1
|
Ma H, Ramanujam AA, Linnes JC, Kinzer-Ursem TL. Biomolecular Interaction Analysis Quantification with a Low-Volume Microfluidic Chip and Particle Diffusometry. Anal Chem 2024; 96:5815-5823. [PMID: 38575144 PMCID: PMC11025547 DOI: 10.1021/acs.analchem.3c04840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 04/06/2024]
Abstract
Microfluidic techniques are widely applied in biomolecular analysis and disease diagnostic assays. While the volume of the sample that is directly used in such assays is often only femto-to microliters, the "dead volume" of solutions supplied in syringes and tubing can be much larger, even up to milliliters, increasing overall reagent use and making analysis significantly more expensive. To reduce the difficulty and cost, we designed a new chip using a low volume solution for analysis and applied it to obtain real-time data for protein-protein interaction measurements. The chip takes advantage of air/aqueous two-phase droplet flow, on-chip rapid mixing within milliseconds, and a droplet capture method, that ultimately requires only 2 μL of reagent solution. The interaction is analyzed by particle diffusometry, a nonintrusive and precise optical detection method to analyze the properties of microparticle diffusion in solution. Herein, we demonstrate on-chip characterization of human immunodeficiency virus p24 antibody-antigen protein binding kinetics imaged via fluorescence microscopy and analyzed by PD. The measured kon and koff are 1 × 106 M-1 s-1 and 3.3 × 10-4 s-1, respectively, and agree with independent measurement via biolayer interferometry and previously calculated p24-antibody binding kinetics. This new microfluidic chip and the protein-protein interaction analysis method can also be applied in other fields that require low-volume solutions to perform accurate measurement, analysis, and detection.
Collapse
Affiliation(s)
- Hui Ma
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Aiswarya A. Ramanujam
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jacqueline C. Linnes
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Tamara L. Kinzer-Ursem
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| |
Collapse
|
2
|
Janezic EM, Doan A, Mai E, Bravo DD, Wang J, Kim HS, Spiess C, Bewley K, ElSohly A, Liang WC, Koerber JT, Richalet P, Vanhove M, Comps-Agrar L. A novel, label-free, pre-equilibrium assay to determine the association and dissociation rate constants of therapeutic antibodies on living cells. Br J Pharmacol 2023. [PMID: 37783572 DOI: 10.1111/bph.16258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 09/19/2023] [Accepted: 09/23/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND AND PURPOSE Monoclonal antibodies (Ab) represent the fastest growing drug class. Knowledge of the biophysical parameters (kon , koff and KD ) that dictate Ab:receptor interaction is critical during the drug discovery process. However, with the increasing complexity of Ab formats and their targets, it became apparent that existing technologies present limitations and are not always suitable to determine these parameters. Therefore, novel affinity determination methods represent an unmet assay need. EXPERIMENTAL APPROACH We developed a pre-equilibrium kinetic exclusion assay using recent mathematical advances to determine the kon , koff and KD of monoclonal Ab:receptor interactions on living cells. The assay is amenable to all human IgG1 and rabbit Abs. KEY RESULTS Using our novel assay, we demonstrated for several monoclonal Ab:receptor pairs that the calculated kinetic rate constants were comparable with orthogonal methods that were lower throughput or more resource consuming. We ran simulations to predict the critical conditions to improve the performance of the assays. We further showed that this method could successfully be applied to both suspension and adherent cells. Finally, we demonstrated that kon and koff , but not KD , correlate with in vitro potency for a panel of monoclonal Abs. CONCLUSIONS AND IMPLICATIONS Our novel assay has the potential to systematically probe binding kinetics of monoclonal Abs to cells and can be incorporated in a screening cascade to identify new therapeutic candidates. Wide-spread adoption of pre-equilibrium assays using physiologically relevant systems will lead to a more holistic understanding of how Ab binding kinetics influence their potency.
Collapse
Affiliation(s)
| | | | - Elaine Mai
- Genentech, Inc, South San Francisco, California, USA
| | | | - Jianyong Wang
- Genentech, Inc, South San Francisco, California, USA
| | - Hok Seon Kim
- Genentech, Inc, South San Francisco, California, USA
| | | | | | - Adel ElSohly
- Genentech, Inc, South San Francisco, California, USA
| | | | | | | | | | | |
Collapse
|
3
|
Abstract
In the computational design of antibodies, the interaction analysis between target antigen and antibody is an essential process to obtain feedback for validation and optimization of the design. Kinetic and thermodynamic parameters as well as binding affinity (KD) allow for a more detailed evaluation and understanding of the molecular recognition. In this chapter, we summarize the conventional experimental methods which can calculate KD value (ELISA, FP), analyze a binding activity to actual cells (FCM), and evaluate the kinetic and thermodynamic parameters (ITC, SPR, BLI), including high-throughput analysis and a recently developed experimental technique.
Collapse
Affiliation(s)
- Aki Tanabe
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
4
|
A method to assess the robustness of complex mathematical models used for quantitative interpretation of experimental data by nonlinear regression analysis: application to high-affinity binding models. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:1045-1054. [PMID: 34142204 DOI: 10.1007/s00249-021-01556-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/06/2021] [Accepted: 06/09/2021] [Indexed: 10/21/2022]
Abstract
Nonlinear regression is widely used to fit experimental data to a specific mathematical model to extract numerical values for parameters representing the studied process. However, assessing the degree of precision that can be expected from such an analysis for a given parameter can be quite challenging for complex mathematical models. To address this issue, we propose here a method based on the analysis of a large number of data sets generated in such a way to mimic specific experimental conditions. Applying this methodology to high-affinity binding models, we report here a quantitative analysis of the robustness of such models, and how the precision on the fitting parameters can be expected to vary based on, e.g., the initial experimental conditions, the number or distribution of experimental points, or the experimental variability. We also show that these models, although widely used, are intrinsically limited by the fact that the two main fitting parameters, one representing the concentration of the studied species and the other its affinity, are inversely correlated, but demonstrate that this limitation can be overcome by global analysis of multiple data series generated at different concentrations of the titrated species.
Collapse
|
5
|
Torrini F, Palladino P, Baldoneschi V, Scarano S, Minunni M. Sensitive 'two-steps' competitive assay for gonadotropin-releasing hormone detection via SPR biosensing and polynorepinephrine-based molecularly imprinted polymer. Anal Chim Acta 2021; 1161:338481. [PMID: 33896555 DOI: 10.1016/j.aca.2021.338481] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/25/2021] [Accepted: 04/03/2021] [Indexed: 12/12/2022]
Abstract
The work reports an innovative bioassay for the detection of gonadorelin in urine, a gonadotropin-releasing hormone agonist widely used in fertility medicine and to treat hormonal dysfunctions. Gonadorelin is also a synthetic hormone listed by the World Anti-Doping Agency (WADA) and of interest in anti-doping controls. The main novelty relies on the development of a biocompatible, stable, and low-cost biomimetic receptor alternative to classic antibodies. Starting from norepinephrine monomer, a highly selective and sensitive molecularly imprinted polymer (MIP) was developed and optimized for optical real-time and label-free SPR biosensing. The selectivity has been addressed by testing a series of peptides, from high to low similarity, both in terms of molecular weight and primary sequence. Due to the very low molecular weight of gonadorelin (1182 Da), a 'two-steps' competitive assay was developed. Particular attention has been paid to the design of the competitor and its binding affinity constant towards the MIP, being a key step for the success of the competitive strategy. The SPR assay was first optimized in standard conditions and finally applied to untreated urine samples, achieving the sensitivity required by WADA guidelines. The MIP, tested in parallel with a monoclonal antibody, gave comparable results in terms of affinity constants and selectivity towards possible interfering analytes. However, the biomimetic receptor appears clearly superior in terms of sensitivity and reproducibility. This, together with its preparation simplicity, the extremely low-cost of the monomer and its reusability for hundreds of measurements, make polynorepinephrine-based MIPs powerful rivals to immune-based approaches in the near future for similar applications.
Collapse
Affiliation(s)
- Francesca Torrini
- Department of Chemistry "Ugo Schiff", University of Florence, 50019, Sesto Fiorentino (FI), Italy.
| | - Pasquale Palladino
- Department of Chemistry "Ugo Schiff", University of Florence, 50019, Sesto Fiorentino (FI), Italy.
| | - Veronica Baldoneschi
- Department of Chemistry "Ugo Schiff", University of Florence, 50019, Sesto Fiorentino (FI), Italy.
| | - Simona Scarano
- Department of Chemistry "Ugo Schiff", University of Florence, 50019, Sesto Fiorentino (FI), Italy.
| | - Maria Minunni
- Department of Chemistry "Ugo Schiff", University of Florence, 50019, Sesto Fiorentino (FI), Italy.
| |
Collapse
|
6
|
Sharifian Gh M. Recent Experimental Developments in Studying Passive Membrane Transport of Drug Molecules. Mol Pharm 2021; 18:2122-2141. [PMID: 33914545 DOI: 10.1021/acs.molpharmaceut.1c00009] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The ability to measure the passive membrane permeation of drug-like molecules is of fundamental biological and pharmaceutical importance. Of significance, passive diffusion across the cellular membranes plays an effective role in the delivery of many pharmaceutical agents to intracellular targets. Hence, approaches for quantitative measurement of membrane permeability have been the topics of research for decades, resulting in sophisticated biomimetic systems coupled with advanced techniques. In this review, recent developments in experimental approaches along with theoretical models for quantitative and real-time analysis of membrane transport of drug-like molecules through mimetic and living cell membranes are discussed. The focus is on time-resolved fluorescence-based, surface plasmon resonance, and second-harmonic light scattering approaches. The current understanding of how properties of the membrane and permeant affect the permeation process is discussed.
