1
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De Silva M, Dunn RC. Electric field-enhanced backscatter interferometry detection for capillary electrophoresis. Sci Rep 2024; 14:2110. [PMID: 38267528 PMCID: PMC10808210 DOI: 10.1038/s41598-024-52621-3] [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: 12/18/2023] [Accepted: 01/22/2024] [Indexed: 01/26/2024] Open
Abstract
Backscatter interferometry (BSI) is a refractive index (RI) detection method that is easily integrated with capillary electrophoresis (CE) and is capable of detecting species ranging from inorganic ions to proteins without additional labels or contrast agents. The BSI signal changes linearly with the square of the separation voltage which has been used to quantify sample injection, but has not been explored as a potential signal enhancement mechanism in CE. Here we develop a mathematical model that predicts a signal enhancement at high field strengths, where the BSI signal is dominated by the voltage dependent mechanism. This is confirmed in both simulation and experiment, which show that the analyte peak area grows linearly with separation voltage at high field strengths. This effect can be exploited by adjusting the background electrolyte (BGE) to increase the conductivity difference between the BGE and analyte zones, which is shown to improve BSI performance. We also show that this approach has utility in small bore capillaries where larger separation fields can be applied before excess Joule heating degrades the separation. Unlike other optical detection methods that generally degrade as the optical pathlength is reduced, the BSI signal-to-noise can improve in small bore capillaries as the larger separation fields enhance the signal.
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Affiliation(s)
- Miyuru De Silva
- Department of Chemistry, University of Kansas, Lawrence, KS, 66047, USA
| | - Robert C Dunn
- Department of Chemistry, University of Kansas, Lawrence, KS, 66047, USA.
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2
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Ray M, Sayeed A, Ganshert M, Saha A. Direct Binding Methods to Measure Receptor-Ligand Interactions. J Phys Chem B 2024; 128:3-19. [PMID: 38134048 DOI: 10.1021/acs.jpcb.3c05041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
G-protein-coupled receptors (GPCRs) contribute to numerous physiological processes via complex network mechanisms. While indirect signaling assays (Ca2+ mobilization, cAMP production, and GTPγS binding) have been useful in identifying and characterizing downstream signaling mechanisms of GPCRs, these methods lack measurements of direct binding affinities, kinetics, binding specificity, and selectivity that are important parameters in GPCR drug discovery. In comparison to existing direct methods that use radio- or fluorescent labels, label-free techniques can closely emulate the native interactions around binding partners. Surface plasmon resonance (SPR) is a label-free technique that utilizes the refractive index (RI) property and is applied widely in quantitative GPCR-ligand binding kinetics measurement including small molecules screening. However, purified GPCRs are further embedded in a synthetic lipid environment which is immobilized through different tags to the SPR sensor surface, resulting in a non-native environment. Here, we introduced a methodology that also uses the RI property to measure binding interactions in a label-free, immobilization-free arrangement. The free-solution technique is successfully applied in quantifying the interaction of bioactive lipids to cognate lipid GPCRs, which is not purified but rather present in near-native conditions, i.e., in milieu of other cytoplasmic lipids and proteins. To further consider the wide applicability of these free-solution approaches in biomolecular interaction research, additional applications on a variety of receptor-ligand pairs are imperative.
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Affiliation(s)
- Manisha Ray
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Road, Chicago, Illinois 60660, United States
| | - Aryana Sayeed
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Road, Chicago, Illinois 60660, United States
| | - Madeline Ganshert
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Road, Chicago, Illinois 60660, United States
| | - Arjun Saha
- Department of Chemistry and Biochemistry, University of Wisconsin, Milwaukee Chemistry Bldg, 144, 3210 N Cramer Street, Milwaukee, Wisconsin 53211, United States
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3
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Russell Lewis B, Lawrence R, Hammerschmid D, Reading E. Structural mass spectrometry approaches to understand multidrug efflux systems. Essays Biochem 2022; 67:255-267. [PMID: 36504255 PMCID: PMC10070475 DOI: 10.1042/ebc20220190] [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: 10/27/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022]
Abstract
Multidrug efflux pumps are ubiquitous across both eukaryotes and prokaryotes, and have major implications in antimicrobial and multidrug resistance. They reside within cellular membranes and have proven difficult to study owing to their hydrophobic character and relationship with their compositionally complex lipid environment. Advances in structural mass spectrometry (MS) techniques have made it possible to study these systems to elucidate critical information on their structure-function relationships. For example, MS techniques can report on protein structural dynamics, stoichiometry, connectivity, solvent accessibility, and binding interactions with ligands, lipids, and other proteins. This information proving powerful when used in conjunction with complementary structural biology methods and molecular dynamics (MD) simulations. In the present review, aimed at those not experts in MS techniques, we report on the current uses of MS in studying multidrug efflux systems, practical considerations to consider, and the future direction of the field. In the first section, we highlight the importance of studying multidrug efflux proteins, and introduce a range of different MS techniques and explain what information they yield. In the second section, we review recent studies that have utilised MS techniques to study and characterise a range of different multidrug efflux systems.
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Affiliation(s)
- Benjamin Russell Lewis
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Ryan Lawrence
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Dietmar Hammerschmid
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Eamonn Reading
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
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4
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Zhang P, Zhou X, Jiang J, Kolay J, Wang R, Ma G, Wan Z, Wang S. In Situ Analysis of Membrane-Protein Binding Kinetics and Cell-Surface Adhesion Using Plasmonic Scattering Microscopy. Angew Chem Int Ed Engl 2022; 61:e202209469. [PMID: 35922374 PMCID: PMC9561081 DOI: 10.1002/anie.202209469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Indexed: 11/09/2022]
Abstract
Surface plasmon resonance microscopy (SPRM) is an excellent platform for in situ studying cell-substrate interactions. However, SPRM suffers from poor spatial resolution and small field of view. Herein, we demonstrate plasmonic scattering microscopy (PSM) by adding a dry objective on a popular prism-coupled surface plasmon resonance (SPR) system. PSM not only retains SPRM's high sensitivity and real-time analysis capability, but also provides ≈7 times higher spatial resolution and ≈70 times larger field of view than the typical SPRM, thus providing more details about membrane protein response to ligand binding on over 100 cells simultaneously. In addition, PSM allows quantifying the target movements in the axial direction with a high spatial resolution, thus allowing mapping adhesion spring constants for quantitatively describing the mechanical properties of the cell-substrate contacts. This work may offer a powerful and cost-effective strategy for upgrading current SPR products.
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Affiliation(s)
- Pengfei Zhang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ 85287, USA
| | - Xinyu Zhou
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ 85287, USA
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Jiapei Jiang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ 85287, USA
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Jayeeta Kolay
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ 85287, USA
| | - Rui Wang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ 85287, USA
| | - Guangzhong Ma
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ 85287, USA
| | - Zijian Wan
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ 85287, USA
- School of Electrical, Energy and Computer Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Shaopeng Wang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ 85287, USA
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
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5
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Kussrow A, Kammer MN, Massion PP, Webster R, Bornhop DJ. Assay Performance of a Label-Free, Solution-Phase CYFRA 21-1 Determination. ACS OMEGA 2022; 7:31916-31923. [PMID: 36120008 PMCID: PMC9476196 DOI: 10.1021/acsomega.2c02763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
CYFRA 21.1, a cytokeratin fragment of epithelial origin, has long been a valuable blood-based biomarker. As with most biomarkers, the clinical diagnostic value of CYFRA 21.1 is dependent on the quantitative performance of the assay. Looking toward translation, it is shown here that a free-solution assay (FSA) coupled with a compensated interferometric reader (CIR) can be used to provide excellent analytical performance in quantifying CYFRA 21.1 in patient serum samples. This report focuses on the analytical performance of the high-sensitivity (hs)-CYFRA 21.1 assay in the context of quantifying the biomarker in two indeterminate pulmonary nodule (IPN) patient cohorts totaling 179 patients. Each of the ten assay calibrations consisted of 6 concentrations, each run as 7 replicates (e.g., 10 × 6 × 7 data points) and were performed on two different instruments by two different operators. Coefficients of variation (CVs) for the hs-CYFRA 21.1 analytical figures of merit, limit of quantification (LOQ) of ca. 60 pg/mL, B max, initial slope, probe-target binding affinity, and reproducibility of quantifying an unknown were found to range from 2.5 to 8.3%. Our results demonstrate the excellent performance of our FSA-CIR hs-CYFRA 21-1 assay and a proof of concept for potentially redefining the performance characteristics of this existing important candidate biomarker.
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Affiliation(s)
- Amanda
K. Kussrow
- Department
of Chemistry and The Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Michael N. Kammer
- Division
of Allergy, Pulmonary and Critical Care Medicine and Vanderbilt-Ingram
Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Pierre P. Massion
- Division
of Allergy, Pulmonary and Critical Care Medicine and Vanderbilt-Ingram
Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Rebekah Webster
- Department
of Chemistry and The Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Darryl J. Bornhop
- Department
of Chemistry and The Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
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6
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Khiar-Fernández N, Zian D, Vázquez-Villa H, Martínez RF, Escobar-Peña A, Foronda-Sainz R, Ray M, Puigdomenech-Poch M, Cincilla G, Sánchez-Martínez M, Kihara Y, Chun J, López-Vales R, López-Rodríguez ML, Ortega-Gutiérrez S. Novel Antagonist of the Type 2 Lysophosphatidic Acid Receptor (LPA 2), UCM-14216, Ameliorates Spinal Cord Injury in Mice. J Med Chem 2022; 65:10956-10974. [PMID: 35948083 PMCID: PMC9421655 DOI: 10.1021/acs.jmedchem.2c00046] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Spinal cord injuries (SCIs) irreversibly disrupt spinal
connectivity,
leading to permanent neurological disabilities. Current medical treatments
for reducing the secondary damage that follows the initial injury
are limited to surgical decompression and anti-inflammatory drugs,
so there is a pressing need for new therapeutic strategies. Inhibition
of the type 2 lysophosphatidic acid receptor (LPA2) has
recently emerged as a new potential pharmacological approach to decrease
SCI-associated damage. Toward validating this receptor as a target
in SCI, we have developed a new series of LPA2 antagonists,
among which compound 54 (UCM-14216) stands out as a potent
and selective LPA2 receptor antagonist (Emax = 90%, IC50 = 1.9 μM, KD = 1.3 nM; inactive at LPA1,3–6 receptors).
This compound shows efficacy in an in vivo mouse model of SCI in an
LPA2-dependent manner, confirming the potential of LPA2 inhibition for providing a new alternative for treating SCI.
