in surface fluorescence sensing and imaging, leading to a paradigm shift of surface plasmon-assisted fluorescence techniques, for example, surface plasmon enhanced field fluorescence spectroscopy, surface plasmon coupled emission (SPCE), and SPCE imaging. This Review aims to characterize the unique optical property with a common physical interpretation and diverse surface architecture-based measurements. The fundamental electromagnetic theory is employed to comprehensively unveil the fluorophore-surface plasmon interaction, and the associated surface-modification design is liberally highlighted to balance the surface plasmon-induced fluorescence-enhancement efforts and the surface plasmon-caused fluorescence-quenching effects. In particular, all types of surface structures, for example, silicon, carbon, protein, DNA, polymer, and multilayer, are systematically interrogated in terms of component, thickness, stiffness, and functionality. As a highly interdisciplinary and expanding field in physics, optics, chemistry, and surface chemistry, this Review could be of great interest to a broad readership, in particular, among physical chemists, analytical chemists, and in surface-based sensing and imaging studies.
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Affiliation(s)
- Qiang Su
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Carson International Cancer Center, Shenzhen University, 1066 Xueyuan Street, Nanshan District, Shenzhen 518055, Guangdong, China.,School of Chemistry, University of Birmingham, Edgbaston B15 2TT, Birmingham, United Kingdom
| | - Cheng Jiang
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom.,Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Deming Gou
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Carson International Cancer Center, Shenzhen University, 1066 Xueyuan Street, Nanshan District, Shenzhen 518055, Guangdong, China
| | - Yi Long
- Clinical Research Center, Southern University of Science and Technology Hospital, 6019 Liuxian Street, Xili Avenue, Nanshan District, Shenzhen 518055, Guangdong, China
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5
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Tiwari PB, Bencheqroun C, Lemus M, Shaw T, Kouassi-Brou M, Alaoui A, Üren A. SPRD: a surface plasmon resonance database of common factors for better experimental planning. BMC Mol Cell Biol 2021; 22:17. [PMID: 33676410 PMCID: PMC7937274 DOI: 10.1186/s12860-021-00354-w] [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: 12/15/2020] [Accepted: 02/22/2021] [Indexed: 12/17/2022] Open
Abstract
Background Surface plasmon resonance is a label-free biophysical technique that is widely used in investigating biomolecular interactions, including protein-protein, protein-DNA, and protein-small molecule binding. Surface plasmon resonance is a very powerful tool in different stages of small molecule drug development and antibody characterization. Both academic institutions and pharmaceutical industry extensively utilize this method for screening and validation studies involving direct molecular interactions. In most applications of the surface plasmon resonance technology, one of the studied molecules is immobilized on a microchip, while the second molecule is delivered through a microfluidic system over the immobilized molecules. Changes in total mass on the chip surface is recorded in real time as an indicator of the molecular interactions. Main body Quality and accuracy of the surface plasmon resonance data depend on experimental variables, including buffer composition, type of sensor chip, coupling chemistry of molecules on the sensor surface, and surface regeneration conditions. These technical details are generally included in materials and methods sections of published manuscripts and are not easily accessible using the common internet browser search engines or PubMed. Herein, we introduce a surface plasmon resonance database, www.sprdatabase.info that contains technical details extracted from 5140 publications with surface plasmon resonance data. We also provide an analysis of experimental conditions preferred by different laboratories. These experimental variables can be searched within the database and help future users of this technology to design better experiments. Conclusion Amine coupling and CM5 chips were the most common methods used for immobilizing proteins in surface plasmon resonance experiments. However, number of different chips, capture methods and buffer conditions were used by multiple investigators. We predict that the database will significantly help the scientific community using this technology and hope that users will provide feedback to improve and expand the database indefinitely. Publicly available information in the database can save a great amount of time and resources by assisting initial optimization and troubleshooting of surface plasmon resonance experiments.
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Affiliation(s)
| | - Camelia Bencheqroun
- Innovation Center for Biomedical Informatics (ICBI), Georgetown University, Washington, DC, 20057, USA
| | - Mario Lemus
- Department of Oncology, Georgetown University, Washington, DC, 20057, USA
| | - Taryn Shaw
- Department of Oncology, Georgetown University, Washington, DC, 20057, USA
| | - Marilyn Kouassi-Brou
- Department of Oncology, Georgetown University, Washington, DC, 20057, USA.,Geisel School of Medicine, Dartmouth College, NH, 03755, Hanover, USA
| | - Adil Alaoui
- Innovation Center for Biomedical Informatics (ICBI), Georgetown University, Washington, DC, 20057, USA
| | - Aykut Üren
- Department of Oncology, Georgetown University, Washington, DC, 20057, USA.
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6
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Multiplex Immunoassay Techniques for On-Site Detection of Security Sensitive Toxins. Toxins (Basel) 2020; 12:toxins12110727. [PMID: 33233770 PMCID: PMC7699850 DOI: 10.3390/toxins12110727] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 12/12/2022] Open
Abstract
Biological toxins are a heterogeneous group of high molecular as well as low molecular weight toxins produced by living organisms. Due to their physical and logistical properties, biological toxins are very attractive to terrorists for use in acts of bioterrorism. Therefore, among the group of biological toxins, several are categorized as security relevant, e.g., botulinum neurotoxins, staphylococcal enterotoxins, abrin, ricin or saxitoxin. Additionally, several security sensitive toxins also play a major role in natural food poisoning outbreaks. For a prompt response to a potential bioterrorist attack using biological toxins, first responders need reliable, easy-to-use and highly sensitive methodologies for on-site detection of the causative agent. Therefore, the aim of this review is to present on-site immunoassay platforms for multiplex detection of biological toxins. Furthermore, we introduce several commercially available detection technologies specialized for mobile or on-site identification of security sensitive toxins.
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7
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Zhou L, Su Q, Wu F, Wan Y, Xu P, Dong A, Li Q, Qian W. Using Reflectometric Interference Spectroscopy to Real-Time Monitor Amphiphile-Induced Orientational Responses of Liquid-Crystal-Loaded Silica Colloidal Crystal Films. Anal Chem 2020; 92:12071-12078. [DOI: 10.1021/acs.analchem.0c02749] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lele Zhou
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qianqian Su
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Feng Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yizhen Wan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Pengfei Xu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Ao Dong
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qiang Li
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Weiping Qian
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
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8
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Sergeeva AP, Katsamba PS, Cosmanescu F, Brewer JJ, Ahlsen G, Mannepalli S, Shapiro L, Honig B. DIP/Dpr interactions and the evolutionary design of specificity in protein families. Nat Commun 2020; 11:2125. [PMID: 32358559 PMCID: PMC7195491 DOI: 10.1038/s41467-020-15981-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 04/06/2020] [Indexed: 01/10/2023] Open
Abstract
Differential binding affinities among closely related protein family members underlie many biological phenomena, including cell-cell recognition. Drosophila DIP and Dpr proteins mediate neuronal targeting in the fly through highly specific protein-protein interactions. We show here that DIPs/Dprs segregate into seven specificity subgroups defined by binding preferences between their DIP and Dpr members. We then describe a sequence-, structure- and energy-based computational approach, combined with experimental binding affinity measurements, to reveal how specificity is coded on the canonical DIP/Dpr interface. We show that binding specificity of DIP/Dpr subgroups is controlled by "negative constraints", which interfere with binding. To achieve specificity, each subgroup utilizes a different combination of negative constraints, which are broadly distributed and cover the majority of the protein-protein interface. We discuss the structural origins of negative constraints, and potential general implications for the evolutionary origins of binding specificity in multi-protein families.
