1
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Drozd M, Kobylska E, Żmieńko M, Chudy M. Sensitive and label-free SPR biosensing platforms for high-throughput screening of plasma membrane receptors interactions with insulin-like targets of hypoglycaemic activity. Talanta 2024; 274:125914. [PMID: 38537356 DOI: 10.1016/j.talanta.2024.125914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 05/04/2024]
Abstract
Progress in medical sciences aims for tailored therapy of civilization diseases like diabetes. Preclinical screening of new medicines superior to insulin should include the verification of their affinity to the membrane receptors naturally stimulated by this hormone: insulin receptor isoforms A and B and insulin-like growth factor receptor. Considering that the affinity constants obtained using different experimental conditions are incomparable, it is essential to develop a robust and reliable method to analyze these interactions. The versatile SPR platform developed in this study enables the evaluation of the bioactivity of hypoglycaemic molecules. Thanks to the comprehensive characterization of miscellaneous aspects of the analytical platform, including the design of the SPR biosensor receptor layer, ensuring interaction specificity, as well as the quality control of the standards used (human insulin, HI; long-acting insulin analog: glargine, Gla), the feasibility of the method of equilibrium and kinetic constants determination for insulin-like targets was confirmed. SPR assays constructed in the direct format using IR-A, IR-B, and IGF1-R receptor proteins show high sensitivities and low detection limits towards insulin and glargine detection in the range of 18.3-53.3 nM with no signs of mass transport limitations. The improved analytical performance and stability of SPR biosensors favor the acquisition of good-quality kinetic data, while preservation of receptors activity after binding to long-chain carboxymethyldextran, combined with spontaneous regeneration, results in stability and long shelf life of the biosensor, which makes it useful for label-free insulin analogs biosensing and thus extensive screening in diabetic drugs discovery.
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Affiliation(s)
- Marcin Drozd
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664, Warsaw, Poland; Centre for Advanced Materials and Technologies CEZAMAT, Poleczki 19, 02-822, Warsaw, Poland
| | - Ewa Kobylska
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664, Warsaw, Poland; Łukasiewicz - Industrial Chemistry Institute, Rydygiera 8, 01-793, Warsaw, Poland
| | - Małgorzata Żmieńko
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664, Warsaw, Poland
| | - Michał Chudy
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664, Warsaw, Poland.
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2
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Schedler B, Yukhnovets O, Lindner L, Meyer A, Fitter J. The Thermodynamic Fingerprints of Ultra-Tight Nanobody-Antigen Binding Probed via Two-Color Single-Molecule Coincidence Detection. Int J Mol Sci 2023; 24:16379. [PMID: 38003569 PMCID: PMC10671529 DOI: 10.3390/ijms242216379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Life on the molecular scale is based on a versatile interplay of biomolecules, a feature that is relevant for the formation of macromolecular complexes. Fluorescence-based two-color coincidence detection is widely used to characterize molecular binding and was recently improved by a brightness-gated version which gives more accurate results. We developed and established protocols which make use of coincidence detection to quantify binding fractions between interaction partners labeled with fluorescence dyes of different colors. Since the applied technique is intrinsically related to single-molecule detection, the concentration of diffusing molecules for confocal detection is typically in the low picomolar regime. This makes the approach a powerful tool for determining bi-molecular binding affinities, in terms of KD values, in this regime. We demonstrated the reliability of our approach by analyzing very strong nanobody-EGFP binding. By measuring the affinity at different temperatures, we were able to determine the thermodynamic parameters of the binding interaction. The results show that the ultra-tight binding is dominated by entropic contributions.
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Affiliation(s)
- Benno Schedler
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
| | - Olessya Yukhnovets
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
| | - Lennart Lindner
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
| | - Alida Meyer
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
| | - Jörg Fitter
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
- ER-C-3 Structural Biology & IBI-6 Cellular Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
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3
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Behan J, Xie Z, Wang YF, Yang X, Aastrup T, Yan Y, Adumeau L, Dawson KA. Quartz Crystal Microbalance Method to Measure Nanoparticle-Receptor Interactions and Evaluate Nanoparticle Design Efficiency. JACS AU 2023; 3:1623-1633. [PMID: 37388690 PMCID: PMC10301671 DOI: 10.1021/jacsau.3c00084] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/03/2023] [Accepted: 04/24/2023] [Indexed: 07/01/2023]
Abstract
Conjugation of biomolecules on the surface of nanoparticles (NPs) to achieve active targeting is widely investigated within the scientific community. However, while a basic framework of the physicochemical processes underpinning bionanoparticle recognition is now emerging, the precise evaluation of the interactions between engineered NPs and biological targets remains underdeveloped. Here, we show how the adaptation of a method currently used to evaluate molecular ligand-receptor interactions by quartz crystal microbalance (QCM) can be used to obtain concrete insights into interactions between different NP architectures and assemblies of receptors. Using a model bionanoparticle grafted with oriented apolipoprotein E (ApoE) fragments, we examine key aspects of bionanoparticle engineering for effective interactions with target receptors. We show that the QCM technique can be used to rapidly measure construct-receptor interactions across biologically relevant exchange times. We contrast random adsorption of the ligand at the surface of the NPs, resulting in no measurable interaction with target receptors, to grafted oriented constructs, which are strongly recognized even at lower graft densities. The effects of other basic parameters impacting the interaction such as ligand graft density, receptor immobilization density, and linker length were also efficiently evaluated with this technique. Dramatic changes in interaction outcomes with subtle alterations in these parameters highlight the general importance of measuring the interactions between engineered NPs and target receptors ex situ early on in the construct development process for the rational design of bionanoparticles.
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Affiliation(s)
- James
A. Behan
- Centre
for BioNano Interactions, School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Zengchun Xie
- Centre
for BioNano Interactions, School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Yi-Feng Wang
- Centre
for BioNano Interactions, School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Xiaoliang Yang
- Centre
for BioNano Interactions, School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Teodor Aastrup
- Attana
AB, Greta Arwidssons
Väg 21, Stockholm SE-11419, Sweden
| | - Yan Yan
- UCD
Conway Institute of Biomolecular and Biomedical Research, School of
Biomolecular and Biomedical Science, University
College Dublin, Belfield, Dublin 4, Ireland
| | - Laurent Adumeau
- Centre
for BioNano Interactions, School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kenneth A. Dawson
- Centre
for BioNano Interactions, School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
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4
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Kinetic Modeling of Time-Dependent Enzyme Inhibition by Pre-Steady-State Analysis of Progress Curves: The Case Study of the Anti-Alzheimer's Drug Galantamine. Int J Mol Sci 2022; 23:ijms23095072. [PMID: 35563466 PMCID: PMC9105972 DOI: 10.3390/ijms23095072] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 01/27/2023] Open
Abstract
The Michaelis–Menten model of enzyme kinetic assumes the free ligand approximation, the steady-state approximation and the rapid equilibrium approximation. Analytical methods to model slow-binding inhibitors by the analysis of initial velocities have been developed but, due to their inherent complexity, they are seldom employed. In order to circumvent the complications that arise from the violation of the rapid equilibrium assumption, inhibition is commonly evaluated by pre-incubating the enzyme and the inhibitors so that, even for slow inhibitors, the binding equilibrium is established before the reaction is started. Here, we show that for long drug-target residence time inhibitors, the conventional analysis of initial velocities by the linear regression of double-reciprocal plots fails to provide a correct description of the inhibition mechanism. As a case study, the inhibition of acetylcholinesterase by galantamine, a drug approved for the symptomatic treatment of Alzheimer’s disease, is reported. For over 50 years, analysis based on the conventional steady-state model has overlooked the time-dependent nature of galantamine inhibition, leading to an erroneous assessment of the drug potency and, hence, to discrepancies between biochemical data and the pharmacological evidence. Re-examination of acetylcholinesterase inhibition by pre-steady state analysis of the reaction progress curves showed that the potency of galantamine has indeed been underestimated by a factor of ~100.