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Affiliation(s)
- Nora Khiar-Fernández
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - Debora Zian
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - Henar Vázquez-Villa
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - R Fernando Martínez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - Andrea Escobar-Peña
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - Román Foronda-Sainz
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - Manisha Ray
- Translational Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Maria Puigdomenech-Poch
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Institut de Neurociències, Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Universitat Autònoma de Barcelona, Bellaterra, BarcelonaE-08193, Spain
| | - Giovanni Cincilla
- Molomics, Barcelona Science Park, Baldiri i Reixac 4-8, Barcelona E-08028, Spain
| | - Melchor Sánchez-Martínez
- Molomics, Barcelona Science Park, Baldiri i Reixac 4-8, Barcelona E-08028, Spain.,Burua Scientific, Sant Pere de Ribes E-08810, Spain
| | - Yasuyuki Kihara
- Translational Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jerold Chun
- Translational Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Rubèn López-Vales
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Institut de Neurociències, Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Universitat Autònoma de Barcelona, Bellaterra, BarcelonaE-08193, Spain
| | - María L López-Rodríguez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - Silvia Ortega-Gutiérrez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain
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7
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Zhang P, Zhou X, Jiang J, Kolay J, Wang R, Ma G, Wan Z, Wang S. In Situ Analysis of Membrane‐Protein Binding Kinetics and Cell–Surface Adhesion Using Plasmonic Scattering Microscopy. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202209469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Pengfei Zhang
- Arizona State University Biodesign Center for Bioelectronics and Biosensors 1001 S. McAllister Ave. 85287 Tempe UNITED STATES
| | - Xinyu Zhou
- Arizona State University Biodesign Institute Biodesign Center for Bioelectronics and Biosensors UNITED STATES
| | - Jiapei Jiang
- Arizona State University Biodesign Institute Biodesign Center for Bioelectronics and Biosensors UNITED STATES
| | - Jayeeta Kolay
- Arizona State University Biodesign Institute Biodesign Center for Bioelectronics and Biosensors UNITED STATES
| | - Rui Wang
- Arizona State University Biodesign Institute Biodesign Center for Bioelectronics and Biosensors UNITED STATES
| | - Guangzhong Ma
- Arizona State University Biodesign Institute Biodesign Center for Bioelectronics and Biosensors UNITED STATES
| | - Zijian Wan
- Arizona State University Biodesign Institute Biodesign Center for Bioelectronics and Biosensors UNITED STATES
| | - Shaopeng Wang
- Arizona State University Biodesign Institute Center for Bioelectronics and Biosensors 1001 S McAllister AvenuePO BOX 875801 85248 Tempe UNITED STATES
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8
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Zhu H, Chen Z, Chen Y, Zhu JJ. Affinities and Kinetics Detection of Protein-Small Molecule Interactions with a Monolayer MoS 2 -Based Optical Imaging Platform. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2202622. [PMID: 35726050 DOI: 10.1002/smll.202202622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Quantifying the binding kinetics and affinities of protein-small molecule interactions is critical for biomarker validation, drug discovery, and deep understanding of various biological processes at the molecular-scale. Novel approaches are demanded as most common label-free techniques are mass-sensitive, which are not suitable for the detection of small molecule interactions. Here, an optical imaging platform is developed to measure the binding kinetics of both protein-small molecules and protein-ions based on monolayer MoS2 , an ultra-thin 2D material whose optical absorption is extremely sensitive to charge. A model is established to calibrate the optical response due to the charged analyte binding and it is applied to quantify the interactions between abl1 kinase and different small-molecule inhibitors. Such a presented method is capable of distinguishing different inhibitors binding to a wild or mutated kinase, which provides guidance for drug evaluation and drug mechanism exploration. The binding kinetics of calcium ions to calmodulin is also measured, further broadening the application field of the method. In addition, the imaging capability allows mapping the local binding kinetics of the molecular interactions with a high resolution, which reveals visible spatial variability and offers a promising tool for studying heterogeneous local interfacial interactions.
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Affiliation(s)
- Hao Zhu
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, P. R. China
| | - Zixuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, P. R. China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
- Shenzhen Research Institute of Nanjing University, Shenzhen, 518000, P. R. China
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9
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Stein JAC, Ianeselli A, Braun D. Kinetic Microscale Thermophoresis for Simultaneous Measurement of Binding Affinity and Kinetics. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Julian A. C. Stein
- Systems Biophysics Department of Physics Ludwig-Maximilians-Universität München and Center for NanoScience Amalienstasse 54 80799 München Germany
| | - Alan Ianeselli
- Systems Biophysics Department of Physics Ludwig-Maximilians-Universität München and Center for NanoScience Amalienstasse 54 80799 München Germany
| | - Dieter Braun
- Systems Biophysics Department of Physics Ludwig-Maximilians-Universität München and Center for NanoScience Amalienstasse 54 80799 München Germany
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10
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Stein JAC, Ianeselli A, Braun D. Kinetic Microscale Thermophoresis for Simultaneous Measurement of Binding Affinity and Kinetics. Angew Chem Int Ed Engl 2021; 60:13988-13995. [PMID: 33793031 PMCID: PMC8251828 DOI: 10.1002/anie.202101261] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/16/2021] [Indexed: 12/11/2022]
Abstract
Microscale thermophoresis (MST) is a versatile technique to measure binding affinities of binder-ligand systems, based on the directional movement of molecules in a temperature gradient. We extended MST to measure binding kinetics as well as binding affinity in a single experiment by increasing the thermal dissipation of the sample. The kinetic relaxation fingerprints were derived from the fluorescence changes during thermodynamic re-equilibration of the sample after local heating. Using this method, we measured DNA hybridization on-rates and off-rates in the range 104 -106 m-1 s-1 and 10-4 -10-1 s-1 , respectively. We observed the expected exponential dependence of the DNA hybridization off-rates on salt concentration, strand length and inverse temperature. The measured on-rates showed a linear dependence on salt concentration and weak dependence on strand length and temperature. For biomolecular interactions with large enthalpic contributions, the kinetic MST technique offers a robust, cost-effective and immobilization-free determination of kinetic rates and binding affinity simultaneously, even in crowded solutions.
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Affiliation(s)
- Julian A C Stein
- Systems Biophysics, Department of Physics, Ludwig-Maximilians-Universität München and Center for NanoScience, Amalienstasse 54, 80799, München, Germany
| | - Alan Ianeselli
- Systems Biophysics, Department of Physics, Ludwig-Maximilians-Universität München and Center for NanoScience, Amalienstasse 54, 80799, München, Germany
| | - Dieter Braun
- Systems Biophysics, Department of Physics, Ludwig-Maximilians-Universität München and Center for NanoScience, Amalienstasse 54, 80799, München, Germany
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11
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Liang R, Ma G, Jing W, Wang Y, Yang Y, Tao N, Wang S. Charge-Sensitive Optical Detection of Small Molecule Binding Kinetics in Normal Ionic Strength Buffer. ACS Sens 2021; 6:364-370. [PMID: 32842724 DOI: 10.1021/acssensors.0c01063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Most label-free detection technologies detect the masses of molecules, and their sensitivities thus decrease with molecular weight, making it challenging to detect small molecules. To address this need, we have developed a charge-sensitive optical detection (CSOD) technique, which detects the charge rather than the mass of a molecule with an optical fiber. However, the effective charge of a molecule decreases with the buffer ionic strength. For this reason, the previous CSOD works with diluted buffers, which could affect the measured molecular binding kinetics. Here, we show a technique capable of detecting molecular binding kinetics in normal ionic strength buffers. An H-shaped sample well was developed to increase the current density at the sensing area to compensate the signal loss due to ionic screening at normal ionic strength buffer, while keeping the current density low at the electrodes to minimize the electrode reaction. In addition, agarose gels were used to cover the electrodes to prevent electrode reaction generated bubbles from entering the sensing area. With this new design, we have measured the binding kinetics between G-protein-coupled receptors (GPCRs) and their small molecule ligands in normal buffer. We found that the affinities measured in normal buffer are stronger than those measured in diluted buffer, likely due to the stronger electrostatic repulsion force between the same charged ligands and receptors in the diluted buffer.
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12
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Jiang H, Cole PA. N-Terminal Protein Labeling with N-Hydroxysuccinimide Esters and Microscale Thermophoresis Measurements of Protein-Protein Interactions Using Labeled Protein. Curr Protoc 2021; 1:e14. [PMID: 33484499 PMCID: PMC7839251 DOI: 10.1002/cpz1.14] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein labeling strategies have been explored for decades to study protein structure, function, and regulation. Fluorescent labeling of a protein enables the study of protein-protein interactions through biophysical methods such as microscale thermophoresis (MST). MST measures the directed motion of a fluorescently labeled protein in response to microscopic temperature gradients, and the protein's thermal mobility can be used to determine binding affinity. However, the stoichiometry and site specificity of fluorescent labeling are hard to control, and heterogeneous labeling can generate inaccuracies in binding measurements. Here, we describe an easy-to-apply protocol for high-stoichiometric, site-specific labeling of a protein at its N-terminus with N-hydroxysuccinimide (NHS) esters as a means to measure protein-protein interaction affinity by MST. This protocol includes guidelines for NHS ester labeling, fluorescent-labeled protein purification, and MST measurement using a labeled protein. As an example of the entire workflow, we additionally provide a protocol for labeling a ubiquitin E3 enzyme and testing ubiquitin E2-E3 enzyme binding affinity. These methods are highly adaptable and can be extended for protein interaction studies in various biological and biochemical circumstances. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Labeling a protein of interest at its N-terminus with NHS esters through stepwise reaction Alternate Protocol: Labeling a protein of interest at its N-terminus with NHS esters through a one-pot reaction Basic Protocol 2: Purifying the N-terminal fluorescent-labeled protein and determining its concentration and labeling efficiency Basic Protocol 3: Using MST to determine the binding affinity of an N-terminal fluorescent-labeled protein to a binding partner. Basic Protocol 4: NHS ester labeling of ubiquitin E3 ligase WWP2 and measurement of the binding affinity between WWP2 and an E2 conjugating enzyme by the MST binding assay.
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Affiliation(s)
- Hanjie Jiang
- Division of Genetics, Brigham and Women’s Hospital,
Department of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard
Medical School, Boston, Massachusetts 02115, United States
- Department of Pharmacology and Molecular Sciences, Johns
Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Philip A. Cole
- Division of Genetics, Brigham and Women’s Hospital,
Department of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard
Medical School, Boston, Massachusetts 02115, United States
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13
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Crump GM, Zhou J, Mashayekh S, Grimes CL. Revisiting peptidoglycan sensing: interactions with host immunity and beyond. Chem Commun (Camb) 2020; 56:13313-13322. [PMID: 33057506 PMCID: PMC7642115 DOI: 10.1039/d0cc02605k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The interaction between host immunity and bacterial cells plays a pivotal role in a variety of human diseases. The bacterial cell wall component peptidoglycan (PG) is known to stimulate an immune response, which makes PG a distinctive recognition element for unveiling these complicated molecular interactions. Pattern recognition receptor (PRR) proteins are among the critical components of this system that initially recognize molecular patterns associated with microorganisms such as bacteria and fungi. These molecular patterns are mostly embedded in the bacterial or fungal cell wall structure and can be released and presented to the immune system in various situations. Nonetheless, detailed knowledge of this recognition is limited due to the diversity among the PG polymer and its fragments; the subsequent responses by multiple hosts add more complexity. Here, we discuss how our understanding of the role and molecular mechanisms of the well-studied PRR, the NOD-like receptors (NLRs), in the human immune system has evolved in recent years. We highlight the instances of other classes of proteins with similar behavior in the recognition of PG that have been identified in other microorganisms such as yeasts. These proteins are particularly interesting because a network of cellular interactions exists between human host cells, bacteria and yeast as a part of the normal human flora. To support our understanding of these interactions, we provide insight into the chemist's toolbox of peptidoglycan probes that aid in the investigations of the behaviors of these proteins and other biological contexts relevant to the sensing and recognition of peptidoglycan. The importance of these interactions in human health for the development of biomarkers and biotherapy is highlighted.