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Affiliation(s)
- Alina P Sergeeva
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Phinikoula S Katsamba
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA
| | - Filip Cosmanescu
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA
| | - Joshua J Brewer
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Goran Ahlsen
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA
| | - Seetha Mannepalli
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA
| | - Lawrence Shapiro
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
| | - Barry Honig
- Department of Systems Biology, Columbia University, New York, NY, USA.
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
- Department of Medicine, Columbia University, New York, NY, USA.
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9
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Family-wide Structural and Biophysical Analysis of Binding Interactions among Non-clustered δ-Protocadherins. Cell Rep 2020; 30:2655-2671.e7. [PMID: 32101743 PMCID: PMC7082078 DOI: 10.1016/j.celrep.2020.02.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 11/02/2019] [Accepted: 01/31/2020] [Indexed: 01/21/2023] Open
Abstract
Non-clustered δ1- and δ2-protocadherins, close relatives of clustered protocadherins, function in cell adhesion and motility and play essential roles in neural patterning. To understand the molecular interactions underlying these functions, we used solution biophysics to characterize binding of δ1- and δ2-protocadherins, determined crystal structures of ectodomain complexes from each family, and assessed ectodomain assembly in reconstituted intermembrane junctions by cryoelectron tomography (cryo-ET). Homophilic trans (cell-cell) interactions were preferred for all δ-protocadherins, with additional weaker heterophilic interactions observed exclusively within each subfamily. As expected, δ1- and δ2-protocadherin trans dimers formed through antiparallel EC1-EC4 interfaces, like clustered protocadherins. However, no ectodomain-mediated cis (same-cell) interactions were detectable in solution; consistent with this, cryo-ET of reconstituted junctions revealed dense assemblies lacking the characteristic order observed for clustered protocadherins. Our results define non-clustered protocadherin binding properties and their structural basis, providing a foundation for interpreting their functional roles in neural patterning.
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10
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Kim DM, Yao X, Vanam RP, Marlow MS. Measuring the effects of macromolecular crowding on antibody function with biolayer interferometry. MAbs 2019; 11:1319-1330. [PMID: 31401928 PMCID: PMC6748605 DOI: 10.1080/19420862.2019.1647744] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Biotherapeutic proteins are commonly dosed at high concentrations into the blood, which is an inherently complex, crowded solution with substantial protein content. The effects of macromolecular crowding may lead to an appreciable level of non-specific hetero-association in this physiological environment. Therefore, developing a method to characterize the diverse consequences of non-specific interactions between proteins under such non-ideal, crowded conditions, which deviate substantially from those commonly employed for in vitro characterization, is vital to achieving a more complete picture of antibody function in a biological context. In this study, we investigated non-specific interactions between human serum albumin (HSA) and two monoclonal antibodies (mAbs) by static light scattering and determined these interactions are both ionic strength-dependent and mAb-dependent. Using biolayer interferometry (BLI), we assessed the effect of HSA on antigen binding by mAbs, demonstrating that these non-specific interactions have a functional impact on mAb:antigen interactions, particularly at low ionic strength. While this effect is mitigated at physiological ionic strength, our in vitro data support the notion that HSA in the blood may lead to non-specific interactions with mAbs in vivo, with a potential impact on their interactions with antigen. Furthermore, the BLI method offers a high-throughput advantage compared to orthogonal techniques such as analytical ultracentrifugation and is amenable to a greater variety of solution conditions compared to nuclear magnetic resonance spectroscopy. Our study demonstrates that BLI is a viable technology for examining the impact of non-specific interactions on specific biologically relevant interactions, providing a direct method to assess binding events in crowded conditions.
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Affiliation(s)
- Dorothy M Kim
- Pre-Clinical Development and Protein Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA
| | - Xiao Yao
- Pre-Clinical Development and Protein Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA
| | - Ram P Vanam
- Pre-Clinical Development and Protein Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA
| | - Michael S Marlow
- Pre-Clinical Development and Protein Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA.,Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc ., Ridgefield , CT , USA
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11
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Su Q, Wu F, Xu P, Dong A, Liu C, Wan Y, Qian W. Interference Effect of Silica Colloidal Crystal Films and Their Applications to Biosensing. Anal Chem 2019; 91:6080-6087. [PMID: 30994327 DOI: 10.1021/acs.analchem.9b00620] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
With the aim to develop better and more reliable interference effective substrates, silica colloidal crystal films with different sphere diameters and film thicknesses were successfully made by an improved vertical deposition method and a systematic investigation of their reflectometric interference spectroscopy (RIfS) properties are presented in this work. The influence of silica sphere diameter and film thickness on the RIfS signals was studied. The results showed that the film thickness is the key factor of RIfS signals. An RIfS system was set up by using a silica colloidal crystal film as an interference effective substrate. The influence of film thickness on the response to refractive index changes of the proposed system was also investigated. When the influence of film thickness on RIfS signals and refractive index response we considered together, silica colloidal crystal films with a thickness between 4 and 6 μm were chosen for sensor construction. Monitoring the digestive process of gelatin with trypsin was also demonstrated by combining gelatin-modified silica colloidal crystal films with RIfS. The system showed excellent sensitivity with a wide linear range and could achieve real-time measurement of each process. It has been proved that this is a promising method to construct biosensors using silica colloidal crystal films as interference-sensitive substrates.
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Affiliation(s)
- Qianqian Su
- State Key Laboratory of Bioelectronics , Southeast University , Nanjing , People's Republic of China
| | - Feng Wu
- State Key Laboratory of Bioelectronics , Southeast University , Nanjing , People's Republic of China
| | - Pengfei Xu
- State Key Laboratory of Bioelectronics , Southeast University , Nanjing , People's Republic of China
| | - Ao Dong
- State Key Laboratory of Bioelectronics , Southeast University , Nanjing , People's Republic of China
| | - Chang Liu
- State Key Laboratory of Bioelectronics , Southeast University , Nanjing , People's Republic of China
| | - Yizhen Wan
- State Key Laboratory of Bioelectronics , Southeast University , Nanjing , People's Republic of China
| | - Weiping Qian
- State Key Laboratory of Bioelectronics , Southeast University , Nanjing , People's Republic of China
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12
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Walper SA, Lasarte Aragonés G, Sapsford KE, Brown CW, Rowland CE, Breger JC, Medintz IL. Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies. ACS Sens 2018; 3:1894-2024. [PMID: 30080029 DOI: 10.1021/acssensors.8b00420] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Although a fundamental understanding of the pathogenicity of most biothreat agents has been elucidated and available treatments have increased substantially over the past decades, they still represent a significant public health threat in this age of (bio)terrorism, indiscriminate warfare, pollution, climate change, unchecked population growth, and globalization. The key step to almost all prevention, protection, prophylaxis, post-exposure treatment, and mitigation of any bioagent is early detection. Here, we review available methods for detecting bioagents including pathogenic bacteria and viruses along with their toxins. An introduction placing this subject in the historical context of previous naturally occurring outbreaks and efforts to weaponize selected agents is first provided along with definitions and relevant considerations. An overview of the detection technologies that find use in this endeavor along with how they provide data or transduce signal within a sensing configuration follows. Current "gold" standards for biothreat detection/diagnostics along with a listing of relevant FDA approved in vitro diagnostic devices is then discussed to provide an overview of the current state of the art. Given the 2014 outbreak of Ebola virus in Western Africa and the recent 2016 spread of Zika virus in the Americas, discussion of what constitutes a public health emergency and how new in vitro diagnostic devices are authorized for emergency use in the U.S. are also included. The majority of the Review is then subdivided around the sensing of bacterial, viral, and toxin biothreats with each including an overview of the major agents in that class, a detailed cross-section of different sensing methods in development based on assay format or analytical technique, and some discussion of related microfluidic lab-on-a-chip/point-of-care devices. Finally, an outlook is given on how this field will develop from the perspective of the biosensing technology itself and the new emerging threats they may face.