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5
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Vander Mause ER, Atanackovic D, Lim CS, Luetkens T. Roadmap to affinity-tuned antibodies for enhanced chimeric antigen receptor T cell function and selectivity. Trends Biotechnol 2022; 40:875-890. [DOI: 10.1016/j.tibtech.2021.12.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 12/29/2022]
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6
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Stein JAC, Ianeselli A, Braun D. Kinetic Microscale Thermophoresis for Simultaneous Measurement of Binding Affinity and Kinetics. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Julian A. C. Stein
- Systems Biophysics Department of Physics Ludwig-Maximilians-Universität München and Center for NanoScience Amalienstasse 54 80799 München Germany
| | - Alan Ianeselli
- Systems Biophysics Department of Physics Ludwig-Maximilians-Universität München and Center for NanoScience Amalienstasse 54 80799 München Germany
| | - Dieter Braun
- Systems Biophysics Department of Physics Ludwig-Maximilians-Universität München and Center for NanoScience Amalienstasse 54 80799 München Germany
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7
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Stein JAC, Ianeselli A, Braun D. Kinetic Microscale Thermophoresis for Simultaneous Measurement of Binding Affinity and Kinetics. Angew Chem Int Ed Engl 2021; 60:13988-13995. [PMID: 33793031 PMCID: PMC8251828 DOI: 10.1002/anie.202101261] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/16/2021] [Indexed: 12/11/2022]
Abstract
Microscale thermophoresis (MST) is a versatile technique to measure binding affinities of binder-ligand systems, based on the directional movement of molecules in a temperature gradient. We extended MST to measure binding kinetics as well as binding affinity in a single experiment by increasing the thermal dissipation of the sample. The kinetic relaxation fingerprints were derived from the fluorescence changes during thermodynamic re-equilibration of the sample after local heating. Using this method, we measured DNA hybridization on-rates and off-rates in the range 104 -106 m-1 s-1 and 10-4 -10-1 s-1 , respectively. We observed the expected exponential dependence of the DNA hybridization off-rates on salt concentration, strand length and inverse temperature. The measured on-rates showed a linear dependence on salt concentration and weak dependence on strand length and temperature. For biomolecular interactions with large enthalpic contributions, the kinetic MST technique offers a robust, cost-effective and immobilization-free determination of kinetic rates and binding affinity simultaneously, even in crowded solutions.
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Affiliation(s)
- Julian A C Stein
- Systems Biophysics, Department of Physics, Ludwig-Maximilians-Universität München and Center for NanoScience, Amalienstasse 54, 80799, München, Germany
| | - Alan Ianeselli
- Systems Biophysics, Department of Physics, Ludwig-Maximilians-Universität München and Center for NanoScience, Amalienstasse 54, 80799, München, Germany
| | - Dieter Braun
- Systems Biophysics, Department of Physics, Ludwig-Maximilians-Universität München and Center for NanoScience, Amalienstasse 54, 80799, München, Germany
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8
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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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9
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Robin M, Tayakout-Fayolle M, Pitault I, Jallut C, Drazek L. Estimation of Kinetic Parameters Involved in Solid-Phase Immunoassays by Affinity Chromatography. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.0c00922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maëlenn Robin
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, 43 boulevard du 11 novembre 1918, F-69100 Villeurbanne, France
- bioMérieux SA, Immuno Innovation Department, 376 chemin de l’Orme, 69280 Marcy l’Etoile, France
| | - Mélaz Tayakout-Fayolle
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, 43 boulevard du 11 novembre 1918, F-69100 Villeurbanne, France
| | - Isabelle Pitault
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, 43 boulevard du 11 novembre 1918, F-69100 Villeurbanne, France
| | - Christian Jallut
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, 43 boulevard du 11 novembre 1918, F-69100 Villeurbanne, France
| | - Laurent Drazek
- bioMérieux SA, Biomathematics Departement, 5 rue des Berges, 38024 Grenoble, France
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10
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Quantitative and Selective Surface Plasmon Resonance Response Based on a Reduced Graphene Oxide-Polyamidoamine Nanocomposite for Detection of Dengue Virus E-Proteins. NANOMATERIALS 2020; 10:nano10030569. [PMID: 32245185 PMCID: PMC7153703 DOI: 10.3390/nano10030569] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/31/2020] [Accepted: 02/11/2020] [Indexed: 12/12/2022]
Abstract
Dengue viral infection is one of the most common deadliest diseases and has become a recurrent issue for public health in tropical countries. Although the spectrum of clinical diagnosis and treatment have recently been established, the efficient and rapid detection of dengue virus (DENV) during viremia and the early febrile phase is still a great challenge. In this study, a dithiobis (succinimidyl undecanoate, DSU)/amine-functionalized reduced graphene oxide--polyamidoamine dendrimer (DSU/amine-functionalized rGO-PAMAM) thin film-based surface plasmon resonance (SPR) sensor was developed for the detection of DENV 2 E-proteins. Different concentrations of DENV 2 E-proteins were successfully tested by the developed SPR sensor-based system. The performance of the developed sensor showed increased shift in the SPR angle, narrow full-width-half-maximum of the SPR curve, high detection accuracy, excellent figure of merit and signal-to-noise ratio, good sensitivity values in the range of 0.08-0.5 pM (S = 0.2576°/pM, R2 = 0.92), and a high equilibrium association constant (KA) of 7.6452 TM-1. The developed sensor also showed a sensitive and selective response towards DENV 2 E-proteins compared to DENV 1 E-proteins and ZIKV (Zika virus) E-proteins. Overall, it was concluded that the Au/DSU/amine-functionalized rGO-PAMAM thin film-based SPR sensor has potential to serve as a rapid clinical diagnostic tool for DENV infection.
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11
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Yang J, Talibov VO, Peintner S, Rhee C, Poongavanam V, Geitmann M, Sebastiano MR, Simon B, Hennig J, Dobritzsch D, Danielson UH, Kihlberg J. Macrocyclic Peptides Uncover a Novel Binding Mode for Reversible Inhibitors of LSD1. ACS OMEGA 2020; 5:3979-3995. [PMID: 32149225 PMCID: PMC7057333 DOI: 10.1021/acsomega.9b03493] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 01/30/2020] [Indexed: 06/10/2023]
Abstract
Lysine-specific demethylase 1 (LSD1) is an epigenetic enzyme which regulates the methylation of Lys4 of histone 3 (H3) and is overexpressed in certain cancers. We used structures of H3 substrate analogues bound to LSD1 to design macrocyclic peptide inhibitors of LSD1. A linear, Lys4 to Met-substituted, 11-mer (4) was identified as the shortest peptide distinctly interacting with LSD1. It was evolved into macrocycle 31, which was >40 fold more potent (K i = 2.3 μM) than 4. Linear and macrocyclic peptides exhibited unexpected differences in structure-activity relationships for interactions with LSD1, indicating that they bind LSD1 differently. This was confirmed by the crystal structure of 31 in complex with LSD1-CoREST1, which revealed a novel binding mode at the outer rim of the LSD1 active site and without a direct interaction with FAD. NMR spectroscopy of 31 suggests that macrocyclization restricts its solution ensemble to conformations that include the one in the crystalline complex. Our results provide a solid basis for the design of optimized reversible LSD1 inhibitors.
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Affiliation(s)
- Jie Yang
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
| | - Vladimir O. Talibov
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
| | - Stefan Peintner
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
| | - Claire Rhee
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
| | | | - Matthis Geitmann
- Beactica
AB, Uppsala Business Park, Virdings allé 2, SE-75450 Uppsala, Sweden
| | | | - Bernd Simon
- Structural
and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Janosch Hennig
- Structural
and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Doreen Dobritzsch
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
| | - U. Helena Danielson
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
- Science
for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Jan Kihlberg
- Department
of Chemistry—BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden
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12
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Fernandez M, Urvoas A, Even-Hernandez P, Burel A, Mériadec C, Artzner F, Bouceba T, Minard P, Dujardin E, Marchi V. Hybrid gold nanoparticle-quantum dot self-assembled nanostructures driven by complementary artificial proteins. NANOSCALE 2020; 12:4612-4621. [PMID: 32043516 DOI: 10.1039/c9nr09987e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Hybrid nanostructures are constructed by the direct coupling of fluorescent quantum dots and plasmonic gold nanoparticles. Self-assembly is directed by the strong affinity between two artificial α-repeat proteins that are introduced in the capping layers of the nanoparticles at a controlled surface density. The proteins have been engineered to exhibit a high mutual affinity, corresponding to a dissociation constant in the nanomolar range, towards the protein-functionalized quantum dots and gold nanoparticles. Protein-mediated self-assembly is evidenced by surface plasmon resonance and gel electrophoresis. The size and the structure of colloidal superstructures of complementary nanoparticles are analyzed by transmission electron microscopy and small angle X-ray scattering. The size of the superstructures is determined by the number of proteins per nanoparticle. The well-defined geometry of the rigid protein complex sets a highly uniform interparticle distance of 8 nm that affects the emission properties of the quantum dots in the hybrid ensembles. Our results open the route to the design of hybrid emitter-plasmon colloidal assemblies with controlled near-field coupling and better optical response.
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Affiliation(s)
- Maxence Fernandez
- University Rennes 1, Institute of Chemical Sciences, UMR 6226 CNRS, Campus Beaulieu, F-35042 Rennes, France.
