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Tiwari PB, Kamgar-Dayhoff P, Tiwari P, McKillop MI, Brelidze TI. Use of Surface Plasmon Resonance Technique for Studies of Inter-domain Interactions in Ion Channels. Methods Mol Biol 2024; 2796:105-118. [PMID: 38856898 PMCID: PMC11225882 DOI: 10.1007/978-1-0716-3818-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Ion channels are transmembrane proteins essential for cellular functions and are important drug targets. Surface plasmon resonance (SPR) is a powerful technique for investigating protein-protein and protein-small molecule ligand interactions. SPR has been underutilized for studies of ion channels, even though it could provide a wealth of information on the mechanisms of ion channel regulation and aid in ion channel drug discovery. Here we provide a detailed description of the use of SPR technology for investigating inter-domain interactions in KCNH potassium-selective and voltage-gated ion channels.
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Affiliation(s)
- Purushottam B Tiwari
- Department of Oncology, Georgetown University Medical Center, Washington, DC, USA
| | - Pareesa Kamgar-Dayhoff
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, DC, USA
| | - Prakriti Tiwari
- Department of Oncology, Georgetown University Medical Center, Washington, DC, USA
- Department of Biology, College of Arts & Sciences, Georgetown University, Washington, DC, USA
| | - Maria I McKillop
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, DC, USA
| | - Tinatin I Brelidze
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, DC, USA.
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Nguyen K, Li K, Flores K, Tomaras GD, Dennison SM, McCarthy JM. Parameter estimation and identifiability analysis for a bivalent analyte model of monoclonal antibody-antigen binding. Anal Biochem 2023; 679:115263. [PMID: 37549723 PMCID: PMC10511885 DOI: 10.1016/j.ab.2023.115263] [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: 04/02/2023] [Revised: 07/10/2023] [Accepted: 07/23/2023] [Indexed: 08/09/2023]
Abstract
Surface plasmon resonance (SPR) is an extensively used technique to characterize antigen-antibody interactions. Affinity measurements by SPR typically involve testing the binding of antigen in solution to monoclonal antibodies (mAbs) immobilized on a chip and fitting the kinetics data using 1:1 Langmuir binding model to derive rate constants. However, when it is necessary to immobilize antigens instead of the mAbs, a bivalent analyte (1:2) binding model is required for kinetics analysis. This model is lacking in data analysis packages associated with high throughput SPR instruments and the packages containing this model do not explore multiple local minima and parameter identifiability issues that are common in non-linear optimization. Therefore, we developed a method to use a system of ordinary differential equations for analyzing 1:2 binding kinetics data. Salient features of this method include a grid search on parameter initialization and a profile likelihood approach to determine parameter identifiability. Using this method we found a non-identifiable parameter in data set collected under the standard experimental design. A simulation-guided improved experimental design led to reliable estimation of all rate constants. The method and approach developed here for analyzing 1:2 binding kinetics data will be valuable for expeditious therapeutic antibody discovery research.
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Affiliation(s)
- Kyle Nguyen
- Biomathematics Graduate Program, North Carolina State University, Raleigh, 27607, NC, USA; Center for Research in Scientific Computation, North Carolina State University, Raleigh, 27607, NC, USA.
| | - Kan Li
- Center for Human Systems Immunology, Duke University, Durham, 27701, NC, USA; Department of Surgery, Duke University, Durham, 27710, NC, USA
| | - Kevin Flores
- Center for Research in Scientific Computation, North Carolina State University, Raleigh, 27607, NC, USA; Department of Mathematics, North Carolina State University, Raleigh, 27607, NC, USA
| | - Georgia D Tomaras
- Center for Human Systems Immunology, Duke University, Durham, 27701, NC, USA; Department of Surgery, Duke University, Durham, 27710, NC, USA; Department of Integrative Immunobiology, Duke University, Durham, 27710, NC, USA; Department of Molecular Genetics and Microbiology, Duke University, Durham, 27710, NC, USA; Duke Human Vaccine Institute, Duke University, Durham, 27710, NC, USA
| | - S Moses Dennison
- Center for Human Systems Immunology, Duke University, Durham, 27701, NC, USA; Department of Surgery, Duke University, Durham, 27710, NC, USA
| | - Janice M McCarthy
- Center for Human Systems Immunology, Duke University, Durham, 27701, NC, USA; Department of Biostatistics and Bioinformatics, Duke University, Durham, 27710, NC, USA
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On the Use of Surface Plasmon Resonance Biosensing to Understand IgG-FcγR Interactions. Int J Mol Sci 2021; 22:ijms22126616. [PMID: 34205578 PMCID: PMC8235063 DOI: 10.3390/ijms22126616] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 01/01/2023] Open