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Affiliation(s)
- Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Guillermo Lasarte Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Kim E. Sapsford
- OMPT/CDRH/OIR/DMD Bacterial Respiratory and Medical Countermeasures Branch, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Carl W. Brown
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Clare E. Rowland
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20036, United States
| | - Joyce C. Breger
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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13
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Monitoring drug–serum protein interactions for early ADME prediction through Surface Plasmon Resonance technology. J Pharm Biomed Anal 2017; 144:188-194. [DOI: 10.1016/j.jpba.2017.03.054] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 03/03/2017] [Accepted: 03/26/2017] [Indexed: 12/16/2022]
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14
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Heterotypic Coiled-Coil Formation is Essential for the Correct Assembly of the Septin Heterofilament. Biophys J 2017; 111:2608-2619. [PMID: 28002737 DOI: 10.1016/j.bpj.2016.10.032] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 10/03/2016] [Accepted: 10/05/2016] [Indexed: 11/20/2022] Open
Abstract
Protein-protein interactions play a critical role in promoting the stability of protein quaternary structure and in the assembly of large macromolecular complexes. What drives the stabilization of such assemblies is a central question in biology. A limiting factor in fully understanding such systems is the transient nature of many complexes, making structural studies difficult. Septins comprise a conserved family of guanine nucleotide binding proteins that polymerize in the form of heterofilaments. In structural terms, they have a common organization: a central GTPase domain, an N-terminal domain, and a C-terminal domain; the latter is predicted to form a coiled coil. Currently, even for the best characterized human septin heterocomplex (SEPT2/SEPT6/SEPT7), the role of C-terminal domain is not fully established, and this is partly due to the absence of electron density for the C-terminal domains in the x-ray structure. Here we present results on the homo/heterotypical affinity for the C-terminal domains of human septins belonging to the SEPT6 and SEPT7 groups (SEPT6C/8C/10C/11C and SEPT7C, respectively) and provide clear evidence that this domain determines the preference for heterotypic interactions at one specific interface during the assembly of the heterofilament. This observation has wider implications where macromolecular assemblies are defined by coiled-coil protein interactions.
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15
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Abstract
The use of optical biosensors for studying macromolecular interactions is gaining increasing popularity. In one study, 1514 papers that involved the application of biosensor data were identified for the year 2009 alone (Rich and Myszka, J Mol Recognit 24:892-914, 2011), the sheer volume and variety of which present a daunting task for the burgeoning biosensor user to accumulate and decipher. This chapter is designed to provide the reader with the tools necessary to prepare, design, and efficiently execute a kinetic experiment on Biacore. It is written to guide the Biacore user through basic theory, system maintenance, and assay setup while also offering some practical tips that we find useful for Biacore-based studies. Many kinetic-based screening assays require rigorous sample preparation and purification prior to analysis. To highlight these procedures, this protocol describes the kinetic characterization of single chain Fv (scFv) antibody fragments from crude bacterial lysates using an antibody affinity capture approach. Even though we specifically describe the capture of HA-tagged scFv antibody fragments to an anti-HA tag monoclonal antibody-immobilized surface prior to kinetic analysis, the same methodologies are universally applicable and can be used for practically any affinity pair and most Biacore systems.
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Affiliation(s)
- Paul Leonard
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
- School of Biotechnology, Dublin City University, Dublin 9, Ireland
- National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
| | - Stephen Hearty
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
- School of Biotechnology, Dublin City University, Dublin 9, Ireland
- National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
| | - Hui Ma
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
| | - Richard O'Kennedy
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland.
- School of Biotechnology, Dublin City University, Dublin 9, Ireland.
- National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland.
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16
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Wang X, McKay P, Yee LT, Dutina G, Hass PE, Nijem I, Allison D, Cowan KJ, Lin K, Quarmby V, Yang J. Impact of SPR biosensor assay configuration on antibody: Neonatal Fc receptor binding data. MAbs 2016; 9:319-332. [PMID: 28001487 DOI: 10.1080/19420862.2016.1261774] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Binding interactions with the neonatal Fc receptor (FcRn) are one determinant of pharmacokinetic properties of recombinant human monoclonal antibody (rhumAb) therapeutics, and a conserved binding motif in the crystallizable fragment (Fc) region of IgG molecules interacts with FcRn. Surface plasmon resonance (SPR) biosensor assays are often used to characterize interactions between FcRn and rhumAb therapeutics. In such assays, generally either the rhumAb (format 1) or the FcRn protein (format 2) is immobilized on a biosensor chip. However, because evidence suggests that, in some cases, the variable domains of a rhumAb may also affect FcRn binding, we evaluated the effect of SPR assay configuration on binding data. We sought to assess FcRn binding properties of 2 rhumAbs (rhumAb1 and rhumAb2) to FcRn proteins using these 2 biosensor assay formats. The two rhumAbs have greater than 99% sequence identity in the Fc domain but differ in their Fab regions. rhumAb2 contains a positively charged patch in the variable domain that is absent in rhumAb1. Our results showed that binding of rhumAb1 to FcRn was independent of biosensor assay configuration, while binding of rhumAb2 to FcRn was highly SPR assay configuration dependent. Further investigations revealed that the format dependency of rhumAb2-FcRn binding is linked to the basic residues that form a positively charged patch in the variable domain of rhumAb2. Our work highlights the importance of analyzing rhumAb-FcRn binding interactions using 2 alternate SPR biosensor assay configurations. This approach may also provide a simple way to identify the potential for non-Fc-driven FcRn binding interactions in otherwise typical IgGs.