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Pascale Even-Hernandez
- University Rennes 1, Institute of Chemical Sciences, UMR 6226 CNRS, Campus Beaulieu, F-35042 Rennes, France.
| | - Agnès Burel
- University Rennes 1, Microscopy Rennes Imaging Center, UMS3480 BIOSIT, Campus Villejean, Rennes, France
| | - Cristelle Mériadec
- University Rennes 1, Institut de Physique de Rennes, UMR 6251 CNRS, Campus Beaulieu, F-35042 Rennes, France
| | - Franck Artzner
- University Rennes 1, Institut de Physique de Rennes, UMR 6251 CNRS, Campus Beaulieu, F-35042 Rennes, France
| | - Tahar Bouceba
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Protein engineering platform, Molecular Interaction Service, F-75005 Paris, France
| | - Philippe Minard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France
| | - Erik Dujardin
- Groupe NanoSciences-CEMES, CNRS UPR 8011, 29 rue J. Marvig, B.P. 94347, F-31055 Toulouse, France
| | - Valérie Marchi
- University Rennes 1, Institute of Chemical Sciences, UMR 6226 CNRS, Campus Beaulieu, F-35042 Rennes, France.
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13
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Krämer SD, Wöhrle J, Rath C, Roth G. Anabel: An Online Tool for the Real-Time Kinetic Analysis of Binding Events. Bioinform Biol Insights 2019; 13:1177932218821383. [PMID: 30670920 PMCID: PMC6328958 DOI: 10.1177/1177932218821383] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 11/23/2018] [Indexed: 11/17/2022] Open
Abstract
Anabel (Analysis of binding events + l) is an open source online software tool (www.skscience.org/anabel) for the convenient analysis of molecular binding interactions. Currently, exported datasets from Biacore (surface plasmon resonance [SPR]), FortéBio (biolayer interference [BLI]), and Biametrics (single color reflectometry [SCORE]) can be uploaded and evaluated in Anabel using 2 different evaluation methods. Moreover, a universal data template format is provided to upload any other binding dataset to Anabel. This enables an easier comparison of different analysis methods for all users. Furthermore, a guide was established in Anabel to help inexperienced users to obtain optimal results. In addition, expert features can be used to optimize and control the fit of the binding model to the measured data. We tried to make the process of fitting and evaluating as easy as possible through the use of an intuitive user interface. At the end of every analysis, a single excel file, containing all results and graphs of the performed analysis, can be downloaded.
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Affiliation(s)
- Stefan D Krämer
- Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany.,Faculty for Biology, University of Freiburg, Freiburg, Germany
| | - Johannes Wöhrle
- Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany.,Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
| | - Christin Rath
- Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany.,Faculty for Biology, University of Freiburg, Freiburg, Germany.,BioCopy GmbH, Freiburg, Germany.,BIOSS Center for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Günter Roth
- Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany.,Faculty for Biology, University of Freiburg, Freiburg, Germany.,BioCopy GmbH, Freiburg, Germany.,BIOSS Center for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
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14
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Brambilla D, Chiari M, Gori A, Cretich M. Towards precision medicine: the role and potential of protein and peptide microarrays. Analyst 2019; 144:5353-5367. [DOI: 10.1039/c9an01142k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Techniques to comprehensively analyze protein signatures are pivotal to unravel disease mechanisms, develop novel biomarkers and targeted therapies. In this frame, protein and peptide microarrays can play a major role in fuelling precision medicine.
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Affiliation(s)
- Dario Brambilla
- Consiglio Nazionale delle Ricerche
- Istituto di Chimica del Riconoscimento Molecolare (ICRM)
- Milano
- Italy
| | - Marcella Chiari
- Consiglio Nazionale delle Ricerche
- Istituto di Chimica del Riconoscimento Molecolare (ICRM)
- Milano
- Italy
| | - Alessandro Gori
- Consiglio Nazionale delle Ricerche
- Istituto di Chimica del Riconoscimento Molecolare (ICRM)
- Milano
- Italy
| | - Marina Cretich
- Consiglio Nazionale delle Ricerche
- Istituto di Chimica del Riconoscimento Molecolare (ICRM)
- Milano
- Italy
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15
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McDermott JJ, Civic B, Barkan A. Effects of RNA structure and salt concentration on the affinity and kinetics of interactions between pentatricopeptide repeat proteins and their RNA ligands. PLoS One 2018; 13:e0209713. [PMID: 30576379 PMCID: PMC6303017 DOI: 10.1371/journal.pone.0209713] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 12/10/2018] [Indexed: 11/19/2022] Open
Abstract
Pentatricopeptide repeat (PPR) proteins are helical repeat proteins that bind specific RNA sequences via modular 1-repeat:1-nucleotide interactions. Binding specificity is dictated, in part, by hydrogen bonds between the amino acids at two positions in each PPR motif and the Watson-Crick face of the aligned nucleobase. There is evidence that PPR-RNA interactions can compete with RNA-RNA interactions in vivo, and that this competition underlies some effects of PPR proteins on gene expression. Conversely, RNA secondary structure can inhibit the binding of a PPR protein to its specific binding site. The parameters that influence whether PPR-RNA or RNA-RNA interactions prevail are unknown. Understanding these parameters will be important for understanding the functions of natural PPR proteins and for the design of engineered PPR proteins for synthetic biology purposes. We addressed this question by analyzing the effects of RNA structures of varying stability and position on the binding of the model protein PPR10 to its atpH RNA ligand. Our results show that even very weak RNA structures (ΔG° ~ 0 kcal/mol) involving only one nucleotide at either end of the minimal binding site impede PPR10 binding. Analysis of binding kinetics using Surface Plasmon Resonance showed that RNA structures reduce PPR10’s on-rate and increase its off-rate. Complexes between the PPR proteins PPR10 and HCF152 and their respective RNA ligands have long half-lives (one hour or more), correlating with their functions as barriers to exonucleolytic RNA decay in vivo. The effects of salt concentration on PPR10-RNA binding kinetics showed that electrostatic interactions play an important role in establishing PPR10-RNA interactions but play a relatively small role in maintaining specific interactions once established.
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Affiliation(s)
- James J. McDermott
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Bryce Civic
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
- * E-mail:
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16
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Lowe BM, Sun K, Zeimpekis I, Skylaris CK, Green NG. Field-effect sensors - from pH sensing to biosensing: sensitivity enhancement using streptavidin-biotin as a model system. Analyst 2018; 142:4173-4200. [PMID: 29072718 DOI: 10.1039/c7an00455a] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Field-Effect Transistor sensors (FET-sensors) have been receiving increasing attention for biomolecular sensing over the last two decades due to their potential for ultra-high sensitivity sensing, label-free operation, cost reduction and miniaturisation. Whilst the commercial application of FET-sensors in pH sensing has been realised, their commercial application in biomolecular sensing (termed BioFETs) is hindered by poor understanding of how to optimise device design for highly reproducible operation and high sensitivity. In part, these problems stem from the highly interdisciplinary nature of the problems encountered in this field, in which knowledge of biomolecular-binding kinetics, surface chemistry, electrical double layer physics and electrical engineering is required. In this work, a quantitative analysis and critical review has been performed comparing literature FET-sensor data for pH-sensing with data for sensing of biomolecular streptavidin binding to surface-bound biotin systems. The aim is to provide the first systematic, quantitative comparison of BioFET results for a single biomolecular analyte, specifically streptavidin, which is the most commonly used model protein in biosensing experiments, and often used as an initial proof-of-concept for new biosensor designs. This novel quantitative and comparative analysis of the surface potential behaviour of a range of devices demonstrated a strong contrast between the trends observed in pH-sensing and those in biomolecule-sensing. Potential explanations are discussed in detail and surface-chemistry optimisation is shown to be a vital component in sensitivity-enhancement. Factors which can influence the response, yet which have not always been fully appreciated, are explored and practical suggestions are provided on how to improve experimental design.
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Affiliation(s)
- Benjamin M Lowe
- Department of Electronics and Computer Science, Nano Research Group, University of Southampton, UK.
| | - Kai Sun
- Department of Electronics and Computer Science, Nano Research Group, University of Southampton, UK.
| | - Ioannis Zeimpekis
- Department of Electronics and Computer Science, Nano Research Group, University of Southampton, UK.
| | | | - Nicolas G Green
- Department of Electronics and Computer Science, Nano Research Group, University of Southampton, UK.
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17
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Forssén P, Multia E, Samuelsson J, Andersson M, Aastrup T, Altun S, Wallinder D, Wallbing L, Liangsupree T, Riekkola ML, Fornstedt T. Reliable Strategy for Analysis of Complex Biosensor Data. Anal Chem 2018; 90:5366-5374. [PMID: 29589451 PMCID: PMC6150654 DOI: 10.1021/acs.analchem.8b00504] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
![]()
When
using biosensors, analyte biomolecules of several different
concentrations are percolated over a chip with immobilized ligand
molecules that form complexes with analytes. However, in many cases
of biological interest, e.g., in antibody interactions, complex formation
steady-state is not reached. The data measured are so-called sensorgram,
one for each analyte concentration, with total complex concentration
vs time. Here we present a new four-step strategy for more reliable
processing of this complex kinetic binding data and compare it with
the standard global fitting procedure. In our strategy, we first calculate
a dissociation graph to reveal if there are any heterogeneous interactions.