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Affiliation(s)
- Geneva Maddison Crump
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
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14
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Gabellieri E, Capotosti F, Molette J, Sreenivasachary N, Mueller A, Berndt M, Schieferstein H, Juergens T, Varisco Y, Oden F, Schmitt-Willich H, Hickman D, Dinkelborg L, Stephens A, Pfeifer A, Kroth H. Discovery of 2-(4-(2-fluoroethoxy)piperidin-1-yl)-9-methyl-9H-pyrrolo[2,3-b:4,5-c']dipyridine ([18F]PI-2014) as PET tracer for the detection of pathological aggregated tau in Alzheimer's disease and other tauopathies. Eur J Med Chem 2020; 204:112615. [PMID: 32771872 DOI: 10.1016/j.ejmech.2020.112615] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/04/2020] [Accepted: 06/21/2020] [Indexed: 12/29/2022]
Abstract
The compound screening was initiated with a direct staining assay to identify compounds binding to Tau aggregates and not Abeta plaques using human brain sections derived from late stage Alzheimer's disease donors. The binding of Tau aggregate selective compounds was then quantitatively assessed with human brain derived paired helical filaments utilizing the label-free Back Scattering Interferometry assay. In vivo biodistribution experiments of selected fluorine-18 labeled compounds were performed in mice to assess brain uptake, brain washout, and defluorination. Compound 11 emerged as the most promising candidate, displaying high in vitro binding affinity and selectivity to neurofibrillary tangles. Fluorine-18 labeled compound 11 showed high brain uptake and rapid washout from the mouse brain with no observed bone uptake. Furthermore, compound 11 was able to detect Tau aggregates in tauopathy brain sections from corticobasal degeneration, progressive supranuclear palsy, and Pick's disease donors. Thus, 2-(4-(2-fluoroethoxy)piperidin-1-yl)-9-methyl-9H-pyrrolo[2,3-b:4,5-c']dipyridine (PI-2014, compound 11) was selected for characterization in a first-in-human study.
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Affiliation(s)
| | | | - Jerome Molette
- AC Immune SA, EPFL Innovation Park, Building B, 1015, Lausanne, Switzerland
| | | | - Andre Mueller
- Life Molecular Imaging GmbH, Tegeler Strasse 6-7, 13353, Berlin, Germany
| | - Mathias Berndt
- Life Molecular Imaging GmbH, Tegeler Strasse 6-7, 13353, Berlin, Germany
| | - Hanno Schieferstein
- Formerly Piramal Imaging GmbH, Tegeler Strasse 6-7, 13353, Berlin, Germany; Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Tanja Juergens
- AC Immune SA, EPFL Innovation Park, Building B, 1015, Lausanne, Switzerland
| | - Yvan Varisco
- AC Immune SA, EPFL Innovation Park, Building B, 1015, Lausanne, Switzerland
| | - Felix Oden
- Life Molecular Imaging GmbH, Tegeler Strasse 6-7, 13353, Berlin, Germany
| | | | - David Hickman
- AC Immune SA, EPFL Innovation Park, Building B, 1015, Lausanne, Switzerland
| | - Ludger Dinkelborg
- Life Molecular Imaging GmbH, Tegeler Strasse 6-7, 13353, Berlin, Germany
| | - Andrew Stephens
- Life Molecular Imaging GmbH, Tegeler Strasse 6-7, 13353, Berlin, Germany
| | - Andrea Pfeifer
- AC Immune SA, EPFL Innovation Park, Building B, 1015, Lausanne, Switzerland
| | - Heiko Kroth
- AC Immune SA, EPFL Innovation Park, Building B, 1015, Lausanne, Switzerland.
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15
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Ray M, Nagai K, Kihara Y, Kussrow A, Kammer MN, Frantz A, Bornhop DJ, Chun J. Unlabeled lysophosphatidic acid receptor binding in free solution as determined by a compensated interferometric reader. J Lipid Res 2020; 61:1244-1251. [PMID: 32513900 PMCID: PMC7397748 DOI: 10.1194/jlr.d120000880] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/01/2020] [Indexed: 12/11/2022] Open
Abstract
Native interactions between lysophospholipids (LPs) and their cognate LP receptors are difficult to measure because of lipophilicity and/or the adhesive properties of lipids, which contribute to high levels of nonspecific binding in cell membrane preparations. Here, we report development of a free-solution assay (FSA) where label-free LPs bind to their cognate G protein-coupled receptors (GPCRs), combined with a recently reported compensated interferometric reader (CIR) to quantify native binding interactions between receptors and ligands. As a test case, the binding parameters between lysophosphatidic acid (LPA) receptor 1 (LPA1; one of six cognate LPA GPCRs) and LPA were determined. FSA-CIR detected specific binding through the simultaneous real-time comparison of bound versus unbound species by measuring the change in the solution dipole moment produced by binding-induced conformational and/or hydration changes. FSA-CIR identified KD values for chemically distinct LPA species binding to human LPA1 and required only a few nanograms of protein: 1-oleoyl (18:1; KD = 2.08 ± 1.32 nM), 1-linoleoyl (18:2; KD = 2.83 ± 1.64 nM), 1-arachidonoyl (20:4; KD = 2.59 ± 0.481 nM), and 1-palmitoyl (16:0; KD = 1.69 ± 0.1 nM) LPA. These KD values compared favorably to those obtained using the previous generation back-scattering interferometry system, a chip-based technique with low-throughput and temperature sensitivity. In conclusion, FSA-CIR offers a new increased-throughput approach to assess quantitatively label-free lipid ligand-receptor binding, including nonactivating antagonist binding, under near-native conditions.
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Affiliation(s)
- Manisha Ray
- Degenerative Disease Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Kazufumi Nagai
- Degenerative Disease Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Yasuyuki Kihara
- Degenerative Disease Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Amanda Kussrow
- Department of Chemistry and Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37235
| | - Michael N Kammer
- Department of Chemistry and Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37235
| | - Aaron Frantz
- Degenerative Disease Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037.,Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA 92037
| | - Darryl J Bornhop
- Department of Chemistry and Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37235
| | - Jerold Chun
- Degenerative Disease Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
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16
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Rohrbach A, Meyer T, Stelzer EHK, Kress H. Measuring Stepwise Binding of Thermally Fluctuating Particles to Cell Membranes without Fluorescence. Biophys J 2020; 118:1850-1860. [PMID: 32229315 DOI: 10.1016/j.bpj.2020.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 02/28/2020] [Accepted: 03/03/2020] [Indexed: 01/07/2023] Open
Abstract
Thermal motions enable a particle to probe the optimal interaction state when binding to a cell membrane. However, especially on the scale of microseconds and nanometers, position and orientation fluctuations are difficult to observe with common measurement technologies. Here, we show that it is possible to detect single binding events of immunoglobulin-G-coated polystyrene beads, which are held in an optical trap near the cell membrane of a macrophage. Changes in the spatial and temporal thermal fluctuations of the particle were measured interferometrically, and no fluorophore labeling was required. We demonstrate both by Brownian dynamic simulations and by experiments that sequential stepwise increases in the force constant of the bond between a bead and a cell of typically 20 pN/μm are clearly detectable. In addition, this technique provides estimates about binding rates and diffusion constants of membrane receptors. The simple approach of thermal noise tracking points out new strategies in understanding interactions between cells and particles, which are relevant for a large variety of processes, including phagocytosis, drug delivery, and the effects of small microplastics and particulates on cells.
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Affiliation(s)
- Alexander Rohrbach
- Laboratory for Bio- and Nano-Photonics, University of Freiburg, Department of Microsystems Engineering, Freiburg, Germany; Centre for integrative Biological Signalling Studies, Freiburg, Germany.
| | - Tim Meyer
- Laboratory for Bio- and Nano-Photonics, University of Freiburg, Department of Microsystems Engineering, Freiburg, Germany
| | - Ernst H K Stelzer
- Laboratory for Physical Biology, Buchmann Institute for Molecular Life Sciences, University of Frankfurt, Frankfurt Main, Germany
| | - Holger Kress
- Department of Physics, University of Bayreuth, Bayreuth, Germany.
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17
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Wang Y, Guo W, Yang Q, Su B. Electrochemiluminescence Self-Interference Spectroscopy with Vertical Nanoscale Resolution. J Am Chem Soc 2020; 142:1222-1226. [DOI: 10.1021/jacs.9b12833] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yafeng Wang
- Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Weiliang Guo
- Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Qian Yang
- Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Bin Su
- Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
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18
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Wang Y, Yang Q, Su B. Spatially resolved electrochemistry enabled by thin-film optical interference. Chem Commun (Camb) 2020; 56:12359-12362. [DOI: 10.1039/d0cc05265e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electrochemical reactions occurring on the local surface can be spatially resolved by successive interferometric imaging of the nanochannel membrane coated electrode.
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Affiliation(s)
- Yafeng Wang
- Institute of Analytical Chemistry
- Department of Chemistry
- Zhejiang University
- Hangzhou 310058
- China
| | - Qian Yang
- Institute of Analytical Chemistry
- Department of Chemistry
- Zhejiang University
- Hangzhou 310058
- China
| | - Bin Su
- Institute of Analytical Chemistry
- Department of Chemistry
- Zhejiang University
- Hangzhou 310058
- China
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19
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González-Gil I, Zian D, Vázquez-Villa H, Hernández-Torres G, Martínez RF, Khiar-Fernández N, Rivera R, Kihara Y, Devesa I, Mathivanan S, Del Valle CR, Zambrana-Infantes E, Puigdomenech M, Cincilla G, Sanchez-Martinez M, Rodríguez de Fonseca F, Ferrer-Montiel AV, Chun J, López-Vales R, López-Rodríguez ML, Ortega-Gutiérrez S. A Novel Agonist of the Type 1 Lysophosphatidic Acid Receptor (LPA 1), UCM-05194, Shows Efficacy in Neuropathic Pain Amelioration. J Med Chem 2019; 63:2372-2390. [PMID: 31790581 DOI: 10.1021/acs.jmedchem.9b01287] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Neuropathic pain (NP) is a complex chronic pain state with a prevalence of almost 10% in the general population. Pharmacological options for NP are limited and weakly effective, so there is a need to develop more efficacious NP attenuating drugs. Activation of the type 1 lysophosphatidic acid (LPA1) receptor is a crucial factor in the initiation of NP. Hence, it is conceivable that a functional antagonism strategy could lead to NP mitigation. Here we describe a new series of LPA1 agonists among which derivative (S)-17 (UCM-05194) stands out as the most potent and selective LPA1 receptor agonist described so far (Emax = 118%, EC50 = 0.24 μM, KD = 19.6 nM; inactive at autotaxin and LPA2-6 receptors). This compound induces characteristic LPA1-mediated cellular effects and prompts the internalization of the receptor leading to its functional inactivation in primary sensory neurons and to an efficacious attenuation of the pain perception in an in vivo model of NP.