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Affiliation(s)
- Xiangdan Wang
- a BioAnalytical Sciences, Genentech , South San Francisco , CA , USA
| | - Patrick McKay
- b Technical Development, Genentech , South San Francisco , CA , USA
| | - Liliana T Yee
- b Technical Development, Genentech , South San Francisco , CA , USA
| | - George Dutina
- c Department of Early Stage Cell Culture , Genentech , South San Francisco , CA , USA
| | - Philip E Hass
- d Protein Chemistry, Genentech , South San Francisco , CA , USA
| | - Ihsan Nijem
- a BioAnalytical Sciences, Genentech , South San Francisco , CA , USA
| | - David Allison
- e Clinical Pharmacology, Genentech , South San Francisco , CA , USA
| | - Kyra J Cowan
- a BioAnalytical Sciences, Genentech , South San Francisco , CA , USA
| | - Kevin Lin
- f Analytical Operations, Genentech , South San Francisco , CA , USA
| | - Valerie Quarmby
- a BioAnalytical Sciences, Genentech , South San Francisco , CA , USA
| | - Jihong Yang
- a BioAnalytical Sciences, Genentech , South San Francisco , CA , USA
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17
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Carroll J, Raum M, Forsten-Williams K, Täuber UC. Ligand-receptor binding kinetics in surface plasmon resonance cells: a Monte Carlo analysis. Phys Biol 2016; 13:066010. [PMID: 27922830 DOI: 10.1088/1478-3975/13/6/066010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Surface plasmon resonance (SPR) chips are widely used to measure association and dissociation rates for the binding kinetics between two species of chemicals, e.g., cell receptors and ligands. It is commonly assumed that ligands are spatially well mixed in the SPR region, and hence a mean-field rate equation description is appropriate. This approximation however ignores the spatial fluctuations as well as temporal correlations induced by multiple local rebinding events, which become prominent for slow diffusion rates and high binding affinities. We report detailed Monte Carlo simulations of ligand binding kinetics in an SPR cell subject to laminar flow. We extract the binding and dissociation rates by means of the techniques frequently employed in experimental analysis that are motivated by the mean-field approximation. We find major discrepancies in a wide parameter regime between the thus extracted rates and the known input simulation values. These results underscore the crucial quantitative importance of spatio-temporal correlations in binary reaction kinetics in SPR cell geometries, and demonstrate the failure of a mean-field analysis of SPR cells in the regime of high Damköhler number [Formula: see text], where the spatio-temporal correlations due to diffusive transport and ligand-receptor rebinding events dominate the dynamics of SPR systems.
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Affiliation(s)
- Jacob Carroll
- Department of Physics & Center for Soft Matter and Biological Physics (MC 0435), Robeson Hall, 850 West Campus Drive, Virginia Tech, Blacksburg, VA 24061, USA
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18
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Jalali-Yazdi F, Takahashi TT, Roberts RW. General, Label-Free Method for Determining K(d) and Ligand Concentration Simultaneously. Anal Chem 2015; 87:11755-62. [PMID: 26485531 DOI: 10.1021/acs.analchem.5b03069] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Some of the most commonly used affinity reagents (e.g., antibodies) are often developed and used in conditions where their input concentrations ([L]0) and affinities (K(d)) are not known. Here, we have developed a general approach to determine both [L]0 and K(d) values simultaneously for affinity reagents (small molecules, proteins, and antibodies). To do this, we perform quantitative equilibrium exclusion immunoassays with two different concentrations of target and fit the data simultaneously to determine K(d) and [L]0. The results give accurate and reproducible measures of both values compared to established methods. By performing detailed error analysis, we demonstrate that our fitting gives unique solutions and indicates where K(d) and [L]0 measures are reliable. Furthermore, we found that a divalent model of antibody binding gives accurate K(d) and [L]0 values in both the forward (antibody immobilized) and the reverse (target immobilized) assays-addressing the long-term problem of obtaining quantitative data from reverse assays.
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Affiliation(s)
- Farzad Jalali-Yazdi
- Mork Family Department of Chemical Engineering and Materials Science, ‡Department of Chemistry, §Department of Molecular Computational Biology, and ∥USC Norris Comprehensive Cancer Center, University of Southern California , Los Angeles, California 90089-2905, United States
| | - Terry T Takahashi
- Mork Family Department of Chemical Engineering and Materials Science, ‡Department of Chemistry, §Department of Molecular Computational Biology, and ∥USC Norris Comprehensive Cancer Center, University of Southern California , Los Angeles, California 90089-2905, United States
| | - Richard W Roberts
- Mork Family Department of Chemical Engineering and Materials Science, ‡Department of Chemistry, §Department of Molecular Computational Biology, and ∥USC Norris Comprehensive Cancer Center, University of Southern California , Los Angeles, California 90089-2905, United States
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19
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Abstract
Protein-protein interactions regulate many important cellular processes, including carbohydrate and lipid metabolism, cell cycle and cell death regulation, protein and nucleic acid metabolism, signal transduction, and cellular architecture. A complete understanding of cellular function depends on full characterization of the complex network of cellular protein-protein interactions, including measurements of their kinetic and binding properties. Surface plasmon resonance (SPR) is one of the commonly used technologies for detailed and quantitative studies of protein-protein interactions and determination of their equilibrium and kinetic parameters. SPR provides excellent instrumentation for a label-free, real-time investigation of protein-protein interactions. This chapter details the experimental design and proper use of the instrumentation for a kinetic experiment. It will provide readers with basic theory, assay setup, and the proper way of reporting this type of results with practical tips useful for SPR-based studies. A generic protocol for immobilizing ligands using amino coupling chemistry, also useful if an antibody affinity capture approach is used, performing kinetic studies, and collecting and analyzing data is described.
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Affiliation(s)
- Zaneta Nikolovska-Coleska
- Department of Pathology, University of Michigan Medical School, 4510E MSRB I, 1150 West Medical Center Drive, Ann Arbor, MI, 48109, USA,
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20
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Chu R, Reczek D, Brondyk W. Capture-stabilize approach for membrane protein SPR assays. Sci Rep 2014; 4:7360. [PMID: 25484112 PMCID: PMC5154539 DOI: 10.1038/srep07360] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 11/19/2014] [Indexed: 02/01/2023] Open
Abstract
Measuring the binding kinetics of antibodies to intact membrane proteins by surface plasmon resonance has been challenging largely because of the inherent difficulties in capturing membrane proteins on chip surfaces while retaining their native conformation. Here we describe a method in which His-tagged CXCR5, a GPCR, was purified and captured on a Biacore chip surface via the affinity tag. The captured receptor protein was then stabilized on the chip surface by limited cross-linking. The resulting chip surface retained ligand binding activity and was used for monoclonal antibody kinetics assays by a standard Biacore kinetics assay method with a simple low pH regeneration step. We demonstrate the advantages of this whole receptor assay when compared to available peptide-based binding assays. We further extended the application of the capture-stabilize approach to virus-like particles and demonstrated its utility analyzing antibodies against CD52, a GPI-anchored protein, in its native membrane environment. The results are the first demonstration of chemically stabilized chip surfaces for membrane protein SPR assays.
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Affiliation(s)
- Ruiyin Chu
- Genzyme Corporation, 49 New York Avenue, Framingham, MA 01701, USA
| | - David Reczek
- Genzyme Corporation, 49 New York Avenue, Framingham, MA 01701, USA
| | - William Brondyk
- Genzyme Corporation, 49 New York Avenue, Framingham, MA 01701, USA
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21
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Hill RT. Plasmonic biosensors. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2014; 7:152-68. [PMID: 25377594 DOI: 10.1002/wnan.1314] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 09/19/2014] [Accepted: 09/29/2014] [Indexed: 11/11/2022]
Abstract
The unique optical properties of plasmon resonant nanostructures enable exploration of nanoscale environments using relatively simple optical characterization techniques. For this reason, the field of plasmonics continues to garner the attention of the biosensing community. Biosensors based on propagating surface plasmon resonances (SPRs) in films are the most well-recognized plasmonic biosensors, but there is great potential for the new, developing technologies to surpass the robustness and popularity of film-based SPR sensing. This review surveys the current plasmonic biosensor landscape with emphasis on the basic operating principles of each plasmonic sensing technique and the practical considerations when developing a sensing platform with the various techniques. The 'gold standard' film SPR technique is reviewed briefly, but special emphasis is devoted to the up-and-coming localized surface plasmon resonance and plasmonically coupled sensor technology.