Thereafter, a new numerical algorithm, AIDA, is used to get the number
of different complex formation reactions for each analyte concentration
level. This information is then used to estimate the corresponding
complex formation rate constants by fitting to the measured sensorgram
one by one. Finally, all estimated rate constants are plotted and
clustered, where each cluster represents a complex formation. Synthetic
and experimental data obtained from three different QCM biosensor
experimental systems having fast (close to steady-state), moderate,
and slow kinetics (far from steady-state) were evaluated using the
four-step strategy and standard global fitting. The new strategy allowed
us to more reliably estimate the number of different complex formations,
especially for cases of complex and slow dissociation kinetics. Moreover,
the new strategy proved to be more robust as it enables one to handle
system drift, i.e., data from biosensor chips that deteriorate over
time.
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Affiliation(s)
- Patrik Forssén
- Department of Engineering and Chemical Sciences , Karlstad University , SE-651 88 Karlstad , Sweden
| | - Evgen Multia
- Department of Chemistry , P.O. Box 55, FI-00014 University of Helsinki , Finland
| | - Jörgen Samuelsson
- Department of Engineering and Chemical Sciences , Karlstad University , SE-651 88 Karlstad , Sweden
| | - Marie Andersson
- Department of Engineering and Chemical Sciences , Karlstad University , SE-651 88 Karlstad , Sweden
| | - Teodor Aastrup
- Attana AB , Björnäsvägen 21 , SE-114 19 Stockholm , Sweden
| | - Samuel Altun
- Attana AB , Björnäsvägen 21 , SE-114 19 Stockholm , Sweden
| | | | - Linus Wallbing
- Attana AB , Björnäsvägen 21 , SE-114 19 Stockholm , Sweden
| | | | - Marja-Liisa Riekkola
- Department of Chemistry , P.O. Box 55, FI-00014 University of Helsinki , Finland
| | - Torgny Fornstedt
- Department of Engineering and Chemical Sciences , Karlstad University , SE-651 88 Karlstad , Sweden
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18
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Label-free Microarray-based Binding Affinity Constant Measurement with Modified Fluidic Arrangement. BIOCHIP JOURNAL 2018. [DOI: 10.1007/s13206-017-2102-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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19
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Sotnikov DV, Zherdev AV, Dzantiev BB. Mathematical Modeling of Bioassays. BIOCHEMISTRY (MOSCOW) 2018. [PMID: 29523069 DOI: 10.1134/s0006297917130119] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The high affinity and specificity of biological receptors determine the demand for and the intensive development of analytical systems based on use of these receptors. Therefore, theoretical concepts of the mechanisms of these systems, quantitative parameters of their reactions, and relationships between their characteristics and ligand-receptor interactions have become extremely important. Many mathematical models describing different bioassay formats have been proposed. However, there is almost no information on the comparative characteristics of these models, their assumptions, and predictive insights. In this review we suggested a set of criteria to classify various bioassays and reviewed classical and contemporary publications on these bioassays with special emphasis on immunochemical analysis systems as the most common and in-demand techniques. The possibilities of analytical and numerical modeling are discussed, as well as estimations of the minimum concentrations that may be detected in bioassays and recommendations for the choice of assay conditions.
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Affiliation(s)
- D V Sotnikov
- Bach Institute of Biochemistry, Research Center for Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.
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20
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Artificial antibody created by conformational reconstruction of the complementary-determining region on gold nanoparticles. Proc Natl Acad Sci U S A 2017; 115:E34-E43. [PMID: 29255034 PMCID: PMC5776806 DOI: 10.1073/pnas.1713526115] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mimicking protein-like specific interactions and functions has been a long-pursued goal in nanotechnology. The key challenge is to precisely organize nonfunctional surface groups on nanoparticles into specific 3D conformations to function in a concerted and orchestrated manner. Here, we develop a method to graft the complementary-determining regions of natural antibodies onto nanoparticles and reconstruct their “active” conformation to create nanoparticle-based artificial antibodies that recognize the corresponding antigens. Our work demonstrates that it is possible to create functions on nanoparticles by conformational engineering, namely tuning flexible surface groups into specific conformations. Our straightforward strategy could be used further to create other artificial antibodies for various applications and provides a new tool to understand the structure and folding of natural proteins. To impart biomedical functions to nanoparticles (NPs), the common approach is to conjugate functional groups onto NPs by dint of the functions of those groups per se. It is still beyond current reach to create protein-like specific interactions and functions on NPs by conformational engineering of nonfunctional groups on NPs. Here, we develop a conformational engineering method to create an NP-based artificial antibody, denoted “Goldbody,” through conformational reconstruction of the complementary-determining regions (CDRs) of natural antibodies on gold NPs (AuNPs). The seemingly insurmountable task of controlling the conformation of the CDR loops, which are flexible and nonfunctional in the free form, was accomplished unexpectedly in a simple way. Upon anchoring both terminals of the free CDR loops on AuNPs, we managed to reconstruct the “active” conformation of the CDR loops by tuning the span between the two terminals and, as a result, the original specificity was successfully reconstructed on the AuNPs. Two Goldbodies have been created by this strategy to specifically bind with hen egg white lysozyme and epidermal growth factor receptor, with apparent affinities several orders of magnitude stronger than that of the original natural antibodies. Our work demonstrates that it is possible to create protein-like functions on NPs in a protein-like way, namely by tuning flexible surface groups to the correct conformation. Given the apparent merits, including good stability, of Goldbodies, we anticipate that a category of Goldbodies could be created to target different antigens and thus used as substitutes for natural antibodies in various applications.
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21
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Berto M, Diacci C, D'Agata R, Pinti M, Bianchini E, Lauro MD, Casalini S, Cossarizza A, Berggren M, Simon D, Spoto G, Biscarini F, Bortolotti CA. EGOFET Peptide Aptasensor for Label-Free Detection of Inflammatory Cytokines in Complex Fluids. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/adbi.201700072] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Marcello Berto
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Chiara Diacci
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Roberta D'Agata
- Dipartimento di Scienze Chimiche; Università di Catania; V.le A. Doria 6 95131 Catania
| | - Marcello Pinti
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Elena Bianchini
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Michele Di Lauro
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Stefano Casalini
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Andrea Cossarizza
- Dipartimento di Scienze Mediche e Chirurgiche Materno-Infantili e dell'Adulto; Università di Modena e Reggio Emilia; Via Campi 287 41125 Modena Italy
| | - Magnus Berggren
- Laboratory of Organic Electronics; Department of Science and Technology; ITN; Linköping University; S-601 74 Norrköping Sweden
| | - Daniel Simon
- Laboratory of Organic Electronics; Department of Science and Technology; ITN; Linköping University; S-601 74 Norrköping Sweden
| | - Giuseppe Spoto
- Dipartimento di Scienze Chimiche; Università di Catania; V.le A. Doria 6 95131 Catania
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici; c/o Dipartimento di Scienze Chimiche; Università di Catania; Viale Andrea Doria 6 95131 Catania Italy
| | - Fabio Biscarini
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Carlo A. Bortolotti
- Dipartimento di Scienze della Vita; Università di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
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22
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Piche-Nicholas NM, Avery LB, King AC, Kavosi M, Wang M, O'Hara DM, Tchistiakova L, Katragadda M. Changes in complementarity-determining regions significantly alter IgG binding to the neonatal Fc receptor (FcRn) and pharmacokinetics. MAbs 2017; 10:81-94. [PMID: 28991504 PMCID: PMC5800364 DOI: 10.1080/19420862.2017.1389355] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
A large body of data exists demonstrating that neonatal Fc receptor (FcRn) binding of an IgG via its Fc CH2-CH3 interface trends with the pharmacokinetics (PK) of IgG. We have observed that PK of IgG molecules vary widely, even when they share identical Fc domains. This led us to hypothesize that domains distal from the Fc could contribute to FcRn binding and affect PK. In this study, we explored the role of these IgG domains in altering the affinity between IgG and FcRn. Using a surface plasmon resonance-based assay developed to examine the steady-state binding affinity (KD) of IgG molecules to FcRn, we dissected the contributions of IgG domains in modulating the affinity between FcRn and IgG. Through analysis of a broad collection of therapeutic antibodies containing more than 50 unique IgG molecules, we demonstrated that variable domains, and in particular complementarity-determining regions (CDRs), significantly alter binding affinity to FcRn in vitro. Furthermore, a panel of IgG molecules differing only by 1–5 mutations in CDRs altered binding affinity to FcRn in vitro, by up to 79-fold, and the affinity values correlated with calculated isoelectric point values of both variable domains and CDR-L3. In addition, tighter affinity values trend with faster in vivo clearance of a set of IgG molecules differing only by 1–3 mutations in human FcRn transgenic mice. Understanding the role of CDRs in modulation of IgG affinity to FcRn in vitro and their effect on PK of IgG may have far-reaching implications in the optimization of IgG therapeutics.