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Affiliation(s)
- Inés González-Gil
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Debora Zian
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Henar Vázquez-Villa
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Gloria Hernández-Torres
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - R Fernando Martínez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Nora Khiar-Fernández
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Richard Rivera
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yasuyuki Kihara
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Isabel Devesa
- IDiBE, Universidad Miguel Hernández de Elche, E-03202 Alicante, Spain
| | | | - Cristina Rosell Del Valle
- Instituto de Investigación Biomédica de Málaga, UGC Salud Mental, Universidad de Málaga, Hospital Universitario Regional de Málaga, E-29010 Málaga, Spain
| | - Emma Zambrana-Infantes
- Instituto de Investigación Biomédica de Málaga, UGC Salud Mental, Universidad de Málaga, Hospital Universitario Regional de Málaga, E-29010 Málaga, Spain
| | - María Puigdomenech
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Institut de Neurociències, Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Universitat Autònoma de Barcelona, Bellaterra, E-08193 Barcelona, Spain
| | - Giovanni Cincilla
- Molomics, Barcelona Science Park, Baldiri i Reixac 4-8, E-08028 Barcelona, Spain
| | | | - Fernando Rodríguez de Fonseca
- Instituto de Investigación Biomédica de Málaga, UGC Salud Mental, Universidad de Málaga, Hospital Universitario Regional de Málaga, E-29010 Málaga, Spain.,Departamento de Psicobiología, Facultad de Psicología, Universidad Complutense de Madrid, Pozuelo de Alarcón, E-28223 Madrid, Spain
| | | | - Jerold Chun
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Rubén López-Vales
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Institut de Neurociències, Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Universitat Autònoma de Barcelona, Bellaterra, E-08193 Barcelona, Spain
| | - María L López-Rodríguez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Silvia Ortega-Gutiérrez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
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20
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Jordan LR, Blauch ME, Baxter AM, Cawley JL, Wittenberg NJ. Influence of brain gangliosides on the formation and properties of supported lipid bilayers. Colloids Surf B Biointerfaces 2019; 183:110442. [DOI: 10.1016/j.colsurfb.2019.110442] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 07/30/2019] [Accepted: 08/15/2019] [Indexed: 01/04/2023]
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21
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Korshunova AV, Lopanskaia IN, Gudimchuk NB. Modern Approaches to Analysis of Protein–Ligand Interactions. Biophysics (Nagoya-shi) 2019. [DOI: 10.1134/s0006350919040079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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22
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Ma G, Shan X, Wang S, Tao N. Quantifying Ligand-Protein Binding Kinetics with Self-Assembled Nano-oscillators. Anal Chem 2019; 91:14149-14156. [PMID: 31593433 DOI: 10.1021/acs.analchem.9b04195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Measuring ligand-protein interactions is critical for unveiling molecular-scale biological processes in living systems and for screening drugs. Various detection technologies have been developed, but quantifying the binding kinetics of small molecules to the proteins remains challenging because the sensitivities of the mainstream technologies decrease with the size of the ligand. Here, we report a method to measure and quantify the binding kinetics of both large and small molecules with self-assembled nano-oscillators, each consisting of a nanoparticle tethered to a surface via long polymer molecules. By applying an oscillating electric field normal to the surface, the nanoparticle oscillates, and the oscillation amplitude is proportional to the number of charges on the nano-oscillator. Upon the binding of ligands onto the nano-oscillator, the oscillation amplitude will change. Using a plasmonic imaging approach, the oscillation amplitude is measured with subnanometer precision, allowing us to accurately quantify the binding kinetics of ligands, including small molecules, to their protein receptors. This work demonstrates the capability of nano-oscillators as an useful tool for measuring the binding kinetics of both large and small molecules.
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Affiliation(s)
- Guangzhong Ma
- Biodesign Center for Bioelectronics and Biosensors , Arizona State University , Tempe , Arizona 85287 , United States.,School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
| | - Xiaonan Shan
- Biodesign Center for Bioelectronics and Biosensors , Arizona State University , Tempe , Arizona 85287 , United States.,School of Electrical, Computer and Energy Engineering , Arizona State University , Tempe , Arizona 85287 , United States
| | - Shaopeng Wang
- Biodesign Center for Bioelectronics and Biosensors , Arizona State University , Tempe , Arizona 85287 , United States
| | - Nongjian Tao
- Biodesign Center for Bioelectronics and Biosensors , Arizona State University , Tempe , Arizona 85287 , United States.,School of Electrical, Computer and Energy Engineering , Arizona State University , Tempe , Arizona 85287 , United States
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23
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Kammer MN, Kussrow A, Gandhi I, Drabek R, Batchelor RH, Jackson GW, Bornhop DJ. Quantification of Opioids in Urine Using an Aptamer-Based Free-Solution Assay. Anal Chem 2019; 91:10582-10588. [PMID: 31314489 DOI: 10.1021/acs.analchem.9b01638] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The opioid epidemic continues in the United States. Many have been impacted by this epidemic, including neonates who exhibit Neonatal Abstinence Syndrome (NAS). Opioid diagnosis and NAS can be negatively impacted by limited testing options outside the hospital, due to poor assay performance, false-negatives, rapid drug clearance rates, and difficulty in obtaining enough specimen for testing. Here we report a small volume urine assay for oxycodone, hydrocodone, fentanyl, noroxycodone, norhydrocodone, and norfentanyl with excellent LODs and LOQs. The free-solution assay (FSA), coupled with high affinity DNA aptamer probes and a compensated interferometric reader (CIR), represents a potential solution for quantifying opioids rapidly, at high sensitivity, and noninvasively on small sample volumes. The mix-and-read test is 5- to 275-fold and 50- to 1250-fold more sensitive than LC-MS/MS and immunoassays, respectively. Using FSA, oxycodone, hydrocodone, fentanyl, and their urinary metabolites were quantified using 10 μL of urine at 28-81 pg/mL, with >95% specificity and excellent accuracy in ∼1 h. The assay sensitivity, small sample size requirement, and speed could enable opioid screening, particularly for neonates, and points to the potential for pharmacokinetic tracking.
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Affiliation(s)
- Michael N Kammer
- Department of Chemistry and Vanderbilt Institute of Chemical Biology , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Amanda Kussrow
- Department of Chemistry and Vanderbilt Institute of Chemical Biology , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Ilavarasi Gandhi
- Base Pair Biotechnologies, Inc. , Pearland , Texas 77584 , United States
| | - Rafal Drabek
- Base Pair Biotechnologies, Inc. , Pearland , Texas 77584 , United States
| | - Robert H Batchelor
- Base Pair Biotechnologies, Inc. , Pearland , Texas 77584 , United States
| | - George W Jackson
- Base Pair Biotechnologies, Inc. , Pearland , Texas 77584 , United States
| | - Darryl J Bornhop
- Department of Chemistry and Vanderbilt Institute of Chemical Biology , Vanderbilt University , Nashville , Tennessee 37235 , United States
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24
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Mizuno H, Kihara Y, Kussrow A, Chen A, Ray M, Rivera R, Bornhop DJ, Chun J. Lysophospholipid G protein-coupled receptor binding parameters as determined by backscattering interferometry. J Lipid Res 2019; 60:212-217. [PMID: 30463988 PMCID: PMC6314248 DOI: 10.1194/jlr.d089938] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/13/2018] [Indexed: 12/23/2022] Open
Abstract
Lysophosphatidic acid (LPA) activates cognate G protein-coupled receptors (GPCRs) to initiate biological signaling cascades. Lysophospholipid (LP) receptor binding properties remain incompletely assessed because of difficulties with ligand lipophilicity and lipid "stickiness." These inherent attributes produce high levels of nonspecific binding within cell-membrane preparations used to assess GPCRs, as has been shown in classical binding assays using radiolabeled ligands, making accurate measurements of lipid binding kinetics difficult to achieve. Backscattering interferometry (BSI) is an optical technology that measures molecular binding interactions by reporting changes in the refractive index of a solution after binding events. Here, we report the use of BSI to assess LPA1 for its ability to bind to naturally occurring lipids and a synthetic LPA1 antagonist (ONO-9780307), under both primary- and competition-binding conditions. Assessment of 12 different lipids demonstrated that the known LP ligand, 1-oleoyl-LPA, as well as an endocannabinoid metabolite, anandamide phosphate, are specific ligands for LPA1, whereas other LPs tested were not. Newly determined dissociation constants (Kd values) for orthosteric lipid ligands approximated 10-9 M, substantially lower (i.e., with higher affinity) than measured Kd values in classical binding or cell-based assays. These results demonstrate that BSI may have particular utility in assessing binding interactions between lipid receptors and their lipid ligands and could provide new screening approaches for lipid receptor identification and drug discovery.
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Affiliation(s)
- Hirotaka Mizuno
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
- Discovery Technology Research Laboratories, Ono Pharmaceutical Co., Ltd., Osaka 618-8585, Japan
| | - Yasuyuki Kihara
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Amanda Kussrow
- Department of Chemistry Vanderbilt University, Nashville, TN 37235
- Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37235
| | - Allison Chen
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Manisha Ray
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Richard Rivera
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Darryl J Bornhop
- Department of Chemistry Vanderbilt University, Nashville, TN 37235
- Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37235
| | - Jerold Chun
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
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25
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Ma G, Syu GD, Shan X, Henson B, Wang S, Desai PJ, Zhu H, Tao N. Measuring Ligand Binding Kinetics to Membrane Proteins Using Virion Nano-oscillators. J Am Chem Soc 2018; 140:11495-11501. [PMID: 30114365 DOI: 10.1021/jacs.8b07461] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Membrane proteins play vital roles in cellular signaling processes and serve as the most popular drug targets. A key task in studying cellular functions and developing drugs is to measure the binding kinetics of ligands with the membrane proteins. However, this has been a long-standing challenge because one must perform the measurement in a membrane environment to maintain the conformations and functions of the membrane proteins. Here, we report a new method to measure ligand binding kinetics to membrane proteins using self-assembled virion oscillators. Virions of human herpesvirus were used to display human G-protein-coupled receptors (GPCRs) on their viral envelopes. Each virion was then attached to a gold-coated glass surface via a flexible polymer to form an oscillator and driven into oscillation with an alternating electric field. By tracking changes in the oscillation amplitude in real-time with subnanometer precision, the binding kinetics between ligands and GPCRs was measured. We anticipate that this new label-free detection technology can be readily applied to measure small or large ligand binding to any type of membrane proteins and thus contribute to the understanding of cellular functions and screening of drugs.