Collapse
Affiliation(s)
- Mohammad Sharifian Gh
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia 22908, United States
| |
Collapse
|
7
|
Quinn JG. A rebinding-assay for measuring extreme kinetics using label-free biosensors. Sci Rep 2021; 11:8301. [PMID: 33859320 PMCID: PMC8050309 DOI: 10.1038/s41598-021-87880-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/06/2021] [Indexed: 12/25/2022] Open
Abstract
In vitro kinetic measurements allow mechanistic characterization of binding interactions and are particularly valuable throughout drug discovery, from confirmation of on-target binding in early discovery to fine-tuning of drug-binding properties in pre-clinical development. Early chemical matter often exhibits transient kinetics, which remain challenging to measure in a routine drug discovery setting. For example, characterization of irreversible inhibitors has classically relied on the alkylation rate constant, yet this metric fails to resolve its fundamental constituent rate constants, which drive reversible binding kinetics and affinity complex inactivation. In other cases, extremely rapid association processes, which can approach the diffusion limit, also remain challenging to measure. To address these limitations, a practical kinetic rebinding assay is introduced that may be applied for kinetic screening and characterization of compounds. The new capabilities afforded by this probe-based assay emerge from mixed-phase partitioning in a flow-injection configuration and have been implemented using label-free biosensing. A finite element analysis-based biosensor model, simulating inhibition of rebinding within a crowded hydrogel milieu, provided surrogate test data that enabled development and validation of an algebraic model for estimation of kinetic interaction constants. An experimental proof-of-principle demonstrating estimation of the association rate constant, decoupled from the dissociation process, provided further validation.
Collapse
Affiliation(s)
- John G Quinn
- Biophysical Group, Biochemical and Cellular Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
| |
Collapse
|
8
|
Melentiev PN, Son LV, Kudryavtsev DS, Kasheverov IE, Tsetlin VI, Esenaliev RO, Balykin VI. Ultrafast, Ultrasensitive Detection and Imaging of Single Cardiac Troponin-T Molecules. ACS Sens 2020; 5:3576-3583. [PMID: 33124416 DOI: 10.1021/acssensors.0c01790] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The fluorescence-based methods of single-molecule optical detection have opened up unprecedented possibilities for imaging, monitoring, and sensing at a single-molecule level. However, single-molecule detection methods are very slow, making them practically inapplicable. In this paper, we show how to overcome this key limitation using the expanded laser spot, laser excitation in a nonfluorescent spectral window of biomolecules, and more binding fluorescent molecules on a biomolecule that increases the detection volume and the number of collected photons. We demonstrate advantages of the developed approach unreachable by any other technique using detection of single cardiac troponin-T molecules: (i) 1000-fold faster than by known approaches, (ii) real-time imaging of single troponin-T molecules dissolved in human blood serum, (iii) measurement of troponin-T concentration with a clinically important sensitivity of about 1 pg/mL. The developed approach can be used for ultrafast, ultrasensitive detection, monitoring, and real-time imaging of other biomolecules as well as of larger objects including pathogenic viruses and bacteria.
Collapse
Affiliation(s)
- Pavel N. Melentiev
- Institute of Spectroscopy RAS, Troitsk, Moscow 108840, Russia
- Higher School of Economics, National Research University, Moscow 101000, Russia
| | - Lina V. Son
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the RAS, Moscow 117997, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow reg. 141700, Russia
| | - Denis S. Kudryavtsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the RAS, Moscow 117997, Russia
| | - Igor E. Kasheverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the RAS, Moscow 117997, Russia
| | - Victor I. Tsetlin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the RAS, Moscow 117997, Russia
| | - Rinat O. Esenaliev
- The University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555, United States
| | - Victor I. Balykin
- Institute of Spectroscopy RAS, Troitsk, Moscow 108840, Russia
- Higher School of Economics, National Research University, Moscow 101000, Russia
| |
Collapse
|
9
|
Sandmark J, Tigerström A, Akerud T, Althage M, Antonsson T, Blaho S, Bodin C, Boström J, Chen Y, Dahlén A, Eriksson PO, Evertsson E, Fex T, Fjellström O, Gustafsson D, Herslöf M, Hicks R, Jarkvist E, Johansson C, Kalies I, Karlsson Svalstedt B, Kartberg F, Legnehed A, Martinsson S, Moberg A, Ridderström M, Rosengren B, Sabirsh A, Thelin A, Vinblad J, Wellner AU, Xu B, Östlund-Lindqvist AM, Knecht W. Identification and analyses of inhibitors targeting apolipoprotein(a) kringle domains KIV-7, KIV-10, and KV provide insight into kringle domain function. J Biol Chem 2020; 295:5136-5151. [PMID: 32132173 DOI: 10.1074/jbc.ra119.011251] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/17/2020] [Indexed: 11/06/2022] Open
Abstract
Increased plasma concentrations of lipoprotein(a) (Lp(a)) are associated with an increased risk for cardiovascular disease. Lp(a) is composed of apolipoprotein(a) (apo(a)) covalently bound to apolipoprotein B of low-density lipoprotein (LDL). Many of apo(a)'s potential pathological properties, such as inhibition of plasmin generation, have been attributed to its main structural domains, the kringles, and have been proposed to be mediated by their lysine-binding sites. However, available small-molecule inhibitors, such as lysine analogs, bind unselectively to kringle domains and are therefore unsuitable for functional characterization of specific kringle domains. Here, we discovered small molecules that specifically bind to the apo(a) kringle domains KIV-7, KIV-10, and KV. Chemical synthesis yielded compound AZ-05, which bound to KIV-10 with a Kd of 0.8 μm and exhibited more than 100-fold selectivity for KIV-10, compared with the other kringle domains tested, including plasminogen kringle 1. To better understand and further improve ligand selectivity, we determined the crystal structures of KIV-7, KIV-10, and KV in complex with small-molecule ligands at 1.6-2.1 Å resolutions. Furthermore, we used these small molecules as chemical probes to characterize the roles of the different apo(a) kringle domains in in vitro assays. These assays revealed the assembly of Lp(a) from apo(a) and LDL, as well as potential pathophysiological mechanisms of Lp(a), including (i) binding to fibrin, (ii) stimulation of smooth-muscle cell proliferation, and (iii) stimulation of LDL uptake into differentiated monocytes. Our results indicate that a small-molecule inhibitor targeting the lysine-binding site of KIV-10 can combat the pathophysiological effects of Lp(a).