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Affiliation(s)
| | | | - Amy C King
- a BioMedicine Design, Pfizer Inc. , Cambridge , MA , USA
| | - Mania Kavosi
- b BioMedicine Design, Pfizer Inc. , Andover , MA , USA
| | - Mengmeng Wang
- b BioMedicine Design, Pfizer Inc. , Andover , MA , USA
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23
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Wear MA, Nowicki MW, Blackburn EA, McNae IW, Walkinshaw MD. Thermo-kinetic analysis space expansion for cyclophilin-ligand interactions - identification of a new nonpeptide inhibitor using Biacore™ T200. FEBS Open Bio 2017; 7:533-549. [PMID: 28396838 PMCID: PMC5377415 DOI: 10.1002/2211-5463.12201] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 01/18/2017] [Accepted: 01/23/2017] [Indexed: 12/31/2022] Open
Abstract
We have established a refined methodology for generating surface plasmon resonance sensor surfaces of recombinant his‐tagged human cyclophilin‐A. Our orientation‐specific stabilisation approach captures his‐tagged protein under ‘physiological conditions’ (150 mm NaCl, pH 7.5) and covalently stabilises it on Ni2+‐nitrilotriacetic acid surfaces, very briefly activated for primary amine‐coupling reactions, producing very stable and active surfaces (≥ 95% specific activity) of cyclophilin‐A. Variation in protein concentration with the same contact time allows straightforward generation of variable density surfaces, with essentially no loss of activity, making the protocol easily adaptable for studying numerous interactions; from very small fragments, ~ 100 Da, to large protein ligands. This new method results in an increased stability and activity of the immobilised protein and allowed us to expand the thermo‐kinetic analysis space, and to determine accurate and robust thermodynamic parameters for the cyclophilin‐A–cyclosporin‐A interaction. Furthermore, the increased sensitivity of the surface allowed identification of a new nonpeptide inhibitor of cyclophilin‐A, from a screen of a fragment library. This fragment, 2,3‐diaminopyridine, bound specifically with a mean affinity of 248 ± 60 μm. The X‐ray structure of this 109‐Da fragment bound in the active site of cyclophilin‐A was solved to a resolution of 1.25 Å (PDB: 5LUD), providing new insight into the molecular details for a potential new series of nonpeptide cyclophilin‐A inhibitors.
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Affiliation(s)
- Martin A Wear
- The Edinburgh Protein Production Facility (EPPF) Wellcome Trust Centre for Cell Biology (WTCCB) University of Edinburgh UK
| | - Matthew W Nowicki
- The Edinburgh Protein Production Facility (EPPF) Wellcome Trust Centre for Cell Biology (WTCCB) University of Edinburgh UK
| | - Elizabeth A Blackburn
- The Edinburgh Protein Production Facility (EPPF) Wellcome Trust Centre for Cell Biology (WTCCB) University of Edinburgh UK
| | - Iain W McNae
- The Edinburgh Protein Production Facility (EPPF) Wellcome Trust Centre for Cell Biology (WTCCB) University of Edinburgh UK
| | - Malcolm D Walkinshaw
- The Edinburgh Protein Production Facility (EPPF) Wellcome Trust Centre for Cell Biology (WTCCB) University of Edinburgh UK
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24
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Multia E, Sirén H, Andersson K, Samuelsson J, Forssén P, Fornstedt T, Öörni K, Jauhiainen M, Riekkola ML. Thermodynamic and kinetic approaches for evaluation of monoclonal antibody - Lipoprotein interactions. Anal Biochem 2017; 518:25-34. [DOI: 10.1016/j.ab.2016.10.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 09/30/2016] [Accepted: 10/26/2016] [Indexed: 11/16/2022]
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25
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Blevins SJ, Baker BM. Using Global Analysis to Extend the Accuracy and Precision of Binding Measurements with T cell Receptors and Their Peptide/MHC Ligands. Front Mol Biosci 2017; 4:2. [PMID: 28197404 PMCID: PMC5281623 DOI: 10.3389/fmolb.2017.00002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 01/11/2017] [Indexed: 11/13/2022] Open
Abstract
In cellular immunity, clonally distributed T cell receptors (TCRs) engage complexes of peptides bound to major histocompatibility complex proteins (pMHCs). In the interactions of TCRs with pMHCs, regions of restricted and variable diversity align in a structurally complex fashion. Many studies have used mutagenesis to attempt to understand the "roles" played by various interface components in determining TCR recognition properties such as specificity and cross-reactivity. However, these measurements are often complicated or even compromised by the weak affinities TCRs maintain toward pMHC. Here, we demonstrate how global analysis of multiple datasets can be used to significantly extend the accuracy and precision of such TCR binding experiments. Application of this approach should positively impact efforts to understand TCR recognition and facilitate the creation of mutational databases to help engineer TCRs with tuned molecular recognition properties. We also show how global analysis can be used to analyze double mutant cycles in TCR-pMHC interfaces, which can lead to new insights into immune recognition.
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Affiliation(s)
- Sydney J Blevins
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame Notre Dame, IN, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame Notre Dame, IN, USA
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26
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Reinhard A, Nürnberger T. Steady-State and Kinetics-Based Affinity Determination in Effector-Effector Target Interactions. Methods Mol Biol 2017; 1578:81-108. [PMID: 28220417 DOI: 10.1007/978-1-4939-6859-6_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Dissecting the functional basis of pathogenicity and resistance in the context of plant innate immunity benefits greatly from detailed knowledge about biomolecular interactions, as both resistance and virulence depend on specific interactions between pathogen and host biomolecules. While in vivo systems provide biological context to host-pathogen interactions, these experiments typically cannot provide quantitative biochemical characterization of biomolecular interactions. However, in many cases, the biological function does not only depend on whether an interaction occurs at all, but rather on the "intensity" of the interaction, as quantified by affinity. Specifically, microbial effector proteins may bind more than one host target to exert virulence functions, and looking at these interactions more closely than would be possible in a purely black-and-white qualitative assay (as classically based on plant or yeast systems) can reveal new insights into the evolutionary arms race between host and pathogen. Recent advances in biomolecular interaction assays that can be performed in vitro allow quantification of binding events with ever greater fidelity and application range. Here, we describe assays based on microscale thermophoresis (MST) and surface plasmon resonance (SPR). Using these technologies allows affinity determination both in steady-state and in kinetic configurations, providing two conceptually independent pathways to arrive at quantitative affinity data describing the interactions of pathogen and host biomolecules.
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Affiliation(s)
- André Reinhard
- Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University Tübingen, Auf der Morgenstelle 32, D-72076, Tübingen, Germany
| | - Thorsten Nürnberger
- Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University Tübingen, Auf der Morgenstelle 32, D-72076, Tübingen, Germany.
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27
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Integration of Curved D-Type Optical Fiber Sensor with Microfluidic Chip. SENSORS 2016; 17:s17010063. [PMID: 28042821 PMCID: PMC5298636 DOI: 10.3390/s17010063] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 12/16/2016] [Accepted: 12/27/2016] [Indexed: 12/30/2022]
Abstract
A curved D-type optical fiber sensor (OFS) combined with a microfluidic chip is proposed. This OFS, based on surface plasmon resonance (SPR) of the Kretchmann’s configuration, is applied as a biosensor to measure the concentrations of different bio-liquids such as ethanol, methanol, and glucose solutions. The SPR phenomenon is attained by using the optical fiber to guide the light source to reach the side-polished, gold-coated region. Integrating this OFS with a polymethylmethacrylate (PMMA)-based microfluidic chip, the SPR spectra for liquids with different refractive indices are recorded. Experimentally, the sensitivity of the current biosensor was calculated to be in the order of 10−5 RIU. This microfluidic chip-integrated OFS could be valuable for monitoring subtle changes in biological samples such as blood sugar, allergen, and biomolecular interactions.