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Affiliation(s)
- Ryan T Hill
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
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22
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Abstract
The demand for rapid and accurate diagnosis of plant diseases has risen in the last decade. On-site diagnosis of single or multiple pathogens using portable devices is the first step in this endeavour. Despite extensive attempts to develop portable devices for pathogen detection, current technologies are still restricted to detecting known pathogens with limited detection accuracy. Developing new detection techniques for rapid and accurate detection of multiple plant pathogens and their associated variants is essential. Recent single DNA sequencing technologies are a promising new avenue for developing future portable devices for plant pathogen detection. In this review, we detail the current progress in portable devices and technologies used for detecting plant pathogens, the current position of emerging sequencing technologies for analysis of plant genomics, and the future of portable devices for rapid pathogen diagnosis.
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Affiliation(s)
- Amir Sanati Nezhad
- McGill University and Genome Quebec Innovation Centre, Department of Biomedical Engineering, McGill University, Montreal, Quebec, Canada.
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23
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Unconventional surface plasmon resonance signals reveal quantitative inhibition of transcriptional repressor EthR by synthetic ligands. Anal Biochem 2014; 452:54-66. [DOI: 10.1016/j.ab.2014.02.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 02/04/2014] [Accepted: 02/07/2014] [Indexed: 11/22/2022]
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24
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YANG F, YANG XR. Kinetic Analysis of Interaction Between Tumor Necrosis Factor and Its Soluble Receptors. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2013. [DOI: 10.1016/s1872-2040(13)60647-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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25
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Šípová H, Homola J. Surface plasmon resonance sensing of nucleic acids: a review. Anal Chim Acta 2013; 773:9-23. [PMID: 23561902 DOI: 10.1016/j.aca.2012.12.040] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 12/19/2012] [Accepted: 12/21/2012] [Indexed: 12/12/2022]
Abstract
Biosensors based on surface plasmon resonance (SPR) have become a central tool for the investigation and quantification of biomolecules and their interactions. Nucleic acids (NAs) play a vital role in numerous biological processes and therefore have been one of the major groups of biomolecules targeted by the SPR biosensors. This paper discusses the advances of NA SPR biosensor technology and reviews its applications both in the research of molecular interactions involving NAs (NA-NA, NA-protein, NA-small molecule), as well as for the field of bioanalytics in the areas of food safety, medical diagnosis and environmental monitoring.
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Affiliation(s)
- Hana Šípová
- Institute of Photonics and Electronics, Academy of Sciences of the Czech Republic, Chaberská 57, Prague, Czech Republic
| | - Jiří Homola
- Institute of Photonics and Electronics, Academy of Sciences of the Czech Republic, Chaberská 57, Prague, Czech Republic.
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26
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Fee CJ. Label-free, real-time interaction and adsorption analysis 1: surface plasmon resonance. Methods Mol Biol 2013; 996:287-312. [PMID: 23504431 DOI: 10.1007/978-1-62703-354-1_17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A key requirement for the development of proteins for use in nanotechnology is an understanding of how individual proteins bind to other molecules as they assemble into larger structures. The introduction of labels to enable the detection of biomolecules brings the inherent risk that the labels themselves will influence the nature of biomolecular interactions. Thus, there is a need for label-free interaction and adsorption analysis. In this and the following chapter, two biosensor techniques are reviewed: surface plasmon resonance (SPR) and the quartz crystal microbalance (QCM). Both allow real-time analysis of biomolecular interactions and both are label-free. The first of these, SPR, is an optical technique that is highly sensitive to the changes in refractive index that occur with protein (or other molecule) accumulation near an illuminated gold surface. Unlike QCM ( Chapter 18 ) SPR is not affected by the water that may be associated with the adsorbed layer nor by conformational changes in the adsorbed species. SPR thus provides unique information about the interaction of a protein with its binding partners.
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Affiliation(s)
- Conan J Fee
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
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27
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Fang Y. Ligand-receptor interaction platforms and their applications for drug discovery. Expert Opin Drug Discov 2012; 7:969-88. [PMID: 22860803 DOI: 10.1517/17460441.2012.715631] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
INTRODUCTION The study of drug-target interactions is essential for the understanding of biological processes and for the efforts to develop new therapeutic molecules. Increased ligand-binding assays have coincided with the advances in reagents, detection and instrumentation technologies, the expansion in therapeutic targets of interest, and the increasingly recognized importance of biochemical aspects of drug-target interactions in determining the clinical performance of drug molecules. Nowadays, ligand-binding assays can determine every aspect of many drug-target interactions. AREAS COVERED Given that ligand-target interactions are very diverse, the author has decided to focus on the binding of small molecules to protein targets. This article first reviews the key biochemical aspects of drug-target interactions, and then discusses the detection principles of various ligand-binding techniques in the context of their primary applications for drug discovery and development. EXPERT OPINION Equilibrium-binding affinity should not be used as a solo indicator for the in vivo pharmacology of drugs. The clinical relevance of drug-binding kinetics demands high throughput kinetics early in drug discovery. The dependence of ligand binding and function on the conformation of targets necessitates solution-based and whole cell-based ligand-binding assays. The increasing need to examine ligand binding at the proteome level, driven by the clinical importance of the polypharmacology of ligands, has started to make the structure-based in silico binding screen an indispensable technique for drug discovery and development. Integration of different ligand-binding assays is important to improve the efficiency of the drug discovery and development process.
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Affiliation(s)
- Ye Fang
- Biochemical Technologies, Science and Technology Division, Corning, Inc., Corning, NY 14831, USA.
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28
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de Almeida Marques I, Valadares NF, Garcia W, Damalio JCP, Macedo JNA, de Araújo APU, Botello CA, Andreu JM, Garratt RC. Septin C-terminal domain interactions: implications for filament stability and assembly. Cell Biochem Biophys 2012; 62:317-28. [PMID: 22001952 DOI: 10.1007/s12013-011-9307-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Septins form a conserved family of filament forming GTP binding proteins found in a wide range of eukaryotic cells. They share a common structural architecture consisting of an N-terminal domain, a central GTP binding domain and a C-terminal domain, which is often predicted to adopt a coiled-coil conformation, at least in part. The crystal structure of the human SEPT2/SEPT6/SEPT7 heterocomplex has revealed the importance of the GTP binding domain in filament formation, but surprisingly no electron density was observed for the C-terminal domains and their function remains obscure. The dearth of structural information concerning the C-terminal region has motivated the present study in which the putative C-terminal domains of human SEPT2, SEPT6 and SEPT7 were expressed in E. coli and purified to homogeneity. The thermal stability and secondary structure content of the domains were studied by circular dichroism spectroscopy, and homo- and hetero-interactions were investigated by size exclusion chromatography, chemical cross-linking, analytical ultracentrifugation and surface plasmon resonance. Our results show that SEPT6-C and SEPT7-C are able to form both homo- and heterodimers with a high α-helical content in solution. The heterodimer is elongated and considerably more stable than the homodimers, with a K(D) of 15.8 nM. On the other hand, the homodimer SEPT2-C has a much lower affinity, with a K(D) of 4 μM, and a moderate α-helical content. Our findings present the first direct experimental evidence toward better understanding the biophysical properties and coiled-coil pairings of such domains and their potential role in filament assembly and stability.