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Affiliation(s)
- Guangzhong Ma
- Biodesign Center for Bioelectronics and Biosensors , Arizona State University , Tempe , Arizona 85287 , United States
| | - Guan-Da Syu
- Viral Oncology Program , The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins , Baltimore , Maryland 21231 , United States.,Department of Pharmacology and Molecular Sciences , Johns Hopkins School of Medicine , Baltimore , Maryland 21205 , United States.,Center for High-Throughput Biology , Johns Hopkins School of Medicine , Baltimore , Maryland 21205 , United States
| | - Xiaonan Shan
- Biodesign Center for Bioelectronics and Biosensors , Arizona State University , Tempe , Arizona 85287 , United States.,School of Electrical, Computer and Energy Engineering , Arizona State University , Tempe , Arizona 85287 , United States
| | - Brandon Henson
- Viral Oncology Program , The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins , Baltimore , Maryland 21231 , United States
| | - Shaopeng Wang
- Biodesign Center for Bioelectronics and Biosensors , Arizona State University , Tempe , Arizona 85287 , United States
| | - Prashant J Desai
- Viral Oncology Program , The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins , Baltimore , Maryland 21231 , United States
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences , Johns Hopkins School of Medicine , Baltimore , Maryland 21205 , United States.,Center for High-Throughput Biology , Johns Hopkins School of Medicine , Baltimore , Maryland 21205 , United States
| | - Nongjian Tao
- Biodesign Center for Bioelectronics and Biosensors , Arizona State University , Tempe , Arizona 85287 , United States.,School of Electrical, Computer and Energy Engineering , Arizona State University , Tempe , Arizona 85287 , United States
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Kammer MN, Kussrow AK, Olmsted IR, Bornhop DJ. A Highly Compensated Interferometer for Biochemical Analysis. ACS Sens 2018; 3:1546-1552. [PMID: 29984991 DOI: 10.1021/acssensors.8b00361] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Here we report an improved interferometric sensing approach that facilitates high sensitivity nanovolume refractive index (RI) measurements and molecular interaction assays without a temperature controller. The compensated backscattering interferometer (CBSI) is based on a helium-neon (He-Ne) laser, a microfluidic chip, and a CCD array. The CBSI enables simultaneous differential RI measurements within nanoliter volumes, at a compensation level of ca. 5 × 10-8 RIU in the presence of large thermal perturbations (8 °C). This level of d n/d T compensation is enabled by elongating the laser beam along the central axis of the microfluidic channel and measuring the difference in positional shift of interference patterns from two adjacent regions of the channel. By separating two solutions by an air gap or oil droplet, CBSI can discriminate the difference in RI for the sample and reference at a detection limit of 7 × 10-7 RIU in the absence of electronic filtering. At this level of ΔRI sensitivity, it is possible to perform label-free, free-solution biochemical assays at the 10s of nM level without the typical high-resolution temperature control needed in conventional interferometers. Here we illustrate the effective use of CBSI by quantifying the binding affinities for mannose-concanavalin A and Ca2+-recoverin interactions.
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Affiliation(s)
- Michael N. Kammer
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Amanda K. Kussrow
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ian R. Olmsted
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Darryl J. Bornhop
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
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27
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Dunn RC. Wavelength Modulated Back-Scatter Interferometry for Universal, On-Column Refractive Index Detection in Picoliter Volumes. Anal Chem 2018; 90:6789-6795. [PMID: 29762009 DOI: 10.1021/acs.analchem.8b00771] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Wavelength-modulated back scatter interferometry (M-BSI) is shown to improve the detection metrics for refractive index (RI) sensing in microseparations. In M-BSI, the output of a tunable diode laser is focused into the detection zone of a separation channel as the excitation wavelength is rapidly modulated. This spatially modulates the observed interference pattern, which is measured in the backscattered direction. Phase-sensitive detection using a split photodiode detector aligned on one fringe of the interference pattern is used to monitor RI changes as analytes are separated. Using sucrose standards, we report a detection limit of 700 μg/L in a 75 μm i.d. capillary at the 3σ level, corresponding to a detection volume of 90 pL. To validate the approach for electrophoretic separations, Na+ and Li+ were separated and detected with M-BSI and indirect-UV absorbance on the same capillary. A 4 mg/L NaCl and LiCl mixture leads to comparable separation efficiencies in the two detection schemes, with better signal-to-noise in the M-BSI detection, but less baseline stability. The latter arises in part from Joule heating, which influences RI measurements through the thermo-optic properties of the run buffer. To reduce this effect, a 25 μm i.d. capillary combined with active temperature control was used to detect the separation of sucrose, glucose, and lactose with M-BSI. The lack of suitable UV chromophores makes these analytes challenging to detect directly in ultrasmall volumes. Using a 55 mM NaOH run buffer, M-BSI is shown to detect the separation of a mixture of 174 mg/L sucrose, 97 mg/L glucose, and 172 mg/L lactose in a 15 pL detection volume. The universal on-column detection in ultrasmall volumes adds new capabilities for microanalysis platforms, while potentially reducing the footprint and costs of these systems.
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Affiliation(s)
- Robert C Dunn
- Ralph N. Adams Institute for Bioanalytical Chemistry , University of Kansas , 2030 Becker Drive , Lawrence , Kansas 66047 , United States
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28
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Park A, Uddin O, Li Y, Masri R, Keller A. Pain After Spinal Cord Injury Is Associated With Abnormal Presynaptic Inhibition in the Posterior Nucleus of the Thalamus. THE JOURNAL OF PAIN 2018; 19:727.e1-727.e15. [PMID: 29481977 DOI: 10.1016/j.jpain.2018.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 01/29/2018] [Accepted: 02/12/2018] [Indexed: 01/21/2023]
Abstract
Pain after spinal cord injury (SCI-Pain) is one of the most debilitating sequelae of spinal cord injury, characterized as relentless, excruciating pain that is largely refractory to treatments. Although it is generally agreed that SCI-Pain results from maladaptive plasticity in the pain processing pathway that includes the spinothalamic tract and somatosensory thalamus, the specific mechanisms underlying the development and maintenance of such pain are yet unclear. However, accumulating evidence suggests that SCI-Pain may be causally related to abnormal thalamic disinhibition, leading to hyperactivity in the posterior thalamic nucleus (PO), a higher-order nucleus involved in somatosensory and pain processing. We previously described several presynaptic mechanisms by which activity in PO is regulated, including the regulation of GABAergic as well as glutamatergic release by presynaptic metabotropic gamma-aminobutyric acid (GABAB) receptors. Using acute slices from a mouse model of SCI-Pain, we tested whether such mechanisms are affected by SCI-Pain. We reveal 2 abnormal changes in presynaptic signaling in the SCI-Pain condition. The substantial tonic activation of presynaptic GABAB receptors on GABAergic projections to PO-characteristic of normal animals-was absent in mice with SCI-Pain. Also absent in mice with SCI-Pain was the normal presynaptic regulation of glutamatergic projections to the PO by GABAB receptors. The loss of these regulatory presynaptic mechanisms in SCI-Pain may be an element of maladaptive plasticity leading to PO hyperexcitability and behavioral pain, and may suggest targets for development of novel treatments. PERSPECTIVE This report presents synaptic mechanisms that may underlie the development and maintenance of SCI-Pain. Because of the difficulty in treating SCI-Pain, a better understanding of the underlying neurobiological mechanisms is critical, and may allow development of better treatment modalities.
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Affiliation(s)
- Anthony Park
- Program in Neuroscience and Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Olivia Uddin
- Program in Neuroscience and Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Ying Li
- Program in Neuroscience and Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Radi Masri
- Program in Neuroscience and Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland; Department of Endodontics, Periodontics and Prosthodontics, University of Maryland Baltimore, School of Dentistry, Baltimore, Maryland
| | - Asaf Keller
- Program in Neuroscience and Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland.
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29
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Zhang F, Jing W, Hunt A, Yu H, Yang Y, Wang S, Chen HY, Tao N. Label-Free Quantification of Small-Molecule Binding to Membrane Proteins on Single Cells by Tracking Nanometer-Scale Cellular Membrane Deformation. ACS NANO 2018; 12:2056-2064. [PMID: 29397682 PMCID: PMC5851003 DOI: 10.1021/acsnano.8b00235] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Measuring molecular binding to membrane proteins is critical for understanding cellular functions, validating biomarkers, and screening drugs. Despite the importance, developing such a capability has been a difficult challenge, especially for small-molecule binding to membrane proteins in their native cellular environment. Here we show that the binding of both large and small molecules to membrane proteins can be quantified on single cells by trapping single cells with a microfluidic device and detecting binding-induced cellular membrane deformation on the nanometer scale with label-free optical imaging. We develop a thermodynamic model to describe the binding-induced membrane deformation, validate the model by examining the dependence of membrane deformation on cell stiffness, membrane protein expression level, and binding affinity, and study four major types of membrane proteins, including glycoproteins, ion channels, G-protein coupled receptors, and tyrosine kinase receptors. The single-cell detection capability reveals the importance of local membrane environment on molecular binding and variability in the binding kinetics of different cell lines and heterogeneity of different cells within the same cell line.
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Affiliation(s)
- Fenni Zhang
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- School of Electrical Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, USA
| | - Wenwen Jing
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Ashley Hunt
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Hui Yu
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Yunze Yang
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- School of Electrical Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, USA
| | - Shaopeng Wang
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Nongjian Tao
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
- School of Electrical Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, USA
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30
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Wimberg H, Janssen-Bienhold U, Koch KW. Control of the Nucleotide Cycle in Photoreceptor Cell Extracts by Retinal Degeneration Protein 3. Front Mol Neurosci 2018. [PMID: 29515371 PMCID: PMC5826319 DOI: 10.3389/fnmol.2018.00052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Retinal degeneration protein 3 (RD3) is crucial for photoreceptor cell survival and linked to Leber Congenital Amaurosis type 12 (LCA12), a hereditary retinal disease in humans. RD3 inhibits photoreceptor guanylate cyclases GC-E and GC-F and is involved in transport of GCs from the inner to the outer segments. Otherwise, its role in photoreceptor physiology is poorly understood. Here, we describe a new function of RD3. Purified RD3 evoked an increase in guanylate kinase activity, an enzyme that is involved in the nucleotide cycle in photoreceptors. We demonstrate a direct interaction between guanylate kinase and RD3 using back-scattering interferometry and show by immunohistochemistry of mouse retina sections that RD3 and guanylate kinase co-localize in photoreceptor inner segments and to a lesser extent in the outer plexiform layer. Our findings point toward a more complex function of RD3 in photoreceptors. The RD3 – guanylate kinase interaction may also play a role in other cellular systems, while the GC – RD3 interaction is exclusive to photoreceptors.