Abstract
Surface plasmon resonance (SPR)-based optical biosensors offer real-time and label-free analysis of protein interactions, which has extensively contributed to the discovery and development of therapeutic monoclonal antibodies (mAbs). As the biopharmaceutical market for these biologics and their biosimilars is rapidly growing, the role of SPR biosensors in drug discovery and quality assessment is becoming increasingly prominent. One of the critical quality attributes of mAbs is the N-glycosylation of their Fc region. Other than providing stability to the antibody, the Fc N-glycosylation influences immunoglobulin G (IgG) interactions with the Fcγ receptors (FcγRs), modulating the immune response. Over the past two decades, several studies have relied on SPR-based assays to characterize the influence of N-glycosylation upon the IgG-FcγR interactions. While these studies have unveiled key information, many conclusions are still debated in the literature. These discrepancies can be, in part, attributed to the design of the reported SPR-based assays as well as the methodology applied to SPR data analysis. In fact, the SPR biosensor best practices have evolved over the years, and several biases have been pointed out in the development of experimental SPR protocols. In parallel, newly developed algorithms and data analysis methods now allow taking into consideration complex biomolecular kinetics. In this review, we detail the use of different SPR biosensing approaches for characterizing the IgG-FcγR interactions, highlighting their merit and inherent experimental complexity. Furthermore, we review the latest SPR-derived conclusions on the influence of the N-glycosylation upon the IgG-FcγR interactions and underline the differences and similarities across the literature. Finally, we explore new avenues taking advantage of novel computational analysis of SPR results as well as the latest strategies to control the glycoprofile of mAbs during production, which could lead to a better understanding and modelling of the IgG-FcγRs interactions.
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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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Gomes JCM, Souza LC, Oliveira LC. SmartSPR sensor: Machine learning approaches to create intelligent surface plasmon based sensors. Biosens Bioelectron 2021; 172:112760. [PMID: 33197751 DOI: 10.1016/j.bios.2020.112760] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/14/2020] [Accepted: 10/21/2020] [Indexed: 10/23/2022]
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Aćimović SS, Šípová-Jungová H, Emilsson G, Shao L, Dahlin AB, Käll M, Antosiewicz TJ. Antibody-Antigen Interaction Dynamics Revealed by Analysis of Single-Molecule Equilibrium Fluctuations on Individual Plasmonic Nanoparticle Biosensors. ACS NANO 2018; 12:9958-9965. [PMID: 30165019 DOI: 10.1021/acsnano.8b04016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Antibody-antigen interactions are complex events central to immune response, in vivo and in vitro diagnostics, and development of therapeutic substances. We developed an ultrastable single-molecule localized surface plasmon resonance (LSPR) sensing platform optimized for studying antibody-antigen interaction kinetics over very long time scales. The setup allowed us to perform equilibrium fluctuations analysis of the PEG/anti-PEG interaction. By time and frequency domain analysis, we demonstrate that reversible adsorption of monovalently bound anti-PEG antibodies is the dominant factor affecting the LSPR fluctuations. The results suggest that equilibrium fluctuation analysis can be an alternative to established methods for determination of interaction rates. In particular, the methodology is suited to analyze molecular systems whose properties change during the initial interaction phases, for example, due to mass transport limitations or, as demonstrated here, because the effective association rate constant varies with surface concentration of adsorbed molecules.
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Affiliation(s)
- Srdjan S Aćimović
- Department of Physics , Chalmers University of Technology , 412 96 Göteborg , Sweden
| | - Hana Šípová-Jungová
- Department of Physics , Chalmers University of Technology , 412 96 Göteborg , Sweden
| | - Gustav Emilsson
- Department of Chemistry and Chemical Engineering , Chalmers University of Technology , 412 96 Göteborg , Sweden
| | - Lei Shao
- Department of Physics , Chalmers University of Technology , 412 96 Göteborg , Sweden
| | - Andreas B Dahlin
- Department of Chemistry and Chemical Engineering , Chalmers University of Technology , 412 96 Göteborg , Sweden
| | - Mikael Käll
- Department of Physics , Chalmers University of Technology , 412 96 Göteborg , Sweden
| | - Tomasz J Antosiewicz
- Department of Physics , Chalmers University of Technology , 412 96 Göteborg , Sweden
- Faculty of Physics , University of Warsaw , Pasteura 5 , 02-093 Warsaw , Poland
- Center of New Technologies , University of Warsaw , Banacha 2c , 02-097 Warsaw , Poland
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