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Affiliation(s)
- Ivo de Almeida Marques
- Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador são-carlense 400, São Carlos, SP 13560-970, Brazil
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Federici S, Oliviero G, Maiolo D, Depero LE, Colombo I, Bergese P. On the thermodynamics of biomolecule surface transformations. J Colloid Interface Sci 2012; 375:1-11. [DOI: 10.1016/j.jcis.2012.02.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 02/03/2012] [Accepted: 02/04/2012] [Indexed: 02/06/2023]
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Hansen R, Bruus H, Callisen TH, Hassager O. Transient convection, diffusion, and adsorption in surface-based biosensors. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:7557-63. [PMID: 22509887 DOI: 10.1021/la3000763] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
This paper presents a theoretical and computational investigation of convection, diffusion, and adsorption in surface-based biosensors. In particular, we study the transport dynamics in a model geometry of a surface plasmon resonance (SPR) sensor. The work, however, is equally relevant for other microfluidic surface-based biosensors, operating under flow conditions. A widely adopted approximate quasi-steady theory to capture convective and diffusive mass transport is reviewed, and an analytical solution is presented. An expression of the Damköhler number is derived in terms of the nondimensional adsorption coefficient (Biot number), the nondimensional flow rate (Péclet number), and the model geometry. Transient dynamics is investigated, and we quantify the error of using the quasi-steady-state assumption for experimental data fitting in both kinetically limited and convection-diffusion-limited regimes for irreversible adsorption, in specific. The results clarify the conditions under which the quasi-steady theory is reliable or not. In extension to the well-known fact that the range of validity is altered under convection-diffusion-limited conditions, we show how also the ratio of the inlet concentration to the maximum surface capacity is critical for reliable use of the quasi-steady theory. Finally, our results provide users of surface-based biosensors with a tool for correcting experimentally obtained adsorption rate constants.
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Affiliation(s)
- Rasmus Hansen
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, DTU Chemical Engineering Building 227, DK-2800 Kongens Lyngby, Denmark.
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31
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Naghib SM, Rabiee M, Omidinia E, Khoshkenar P. Investigation of a Biosensor Based on Phenylalanine Dehydrogenase Immobilized on a Polymer-Blend Film for Phenylketonuria Diagnosis. ELECTROANAL 2012. [DOI: 10.1002/elan.201100391] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Target–drug interactions: first principles and their application to drug discovery. Drug Discov Today 2012; 17:10-22. [DOI: 10.1016/j.drudis.2011.06.013] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 06/07/2011] [Accepted: 06/28/2011] [Indexed: 02/06/2023]
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Nagase N, Terao K, Miyanishi N, Tamai K, Uchiyama N, Suzuki T, Takao H, Shimokawa F, Oohira F. Signal enhancement of protein binding by electrodeposited gold nanostructures for applications in Kretschmann-type SPR sensors. Analyst 2012; 137:5034-40. [DOI: 10.1039/c2an35574d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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van den Biggelaar M, Bouwens EAM, Voorberg J, Mertens K. Storage of factor VIII variants with impaired von Willebrand factor binding in Weibel-Palade bodies in endothelial cells. PLoS One 2011; 6:e24163. [PMID: 21909383 PMCID: PMC3166073 DOI: 10.1371/journal.pone.0024163] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 08/01/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Point mutations resulting in reduced factor VIII (FVIII) binding to von Willebrand factor (VWF) are an important cause of mild/moderate hemophilia A. Treatment includes desmopressin infusion, which concomitantly increases VWF and FVIII plasma levels, apparently from storage pools containing both proteins. The source of these VWF/FVIII co-storage pools and the mechanism of granule biogenesis are not fully understood. METHODOLOGY/PRINCIPAL FINDINGS We studied intracellular trafficking of FVIII variants implicated in mild/moderate hemophilia A together with VWF in HEK293 cells and primary endothelial cells. The role of VWF binding was addressed using FVIII variants displaying reduced VWF interaction. Binding studies using purified FVIII proteins revealed moderate (Arg2150His, Del2201, Pro2300Ser) to severe (Tyr1680Phe, Ser2119Tyr) VWF binding defects. Expression studies in HEK293 cells and primary endothelial cells revealed that all FVIII variants were present within VWF-containing organelles. Quantitative studies showed that the relative amount of FVIII storage was independent of various mutations. Substantial amounts of FVIII variants are co-stored in VWF-containing storage organelles, presumably by virtue of their ability to interact with VWF at low pH. CONCLUSIONS Our data suggest that the potential of FVIII co-storage with VWF is not affected in mild/moderate hemophilia A caused by reduced FVIII/VWF interaction in the circulation. These data support the hypothesis that Weibel-Palade bodies comprise the desmopressin-releasable FVIII storage pool in vivo.
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Using Surface Plasmon Resonance Technology to Screen Interactions Between Exopolysaccharides and Milk Proteins. FOOD BIOPHYS 2011. [DOI: 10.1007/s11483-011-9227-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Binding of alpha-thrombin to surface-anchored platelet glycoprotein Ib(alpha) sulfotyrosines through a two-site mechanism involving exosite I. Proc Natl Acad Sci U S A 2011; 108:8628-33. [PMID: 21555542 DOI: 10.1073/pnas.1017042108] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The involvement of exosite I in α-thrombin (FIIa) binding to platelet glycoprotein Ibα (GPIbα), which could influence interactions with other substrates, remains undefined. To address the problem, we generated the GPIbα amino terminal domain (GPIbα-N) fully sulfated on three tyrosine residues and solved the structure of its complex with FIIa. We found that sulfotyrosine (Tys) 278 enhances the interaction mainly by establishing contacts with exosite I. We then evaluated how substituting tyrosine with phenylalanine, which cannot be sulfated, affects FIIa binding to soluble or surface-immobilized GPIbα-N. Mutating Tyr(276), which mostly contacts exosite II residues, markedly reduced FIIa interaction with both soluble and immobilized GPIbα-N; mutating Tyr(278) or Tyr(279), which mostly contact exosite I residues, reduced FIIa complexing in solution by 0-20% but affinity for immobilized GPIbα-N 2 to 6-fold, respectively. Moreover, three exosite I ligands--aptamer HD1, hirugen, and lepirudin--did not interfere with soluble FIIa complexing to GPIbα-N, excluding that their binding caused allosteric effects influencing the interaction; nonetheless, all impaired FIIa binding to immobilized GPIbα-N and platelet GPIb nearly as much as aptamer HD22 and heparin, both exosite II ligands. Bound HD1 and hirugen alter Trp(148) orientation in a loop near exosite I preventing contacts with the sulfate oxygen atoms of Tys(279). These results support a mechanism in which binding occurs when the two exosites of one FIIa molecule independently interact with two immobilized GPIbα molecules. Through exosite engagement, GPIbα may influence FIIa-dependent processes relevant to hemostasis and thrombosis.