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Affiliation(s)
- Hanna Wimberg
- Biochemistry, Department of Neuroscience, University of Oldenburg, Oldenburg, Germany
| | - Ulrike Janssen-Bienhold
- Department of Neuroscience, Visual Neuroscience, University of Oldenburg, Oldenburg, Germany
| | - Karl-Wilhelm Koch
- Biochemistry, Department of Neuroscience, University of Oldenburg, Oldenburg, Germany
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31
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Kammer MN, Kussrow AK, Bornhop DJ. Longitudinal pixel averaging for improved compensation in backscattering interferometry. OPTICS LETTERS 2018; 43:482-485. [PMID: 29400820 DOI: 10.1364/ol.43.000482] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/19/2017] [Indexed: 06/07/2023]
Abstract
Longitudinal averaging of the interference pattern in a compensated backscattering interferometer provides improved compensation for temperature induced refractive index perturbations. Fringe pattern likeness between two discrete detection regions of an off-the-shelf microfluidic chip illuminated by an inexpensive diode laser scales with interrogation length. Averaging the intensity distribution along a 2.75 mm length of the channel results in a 750-fold reduction in sensitivity to temperature and a baseline noise level of 3×10-8 refractive index units (RIU). These observations enable nanoliter-volume interferometric measurements at a level of 10-7 RIU in the presence of a 2°C temperature variation without the need for temperature control.
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32
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Retzlaff CL, Kussrow A, Schorkopf T, Saetear P, Bornhop DJ, Hardaway JA, Sturgeon SM, Wright J, Blakely RD. Metallo-β-lactamase Domain-Containing Protein 1 (MBLAC1) Is a Specific, High-Affinity Target for the Glutamate Transporter Inducer Ceftriaxone. ACS Chem Neurosci 2017; 8:2132-2138. [PMID: 28783953 DOI: 10.1021/acschemneuro.7b00232] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Ceftriaxone, a β-lactam antibiotic, has been reported to act independently of its antimicrobial actions to normalize perturbed central nervous system glutamate levels, principally by elevating expression of glial glutamate transporters. Identification of a specific, high-affinity target for ceftriaxone could significantly impact therapeutic development for multiple brain disorders, ranging from neurodegenerative disorders to addiction. Recently, we identified a glial-expressed Caenorhabditis elegans gene, swip-10, that encodes a metallo-β-lactamase domain-containing protein, and limits glutamate-dependent changes in dopamine neuron excitability. Bioinformatic analyses identified MBLAC1 as the likely mammalian orthologue of swip-10. Using cyanogen bromide immobilized ceftriaxone for affinity capture experiments and backscattering interferometry to monitor MBLAC1 binding of unmodified ceftriaxone, we obtained evidence for specific, high affinity (KD = 2.2 μM) binding of ceftriaxone to MBLAC1. We discuss our findings with respect to MBLAC1 as a potentially exclusive, high-affinity binding partner of ceftriaxone in the CNS, and the path forward in the development of novel, MBLAC1-based therapeutics.
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Affiliation(s)
- Cassandra L. Retzlaff
- Department
of Biomedical Science and Brain Institute, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, Florida 33458, United States
| | | | | | | | | | | | | | | | - Randy D. Blakely
- Department
of Biomedical Science and Brain Institute, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, Florida 33458, United States
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33
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Schaefer AK, Melnyk JE, Baksh MM, Lazor KM, Finn MG, Grimes CL. Membrane Association Dictates Ligand Specificity for the Innate Immune Receptor NOD2. ACS Chem Biol 2017; 12:2216-2224. [PMID: 28708377 PMCID: PMC5569645 DOI: 10.1021/acschembio.7b00469] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
The
human gut must regulate its immune response to resident and
pathogenic bacteria, numbering in the trillions. The peptidoglycan
component of the bacterial cell wall is a dense and rigid structure
that consists of polymeric carbohydrates and highly cross-linked peptides
which offers protection from the host and surrounding environment.
Nucleotide-binding oligomerization domain-containing protein 2 (NOD2),
a human membrane-associated innate immune receptor found in the gut
epithelium and mutated in an estimated 30% of Crohn’s disease
patients, binds to peptidoglycan fragments and initiates an immune
response. Using a combination of chemical synthesis, advanced analytical
assays, and protein biochemistry, we tested the binding of a variety
of synthetic peptidoglycan fragments to wild-type (WT)-NOD2. Only
when the protein was presented in the native membrane did binding
measurements correlate with a NOD2-dependent nuclear factor kappa-light-chain-enhancer
of activated B cells (NF-κB) response, supporting the hypothesis
that the native-membrane environment confers ligand specificity to
the NOD2 receptor for NF-κB signaling. While N-acetyl-muramyl dipeptide (MDP) has been thought to be the minimal
peptidoglycan fragment necessary to activate a NOD2-dependent immune
response, we found that fragments with and without the dipeptide moiety
are capable of binding and activating a NOD2-dependent
NF-κB response, suggesting that the carbohydrate moiety of the
peptidoglycan fragments is the minimal functional epitope. This work
highlights the necessity of studying NOD2-ligand binding in systems
that resemble the receptor’s natural environment, as the cellular
membrane and/or NOD2 interacting partners appear to play a crucial
role in ligand binding and in triggering an innate immune response.
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Affiliation(s)
- Amy K. Schaefer
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - James E. Melnyk
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Michael M. Baksh
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Klare M. Lazor
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - M. G. Finn
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Catherine Leimkuhler Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Department of Biological Sciences, University of Delaware, Newark, Delaware 19716, United States
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Kubicek-Sutherland JZ, Vu DM, Mendez HM, Jakhar S, Mukundan H. Detection of Lipid and Amphiphilic Biomarkers for Disease Diagnostics. BIOSENSORS-BASEL 2017; 7:bios7030025. [PMID: 28677660 PMCID: PMC5618031 DOI: 10.3390/bios7030025] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/27/2017] [Accepted: 06/30/2017] [Indexed: 12/24/2022]
Abstract
Rapid diagnosis is crucial to effectively treating any disease. Biological markers, or biomarkers, have been widely used to diagnose a variety of infectious and non-infectious diseases. The detection of biomarkers in patient samples can also provide valuable information regarding progression and prognosis. Interestingly, many such biomarkers are composed of lipids, and are amphiphilic in biochemistry, which leads them to be often sequestered by host carriers. Such sequestration enhances the difficulty of developing sensitive and accurate sensors for these targets. Many of the physiologically relevant molecules involved in pathogenesis and disease are indeed amphiphilic. This chemical property is likely essential for their biological function, but also makes them challenging to detect and quantify in vitro. In order to understand pathogenesis and disease progression while developing effective diagnostics, it is important to account for the biochemistry of lipid and amphiphilic biomarkers when creating novel techniques for the quantitative measurement of these targets. Here, we review techniques and methods used to detect lipid and amphiphilic biomarkers associated with disease, as well as their feasibility for use as diagnostic targets, highlighting the significance of their biochemical properties in the design and execution of laboratory and diagnostic strategies. The biochemistry of biological molecules is clearly relevant to their physiological function, and calling out the need for consideration of this feature in their study, and use as vaccine, diagnostic and therapeutic targets is the overarching motivation for this review.
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Affiliation(s)
- Jessica Z Kubicek-Sutherland
- Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Dung M Vu
- Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Heather M Mendez
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131, USA.
- The New Mexico Consortium, Los Alamos, NM 87544, USA.
| | - Shailja Jakhar
- Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Harshini Mukundan
- Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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Baksh MM, Finn M. An experimental check of backscattering interferometry. SENSORS AND ACTUATORS. B, CHEMICAL 2017; 243:977-981. [PMID: 28529409 PMCID: PMC5433263 DOI: 10.1016/j.snb.2016.12.055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Backscattering interferometry (BSI) was used to determine the association constants for four well-known biomolecular interactions: protein A + IgG, trypsin + antitrypsin, trypsin + p-aminobenzamidine, and antithrombin + heparin. Each gave well-defined binding curves and Kd values in close agreement with published findings obtained using other techniques. These results stand in direct contrast to the claims in a 2015 publication in this journal (Discussion of "Back Scattering Interferometry revisited-a theoretical and experimental investigation" Jørgensen, T.M.; Jepsen, S.T.; Sørensen, H.S.; di Gennaro, A.K.; Kristensen, S.R. Sensors and Actuators B 2015, 220, 1328-1337, doi: 10.1016/j.snb.2015.06.121), thus invalidating the claim that BSI is unable to make measurements of this kind. The experimental details are discussed, and several potential sources of error in the previous publication are identified. No comments are made here on the discussion of the theoretical aspects of the BSI technique.
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36
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Label-free quantification of calcium-sensor targeting to photoreceptor guanylate cyclase and rhodopsin kinase by backscattering interferometry. Sci Rep 2017; 7:45515. [PMID: 28361875 PMCID: PMC5374524 DOI: 10.1038/srep45515] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/28/2017] [Indexed: 01/26/2023] Open
Abstract
Quantification of protein binding to membrane proteins is challenging and a limited set of methods is available to study such systems. Here we employed backscattering interferometry (BSI), a free-solution label-free method with high sensitivity, to quantify the interaction of neuronal Ca2+-Sensor proteins with their targets operating in phototransduction. We tested direct binding of guanylate cyclase–activating proteins (GCAP1 and GCAP2) to their membrane target guanylate cyclase 1. The regulatory mechanism of GCAPs including their binding interface in the target is unresolved. Here we used a label-free, free-solution assay method based on BSI to determine binding constants of GCAP1 and GCAP2 to the full-length membrane-bound guanylate cyclase type 1. GCAP1 and GCAP2 bound to different regions on the target guanylate cyclase with submicromolar affinity (apparent KD-values of 663 ± 121 nM and 231 ± 63 nM for Ca2+-free GCAP1 and GCAP2, respectively). A guanylate cyclase construct containing the juxta-membrane and kinase homology domain harbored an exclusive binding site for GCAP1 with similar affinities as the full-length protein, whereas GCAP2 did not bind to this region. We provide a model in which GCAP1 and GCAP2 do not share a single binding site to the target, thus cannot exchange upon fluctuating Ca2+ levels.