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28
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Ko HJ, Park TH. Bioelectronic nose and its application to smell visualization. J Biol Eng 2016; 10:17. [PMID: 27999616 PMCID: PMC5154139 DOI: 10.1186/s13036-016-0041-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/05/2016] [Indexed: 11/10/2022] Open
Abstract
There have been many trials to visualize smell using various techniques in order to objectively express the smell because information obtained from the sense of smell in human is very subjective. So far, well-trained experts such as a perfumer, complex and large-scale equipment such as GC-MS, and an electronic nose have played major roles in objectively detecting and recognizing odors. Recently, an optoelectronic nose was developed to achieve this purpose, but some limitations regarding the sensitivity and the number of smells that can be visualized still persist. Since the elucidation of the olfactory mechanism, numerous researches have been accomplished for the development of a sensing device by mimicking human olfactory system. Engineered olfactory cells were constructed to mimic the human olfactory system, and the use of engineered olfactory cells for smell visualization has been attempted with the use of various methods such as calcium imaging, CRE reporter assay, BRET, and membrane potential assay; however, it is not easy to consistently control the condition of cells and it is impossible to detect low odorant concentration. Recently, the bioelectronic nose was developed, and much improved along with the improvement of nano-biotechnology. The bioelectronic nose consists of the following two parts: primary transducer and secondary transducer. Biological materials as a primary transducer improved the selectivity of the sensor, and nanomaterials as a secondary transducer increased the sensitivity. Especially, the bioelectronic noses using various nanomaterials combined with human olfactory receptors or nanovesicles derived from engineered olfactory cells have a potential which can detect almost all of the smells recognized by human because an engineered olfactory cell might be able to express any human olfactory receptor as well as can mimic human olfactory system. Therefore, bioelectronic nose will be a potent tool for smell visualization, but only if two technologies are completed. First, a multi-channel array-sensing system has to be applied for the integration of all of the olfactory receptors into a single chip for mimicking the performance of human nose. Second, the processing technique of the multi-channel system signals should be simultaneously established with the conversion of the signals to visual images. With the use of this latest sensing technology, the realization of a proper smell-visualization technology is expected in the near future.
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Affiliation(s)
- Hwi Jin Ko
- Bio-MAX Institute, Seoul, 151-742 Republic of Korea
| | - Tai Hyun Park
- Bio-MAX Institute, Seoul, 151-742 Republic of Korea ; School of Chemical and Biological Engineering, Seoul National University, Seoul, 151-742 Republic of Korea ; Advanced Institutes of Convergence Technology, Suwon, Gyeonggido 443-270 Republic of Korea
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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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30
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Rogez-Florent T, Goossens L, Drucbert AS, Duban-Deweer S, Six P, Depreux P, Danzé PM, Goossens JF, Foulon C. Amine coupling versus biotin capture for the assessment of sulfonamide as ligands of hCA isoforms. Anal Biochem 2016; 511:42-51. [DOI: 10.1016/j.ab.2016.07.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 07/08/2016] [Accepted: 07/29/2016] [Indexed: 12/11/2022]
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31
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Aykul S, Martinez-Hackert E. Determination of half-maximal inhibitory concentration using biosensor-based protein interaction analysis. Anal Biochem 2016; 508:97-103. [PMID: 27365221 DOI: 10.1016/j.ab.2016.06.025] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/08/2016] [Accepted: 06/24/2016] [Indexed: 01/01/2023]
Abstract
Half-maximal inhibitory concentration (IC50) is the most widely used and informative measure of a drug's efficacy. It indicates how much drug is needed to inhibit a biological process by half, thus providing a measure of potency of an antagonist drug in pharmacological research. Most approaches to determine IC50 of a pharmacological compound are based on assays that utilize whole cell systems. While they generally provide outstanding potency information, results can depend on the experimental cell line used and may not differentiate a compound's ability to inhibit specific interactions. Here we show using the secreted Transforming Growth Factor-β (TGF-β) family ligand BMP-4 and its receptors as example that surface plasmon resonance can be used to accurately determine IC50 values of individual ligand-receptor pairings. The molecular resolution achievable wih this approach can help distinguish inhibitors that specifically target individual complexes, or that can inhibit multiple functional interactions at the same time.
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Affiliation(s)
- Senem Aykul
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824-1319, USA
| | - Erik Martinez-Hackert
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824-1319, USA.
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32
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Anggayasti WL, Mancera RL, Bottomley S, Helmerhorst E. Optimization of surface plasmon resonance experiments: Case of high mobility group box 1 (HMGB1) interactions. Anal Biochem 2016; 499:43-50. [PMID: 26869083 DOI: 10.1016/j.ab.2015.12.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Revised: 12/01/2015] [Accepted: 12/31/2015] [Indexed: 01/06/2023]
Abstract
Surface plasmon resonance (SPR) is a powerful technique for evaluating protein-protein interactions in real time. However, inappropriately optimized experiments can often lead to problems in the interpretation of data, leading to unreliable kinetic constants and binding models. Optimization of SPR experiments involving "sticky" proteins, or proteins that tend to aggregate, represents a typical scenario where it is important to minimize errors in the data and the kinetic analysis of those data. This is the case of High Mobility Group Box 1 and the receptor of advanced glycation end products. A number of improvements in protein purification, buffer composition, immobilization conditions, and the choice of flow rate are shown to result in substantial improvements in the accurate characterization of the interactions of these proteins and the derivation of the corresponding kinetic constants.
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Affiliation(s)
- Wresti L Anggayasti
- School of Biomedical Sciences, CHIRI Biosciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.
| | - Ricardo L Mancera
- School of Biomedical Sciences, CHIRI Biosciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - Steven Bottomley
- School of Biomedical Sciences, CHIRI Biosciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - Erik Helmerhorst
- School of Biomedical Sciences, CHIRI Biosciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
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33
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Vance S, Zeidan E, Henrich VC, Sandros MG. Comparative Analysis of Human Growth Hormone in Serum Using SPRi, Nano-SPRi and ELISA Assays. J Vis Exp 2016. [PMID: 26780354 PMCID: PMC4781177 DOI: 10.3791/53508] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Sensitive and selective methods for the detection of human growth hormone (hGH) over a wide range of concentrations (high levels of 50-100 ng ml−1 and minimum levels of 0.03 ng ml−1) in circulating blood are essential as variable levels may indicate altered physiology. For example, growth disorders occurring in childhood can be diagnosed by measuring levels of hGH in blood. Also, the misuse of recombinant hGH in sports not only poses an ethical issue it also presents serious health threats to the abuser. One popular strategy for measuring hGH misuse, relies on the detection of the ratio of 22 kDa hGH to total hGH, as non-22 kDa endogenous levels drop after exogenous recombinant hGH (rhGH) administration.Surface plasmon resonance imaging (SPRi) is an analytical tool that allows direct (label-free) monitoring and visualization of biomolecular interactions by recording changes of the refractive index adjacent to the sensor surface in real time. In contrast, the most frequently used colorimetric method, enzyme-linked immunosorbent assay (ELISA) uses enzyme labeled detection antibodies to indirectly measure analyte concentration after the addition of a substrate that induces a color change. To increase detection sensitivity, amplified SPRi uses a sandwich assay format and near infrared quantum dots (QDs) to increase signal strength. After direct SPRi detection of recombinant rhGH in spiked human serum, the SPRi signal is amplified by the sequential injection of detection antibody coated with near-infrared QDs (Nano-SPRi). In this study, the diagnostic potential of direct and amplified SPRi was assessed for measuring rhGH spiked in human serum and compared directly with the capabilities of a commercially available ELISA kit.
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Affiliation(s)
- Stephen Vance
- Department of Nanoscience, University of North Carolina at Greensboro
| | - Effat Zeidan
- Department of Nanoscience, University of North Carolina at Greensboro
| | - Vincent C Henrich
- Center for Biotechnology, Genomics, and Health Research, University of North Carolina at Greensboro
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Dunér G, Anderson H, Pei Z, Ingemarsson B, Aastrup T, Ramström O. Signal enhancement in ligand–receptor interactions using dynamic polymers at quartz crystal microbalance sensors. Analyst 2016; 141:3993-6. [DOI: 10.1039/c6an00735j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The signal enhancement properties of QCM sensors based on dynamic, biotinylated poly(acrylic acid) brushes has been studied in interaction studies with an anti-biotin Fab fragment.
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Affiliation(s)
- Gunnar Dunér
- KTH – Royal Institute of Technology
- Department of Chemistry
- S-10044 Stockholm
- Sweden
- Attana AB
| | - Henrik Anderson
- Attana AB
- S-11419 Stockholm
- Sweden
- Uppsala University
- Ångström Laboratory
| | | | | | | | - Olof Ramström
- KTH – Royal Institute of Technology
- Department of Chemistry
- S-10044 Stockholm
- Sweden
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35
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Kruis IC, Löwik DWPM, Boelens WC, van Hest JCM, Pruijn GJM. An integrated, peptide-based approach to site-specific protein immobilization for detection of biomolecular interactions. Analyst 2016; 141:5321-8. [DOI: 10.1039/c6an00154h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Site-specific immobilization of proteins on a biosensor surface, based on leucine zipper interactions.