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Oliviero G, Federici S, Colombi P, Bergese P. On the difference of equilibrium constants of DNA hybridization in bulk solution and at the solid-solution interface. J Mol Recognit 2011; 24:182-7. [DOI: 10.1002/jmr.1019] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Xiong C, Brewer K, Song S, Zhang R, Lu W, Wen X, Li C. Peptide-based imaging agents targeting phosphatidylserine for the detection of apoptosis. J Med Chem 2011; 54:1825-35. [PMID: 21348464 DOI: 10.1021/jm101477d] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A 14-residue phosphatidylserine (PS)-binding peptide FNFRLKAGQKIRFG (PSBP-0) was scanned with Ala. In addition, a radiometal chelator (SAAC) was introduced at selected sites of the lead peptides. Substitution of the Gln(6) residue in PSBP-0 with Ala resulted in a significant increase in binding affinity to PS as determined by surface plasmon resonance sensorgrams. The binding affinity of the resulting peptide FNFRLKAGAKIRFG (PSBP-6, molecular mass = 1623 Da) to PS (K(d) ∼ 100 nM) increased 10-fold as compared to PSBP-0 (K(d) ∼ 1.38 μM). Introduction of SAAC-Re to the N terminus of PSBP-6 further increased the binding affinity of the resulting peptide SAAC(Re)-PSBP-6 (K(d) ∼ 26 nM). SAAC(Re)-PSBP-6 shows specific binding to apoptotic cells in cell-based assays. Biodistribution studies showed significantly higher uptake of SAAC((99 m)Tc)-PSBP-6 in B16/F10 melanoma treated with poly(L-glutamic acid)-paclitaxel than untreated tumors (4.06 ± 0.55% ID/g vs 1.61 ± 0.33% ID/g, P = 0.00011). SAAC((99 m)Tc)-PSBP-6 is a promising probe for noninvasive imaging of apoptotic cells.
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Affiliation(s)
- Chiyi Xiong
- Department of Experimental Diagnostic Imaging, The University of Texas M D Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, United States
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Abstract
The use of optical biosensors for studying macromolecular interactions is gaining increasing popularity. In one study, 1,179 papers that involved the application of biosensor data were identified for the year 2007 alone (Rich and Myszka, J Mol Recognit 21:355-400, 2008), the sheer volume and variety of which present a daunting task for the burgeoning biosensor user to accumulate and decipher. This chapter is designed to provide the reader with the tools necessary to prepare, design, and efficiently execute a kinetic experiment on Biacore. It is written to guide the Biacore user through basic theory, system maintenance, and assay set-up while also offering some practical tips that we find useful for Biacore-based studies. Many kinetic-based screening assays require rigorous sample preparation and purification prior to analysis. To highlight these procedures, this protocol describes the kinetic characterisation of single chain Fv (scFv) antibody fragments from crude bacterial lysates using an antibody affinity capture approach. Even though we specifically describe the capture of HA-tagged scFv antibody fragments to an anti-HA tag monoclonal antibody-immobilised surface prior to kinetic analysis, the same methodologies are universally applicable and can be used for practically any affinity pair and most Biacore systems.
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Affiliation(s)
- Paul Leonard
- School of Biotechnology and Biomedical Diagnostics Institute, Dublin City University, Dublin, Ireland
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Liu X, Li Y, Lin Z. Kinetic Analysis of the Interaction between Nonsteroidal Anti-inflammatory Drugs and Cyclooxygenase-2 Using Wavelength Modulation Surface Plasmon Resonance. CHINESE J CHEM 2011. [DOI: 10.1002/cjoc.201190046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Comparative surface plasmon resonance and enzyme-linked immunosorbent assay characterisation of a monoclonal antibody with N-acyl homoserine lactones. Anal Chim Acta 2010; 683:113-8. [DOI: 10.1016/j.aca.2010.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 10/04/2010] [Accepted: 10/11/2010] [Indexed: 11/18/2022]
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Solbak SM, Reksten TR, Wray V, Bruns K, Horvli O, Raae AJ, Henklein P, Henklein P, Röder R, Mitzner D, Schubert U, Fossen T. The intriguing cyclophilin A-HIV-1 Vpr interaction: prolyl cis/trans isomerisation catalysis and specific binding. BMC STRUCTURAL BIOLOGY 2010; 10:31. [PMID: 20920334 PMCID: PMC2959089 DOI: 10.1186/1472-6807-10-31] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Accepted: 10/04/2010] [Indexed: 11/23/2022]
Abstract
Background Cyclophilin A (CypA) represents a potential target for antiretroviral therapy since inhibition of CypA suppresses human immunodeficiency virus type 1 (HIV-1) replication, although the mechanism through which CypA modulates HIV-1 infectivity still remains unclear. The interaction of HIV-1 viral protein R (Vpr) with the human peptidyl prolyl isomerase CypA is known to occur in vitro and in vivo. However, the nature of the interaction of CypA with Pro-35 of N-terminal Vpr has remained undefined. Results Characterization of the interactions of human CypA with N-terminal peptides of HIV-1 Vpr has been achieved using a combination of nuclear magnetic resonace (NMR) exchange spectroscopy and surface plasmon resonance spectroscopy (SPR). NMR data at atomic resolution indicate prolyl cis/trans isomerisation of the highly conserved proline residues Pro-5, -10, -14 and -35 of Vpr are catalyzed by human CypA and require only very low concentrations of the isomerase relative to that of the peptide substrates. Of the N-terminal peptides of Vpr only those containing Pro-35 bind to CypA in a biosensor assay. SPR studies of specific N-terminal peptides with decreasing numbers of residues revealed that a seven-residue motif centred at Pro-35 consisting of RHFPRIW, which under membrane-like solution conditions comprises the loop region connecting helix 1 and 2 of Vpr and the two terminal residues of helix 1, is sufficient to maintain strong specific binding. Conclusions Only N-terminal peptides of Vpr containing Pro-35, which appears to be vital for manifold functions of Vpr, bind to CypA in a biosensor assay. This indicates that Pro-35 is essential for a specific CypA-Vpr binding interaction, in contrast to the general prolyl cis/trans isomerisation observed for all proline residues of Vpr, which only involve transient enzyme-substrate interactions. Previously suggested models depicting CypA as a chaperone that plays a role in HIV-1 virulence are now supported by our data. In detail the SPR data of this interaction were compatible with a two-state binding interaction model that involves a conformational change during binding. This is in accord with the structural changes observed by NMR suggesting CypA catalyzes the prolyl cis/trans interconversion during binding to the RHFP35RIW motif of N-terminal Vpr.
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Affiliation(s)
- Sara M Solbak
- Department of Chemistry, University of Bergen, N-5007 Bergen, Norway
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Archakov AI, Ivanov YD. Application of AFM and optical biosensor for investigation of complexes formed in P450-containing monooxygenase systems. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:102-10. [PMID: 20832504 DOI: 10.1016/j.bbapap.2010.08.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 08/20/2010] [Accepted: 08/29/2010] [Indexed: 12/12/2022]
Abstract
Atomic force microscopy (AFM) allows to visualize and count the individual protein molecules and their complexes within multiprotein systems. On the other hand, optical biosensor (OB) provides information on complex formation kinetics as well as complex lifetime (τ(LT)) and affinity. Comparison of complex lifetime τ(LT) with the time required for enzyme's catalytic cycle (τ(cat)) enables to characterize productive complexes and distinguish them from non-productive ones. Both these approaches were applied for the analysis of the three cytochrome P450-containing monooxygenase systems: cytochrome P450 101, cytochrome P450 11A1 and cytochrome P450 2B4. By using AFM, the formation of binary and ternary protein complexes was registered in all the three systems. OB analysis enabled to kinetically characterize these binary and ternary complexes. It was shown that the binary complexes putidaredoxin reductase (PdR)/putidaredoxin (Pd) and Pd/cytochrome P450 101 (P450 101) formed within the P450 101 system and, also, the binary complexes adrenodoxin reductase (AdR)/adrenodoxin (Ad) and Ad/cytochrome P450 11A1 (P450 11A1) formed within the P450 11A1 system are non-productive (deadlock). At the same time, the ternary PdR/Pd/P450 101 and AdR/Ad/P450 11A1 complexes proved to be productive. The binary cytochrome P450 reductase (Fp)/cytochrome P450 2B4 (2B4) complexes and the ternary Fp/2B4/cytochrome b5 (b5) complexes formed within P450 2B4 system were productive.