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37
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Park A, Li Y, Masri R, Keller A. Presynaptic and extrasynaptic regulation of posterior nucleus of thalamus. J Neurophysiol 2017; 118:507-519. [PMID: 28331010 DOI: 10.1152/jn.00862.2016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 02/21/2017] [Accepted: 03/16/2017] [Indexed: 11/22/2022] Open
Abstract
The posterior nucleus of thalamus (PO) is a higher-order nucleus involved in sensorimotor processing, including nociception. An important characteristic of PO is its wide range of activity profiles that vary across states of arousal, thought to underlie differences in somatosensory perception subject to attention and degree of consciousness. Furthermore, PO loses the ability to downregulate its activity level in some forms of chronic pain, suggesting that regulatory mechanisms underlying the normal modulation of PO activity may be pathologically altered. However, the mechanisms responsible for regulating such a wide dynamic range of activity are unknown. Here, we test a series of hypotheses regarding the function of several presynaptic receptors on both GABAergic and glutamatergic afferents targeting PO in mouse, using acute slice electrophysiology. We found that presynaptic GABAB receptors are present on both GABAergic and glutamatergic terminals in PO, but only those on GABAergic terminals are tonically active. We also found that release from GABAergic terminals, but not glutamatergic terminals, is suppressed by cholinergic activation and that a subpopulation of GABAergic terminals is regulated by cannabinoids. Finally, we discovered the presence of tonic currents mediated by extrasynaptic GABAA receptors in PO that are heterogeneously distributed across the nucleus. Thus we demonstrate that multiple regulatory mechanisms concurrently exist in PO, and we propose that regulation of inhibition, rather than excitation, is the more consequential mechanism by which PO activity can be regulated.NEW & NOTEWORTHY The posterior nucleus of thalamus (PO) is a key sensorimotor structure, whose activity is tightly regulated by inhibition from several nuclei. Maladaptive plasticity in this inhibition leads to severe pathologies, including chronic pain. We reveal here, for the first time in PO, multiple regulatory mechanisms that modulate synaptic transmission within PO. These findings may lead to targeted therapies for chronic pain and other disorders.
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Affiliation(s)
- Anthony Park
- Program in Neuroscience and Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland; and
| | - Ying Li
- Program in Neuroscience and Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland; and
| | - Radi Masri
- Program in Neuroscience and Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland; and.,Department of Endodontics, Periodontics and Prosthodontics, University of Maryland Baltimore, School of Dentistry, Baltimore, Maryland
| | - Asaf Keller
- Program in Neuroscience and Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland; and
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38
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Zhang Z, Baksh MM, Finn MG, Heidary DK, Richards CI. Direct Measurement of Trafficking of the Cystic Fibrosis Transmembrane Conductance Regulator to the Cell Surface and Binding to a Chemical Chaperone. Biochemistry 2016; 56:240-249. [PMID: 28001373 DOI: 10.1021/acs.biochem.6b00853] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) result in the disease cystic fibrosis. Deletion of Phe508, the most prevalent mutation associated with this disease, disrupts trafficking of the protein. Small molecule correctors yield moderate improvements in the trafficking of ΔF508-CFTR to the plasma membrane. It is currently not known if correctors increase the level of trafficking through improved cargo loading of transport vesicles or through direct binding to CFTR. Real-time measurements of trafficking were utilized to identify the mechanistic details of chemical, biochemical, and thermal factors that impact CFTR correction, using the corrector molecule VX-809, a secondary mutation (I539T), and low-temperature conditions. Each individually improved trafficking of ΔF508-CFTR to approximately 10% of wild-type levels. The combination of VX-809 with either low temperature or the I539T mutation increased the amount of CFTR on the plasma membrane to nearly 40%, indicating synergistic activity. The number of vesicles reaching the surface was significantly altered; however, the amount of channel in each vesicle remained the same. Direct binding measurements of VX-809 in native membranes using backscattering interferometry indicate tight binding to CFTR, which occurred in a manner independent of mutation. The similar values obtained for all forms of the channel indicate that the binding site is not compromised or enhanced by these mutations.
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Affiliation(s)
- Zhihui Zhang
- Department of Chemistry, University of Kentucky , Lexington, Kentucky 40506, United States
| | - Michael M Baksh
- Department of Chemistry, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - M G Finn
- Department of Chemistry, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - David K Heidary
- Department of Chemistry, University of Kentucky , Lexington, Kentucky 40506, United States
| | - Christopher I Richards
- Department of Chemistry, University of Kentucky , Lexington, Kentucky 40506, United States
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Wang M, Kussrow AK, Ocana MF, Chabot JR, Lepsy CS, Bornhop DJ, O'Hara DM. Physiologically relevant binding affinity quantification of monoclonal antibody PF-00547659 to mucosal addressin cell adhesion molecule for in vitro in vivo correlation. Br J Pharmacol 2016; 174:70-81. [PMID: 27760281 PMCID: PMC5221447 DOI: 10.1111/bph.13654] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/30/2016] [Accepted: 10/06/2016] [Indexed: 12/29/2022] Open
Abstract
Background and Purpose A monoclonal antibody (PF‐00547659) against mucosal addressin cell adhesion molecule (MAdCAM), expressed as both soluble (sMAdCAM) and trans‐membrane (mMAdCAM) target forms, showed over 30‐fold difference in antibody‐target KD between in vitro (Biacore) and clinically derived (KD,in‐vivo) values. Back‐scattering interferometry (BSI) was applied to acquire physiologically relevant KD values which were used to establish in vitro and in vivo correlation (IVIVC). Experimental Approach BSI was applied to obtain KD values between PF‐00547659 and recombinant human MAdCAM in buffer or CHO cells and endogenous MAdCAM in human serum or colon tissue. CHO cells and tissue were minimally processed to yield homogenate containing membrane vesicles and soluble proteins. A series of binding affinities in serum with various dilution factors was used to estimate both KD,in‐vivo and target concentrations; MAdCAM concentrations were also measured using LC–MS/MS. Key Results BSI measurements revealed low KD values (higher affinity) for sMAdCAM in buffer and serum, yet a 20‐fold higher KD value (lower affinity) for mMAdCAM in CHO, mMAdCAM and sMAdCAM in tissue. BSI predicted KD,in‐vivo in serum was similar to clinically derived KD,in‐vivo, and the BSI‐estimated serum sMAdCAM concentration also matched the measured concentration by LC–MS/MS. Conclusions and Implications Our results successfully demonstrated that BSI measurements of physiologically relevant KD values can be used to establish IVIVC, for PF‐00547659 to MAdCAM despite the lack of correlation when using Biacore measured KD and accurately estimates endogenous target concentrations. The application of BSI would greatly enhance successful basic pharmacological research and drug development.
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Affiliation(s)
- Mengmeng Wang
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc, Andover, MA, USA
| | - Amanda K Kussrow
- Department of Chemistry, Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN, USA
| | | | - Jeffrey R Chabot
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc, Andover, MA, USA
| | | | - Darryl J Bornhop
- Department of Chemistry, Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN, USA
| | - Denise M O'Hara
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc, Andover, MA, USA
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40
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Renaud JP, Chung CW, Danielson UH, Egner U, Hennig M, Hubbard RE, Nar H. Biophysics in drug discovery: impact, challenges and opportunities. Nat Rev Drug Discov 2016; 15:679-98. [PMID: 27516170 DOI: 10.1038/nrd.2016.123] [Citation(s) in RCA: 209] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Over the past 25 years, biophysical technologies such as X-ray crystallography, nuclear magnetic resonance spectroscopy, surface plasmon resonance spectroscopy and isothermal titration calorimetry have become key components of drug discovery platforms in many pharmaceutical companies and academic laboratories. There have been great improvements in the speed, sensitivity and range of possible measurements, providing high-resolution mechanistic, kinetic, thermodynamic and structural information on compound-target interactions. This Review provides a framework to understand this evolution by describing the key biophysical methods, the information they can provide and the ways in which they can be applied at different stages of the drug discovery process. We also discuss the challenges for current technologies and future opportunities to use biophysical methods to solve drug discovery problems.
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Affiliation(s)
- Jean-Paul Renaud
- NovAliX, Boulevard Sébastien Brant, 67405 Illkirch Cedex, France.,Institut de Génétique et Biologie Moléculaire et Cellulaire, CNRS UMR7104/INSERM U964/Université de Strasbourg, 1 rue Laurent Fries - BP10142, 67404 Illkirch Cedex, France.,RiboStruct, 15 rue Neuve, 67540 Ostwald, France
| | - Chun-Wa Chung
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - U Helena Danielson
- Department of Chemistry - BMC and Science for Life Laboratory, Drug Discovery &Development Platform, Uppsala University, SE-751 05 Uppsala, Sweden.,Beactica AB, Uppsala Business Park, 754 50 Uppsala, Sweden
| | - Ursula Egner
- Bayer Pharma AG, Müllerstrasse 178, 13353 Berlin, Germany
| | - Michael Hennig
- Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland.,leadXpro AG, PARK INNOVAARE, CH-5234 Villigen, Switzerland
| | - Roderick E Hubbard
- University of York, Heslington, York, YO10 5DD, UK.,Vernalis (R&D), Granta Park, Cambridge, CB21 6GB, UK
| | - Herbert Nar
- Boehringer Ingelheim GmbH &Co. KG, Birkendorfer Strasse 65, 88400 Biberach, Germany
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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.
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42
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Reichart TM, Baksh MM, Rhee JK, Fiedler JD, Sligar SG, Finn MG, Zwick MB, Dawson PE. Trimerization of the HIV Transmembrane Domain in Lipid Bilayers Modulates Broadly Neutralizing Antibody Binding. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201508421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Timothy M. Reichart
- Department of Chemistry; The Scripps Research Institute; 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Michael M. Baksh
- Department of Chemistry; The Scripps Research Institute; 10550 North Torrey Pines Road La Jolla CA 92037 USA
- School of Chemistry & Biochemistry; Georgia Institute of Technology; 901 Atlantic Drive Atlanta GA 30332 USA
| | - Jin-Kyu Rhee
- Department of Food Science and Engineering; Ewha Womans University; Seoul 03760 Korea
| | - Jason D. Fiedler
- Department of Chemistry; The Scripps Research Institute; 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Stephen G. Sligar
- Department of Biochemistry; University of Illinois; Urbana IL 61801 USA
| | - M. G. Finn
- Department of Chemistry; The Scripps Research Institute; 10550 North Torrey Pines Road La Jolla CA 92037 USA
- School of Chemistry & Biochemistry; Georgia Institute of Technology; 901 Atlantic Drive Atlanta GA 30332 USA
| | - Michael B. Zwick
- Department of Immunology and Microbial Science; The Scripps Research Institute; 10550 North Torrey Pines Road La Jolla CA USA
| | - Philip E. Dawson
- Department of Chemistry; The Scripps Research Institute; 10550 North Torrey Pines Road La Jolla CA 92037 USA
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43
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Reichart TM, Baksh MM, Rhee JK, Fiedler JD, Sligar SG, Finn MG, Zwick MB, Dawson PE. Trimerization of the HIV Transmembrane Domain in Lipid Bilayers Modulates Broadly Neutralizing Antibody Binding. Angew Chem Int Ed Engl 2016; 55:2688-92. [PMID: 26799917 PMCID: PMC5405556 DOI: 10.1002/anie.201508421] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/04/2015] [Indexed: 12/18/2022]
Abstract
The membrane-proximal external region (MPER) of HIV gp41 is an established target of antibodies that neutralize a broad range of HIV isolates. To evaluate the role of the transmembrane (TM) domain, synthetic MPER-derived peptides were incorporated into lipid nanoparticles using natural and designed TM domains, and antibody affinity was measured using immobilized and solution-based techniques. Peptides incorporating the native HIV TM domain exhibit significantly stronger interactions with neutralizing antibodies than peptides with a monomeric TM domain. Furthermore, a peptide with a trimeric, three-helix bundle TM domain recapitulates the binding profile of the native sequence. These studies suggest that neutralizing antibodies can bind the MPER when the TM domain is a three-helix bundle and this presentation could influence the binding of neutralizing antibodies to the virus. Lipid-bilayer presentation of viral antigens in Nanodiscs is a new platform for evaluating neutralizing antibodies.