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Affiliation(s)
- Ilmar C. Kruis
- Radboud University
- Department of Biomolecular Chemistry
- Institute for Molecules and Materials and Radboud Institute for Molecular Life Science
- Nijmegen
- The Netherlands
| | - Dennis W. P. M. Löwik
- Radboud University
- Department of Bio-organic Chemistry
- Institute for Molecules and Materials
- Nijmegen
- The Netherlands
| | - Wilbert C. Boelens
- Radboud University
- Department of Biomolecular Chemistry
- Institute for Molecules and Materials and Radboud Institute for Molecular Life Science
- Nijmegen
- The Netherlands
| | - Jan C. M. van Hest
- Radboud University
- Department of Bio-organic Chemistry
- Institute for Molecules and Materials
- Nijmegen
- The Netherlands
| | - Ger J. M. Pruijn
- Radboud University
- Department of Biomolecular Chemistry
- Institute for Molecules and Materials and Radboud Institute for Molecular Life Science
- Nijmegen
- The Netherlands
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36
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Trapaidze A, Hérault JP, Herbert JM, Bancaud A, Gué AM. Investigation of the selectivity of thrombin-binding aptamers for thrombin titration in murine plasma. Biosens Bioelectron 2015; 78:58-66. [PMID: 26594887 DOI: 10.1016/j.bios.2015.11.017] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/26/2015] [Accepted: 11/08/2015] [Indexed: 11/26/2022]
Abstract
Detection of thrombin in plasma raises timely challenges to enable therapeutic management of thrombosis in patients under vital threat. Thrombin binding aptamers represent promising candidates as sensing elements for the development of real-time thrombin biosensors; however implementation of such biosensor requires the clear understanding of thrombin-aptamer interaction properties in real-like environment. In this study, we used Surface Plasmon Resonance technique to answer the questions of specificity and sensitivity of thrombin detection by the thrombin-binding aptamers HD1, NU172 and HD22. We systematically characterized their properties in the presence of thrombin, as well as interfering molecular species such as the thrombin precursor prothrombin, thrombin in complex with some of its natural inhibitors, nonspecific serum proteins, and diluted plasma. Kinetic experiments show the multiple binding modes of HD1 and NU172, which both interact with multiple sites of thrombin with low nanomolar affinities and show little specificity of interaction for prothrombin vs. thrombin. HD22, on the other hand, binds specifically to thrombin exosite II and has no affinity to prothrombin at all. While thrombin in complex with some of its inhibitors could not be recognized by any aptamer, the binding of HD1 and NU172 properties is compromised by thrombin inhibitors alone, as well as with serum albumin. Finally, the complex nature of plasma was overwhelming for HD1, but we define conditions for the thrombin detection at 10nM range in 100-fold diluted plasma by HD22. Consequently HD22 showed key advantage over HD1 and NU172, and appears as the only alternative to design an aptasensor.
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Affiliation(s)
- Ana Trapaidze
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France; Université de Toulouse, LAAS, F-31400 Toulouse, France.
| | | | | | - Aurélien Bancaud
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France; Université de Toulouse, LAAS, F-31400 Toulouse, France.
| | - Anne-Marie Gué
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France; Université de Toulouse, LAAS, F-31400 Toulouse, France
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37
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Nakka SS, Lönn J, Starkhammar Johansson C, Bengtsson T, Nayeri F. Antibodies produced in vitro in the detection of periodontal bacteria by using surface plasmon resonance analysis. Clin Exp Dent Res 2015; 1:32-44. [PMID: 29744138 PMCID: PMC5839181 DOI: 10.1002/cre2.6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 08/14/2015] [Accepted: 08/24/2015] [Indexed: 12/17/2022] Open
Abstract
Porphyromonas gingivalis (P. gingivalis) is a major etiological agent associated with periodontitis. This study aims to develop antibodies to P. gingivalis in vitro for real-time detection of bacteria in clinical samples. Lymphocytes were isolated from whole blood of patient treated for periodontitis and were stimulated with P. gingivalis ATCC 33277. B-cell maturation to long-living antibody secreting-plasma cells was studied using flow cytometry and immunofluorescence staining. The antibodies developed in vitro were immobilized onto a CM-5 sensor chip of a biosensor to detect the presence of P. gingivalis in the gingival crevicular fluid of patients with periodontitis compared to periodontally healthy controls (n = 30). Surface plasmon resonance (SPR) analysis was performed to evaluate specific interactions of bacteria in samples with the immobilized antibodies. The results of SPR analysis were compared to the detection of P. gingivalis in the samples using DNA-DNA checkerboard hybridization technique. A clear and distinct change in lymphocyte morphology upon stimulation with P. gingivalis was observed. Anti-P. gingivalis antibodies secreted by CD38+ plasma cells showed the presence of all the four IgG subclasses. The results of DNA-DNA checkerboard analysis were in agreement with that of SPR analysis for the detection of P. gingivalis in patient samples. Furthermore, incubation with anti-P. gingivalis attenuated the bacterial response in SPR. The in vitro method for antibody production developed during this study could be used for an efficient real-time detection of periodontitis, and the attenuating effects of in vitro antibodies suggest their role in passive immunization to prevent periodontitis and their associated risk factors.
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Affiliation(s)
- Sravya Sowdamini Nakka
- The Institution for Protein Environmental Affinity SurveysPEAS Institut ABLinköpingSweden
- Clinical Research Center, School of Health and Medical SciencesÖrebro UniversityÖrebroSweden
| | - Johanna Lönn
- The Institution for Protein Environmental Affinity SurveysPEAS Institut ABLinköpingSweden
- Clinical Research Center, School of Health and Medical SciencesÖrebro UniversityÖrebroSweden
| | | | - Torbjörn Bengtsson
- Clinical Research Center, School of Health and Medical SciencesÖrebro UniversityÖrebroSweden
| | - Fariba Nayeri
- The Institution for Protein Environmental Affinity SurveysPEAS Institut ABLinköpingSweden
- Division of Infectious DiseasesUniversity HospitalLinköpingSweden
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38
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Vauquelin G, Huber W, Swinney DC. Experimental Methods to Determine Binding Kinetics. THERMODYNAMICS AND KINETICS OF DRUG BINDING 2015. [DOI: 10.1002/9783527673025.ch9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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39
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Study of the interaction of trastuzumab and SKOV3 epithelial cancer cells using a quartz crystal microbalance sensor. SENSORS 2015; 15:5884-94. [PMID: 25763651 PMCID: PMC4435181 DOI: 10.3390/s150305884] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 12/31/2014] [Accepted: 03/02/2015] [Indexed: 12/20/2022]
Abstract
Analytical methods founded upon whole cell-based assays are of importance in early stage drug development and in fundamental studies of biomolecular recognition. Here we have studied the binding of the monoclonal antibody trastuzumab to human epidermal growth factor receptor 2 (HER2) on human ovary adenocarcinoma epithelial cancer cells (SKOV3) using quartz crystal microbalance (QCM) technology. An optimized procedure for immobilizing the cells on the chip surface was established with respect to fixation procedure and seeding density. Trastuzumab binding to the cell decorated sensor surface was studied, revealing a mean dissociation constant, KD, value of 7 ± 1 nM (standard error of the mean). This study provides a new perspective on the affinity of the antibody-receptor complex presented a more natural context compared to purified receptors. These results demonstrate the potential for using whole cell-based QCM assay in drug development, the screening of HER2 selective antibody-based drug candidates, and for the study of biomolecular recognition. This real time, label free approach for studying interactions with target receptors present in their natural environment afforded sensitive and detailed kinetic information about the binding of the analyte to the target.
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40
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Peess C, von Proff L, Goller S, Andersson K, Gerg M, Malmqvist M, Bossenmaier B, Schräml M. Deciphering the stepwise binding mode of HRG1β to HER3 by surface plasmon resonance and interaction map. PLoS One 2015; 10:e0116870. [PMID: 25658697 PMCID: PMC4319926 DOI: 10.1371/journal.pone.0116870] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 12/15/2014] [Indexed: 11/25/2022] Open
Abstract
For the development of efficient anti-cancer therapeutics against the HER receptor family it is indispensable to understand the mechanistic model of the HER receptor activation upon ligand binding. Due to its high complexity the binding mode of Heregulin 1 beta (HRG1β) with its receptor HER3 is so far not understood. Analysis of the interaction of HRG1β with surface immobilized HER3 extracellular domain by time-resolved Surface Plasmon Resonance (SPR) was so far not interpretable using any regular analysis method as the interaction was highly complex. Here, we show that Interaction Map (IM) made it possible to shed light on this interaction. IM allowed deciphering the rate limiting kinetic contributions from complex SPR sensorgrams and thereby enabling the extraction of discrete kinetic rate components from the apparently heterogeneous interactions. We could resolve details from the complex avidity-driven binding mode of HRG1β with HER3 by using a combination of SPR and IM data. Our findings contribute to the general understanding that a major conformational change of HER3 during its activation is induced by a complex sequential HRG1β docking mode.