Collapse
Affiliation(s)
- Jenny Sandmark
- Structure, Biophysics and Fragment-Based Lead Generation, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Anna Tigerström
- Precision Medicine BioPharmaceuticals, Precision Medicine, Oncology R&D, AstraZeneca, Gothenburg, Sweden
| | - Tomas Akerud
- Structure, Biophysics and Fragment-Based Lead Generation, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Magnus Althage
- Translational Science and Experimental Medicine, Early CVRM Biopharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Thomas Antonsson
- Medicinal Chemistry, Cardiovascular, Renal and Metabolism, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Stefan Blaho
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Cristian Bodin
- Structure, Biophysics and Fragment-Based Lead Generation, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Jonas Boström
- Medicinal Chemistry, Cardiovascular, Renal and Metabolism, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Yantao Chen
- Medicinal Chemistry, Cardiovascular, Renal and Metabolism, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Anders Dahlén
- Medicinal Chemistry, Cardiovascular, Renal and Metabolism, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Per-Olof Eriksson
- Structure, Biophysics and Fragment-Based Lead Generation, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Emma Evertsson
- Medicinal Chemistry, Cardiovascular, Renal and Metabolism, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Tomas Fex
- Medicinal Chemistry, Cardiovascular, Renal and Metabolism, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Ola Fjellström
- Research and Early Development, Cardiovascular, Renal and Metabolism, Biopharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - David Gustafsson
- Bioscience Cardiovascular, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Margareta Herslöf
- Medicinal Chemistry, Cardiovascular, Renal and Metabolism, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Ryan Hicks
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Emelie Jarkvist
- Bioscience Cardiovascular, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Carina Johansson
- Structure, Biophysics and Fragment-Based Lead Generation, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Inge Kalies
- Bioscience Cardiovascular, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Birgitta Karlsson Svalstedt
- Bioscience Cardiovascular, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Fredrik Kartberg
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Anne Legnehed
- Bioscience Cardiovascular, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Sofia Martinsson
- Bioscience Cardiovascular, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Andreas Moberg
- Structure, Biophysics and Fragment-Based Lead Generation, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Marianne Ridderström
- Drug Metabolism and Pharmacokinetics, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Birgitta Rosengren
- Bioscience Cardiovascular, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Alan Sabirsh
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Anders Thelin
- Bioscience Cardiovascular, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Johanna Vinblad
- Bioscience Cardiovascular, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Annika U Wellner
- Medicinal Chemistry, Cardiovascular, Renal and Metabolism, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Bingze Xu
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Ann-Margret Östlund-Lindqvist
- Bioscience Cardiovascular, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Wolfgang Knecht
- Bioscience Cardiovascular, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| |
Collapse
|
10
|
The Binding Affinity of Small Molecules with Yam Tyrosinase (Catechol Oxidase): A Biophysical Study. Biochem Res Int 2019; 2019:8284968. [PMID: 31687211 PMCID: PMC6811792 DOI: 10.1155/2019/8284968] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/12/2019] [Accepted: 09/06/2019] [Indexed: 12/30/2022] Open
Abstract
Yam tyrosinase has become an economically essential enzyme due to its ease of purification and abundant availability of yam tubers. However, an efficient biochemical and biophysical characterization of yam tyrosinase has not been reported. In the present study, the interaction of yam (Amorphophallus paeoniifolius) tyrosinase was studied with molecules such as crocin (Crocus sativus), hydroquinone, and kojic acid. Surface plasmon resonance (SPR), fluorescence spectroscopy, and circular dichroism techniques were employed to determine the binding affinities and the changes in secondary and tertiary structures of yam tyrosinase in the presence of four relevant small molecules. Hydroquinone and crocin exhibited very low binding affinities of 0.24 M and 0.0017 M. Due to their apparent weak interactions, competition experiments were used to determine more precisely the binding affinities. Structure-function interrelationships can be correlated in great detail by this study, and the results can be compared with other available tyrosinases.
Collapse
|
11
|
Vanhove E, Vanhove M. Affinity determination of biomolecules: a kinetic model for the analysis of pre-equilibrium titration curves. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:961-966. [DOI: 10.1007/s00249-018-1318-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/13/2018] [Accepted: 07/03/2018] [Indexed: 11/29/2022]
|
12
|
Winzor DJ. Interpretation of results from the competitive Biacore procedure for characterizing immunochemical interactions in solution. J Mol Recognit 2018; 31:e2702. [PMID: 29484741 DOI: 10.1002/jmr.2702] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/08/2017] [Accepted: 01/06/2018] [Indexed: 11/09/2022]
Abstract
Rigorous consideration of the consequences of antibody bivalence in the published competitive kinetic procedure for quantifying the solution characteristics of an antigen-antibody interaction in solution has rendered redundant the practice of substituting the Fab fragment for the antibody to ensure validity of the analysis of results in terms of theory developed for a univalent analyte. Although the quantitative expressions differ for univalent and bivalent analytes, the additional contribution arising from bivalence is likely to be well within the limits of experimental uncertainty in the measured binding constant.
Collapse
Affiliation(s)
- Donald J Winzor
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| |
Collapse
|
13
|
Quantitative monitoring of two simultaneously binding species using Label-Enhanced surface plasmon resonance. Biochem Biophys Res Commun 2018; 497:133-138. [PMID: 29427666 DOI: 10.1016/j.bbrc.2018.02.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 02/05/2018] [Indexed: 11/21/2022]
Abstract
Surface plasmon resonance (SPR) is a well-established method for biomolecular interaction studies. SPR monitors the binding of molecules to a solid surface, embodied as refractive index changes close to the surface. One limitation of conventional SPR is the universal nature of the detection that results in an inability to qualitatively discriminate between different binding species. Furthermore, it is impossible to directly discriminate two species simultaneously binding to different sites on a protein, which limits the utility of SPR, for example, in the study of allosteric binders or bi-specific molecules. It is also impossible in principle to discriminate protein conformation changes from actual binding events. Here we demonstrate how Label-Enhanced SPR can be utilized to discriminate and quantitatively monitor the simultaneous binding of two different species - one dye-labeled and one unlabeled - on a standard, single-wavelength SPR instrument. This new technique increases the versatility of SPR technology by opening up application areas where the usefulness of the approach has previously been limited.
Collapse
|
14
|
Zhang F, Ma J, Watanabe J, Tang J, Liu H, Shen H. Dual Electrophoresis Detection System for Rapid and Sensitive Immunoassays with Nanoparticle Signal Amplification. Sci Rep 2017; 7:42562. [PMID: 28198385 PMCID: PMC5309740 DOI: 10.1038/srep42562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/08/2017] [Indexed: 12/19/2022] Open
Abstract
An electrophoretic technique was combined with an enzyme-linked immunosorbent assay (ELISA) system to achieve a rapid and sensitive immunoassay. A cellulose acetate filter modified with polyelectrolyte multilayer (PEM) was used as a solid substrate for three-dimensional antigen-antibody reactions. A dual electrophoresis process was used to induce directional migration and local condensation of antigens and antibodies at the solid substrate, avoiding the long diffusion times associated with antigen-antibody reactions in conventional ELISAs. The electrophoretic forces drove two steps in the ELISA process, namely the adsorption of antigen, and secondary antibody-labelled polystyrene nanoparticles (NP-Ab). The total time needed for dual electrophoresis-driven detection was just 4 min, nearly 2 h faster than a conventional ELISA system. Moreover, the rapid NP-Ab electrophoresis system simultaneously achieved amplification of the specific signal and a reduction in noise, leading to a more sensitive NP-Ab immunoassay with a limit of detection (LOD) of 130 fM, and wide range of detectable concentrations from 0.13 to 130 pM. These results suggest that the combination of dual electrophoresis detection and NP-Ab signal amplification has great potential for future immunoassay systems.
Collapse
Affiliation(s)
- Fangfang Zhang
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Laboratory of Biomedical Materials, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Junjie Ma
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Laboratory of Biomedical Materials, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Junji Watanabe
- Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Higashinada, Kobe 658-8501, Japan
| | - Jinlong Tang
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Laboratory of Biomedical Materials, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Huiyu Liu
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Laboratory of Biomedical Materials, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Heyun Shen
- Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Laboratory of Biomedical Materials, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| |
Collapse
|
15
|
Bivalent kinetic binding model to surface plasmon resonance studies of antigen-antibody displacement reactions. Anal Biochem 2017; 518:110-125. [DOI: 10.1016/j.ab.2016.11.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 11/09/2016] [Accepted: 11/17/2016] [Indexed: 12/20/2022]
|
16
|
Label-enhanced surface plasmon resonance applied to label-free interaction analysis of small molecules and fragments. Anal Biochem 2016; 510:79-87. [DOI: 10.1016/j.ab.2016.06.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/24/2016] [Accepted: 06/06/2016] [Indexed: 12/30/2022]
|
17
|
Baldacchini C, Bizzarri AR, Cannistraro S. Electron transfer, conduction and biorecognition properties of the redox metalloprotein Azurin assembled onto inorganic substrates. Eur Polym J 2016. [DOI: 10.1016/j.eurpolymj.2016.04.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
|
18
|
Parandoosh Z, Knowles SK, Xiao XY, Zhao C, David GS, Nova MP. Synthesis Coupled to Scintillation Proximity Affinity Screening. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/108705719800300408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The rapidly changing developments in genomics and combinatorial chemistry, generating new drug targets and large numbers of compounds, are beginning to push the limits of screening efficiently. Thus, there is a need for novel tools and strategies to improve high throughput screening. A novel approach is to couple synthesis and screening on a common platform, rather than to increase the rate at which traditional screening methods can be implemented. We have developed a proprietary grafted polymer with special fluorescence characteristics referred to as Electronically Encoded Fluorescence matriX (EFX™), which has the sturdiness and required functionality for direct chemical synthesis as well as suitable surface characteristics for measuring interactions in aqueous solution. This matrix is fabricated into a MicroTube reactor, and each tube is associated with an electronically encoded tag. The system follows a homogenous assay protocol and is based on the scintillation proximity principle. Using solid-phase chemistry, a variety of small molecules may be synthesized onto the EFX. A simple binding assay can be conducted by combining a collection of MicroTubes with any radiolabeled acceptor molecule. The MicroTubes that carry active compounds are selected based on the photon mission or fluorescence characteristics. We validated this approach by evaluating the interactions of biotin with radiolabeled streptavidin.