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Affiliation(s)
- A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia
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Hearty S, Conroy PJ, Ayyar BV, Byrne B, O'Kennedy R. Surface plasmon resonance for vaccine design and efficacy studies: recent applications and future trends. Expert Rev Vaccines 2010; 9:645-64. [PMID: 20518719 DOI: 10.1586/erv.10.52] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The lack of a clear correlation between design and protection continues to present a barrier to progress in vaccine research. In this article, we outline how surface plasmon resonance (SPR) biosensors are emerging as tools to help resolve some of the key biophysical determinants of protection and, thereby, facilitate more rational vaccine design campaigns. SPR technology has contributed significantly to our understanding of the complex biophysical determinants of HIV neutralization and offers a platform for preclinical evaluation of vaccine candidates. In particular, the concept of reverse-engineering HIV vaccine targets based on known broadly neutralizing antibody modalities is explored and extended to include other infectious diseases, such as malaria and influenza, and other diseases such as cancer. The analytical capacity afforded by SPR includes serum screening to monitor immune responses and highly efficient quality-control surveillance measures. These are discussed alongside key technological advances, such as developments in sample throughput, and a perspective predicting continued growth and diversification of the role of SPR in vaccine development is proposed.
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Affiliation(s)
- Stephen Hearty
- Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland
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Albers WM, Munter T, Laaksonen P, Vikholm-Lundin I. Improved functionality of antibody-colloidal gold conjugates with the aid of lipoamide-grafted N-[tris(hydroxymethyl)methyl]acrylamide polymers. J Colloid Interface Sci 2010; 348:1-8. [DOI: 10.1016/j.jcis.2010.03.059] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Revised: 03/25/2010] [Accepted: 03/26/2010] [Indexed: 10/19/2022]
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46
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Plant pectin methylesterase and its inhibitor from kiwi fruit: Interaction analysis by surface plasmon resonance. Food Chem 2010. [DOI: 10.1016/j.foodchem.2009.11.073] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Identification of a gp41 core-binding molecule with homologous sequence of human TNNI3K-like protein as a novel human immunodeficiency virus type 1 entry inhibitor. J Virol 2010; 84:9359-68. [PMID: 20592080 DOI: 10.1128/jvi.00644-10] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) gp41 plays a critical role in the viral fusion process, and its N- and C-terminal heptad repeat domains serve as important targets for developing anti-HIV-1 drugs, like T-20 (generic name, enfuvirtide; brand name, Fuzeon). Here, we conducted a yeast two-hybrid screening on a human bone marrow cDNA library using the recombinant soluble gp41 ectodomain as the bait and identified a novel gp41 core-binding molecule, designated P20. P20 showed no homology with a current HIV fusion inhibitor, T-20, but had sequence homology to a human protein, troponin I type 3 interacting kinase (TNNI3K)-like protein. While it could bind to the six-helix bundle core structure formed by the N- and C-terminal heptad repeats, P20 did not interrupt the formation of the six-helix bundle. P20 was effective in blocking HIV-1 Env-mediated syncytium formation and inhibiting infection by a broad spectrum of HIV-1 strains with distinct subtypes and coreceptor tropism, while it was ineffective against other enveloped viruses, such as vesicular stomatitis virus and influenza A virus. P20 exhibited no significant cytotoxicity to the CD4(+) cells that were used for testing antiviral activity. Among the 11 P20 mutants, four analogous peptides with a common motif (WGRLEGRRT) exhibited significantly reduced anti-HIV-1 activity, suggesting that this region is the critical active site of P20. Therefore, this peptide can be used as a lead for developing novel HIV fusion inhibitors and as a probe for studying the membrane-fusogenic mechanism of HIV.
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Retra K, Geitmann M, Kool J, Smit AB, de Esch IJP, Danielson UH, Irth H. Development of surface plasmon resonance biosensor assays for primary and secondary screening of acetylcholine binding protein ligands. Anal Biochem 2010; 407:58-64. [PMID: 20599657 DOI: 10.1016/j.ab.2010.06.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Accepted: 06/14/2010] [Indexed: 10/19/2022]
Abstract
Surface plasmon resonance (SPR) biosensors recently gained an important place in drug discovery. Here we present a primary and secondary SPR biosensor screening methodology. The primary screening method is based on a direct binding assay with covalent immobilized drug target proteins. For the secondary screening method, a sequential competition assay has been developed where the captured protein is first exposed to an unknown test compound, followed directly by an exposure to a high-molecular-weight reporter ligand. Using the high-molecular-weight reporter ligand to probe the remaining free binding site on the sensor, a significant signal enhancement is obtained. Furthermore, this assay format allows the validation of the primary direct binding assay format, efficiently revealing false positive data. As a model system, acetylcholine binding protein (AChBP), which is a soluble model protein for neuronal nicotinic acetylcholine receptors, has been used. The secondary assay is lower in throughput than the primary assay; however, the signal-to-noise ratio is two times higher compared with the direct assay, and it has a z' factor of 0.96. Using both assays, we identified the compound tacrine as a ligand for AChBP.
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Affiliation(s)
- Kim Retra
- Leiden/Amsterdam Center for Drug Research, Division of Biomolecular Analysis, Faculty of Sciences, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands.
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Abstract
The implementation of surface plasmon-enhanced fluorescence spectroscopy (SPFS) to surface plasmon resonance (SPR) biosensors enables increasing their sensitivity by several orders of magnitude. In SPR-based biosensors, surface plasmons probe the binding of target molecules contained in a liquid sample by their affinity partners attached to a metallic sensor surface. SPR biosensors relying on the detection of refractive index changes allow for direct observation of the binding of large and medium size molecules that produces sufficiently large refractive index changes. In SPR biosensors exploiting SPFS, the capture of fluorophore-labeled molecules to the sensor surface is observed by the detection of fluorescence light emitted from the surface. This technique takes advantage of the enhanced intensity of electromagnetic field accompanied with the resonant excitation of surface plasmons. The interaction with surface plasmons can greatly increase the measured fluorescence signal through enhancing the excitation rate of fluorophores and by more efficient collecting of fluorescence light. SPFS-based biosensors were shown to enable the analysis of samples with extremely low analyte concentrations and the detection of small molecules. In this review, we describe the fundamental principles, implementations, and current state of the art applications of SPFS biosensors. This review focuses on SPFS-based biosensors employing the excitation of surface plasmons on continuous metal-dielectric interfaces.
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Optimizing immobilization on two-dimensional carboxyl surface: pH dependence of antibody orientation and antigen binding capacity. Anal Biochem 2010; 398:161-8. [DOI: 10.1016/j.ab.2009.11.038] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 11/27/2009] [Accepted: 11/30/2009] [Indexed: 11/20/2022]
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