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Affiliation(s)
- Carmen Peess
- Roche Diagnostics GmbH, Penzberg, Germany
- * E-mail:
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41
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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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42
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Davidoff SN, Ditto NT, Brooks AE, Eckman J, Brooks BD. Surface Plasmon Resonance for Therapeutic Antibody Characterization. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/978-1-4939-2617-6_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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43
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Bury D, Dahmane I, Derouaux A, Dumbre S, Herdewijn P, Matagne A, Breukink E, Mueller-Seitz E, Petz M, Terrak M. Positive cooperativity between acceptor and donor sites of the peptidoglycan glycosyltransferase. Biochem Pharmacol 2014; 93:141-50. [PMID: 25462814 DOI: 10.1016/j.bcp.2014.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 11/07/2014] [Accepted: 11/07/2014] [Indexed: 12/01/2022]
Abstract
The glycosyltransferases of family 51 (GT51) catalyze the polymerization of lipid II to form linear glycan chains, which, after cross linking by the transpeptidases, form the net-like peptidoglycan macromolecule. The essential function of the GT makes it an attractive antimicrobial target; therefore a better understanding of its function and its mechanism of interaction with substrates could help in the design and the development of new antibiotics. In this work, we have used a surface plasmon resonance Biacore(®) biosensor, based on an amine derivative of moenomycin A immobilized on a sensor chip surface, to investigate the mechanism of binding of substrate analogous inhibitors to the GT. Addition of increasing concentrations of moenomycin A to the Staphylococcus aureus MtgA led to reduced binding of the protein to the sensor chip as expected. Remarkably, in the presence of low concentrations of the most active disaccharide inhibitors, binding of MtgA to immobilized moenomycin A was found to increase; in contrast competition with moenomycin A occurred only at high concentrations. This finding suggests that at low concentrations, the lipid II analogs bind to the acceptor site and induce a cooperative binding of moenomycin A to the donor site. Our results constitute the first indication of the existence of a positive cooperativity between the acceptor and the donor sites of peptidoglycan GTs. In addition, our study indicates that a modification of two residues (L119N and F120S) within the hydrophobic region of MtgA can yield monodisperse forms of the protein with apparently no change in its secondary structure content, but this is at the expense of the enzyme function.
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Affiliation(s)
- Daniel Bury
- Department of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaussstr. 20, 42119 Wuppertal, Germany.
| | - Ismahene Dahmane
- Centre d'Ingénierie des Protéines, Université de Liège, Allée de la Chimie, B6a, B-4000, Sart Tilman, Liège, Belgium
| | - Adeline Derouaux
- Centre d'Ingénierie des Protéines, Université de Liège, Allée de la Chimie, B6a, B-4000, Sart Tilman, Liège, Belgium
| | - Shrinivas Dumbre
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
| | - André Matagne
- Centre d'Ingénierie des Protéines, Université de Liège, Allée de la Chimie, B6a, B-4000, Sart Tilman, Liège, Belgium
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Erika Mueller-Seitz
- Department of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaussstr. 20, 42119 Wuppertal, Germany
| | - Michael Petz
- Department of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaussstr. 20, 42119 Wuppertal, Germany
| | - Mohammed Terrak
- Centre d'Ingénierie des Protéines, Université de Liège, Allée de la Chimie, B6a, B-4000, Sart Tilman, Liège, Belgium.
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44
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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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45
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Abstract
Surface plasmon resonance (SPR) biosensors have become the mainstream method for biomolecular interaction analysis. It offers many advantages over conventional methods by its label-free, real-time monitoring, low sample consumption, high throughput, and remarkable sensitivity. We have examined dengue virus protein interactions in the context of antibody affinity measurement, protein-protein interaction, and in the screening of small molecule inhibitors as well as the characterization of the interactions between the small molecule binders and the relevant dengue protein. Here we describe the basic methods involved in performing SPR assays as well as in data processing and evaluation using some examples of dengue proteins.
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Affiliation(s)
- Yin Hoe Yau
- Division of Chemical Biology and Biotechnology, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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46
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Glaser RW, Schönherr R, Heinemann SH. Fixed charges in the gel matrix of sensor chips and dissociation in diffusion gradients influence the detection of fast protein-protein interactions. Biosystems 2013; 116:27-35. [PMID: 24342363 DOI: 10.1016/j.biosystems.2013.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 09/01/2013] [Accepted: 09/10/2013] [Indexed: 11/24/2022]
Abstract
In molecular interaction studies based on surface plasmon resonance (SPR) measurements, the ligand is often immobilized in a thin carboxydextran gel matrix. Here we investigated the influence of the charged gel on the results of such SPR measurements. At physiological ionic strength, analytes with a net charge of more than about 5 are considerably enriched or depleted due to the Donnan potential under commonly applied experimental conditions. Below physiological ionic strength, enrichment was found to be even stronger than predicted by Donnan theory. The influence of the gel matrix on the apparent binding is prevented in competition experiments, in which SPR measurements are only used to discriminate between free and complexed analyte while the interaction between analyte and ligand is studied in solution. However, if the analyte-ligand interaction is very fast, thermodynamic equilibrium is disturbed near the interface where free analyte binds to the immobilized ligand due to mass transport limitation. Consequently, the soluble analyte-ligand complex dissociates, which results in an overestimation of free analyte. In experiments of calmodulin binding to fragments of the KCNH1 ion channel protein this mass-transport-induced dissociation led to a systematic underestimation of the affinity. We conclude that the insufficient discrimination between the true analyte-ligand binding and the complex interactions of the analyte with the gel phase may result in systematic errors. The theoretical framework for recognizing and avoiding such errors is provided.
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Affiliation(s)
- Ralf W Glaser
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Hans-Knöll-Straße 2, D-07745 Jena, Germany.
| | - Roland Schönherr
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Hans-Knöll-Straße 2, D-07745 Jena, Germany
| | - Stefan H Heinemann
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Hans-Knöll-Straße 2, D-07745 Jena, Germany
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47
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Xu ZQ, Zhou B, Jiang FL, Dai J, Liu Y. Interaction between a cationic porphyrin and ctDNA investigated by SPR, CV and UV–vis spectroscopy. Colloids Surf B Biointerfaces 2013; 110:321-6. [DOI: 10.1016/j.colsurfb.2013.04.040] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 03/24/2013] [Accepted: 04/17/2013] [Indexed: 11/29/2022]
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48
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Osman B, Uzun L, Beşirli N, Denizli A. Microcontact imprinted surface plasmon resonance sensor for myoglobin detection. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2013; 33:3609-14. [DOI: 10.1016/j.msec.2013.04.041] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 04/12/2013] [Accepted: 04/20/2013] [Indexed: 11/16/2022]
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49
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Cervantes Tellez GA, Hassan S, Tait RN, Berini P, Gordon R. Atomically flat symmetric elliptical nanohole arrays in a gold film for ultrasensitive refractive index sensing. LAB ON A CHIP 2013; 13:2541-6. [PMID: 23478567 DOI: 10.1039/c3lc41411f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Past works on refractive index sensing using nanohole arrays in metal films typically achieved a resolution of around 10(-4) to 10(-5) refractive index units (RIU), up to 10(-6) with complicated detection setups. This is an order of magnitude worse than commercial Kretschmann-based surface-plasmon resonance (SPR) sensors. Here, we demonstrate intensity-based bulk refractive index sensing in an aqueous environment with a resolution of 9.38 × 10(-8) refractive index units (RIU), showing for the first time comparable performance for nanohole SPR with Kretschmann-based SPR. This is achieved by the combination of three advances in the materials properties: (a) template stripping to achieve ultra-flat Au surfaces of ~0.2 nm roughness, (b) elliptical nanoholes to enhance transmission, and (c) a Cytop substrate to symmetrize the refractive index with the aqueous environment above the metal film. The simple optical microscope geometry and microfluidic integration used in this work is promising for multiplexed lab-on-chip analysis.
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50
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Some D. Light-scattering-based analysis of biomolecular interactions. Biophys Rev 2013; 5:147-158. [PMID: 23646069 PMCID: PMC3641300 DOI: 10.1007/s12551-013-0107-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 01/31/2013] [Indexed: 01/06/2023] Open
Abstract
While light scattering has long been applied to the analysis of biomolecular interactions, recent advances have extended the practical use of light scattering techniques to cover a rather broad range of phenomena. In this paper I review essential light scattering theory as applied to specific interactions under thermodynamically ideal conditions and present examples showing how light scattering elucidates the dynamic equilibrium and kinetic behavior of proteins and other biomacromolecules.
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Affiliation(s)
- Daniel Some
- Wyatt Technology Corp, 6300 Hollister Ave, Santa Barbara, CA 93117 USA
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