Collapse
Affiliation(s)
| | - Sue K. Knowles
- IRORI, 11149 North Torrey Pines Road, La Jolla, CA 92037-1031
| | - Xiao-Yi Xiao
- IRORI, 11149 North Torrey Pines Road, La Jolla, CA 92037-1031
| | - Chanfeng Zhao
- IRORI, 11149 North Torrey Pines Road, La Jolla, CA 92037-1031
| | - Gary S. David
- Impact Enterprises, 9477 Poole St., La Jolla, CA 92037
| | - Michael P. Nova
- IRORI, 11149 North Torrey Pines Road, La Jolla, CA 92037-1031
| |
Collapse
|
19
|
Ca-asp bound X-ray structure and inhibition of Bacillus anthracis dihydroorotase (DHOase). Bioorg Med Chem 2016; 24:4536-4543. [PMID: 27499369 DOI: 10.1016/j.bmc.2016.07.055] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/22/2016] [Accepted: 07/25/2016] [Indexed: 01/01/2023]
Abstract
Dihydroorotase (DHOase) is the third enzyme in the de novo pyrimidine synthesis pathway and is responsible for the reversible cyclization of carbamyl-aspartate (Ca-asp) to dihydroorotate (DHO). DHOase is further divided into two classes based on several structural characteristics, one of which is the length of the flexible catalytic loop that interacts with the substrate, Ca-asp, regulating the enzyme activity. Here, we present the crystal structure of Class I Bacillus anthracis DHOase with Ca-asp in the active site, which shows the peptide backbone of glycine in the shorter loop forming the necessary hydrogen bonds with the substrate, in place of the two threonines found in Class II DHOases. Despite the differences in the catalytic loop, the structure confirms that the key interactions between the substrate and active site residues are similar between Class I and Class II DHOase enzymes, which we further validated by mutagenesis studies. B. anthracis DHOase is also a potential antibacterial drug target. In order to identify prospective inhibitors, we performed high-throughput screening against several libraries using a colorimetric enzymatic assay and an orthogonal fluorescence thermal binding assay. Surface plasmon resonance was used for determining binding affinity (KD) and competition analysis with Ca-asp. Our results highlight that the primary difference between Class I and Class II DHOase is the catalytic loop. We also identify several compounds that can potentially be further optimized as potential B. anthracis inhibitors.
Collapse
|
20
|
Origin and prediction of free-solution interaction studies performed label-free. Proc Natl Acad Sci U S A 2016; 113:E1595-604. [PMID: 26960999 DOI: 10.1073/pnas.1515706113] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Interaction/reaction assays have led to significant scientific discoveries in the biochemical, medical, and chemical disciplines. Several fundamental driving forces form the basis of intermolecular and intramolecular interactions in chemical and biochemical systems (London dispersion, hydrogen bonding, hydrophobic, and electrostatic), and in the past three decades the sophistication and power of techniques to interrogate these processes has developed at an unprecedented rate. In particular, label-free methods have flourished, such as NMR, mass spectrometry (MS), surface plasmon resonance (SPR), biolayer interferometry (BLI), and backscattering interferometry (BSI), which can facilitate assays without altering the participating components. The shortcoming of most refractive index (RI)-based label-free methods such as BLI and SPR is the requirement to tether one of the interaction entities to a sensor surface. This is not the case for BSI. Here, our hypothesis is that the signal origin for free-solution, label-free determinations can be attributed to conformation and hydration-induced changes in the solution RI. We propose a model for the free-solution response function (FreeSRF) and show that, when quality bound and unbound structural data are available, FreeSRF correlates well with the experiment (R(2)> 0.99, Spearman rank correlation coefficients >0.9) and the model is predictive within ∼15% of the experimental binding signal. It is also demonstrated that a simple mass-weighted dη/dC response function is the incorrect equation to determine that the change in RI is produced by binding or folding event in free solution.
Collapse
|
21
|
Malkovskiy AV, Wagh DA, Longo FM, Rajadas J. A strategy for analyzing bond strength and interaction kinetics between Pleckstrin homology domains and PI(4,5)P2 phospholipids using force distance spectroscopy and surface plasmon resonance. Analyst 2016; 140:4558-65. [PMID: 26040325 DOI: 10.1039/c5an00498e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phospholipids are important membrane components involved in diverse biological activities ranging from cell signaling to infection by viral particles. A thorough understanding of protein-phospholipid interaction dynamics is thus crucial for deciphering basic cellular processes as well as for targeted drug discovery. For any specific phospholipid-protein binding experiment, various groups have reported different binding constants, which are strongly dependent on applied conditions of interactions. Here, we report a method for accurate determination of the binding affinity and specificity between proteins and phospholipids using a model interaction between PLC-δ1/PH and phosphoinositide phospholipid PtdIns(4,5)P2. We developed an accurate Force Distance Spectroscopy (FDS)-based assay and have attempted to resolve the problem of variation in the observed binding constant by directly measuring the bond force. We confirm the FDS findings of a high bond strength of ∼0.19 ± 0.04 nN by Surface Plasmon Resonance (SPR) data analysis, segregating non-specific interactions, which show a significantly lower K(D) suggesting tight binding.
Collapse
Affiliation(s)
- A V Malkovskiy
- Stanford BioADD Laboratory, Stanford, California 94305, USA.
| | | | | | | |
Collapse
|
22
|
Fjellström O, Akkaya S, Beisel HG, Eriksson PO, Erixon K, Gustafsson D, Jurva U, Kang D, Karis D, Knecht W, Nerme V, Nilsson I, Olsson T, Redzic A, Roth R, Sandmark J, Tigerström A, Öster L. Creating novel activated factor XI inhibitors through fragment based lead generation and structure aided drug design. PLoS One 2015; 10:e0113705. [PMID: 25629509 PMCID: PMC4309560 DOI: 10.1371/journal.pone.0113705] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 10/27/2014] [Indexed: 11/19/2022] Open
Abstract
Activated factor XI (FXIa) inhibitors are anticipated to combine anticoagulant and profibrinolytic effects with a low bleeding risk. This motivated a structure aided fragment based lead generation campaign to create novel FXIa inhibitor leads. A virtual screen, based on docking experiments, was performed to generate a FXIa targeted fragment library for an NMR screen that resulted in the identification of fragments binding in the FXIa S1 binding pocket. The neutral 6-chloro-3,4-dihydro-1H-quinolin-2-one and the weakly basic quinolin-2-amine structures are novel FXIa P1 fragments. The expansion of these fragments towards the FXIa prime side binding sites was aided by solving the X-ray structures of reported FXIa inhibitors that we found to bind in the S1-S1'-S2' FXIa binding pockets. Combining the X-ray structure information from the identified S1 binding 6-chloro-3,4-dihydro-1H-quinolin-2-one fragment and the S1-S1'-S2' binding reference compounds enabled structure guided linking and expansion work to achieve one of the most potent and selective FXIa inhibitors reported to date, compound 13, with a FXIa IC50 of 1.0 nM. The hydrophilicity and large polar surface area of the potent S1-S1'-S2' binding FXIa inhibitors compromised permeability. Initial work to expand the 6-chloro-3,4-dihydro-1H-quinolin-2-one fragment towards the prime side to yield molecules with less hydrophilicity shows promise to afford potent, selective and orally bioavailable compounds.
Collapse
Affiliation(s)
- Ola Fjellström
- Medicinal Chemistry, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
- * E-mail:
| | - Sibel Akkaya
- Medicinal Chemistry, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - Hans-Georg Beisel
- Medicinal Chemistry, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | | | - Karl Erixon
- Medicinal Chemistry, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - David Gustafsson
- Bioscience, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - Ulrik Jurva
- Drug Metabolism and Pharmacokinetics, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - Daiwu Kang
- Bioscience, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - David Karis
- Medicinal Chemistry, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - Wolfgang Knecht
- Bioscience, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - Viveca Nerme
- Bioscience, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - Ingemar Nilsson
- Medicinal Chemistry, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - Thomas Olsson
- Medicinal Chemistry, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - Alma Redzic
- Medicinal Chemistry, Cardiovascular & Metabolic Diseases Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden
| | - Robert Roth
- Discovery Sciences, AstraZeneca R&D, Mölndal, Sweden
| | | | | | - Linda Öster
- Discovery Sciences, AstraZeneca R&D, Mölndal, Sweden
| |
Collapse
|
23
|
Santini S, Bizzarri AR, Yamada T, Beattie CW, Cannistraro S. Binding of azurin to cytochromec551 as investigated by surface plasmon resonance and fluorescence. J Mol Recognit 2014; 27:124-30. [DOI: 10.1002/jmr.2346] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 12/02/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Simona Santini
- Biophysics and Nanoscience Centre, CNISM, Dipartimento DEB; Università della Tuscia; Viterbo Italy
| | - Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, CNISM, Dipartimento DEB; Università della Tuscia; Viterbo Italy
| | - Tohru Yamada
- Department of Surgery, Division of Surgical Oncology; University of Illinois; Chicago IL USA
| | - Craig W. Beattie
- Department of Surgery, Division of Surgical Oncology; University of Illinois; Chicago IL USA
| | - Salvatore Cannistraro
- Biophysics and Nanoscience Centre, CNISM, Dipartimento DEB; Università della Tuscia; Viterbo Italy
| |
Collapse
|
24
|
Label-enhanced surface plasmon resonance: a new concept for improved performance in optical biosensor analysis. SENSORS 2013; 13:15348-63. [PMID: 24217357 PMCID: PMC3871110 DOI: 10.3390/s131115348] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 10/29/2013] [Accepted: 11/02/2013] [Indexed: 11/20/2022]
Abstract
Surface plasmon resonance (SPR) is a well-established optical biosensor technology with many proven applications in the study of molecular interactions as well as in surface and material science. SPR is usually applied in the label-free mode which may be advantageous in cases where the presence of a label may potentially interfere with the studied interactions per se. However, the fundamental challenges of label-free SPR in terms of limited sensitivity and specificity are well known. Here we present a new concept called label-enhanced SPR, which is based on utilizing strongly absorbing dye molecules in combination with the evaluation of the full shape of the SPR curve, whereby the sensitivity as well as the specificity of SPR is significantly improved. The performance of the new label-enhanced SPR method was demonstrated by two simple model assays: a small molecule assay and a DNA hybridization assay. The small molecule assay was used to demonstrate the sensitivity enhancement of the method, and how competitive assays can be used for relative affinity determination. The DNA assay was used to demonstrate the selectivity of the assay, and the capabilities in eliminating noise from bulk liquid composition variations.
Collapse
|
25
|
Day ES, Capili AD, Borysenko CW, Zafari M, Whitty A. Determining the affinity and stoichiometry of interactions between unmodified proteins in solution using Biacore. Anal Biochem 2013; 440:96-107. [PMID: 23711722 DOI: 10.1016/j.ab.2013.05.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 05/03/2013] [Accepted: 05/10/2013] [Indexed: 11/30/2022]
Abstract
We describe a general Biacore method for measuring equilibrium binding affinities and stoichiometries for interactions between unmodified proteins and their unmodified ligands free in solution. Mixtures of protein and ligand are preequilibrated at different ratios in solution and then analyzed by Biacore using a sensor chip surface that detects only unbound analyte. Performing the Biacore analysis under mass transport limited conditions allows the concentration of unbound analyte to be determined from the initial velocity of binding. Plots of initial velocity versus the concentration of the varied binding partner are fitted to a quadratic binding equation to give the affinity and stoichiometry of binding. We demonstrate the method using soluble Her2 extracellular domain binding to monovalent, bivalent, and trivalent forms of an anti-Her2 antibody. The affinity we measured agrees with that obtained from conventional Biacore kinetic analysis, and the stoichiometries for the resulting 1:1, 1:2, and 1:3 complexes were confirmed by gel filtration with in-line light scattering. The method is applicable over an affinity range of approximately 100 pM to 1 μM and is particularly useful when there is concern that covalently modifying one or the other binding partner might affect its binding properties or where multivalency might otherwise complicate a quantitative analysis of binding.
Collapse
|
26
|
Scholten A, Menges B, Juebner M, Rothschild MA, Bender K. A mixed alkanethiol based immunosensor for surface plasmon field-enhanced fluorescence spectroscopy in serum. Analyst 2013; 138:1705-12. [DOI: 10.1039/c3an35657d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
27
|
Surface plasmon resonance, fluorescence, and circular dichroism studies for the characterization of the binding of BACE-1 inhibitors. Anal Bioanal Chem 2012; 405:827-35. [DOI: 10.1007/s00216-012-6312-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Revised: 07/21/2012] [Accepted: 07/30/2012] [Indexed: 10/28/2022]
|
28
|
Zhang X, Lou Z, Wang A, Zhang H. Detection of Wild-Type Hypoxanthine Guanine Phosphoribosyl Transferase of Lymphocytes in Gamma-Irradiated Mice with Surface Plasmon Resonance. ANAL LETT 2012. [DOI: 10.1080/00032719.2012.655677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
29
|
Geschwindner S, Carlsson JF, Knecht W. Application of optical biosensors in small-molecule screening activities. SENSORS 2012; 12:4311-23. [PMID: 22666031 PMCID: PMC3355412 DOI: 10.3390/s120404311] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 03/20/2012] [Accepted: 03/23/2012] [Indexed: 11/16/2022]
Abstract
The last two decades have seen remarkable progress and improvements in optical biosensor systems such that those are currently seen as an important and value-adding component of modern drug screening activities. In particular the introduction of microplate-based biosensor systems holds the promise to match the required throughput without compromising on data quality thus representing a sought-after complement to traditional fluidic systems. This article aims to highlight the application of the two most prominent optical biosensor technologies, namely surface plasmon resonance (SPR) and optical waveguide grating (OWG), in small-molecule screening and will present, review and discuss the advantages and disadvantages of different assay formats on these platforms. A particular focus will be on the specific advantages of the inhibition in solution assay (ISA) format in contrast to traditional direct binding assays (DBA). Furthermore we will discuss different application areas for both fluidic as well as plate-based biosensor systems by considering the individual strength of the platforms.
Collapse
Affiliation(s)
- Stefan Geschwindner
- Discovery Sciences, AstraZeneca R&D Mölndal, 43183 Mölndal, Sweden; E-Mail:
- Authors to whom correspondence should be addressed; E-Mails: (S.G.); (W.K.); Tel.: +46-31-776-2197 (S.G.); Tel.: +46-31-706-5341 (W.K.)
| | - Johan F. Carlsson
- Discovery Sciences, AstraZeneca R&D Mölndal, 43183 Mölndal, Sweden; E-Mail:
| | - Wolfgang Knecht
- CVGI iMed, Bioscience, AstraZeneca R&D Mölndal, 43183 Mölndal, Sweden
- Authors to whom correspondence should be addressed; E-Mails: (S.G.); (W.K.); Tel.: +46-31-776-2197 (S.G.); Tel.: +46-31-706-5341 (W.K.)
| |
Collapse
|
30
|
Solbak SMØ, Wray V, Horvli O, Raae AJ, Flydal MI, Henklein P, Henklein P, Nimtz M, Schubert U, Fossen T. The host-pathogen interaction of human cyclophilin A and HIV-1 Vpr requires specific N-terminal and novel C-terminal domains. BMC STRUCTURAL BIOLOGY 2011; 11:49. [PMID: 22185200 PMCID: PMC3269379 DOI: 10.1186/1472-6807-11-49] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 12/20/2011] [Indexed: 12/26/2022]
Abstract
BACKGROUND Cyclophilin A (CypA) represents a potential key molecule in future antiretroviral therapy since inhibition of CypA suppresses human immunodeficiency virus type 1 (HIV-1) replication. CypA interacts with the virus proteins Capsid (CA) and Vpr, however, the mechanism through which CypA influences HIV-1 infectivity still remains unclear. RESULTS Here the interaction of full-length HIV-1 Vpr with the host cellular factor CypA has been characterized and quantified by surface plasmon resonance spectroscopy. A C-terminal region of Vpr, comprising the 16 residues 75GCRHSRIGVTRQRRAR90, with high binding affinity for CypA has been identified. This region of Vpr does not contain any proline residues but binds much more strongly to CypA than the previously characterized N-terminal binding domain of Vpr, and is thus the first protein binding domain to CypA described involving no proline residues. The fact that the mutant peptide Vpr75-90 R80A binds more weakly to CypA than the wild-type peptide confirms that Arg-80 is a key residue in the C-terminal binding domain. The N- and C-terminal binding regions of full-length Vpr bind cooperatively to CypA and have allowed a model of the complex to be created. The dissociation constant of full-length Vpr to CypA was determined to be approximately 320 nM, indicating that the binding may be stronger than that of the well characterized interaction of HIV-1 CA with CypA. CONCLUSIONS For the first time the interaction of full-length Vpr and CypA has been characterized and quantified. A non-proline-containing 16-residue region of C-terminal Vpr which binds specifically to CypA with similar high affinity as full-length Vpr has been identified. The fact that this is the first non-proline containing binding motif of any protein found to bind to CypA, changes the view on how CypA is able to interact with other proteins. It is interesting to note that several previously reported key functions of HIV-1 Vpr are associated with the identified N- and C-terminal binding domains of the protein to CypA.
Collapse
Affiliation(s)
- Sara M Ø Solbak
- Centre of Pharmacy, University of Bergen, N-5007 Bergen Norway
| | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Frasconi M, Chichiarelli S, Gaucci E, Mazzei F, Grillo C, Chinazzi A, Altieri F. Interaction of ERp57 with calreticulin: Analysis of complex formation and effects of vancomycin. Biophys Chem 2011; 160:46-53. [PMID: 21996511 DOI: 10.1016/j.bpc.2011.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 09/09/2011] [Accepted: 09/09/2011] [Indexed: 10/17/2022]
Abstract
The protein ERp57 (also known as PDIA3) is a widely distributed protein, mainly localized in the endoplasmic reticulum, where it acts as disulfide isomerase, oxidoreductase and chaperone, in concert with the lectins calreticulin (CRT) and calnexin. The ERp57/CRT complex has been detected on the cell surface and previous studies have suggested its involvement in programmed cell death. Although the ERp57-CRT complex has been characterized, little is known about its role in different cellular compartments as well as inhibitors of this interaction. We focused on the kinetic, extent and stability of the ERp57-CRT complex, using the surface plasmon resonance spectroscopy, investigating the possible role as inhibitor of the antibiotic vancomycin. Equilibrium thermodynamic data suggested that vancomycin may hinder the interaction between the two proteins and could interfere with the ERp57 conformational changes that stabilize the complex. Furthermore, by means of confocal microscopy, we evaluated the effect of the in vivo administration of vancomycin on the ERp57/CRT complex on the surface of HeLa cells. The model presented here could be used for the search of other specific inhibitors/interactors of ERp57, which can be extremely helpful to understand the biological pathways where the protein is involved and to modulate its activity.
Collapse
Affiliation(s)
- Marco Frasconi
- Department of Chemistry and Drug Technology, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | | | | | | | | | | | | |
Collapse
|
32
|
Campbell K, Rawn DFK, Niedzwiadek B, Elliott CT. Paralytic shellfish poisoning (PSP) toxin binders for optical biosensor technology: problems and possibilities for the future: a review. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2011; 28:711-25. [PMID: 21623494 PMCID: PMC3118526 DOI: 10.1080/19440049.2010.531198] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
This review examines the developments in optical biosensor technology, which uses the phenomenon of surface plasmon resonance, for the detection of paralytic shellfish poisoning (PSP) toxins. Optical biosensor technology measures the competitive biomolecular interaction of a specific biological recognition element or binder with a target toxin immobilised onto a sensor chip surface against toxin in a sample. Different binders such as receptors and antibodies previously employed in functional and immunological assays have been assessed. Highlighted are the difficulties in detecting this range of low molecular weight toxins, with analogues differing at four chemical substitution sites, using a single binder. The complications that arise with the toxicity factors of each toxin relative to the parent compound, saxitoxin, for the measurement of total toxicity relative to the mouse bioassay are also considered. For antibodies, the cross-reactivity profile does not always correlate to toxic potency, but rather to the toxin structure to which it was produced. Restrictions and availability of the toxins makes alternative chemical strategies for the synthesis of protein conjugate derivatives for antibody production a difficult task. However, when two antibodies with different cross-reactivity profiles are employed, with a toxin chip surface generic to both antibodies, it was demonstrated that the cross-reactivity profile of each could be combined into a single-assay format. Difficulties with receptors for optical biosensor analysis of low molecular weight compounds are discussed, as are the potential of alternative non-antibody-based binders for future assay development in this area.
Collapse
Affiliation(s)
- K Campbell
- Institute of Agri-Food and Land Use, School of Biological Sciences, Queen's University, Belfast, UK.
| | | | | | | |
Collapse
|
33
|
Mavaro A, Abts A, Bakkes PJ, Moll GN, Driessen AJM, Smits SHJ, Schmitt L. Substrate recognition and specificity of the NisB protein, the lantibiotic dehydratase involved in nisin biosynthesis. J Biol Chem 2011; 286:30552-30560. [PMID: 21757717 PMCID: PMC3162415 DOI: 10.1074/jbc.m111.263210] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 07/01/2011] [Indexed: 11/06/2022] Open
Abstract
Nisin is a posttranslationally modified antimicrobial peptide containing the cyclic thioether amino acids lanthionine and methyllanthionine. Although much is known about its antimicrobial activity and mode of action, knowledge about the nisin modification process is still rather limited. The dehydratase NisB is believed to be the initial interaction partner in modification. NisB dehydrates specific serine and threonine residues in prenisin, whereas the cyclase NisC catalyzes the (methyl)lanthionine formation. The fully modified prenisin is exported and the leader peptide is cleaved off by the extracellular protease NisP. Light scattering analysis demonstrated that purified NisB is a dimer in solution. Using size exclusion chromatography and surface plasmon resonance, the interaction of NisB and prenisin, including several of its modified derivatives, was studied. Unmodified prenisin binds to NisB with an affinity of 1.05 ± 0.25 μm, whereas the dehydrated and the fully modified derivatives bind with respective affinities of 0.31 ± 0.07 and 10.5 ± 1.7 μm. The much lower affinity for the fully modified prenisin was related to a >20-fold higher off-rate. For all three peptides the stoichiometry of binding was 1:1. Active nisin, which is the equivalent of fully modified prenisin lacking the leader peptide did not bind to NisB, nor did prenisin in which the highly conserved FNLD box within the leader peptide was mutated to AAAA. Taken together our data indicate that the leader peptide is essential for initial recognition and binding of prenisin to NisB.
Collapse
Affiliation(s)
- Antonino Mavaro
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - André Abts
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Patrick J Bakkes
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Gert N Moll
- BiOMaDe Technology Foundation, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials and the Kluyver Centre for the Genomics of Industrial Microorganisms, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.
| |
Collapse
|
34
|
Sriram R, Yadav AR, Mace CR, Miller BL. Validation of arrayed imaging reflectometry biosensor response for protein-antibody interactions: cross-correlation of theory, experiment, and complementary techniques. Anal Chem 2011; 83:3750-7. [PMID: 21517019 DOI: 10.1021/ac2001302] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the critical steps in the development of an analytical technique is to confirm that its experimental response correlates with predictions derived from the theoretical framework on which it is based. This validates the technique quantitatively and, in the case of a biosensor, facilitates a correlation of the sensor's output signal to the concentration of the analyte being tested. Herein we report studies demonstrating that the quantitative response of arrayed imaging reflectometry (AIR), a highly sensitive label-free biosensing method, is a predictable function of the probe and analyte properties. We first incorporated a standard one-site Langmuir binding model describing probe-analyte interactions at the surface into the theoretical model for thickness-dependent reflectance in AIR. This established a hypothetical correlation between the analyte concentration and the AIR response. Spectroscopic ellipsometry, surface plasmon resonance, and AIR were then used to validate this model for two biomedically important proteins, fibroblast growth factor-2 and vascular endothelial growth factor. While our studies demonstrated that the 1:1 one-site Langmuir model accurately described the observed response of macrospot AIR arrays, either a two-site Langmuir model or a Sips isotherm better described the behavior of AIR microarrays. These studies confirmed the quantitative performance of AIR across a range of probe-analyte affinities. Furthermore, the methodology developed here can be extended to other label-free biosensing platforms, thus facilitating a more accurate and quantitative interpretation of the sensor response.
Collapse
Affiliation(s)
- Rashmi Sriram
- Department of Biomedical Engineering, University of Rochester, Rochester, New York 14642, USA
| | | | | | | |
Collapse
|
35
|
Roy S, Lai H, Zouaoui R, Duffner J, Zhou H, P Jayaraman L, Zhao G, Ganguly T, Kishimoto TK, Venkataraman G. Bioactivity screening of partially desulfated low-molecular-weight heparins: a structure/activity relationship study. Glycobiology 2011; 21:1194-205. [PMID: 21515908 DOI: 10.1093/glycob/cwr053] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A series of size-defined low-molecular-weight heparins were generated by regioselective chemical modifications and profiled for their in vitro and in vivo activities. The compounds displayed reduced anti-coagulant activity, demonstrated varying affinities toward angiogenic growth factors (fibroblast growth factor-2, vascular endothelial growth factor and stromal cell-derived factor-1α), inhibited the P-selectin/P-selectin glycoprotein ligand-1 interaction and, notably, exhibited anti-tumor efficacy in a murine melanoma experimental metastasis model. Our results demonstrate that modulating specific sequences, especially the N-domains (-NS or -NH(2) or -NHCOCH(3)) in these polysaccharide sequences, has a major impact on the participation in a diverse range of biological activities. These results also suggest that the 6-O-sulfates, but not the 2-O-sulfates, critically affect the binding of a desulfated derivative to certain angiogenic proteins as well as its ability to inhibit P-selectin-mediated B16F10 melanoma metastases. Furthermore, N-desulfation followed by N-acetylation regenerates the affinity/inhibition properties to different extents in all the compounds tested in the in vitro assays. This systematic study lays a conceptual foundation for detailed structure function elucidation and will facilitate the rational design of targeted heparan sulfate proteoglycan-based anti-metastatic therapeutic candidates.
Collapse
|
36
|
Kajino M, Fujimoto K, Inouye M. Side-Chain Cross-Linked Short α-Helices That Behave like Original Proteins in Biomacromolecular Interactions. J Am Chem Soc 2010; 133:656-9. [DOI: 10.1021/ja106821x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Masaoki Kajino
- Graduate School of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Kazuhisa Fujimoto
- Graduate School of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Masahiko Inouye
- Graduate School of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| |
Collapse
|
37
|
Comparative surface plasmon resonance and enzyme-linked immunosorbent assay characterisation of a monoclonal antibody with N-acyl homoserine lactones. Anal Chim Acta 2010; 683:113-8. [DOI: 10.1016/j.aca.2010.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 10/04/2010] [Accepted: 10/11/2010] [Indexed: 11/18/2022]
|
38
|
Behar G, Sole V, Defontaine A, Maillasson M, Quemener A, Jacques Y, Tellier C. Evolution of interleukin-15 for higher E. coli expression and solubility. Protein Eng Des Sel 2010; 24:283-90. [DOI: 10.1093/protein/gzq107] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
|
39
|
Shen H, Watanabe J, Akashi M. Polyelectrolyte multilayers-modified membrane filter for rapid immunoassay: protein condensation by centrifugal permeation. Polym J 2010. [DOI: 10.1038/pj.2010.114] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
40
|
Tagaya M, Ikoma T, Hanagata N, Chakarov D, Kasemo B, Tanaka J. Reusable hydroxyapatite nanocrystal sensors for protein adsorption. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2010; 11:045002. [PMID: 27877351 PMCID: PMC5090342 DOI: 10.1088/1468-6996/11/4/045002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2010] [Revised: 09/20/2010] [Accepted: 07/29/2010] [Indexed: 05/12/2023]
Abstract
The repeatability of the adsorption and removal of fibrinogen and fetal bovine serum on hydroxyapatite (HAp) nanocrystal sensors was investigated by Fourier transform infrared (FTIR) spectroscopy and quartz crystal microbalance with dissipation (QCM-D) monitoring technique. The HAp nanocrystals were coated on a gold-coated quartz sensor by electrophoretic deposition. Proteins adsorbed on the HAp sensors were removed by (i) ammonia/hydrogen peroxide mixture (APM), (ii) ultraviolet light (UV), (iii) UV/APM, (iv) APM/UV and (v) sodium dodecyl sulfate (SDS) treatments. FTIR spectra of the reused surfaces revealed that the APM and SDS treatments left peptide fragments or the proteins adsorbed on the surfaces, whereas the other methods successfully removed the proteins. The QCM-D measurements indicated that in the removal treatments, fibrinogen was slowly adsorbed in the first cycle because of the change in surface wettability revealed by contact angle measurements. The SDS treatment was not effective in removing proteins. The APM or UV treatment decreased the frequency shifts for the reused HAp sensors. The UV/APM treatment did not induce the frequency shifts but decreased the dissipation shifts. Therefore, we conclude that the APM/UV treatment is the most useful method for reproducing protein adsorption behavior on HAp sensors.
Collapse
Affiliation(s)
- Motohiro Tagaya
- Biomaterials Center, National Institute for Materials Science, Tsukuba, Ibaraki 305-0047, Japan
- Department of Metallurgy and Ceramics Science, Tokyo Institute of Technology, Tokyo, Tokyo 152-8550, Japan
| | - Toshiyuki Ikoma
- Biomaterials Center, National Institute for Materials Science, Tsukuba, Ibaraki 305-0047, Japan
- Department of Metallurgy and Ceramics Science, Tokyo Institute of Technology, Tokyo, Tokyo 152-8550, Japan
| | - Nobutaka Hanagata
- Biomaterials Center, National Institute for Materials Science, Tsukuba, Ibaraki 305-0047, Japan
| | - Dinko Chakarov
- Department of Applied Physics, Chalmers University of Technology, Göteberg S-41296, Sweden
| | - Bengt Kasemo
- Department of Applied Physics, Chalmers University of Technology, Göteberg S-41296, Sweden
| | - Junzo Tanaka
- Department of Metallurgy and Ceramics Science, Tokyo Institute of Technology, Tokyo, Tokyo 152-8550, Japan
| |
Collapse
|
41
|
Holdgate GA, Anderson M, Edfeldt F, Geschwindner S. Affinity-based, biophysical methods to detect and analyze ligand binding to recombinant proteins: matching high information content with high throughput. J Struct Biol 2010; 172:142-57. [PMID: 20609391 DOI: 10.1016/j.jsb.2010.06.024] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Revised: 06/28/2010] [Accepted: 06/29/2010] [Indexed: 01/21/2023]
Abstract
Affinity-based technologies have become impactful tools to detect, monitor and characterize molecular interactions using recombinant target proteins. This can aid the understanding of biological function by revealing mechanistic details, and even more importantly, enables the identification of new improved ligands that can modulate the biological activity of those targets in a desired fashion. The selection of the appropriate technology is a key step in that process, as each one of the currently available technologies offers a characteristic type of biophysical information about the ligand-binding event. Alongside the indisputable advantages of each of those technologies they naturally display diverse restrictions that are quite frequently related to the target system to be studied but also to the affinity, solubility and molecular size of the ligands. This paper discusses some of the theoretical and experimental aspects of the most common affinity-based methods, what type of information can be gained from each one of those approaches, and what requirements as well as limitations are expected from working with recombinant proteins on those platforms and how those can be optimally addressed.
Collapse
Affiliation(s)
- Geoff A Holdgate
- Lead Generation Sciences, AstraZeneca R&D Alderley Park, Mereside, Alderley Park, United Kingdom
| | | | | | | |
Collapse
|
42
|
Schuck P, Zhao H. The role of mass transport limitation and surface heterogeneity in the biophysical characterization of macromolecular binding processes by SPR biosensing. Methods Mol Biol 2010; 627:15-54. [PMID: 20217612 DOI: 10.1007/978-1-60761-670-2_2] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This chapter presents an introduction to the kinetic analysis of SPR biosensor data for the determination of affinity and kinetic rate constants of biomolecular interactions between an immobilized and a soluble binding partner. The need to be aware of and critically test the assumptions underlying the analysis models is emphasized and the consequences for the experimental design are discussed. The two most common sources of deviation in SPR surface binding kinetics from the ideal pseudo-first-order binding kinetics of bimolecular reactions are mass transport limitations and the heterogeneity of the surface sites. These problems are intrinsic to the use of a biosensor surface for characterizing interactions. The effect of these factors on the observed binding kinetics, and strategies to account for them are reviewed, both in the context of mathematical data analysis, as well as the design of the experiments and controls.
Collapse
Affiliation(s)
- Peter Schuck
- Dynamics of Macromolecular Assembly, Laboratory of Bioengineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health, Bethesda, MD, USA
| | | |
Collapse
|
43
|
Anraku K, Fukuda R, Takamune N, Misumi S, Okamoto Y, Otsuka M, Fujita M. Highly Sensitive Analysis of the Interaction between HIV-1 Gag and Phosphoinositide Derivatives Based on Surface Plasmon Resonance. Biochemistry 2010; 49:5109-16. [DOI: 10.1021/bi9019274] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kensaku Anraku
- Institute of Health Sciences, Kumamoto Health Science University, 325 Izumi-machi, Kumamoto 861-5598, Japan
| | - Ryota Fukuda
- Department of Bioorganic Medicinal Chemistry, Faculty of Life Sciences
| | | | - Shogo Misumi
- Department of Pharmaceutical Biochemistry, Faculty of Life Sciences
| | - Yoshinari Okamoto
- Department of Bioorganic Medicinal Chemistry, Faculty of Life Sciences
| | - Masami Otsuka
- Department of Bioorganic Medicinal Chemistry, Faculty of Life Sciences
| | - Mikako Fujita
- Research Institute for Drug Discovery, School of Pharmacy
| |
Collapse
|
44
|
Maynard JA, Lindquist NC, Sutherland JN, Lesuffleur A, Warrington AE, Rodriguez M, Oh SH. Surface plasmon resonance for high-throughput ligand screening of membrane-bound proteins. Biotechnol J 2009; 4:1542-58. [PMID: 19918786 PMCID: PMC2790208 DOI: 10.1002/biot.200900195] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Technologies based on surface plasmon resonance (SPR) have allowed rapid, label-free characterization of protein-protein and protein-small molecule interactions. SPR has become the gold standard in industrial and academic settings, in which the interaction between a pair of soluble binding partners is characterized in detail or a library of molecules is screened for binding against a single soluble protein. In spite of these successes, SPR is only beginning to be adapted to the needs of membrane-bound proteins which are difficult to study in situ but represent promising targets for drug and biomarker development. Existing technologies, such as BIAcoreTM, have been adapted for membrane protein analysis by building supported lipid layers or capturing lipid vesicles on existing chips. Newer technologies, still in development, will allow membrane proteins to be presented in native or near-native formats. These include SPR nanopore arrays, in which lipid bilayers containing membrane proteins stably span small pores that are addressable from both sides of the bilayer. Here, we discuss current SPR instrumentation and the potential for SPR nanopore arrays to enable quantitative, high-throughput screening of G protein coupled receptor ligands and applications in basic cellular biology.
Collapse
Affiliation(s)
- Jennifer A. Maynard
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, 78705
| | - Nathan C. Lindquist
- Department of Electrical and Computer Engineering, University of Minnesota, Twin Cities, Minneapolis, MN 55455
| | - Jamie N. Sutherland
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, 78705
| | - Antoine Lesuffleur
- Department of Electrical and Computer Engineering, University of Minnesota, Twin Cities, Minneapolis, MN 55455
| | | | - Moses Rodriguez
- Departments of Neurology, Mayo Clinic College of Medicine, Rochester, MN 55905
| | - Sang-Hyun Oh
- Department of Electrical and Computer Engineering, University of Minnesota, Twin Cities, Minneapolis, MN 55455
| |
Collapse
|
45
|
Hoffmann S, Funke SA, Wiesehan K, Moedder S, Glück JM, Feuerstein S, Gerdts M, Mötter J, Willbold D. Competitively selected protein ligands pay their increase in specificity by a decrease in affinity. MOLECULAR BIOSYSTEMS 2009; 6:126-33. [PMID: 20024074 DOI: 10.1039/b910945e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein-ligand interactions characterise and govern the current state and fate of a living cell. The specificity of proteins is mainly determined by the relative affinities to each potential ligand. To investigate the consequences and potentials of ligands with increased specificity in comparison with ligands optimised solely for affinity, it was necessary to identify ligands that are optimised towards specificity instead of a barely optimised affinity to a given target. In the presented example, a modified phage display screening procedure yielded specific ligands for the LckSH3 domain. We found that increased specificity of one of the hereby obtained ligands for LckSH3 is achieved at the cost of a slightly reduced affinity to LckSH3 and a drastically reduced affinity to other SH3 domains. A surface plasmon resonance experiment simulating in vivo-like realistic competitive binding conditions exerted enhanced binding behaviour of the specific ligand under these binding conditions. The experimental data, together with a mathematical model describing the complex experimental situation, and theoretical considerations lead to the conclusion that increased specificity is achieved at the cost of reduced affinity, but after all, it pays if the ligand is applied under realistic, i.e. competitive, conditions.
Collapse
Affiliation(s)
- Silke Hoffmann
- ISB-3, Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Human alpha-defensins inhibit hemolysis mediated by cholesterol-dependent cytolysins. Infect Immun 2009; 77:4028-40. [PMID: 19581399 DOI: 10.1128/iai.00232-09] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Many pathogenic gram-positive bacteria release exotoxins that belong to the family of cholesterol-dependent cytolysins. Here, we report that human alpha-defensins HNP-1 to HNP-3 acted in a concentration-dependent manner to protect human red blood cells from the lytic effects of three of these exotoxins: anthrolysin O (ALO), listeriolysin O, and pneumolysin. HD-5 was very effective against listeriolysin O but less effective against the other toxins. Human alpha-defensins HNP-4 and HD-6 and human beta-defensin-1, -2, and -3 lacked protective ability. HNP-1 required intact disulfide bonds to prevent toxin-mediated hemolysis. A fully linearized analog, in which all six cysteines were replaced by aminobutyric acid (Abu) residues, showed greatly reduced binding and protection. A partially unfolded HNP-1 analog, in which only cysteines 9 and 29 were replaced by Abu residues, showed intact ALO binding but was 10-fold less potent in preventing hemolysis. Surface plasmon resonance assays revealed that HNP-1 to HNP-3 bound all three toxins at multiple sites and also that solution-phase HNP molecules could bind immobilized HNP molecules. Defensin concentrations that inhibited hemolysis by ALO and listeriolysin did not prevent these toxins from binding either to red blood cells or to cholesterol. Others have shown that HNP-1 to HNP-3 inhibit lethal toxin of Bacillus anthracis, toxin B of Clostridium difficile, diphtheria toxin, and exotoxin A of Pseudomonas aeruginosa; however, this is the first time these defensins have been shown to inhibit pore-forming toxins. An "ABCDE mechanism" that can account for the ability of HNP-1 to HNP-3 to inhibit so many different exotoxins is proposed.
Collapse
|
47
|
Doss M, White MR, Tecle T, Gantz D, Crouch EC, Jung G, Ruchala P, Waring AJ, Lehrer RI, Hartshorn KL. Interactions of α-, β-, and θ-Defensins with Influenza A Virus and Surfactant Protein D. THE JOURNAL OF IMMUNOLOGY 2009; 182:7878-87. [DOI: 10.4049/jimmunol.0804049] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
48
|
van Lieshout RML, van Domburg T, Saalmink M, Verbeek R, Wimberger-Friedl R, van Dieijen-Visser MP, Punyadeera C. Three-Dimensional Flow-Through Protein Platform. Anal Chem 2009; 81:5165-71. [DOI: 10.1021/ac801244d] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. M. L. van Lieshout
- Philips Research Europe, High Tech Campus 12, 5656 AE, Eindhoven, The Netherlands and Akademisch Ziekenhuis Maastricht, Maastricht, The Netherlands
| | - T. van Domburg
- Philips Research Europe, High Tech Campus 12, 5656 AE, Eindhoven, The Netherlands and Akademisch Ziekenhuis Maastricht, Maastricht, The Netherlands
| | - M. Saalmink
- Philips Research Europe, High Tech Campus 12, 5656 AE, Eindhoven, The Netherlands and Akademisch Ziekenhuis Maastricht, Maastricht, The Netherlands
| | - R. Verbeek
- Philips Research Europe, High Tech Campus 12, 5656 AE, Eindhoven, The Netherlands and Akademisch Ziekenhuis Maastricht, Maastricht, The Netherlands
| | - R. Wimberger-Friedl
- Philips Research Europe, High Tech Campus 12, 5656 AE, Eindhoven, The Netherlands and Akademisch Ziekenhuis Maastricht, Maastricht, The Netherlands
| | - M. P. van Dieijen-Visser
- Philips Research Europe, High Tech Campus 12, 5656 AE, Eindhoven, The Netherlands and Akademisch Ziekenhuis Maastricht, Maastricht, The Netherlands
| | - C. Punyadeera
- Philips Research Europe, High Tech Campus 12, 5656 AE, Eindhoven, The Netherlands and Akademisch Ziekenhuis Maastricht, Maastricht, The Netherlands
| |
Collapse
|
49
|
Park TJ, Zheng S, Kang YJ, Lee SY. Development of a whole-cell biosensor by cell surface display of a gold-binding polypeptide on the gold surface. FEMS Microbiol Lett 2009; 293:141-7. [DOI: 10.1111/j.1574-6968.2009.01525.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
50
|
Rajamanonmani R, Nkenfou C, Clancy P, Yau YH, Shochat SG, Sukupolvi-Petty S, Schul W, Diamond MS, Vasudevan SG, Lescar J. On a mouse monoclonal antibody that neutralizes all four dengue virus serotypes. J Gen Virol 2009; 90:799-809. [PMID: 19264660 DOI: 10.1099/vir.0.006874-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The flavivirus envelope glycoprotein (E) is responsible for viral attachment and entry by membrane fusion. Its ectodomain is the primary target of the humoral immune response. In particular, the C-terminal Ig-like domain III of E, which is exposed at the surface of the viral particle, forms an attractive antigen for raising protective monoclonal antibodies (mAb). 9F12, a mouse mAb raised against a dengue virus (DENV) serotype 2 recombinant domain III, cross-reacts with corresponding domains from the other three DENV serotypes and also with West Nile virus. mAb 9F12 binds with nanomolar affinity to a conserved epitope that maps to the viral surface comprising residues 305, 307, 310 and 330 of the E protein. mAb 9F12 neutralizes all four DENV serotypes in plaque reduction assays. We expressed a single-chain Fv from 9F12 that retains the binding activity of the parent mAb. Adsorption and fusion inhibition assays indicate that mAb 9F12 prevents early steps of viral entry. Its virus inhibition activity and broad cross-reactivity makes mAb 9F12 a suitable candidate for optimization and humanization into a therapeutic antibody to treat severe infections by dengue.
Collapse
Affiliation(s)
- Ravikumar Rajamanonmani
- Program in Emerging Infectious Diseases, Duke-NUS, Graduate Medical School, Singapore.,School of Biological Sciences, Nanyang Technological University, Biopolis, Singapore
| | - Celine Nkenfou
- Novartis Institute for Tropical Diseases, Biopolis, Singapore
| | - Paula Clancy
- Department of Biochemistry and Molecular Biology, James Cook University, Australia
| | - Yin Hoe Yau
- School of Biological Sciences, Nanyang Technological University, Biopolis, Singapore
| | | | - Soila Sukupolvi-Petty
- Departments of Medicine, Molecular Microbiology, Pathology and Immunology, Washington University School of Medicine, St Louis, USA
| | - Wouter Schul
- Novartis Institute for Tropical Diseases, Biopolis, Singapore
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology and Immunology, Washington University School of Medicine, St Louis, USA
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS, Graduate Medical School, Singapore.,Department of Biochemistry and Molecular Biology, James Cook University, Australia
| | - Julien Lescar
- AFMB CNRS UMR6098, Marseille, France.,School of Biological Sciences, Nanyang Technological University, Biopolis, Singapore
| |
Collapse
|