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Affiliation(s)
- Timothy M Reichart
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Michael M Baksh
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, GA, 30332, USA
| | - Jin-Kyu Rhee
- Department of Food Science and Engineering, Ewha Womans University, Seoul, 03760, Korea
| | - Jason D Fiedler
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Stephen G Sligar
- Department of Biochemistry, University of Illinois, Urbana, IL, 61801, USA
| | - M G Finn
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, GA, 30332, USA
| | - Michael B Zwick
- Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, USA
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
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44
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Jepsen ST, Jørgensen TM, Zong W, Trydal T, Kristensen SR, Sørensen HS. Evaluation of back scatter interferometry, a method for detecting protein binding in solution. Analyst 2015; 140:895-901. [PMID: 25503796 DOI: 10.1039/c4an01129e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Back Scatter Interferometry (BSI) has been proposed to be a highly sensitive and versatile refractive index sensor usable for analytical detection of biomarker and protein interactions in solution. However the existing literature on BSI lacks a physical explanation of why protein interactions in general should contribute to the BSI signal. We have established a BSI system to investigate this subject in further detail. We contribute with a thorough analysis of the robustness of the sensor including unwanted contributions to the interferometric signal caused by temperature variation and dissolved gasses. We report a limit of the effective minimum detectability of refractive index at the 10(-7) level. Long term stability was examined by simultaneously monitoring the temperature inside the capillary revealing an average drift of 2.0 × 10(-7) per hour. Finally we show that measurements on protein A incubated with immunoglobulin G do not result in a signal that can be attributed to binding affinities as otherwise claimed in literature.
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Affiliation(s)
- S T Jepsen
- Dept. of Clinical Biochemistry, Aalborg University Hospital, Hobrovej 18-22, 9000 Aalborg, Denmark
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45
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Kammer MN, Olmsted IR, Kussrow AK, Morris MJ, Jackson GW, Bornhop DJ. Characterizing aptamer small molecule interactions with backscattering interferometry. Analyst 2015; 139:5879-84. [PMID: 25229067 DOI: 10.1039/c4an01227e] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Aptamers are segments of single-strand DNA or RNA used in a wide array of applications, including sensors, therapeutics, and cellular process regulators. Aptamers can bind many target species, including proteins, peptides, and small molecules (SM) with high affinity and specificity. They are advantageous because they can be identified in vitro by SELEX, produced rapidly and relatively economically using oligonucleotide synthesis. The use of aptamers as SM probes has experienced a recent rebirth, and because of their unique properties they represent an attractive alternative to antibodies. Current assay methodology for characterizing small molecule-aptamer binding is limited by either mass sensitivity, as in biolayer interferometry (BLI) and surface plasmon resonance (SPR), or the need for using a fluorophore, as in thermophoresis. Here we report that backscattering interferometry (BSI), a label-free and free-solution sensing technique, can be used to effectively characterize SM-aptamer interactions, providing Kd values on microliter sample quantities and at low nanomolar sensitivity. To demonstrate this capability we measured the aptamer affinity for three previously reported small molecules; bisphenol A, tenofovir, and epirubicin showing BSI provided values consistent with those published previously. We then quantified the Kd values for aptamers to ampicillin, tetracycline and norepinephrine. All measurements produced R(2) values >0.95 and an excellent signal to noise ratio at target concentrations that enable true Kd values to be obtained. No immobilization or labeling chemistry was needed, expediting the assay which is also insensitive to the large relative mass difference between the interacting molecules.
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Affiliation(s)
- Michael N Kammer
- Department of Chemistry, Vanderbilt University, 2201 West End Avenue, Nashville, Tennessee, USA.
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46
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Liu C, Huang D, Yang T, Cremer PS. Simultaneous Detection of Multiple Proteins that Bind to the Identical Ligand in Supported Lipid Bilayers. Anal Chem 2015; 87:7163-70. [DOI: 10.1021/acs.analchem.5b00999] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Chunming Liu
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
| | - Da Huang
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
| | - Tinglu Yang
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
- Department
of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
| | - Paul S. Cremer
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
- Department
of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
- Department
of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania 16802, United States
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47
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Liang B, Ju Y, Joubert JR, Kaleta EJ, Lopez R, Jones IW, Hall HK, Ratnayaka SN, Wysocki VH, Saavedra SS. Label-free detection and identification of protein ligands captured by receptors in a polymerized planar lipid bilayer using MALDI-TOF MS. Anal Bioanal Chem 2015; 407:2777-89. [PMID: 25694144 PMCID: PMC4417943 DOI: 10.1007/s00216-015-8508-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/10/2015] [Accepted: 01/21/2015] [Indexed: 01/27/2023]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) coupled with affinity capture is a well-established method to extract biological analytes from complex samples followed by label-free detection and identification. Many bioanalytes of interest bind to membrane-associated receptors; however, the matrices and high-vacuum conditions inherent to MALDI-TOF MS make it largely incompatible with the use of artificial lipid membranes with incorporated receptors as platforms for detection of captured proteins and peptides. Here we show that cross-linking polymerization of a planar supported lipid bilayer (PSLB) provides the stability needed for MALDI-TOF MS analysis of proteins captured by receptors embedded in the membrane. PSLBs composed of poly(bis-sorbylphosphatidylcholine) (poly(bis-SorbPC)) and doped with the ganglioside receptors GM1 and GD1a were used for affinity capture of the B subunits of cholera toxin, heat-labile enterotoxin, and pertussis toxin. The three toxins were captured simultaneously, then detected and identified by MS on the basis of differences in their molecular weights. Poly(bis-SorbPC) PSLBs are inherently resistant to nonspecific protein adsorption, which allowed selective toxin detection to be achieved in complex matrices (bovine serum and shrimp extract). Using GM1-cholera toxin subunit B as a model receptor-ligand pair, we estimated the minimal detectable concentration of toxin to be 4 nM. On-plate tryptic digestion of bound cholera toxin subunit B followed by MS/MS analysis of digested peptides was performed successfully, demonstrating the feasibility of using the PSLB-based affinity capture platform for identification of unknown, membrane-associated proteins. Overall, this work demonstrates that combining a poly(lipid) affinity capture platform with MALDI-TOF MS detection is a viable approach for capture and proteomic characterization of membrane-associated proteins in a label-free manner.
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Affiliation(s)
- Boying Liang
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721, USA
| | | | - James R. Joubert
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721, USA
| | - Erin J. Kaleta
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721, USA
| | - Rodrigo Lopez
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721, USA
| | - Ian W. Jones
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721, USA
| | - Henry K. Hall
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721, USA
| | - Saliya N. Ratnayaka
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721, USA
| | | | - S. Scott Saavedra
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721, USA
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Saetear P, Perrin AJ, Bartholdson SJ, Wanaguru M, Kussrow A, Bornhop DJ, Wright GJ. Quantification of Plasmodium-host protein interactions on intact, unmodified erythrocytes by back-scattering interferometry. Malar J 2015; 14:88. [PMID: 25889240 PMCID: PMC4349660 DOI: 10.1186/s12936-015-0553-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 01/06/2015] [Indexed: 11/17/2022] Open
Abstract
Background Invasion of host erythrocytes by Plasmodium falciparum is central to the pathogenesis of malaria. Invasion involves recognition events between erythrocyte receptors and ligands on the merozoite, the invasive blood form of the parasite. Identifying and characterizing host-parasite interactions is impeded by the biochemical challenges of working with membrane-embedded glycoprotein receptors. For example, the interaction between P. falciparum erythrocyte binding antigen 175 (PfEBA175) and glycophorin A (GYPA) depends on post-translational modifications that are not easily added in recombinant expression systems, and the use of native GYPA is limited by the hydrophobic transmembrane region, making it difficult to biochemically manipulate. It would, therefore, be desirable to perform quantitative binding assays with receptors embedded within the membranes of intact human erythrocytes. Methods The extracellular region of GYPA was over-expressed as a soluble protein in HEK293E cells. This protein was characterized, sialylated and evaluated for binding to the PfEBA175 protein. The label-free and free-solution assay, backscattering interferometry (BSI), was used to perform binding assays of two well-characterized P. falciparum invasion ligands to intact unmodified human erythrocytes. Results Findings indicate that the post-translational modifications present on native GYPA are required for it to bind recombinant PfEBA175 and that these modifications cannot be recapitulated in vitro using mammalian overexpression methods. Here, BSI was used to obtain quantitative, high fidelity interaction determinations on intact, unmodified erythrocytes. Using BSI and purified recombinant proteins constituting the entire ectodomains of the P. falciparum merozoite ligands PfEBA175 and PfRH5, KDs of 1.1 μM and 50 nM were measured for the PfRH5-BSG and PfEBA175-GYPA interactions, respectively, in good agreement with previous biophysical measurements of these interactions. Conclusions These results demonstrate that BSI can be used to detect and quantify the interactions of two merozoite invasion ligands with their receptors on intact human erythrocytes. BSI assays were performed on unlabelled, free-solution proteins in their native environment, requiring only nanomoles of recombinant protein. This study suggests that BSI can be used to investigate host-parasite protein interactions without the limitations of other assay platforms, and therefore represents a valuable new method to investigate the molecular mechanisms involved in erythrocyte invasion by P. falciparum.
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Affiliation(s)
- Phoonthawee Saetear
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand.
| | - Abigail J Perrin
- Cell Surface Signalling Laboratory and Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
| | - S Josefin Bartholdson
- Cell Surface Signalling Laboratory and Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
| | - Madushi Wanaguru
- Cell Surface Signalling Laboratory and Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
| | - Amanda Kussrow
- Department of Chemistry and the Vanderbilt Institute for Chemical Biology, Vanderbilt University, 4226 Stevenson Center, Nashville, Tennessee, 37235, USA.
| | - Darryl J Bornhop
- Department of Chemistry and the Vanderbilt Institute for Chemical Biology, Vanderbilt University, 4226 Stevenson Center, Nashville, Tennessee, 37235, USA.
| | - Gavin J Wright
- Cell Surface Signalling Laboratory and Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
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Forli S, Olson AJ. Computational challenges of structure-based approaches applied to HIV. Curr Top Microbiol Immunol 2015; 389:31-51. [PMID: 25711462 DOI: 10.1007/82_2015_432] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Here, we review some of the opportunities and challenges that we face in computational modeling of HIV therapeutic targets and structural biology, both in terms of methodology development and structure-based drug design (SBDD). Computational methods have provided fundamental support to HIV research since the initial structural studies, helping to unravel details of HIV biology. Computational models have proved to be a powerful tool to analyze and understand the impact of mutations and to overcome their structural and functional influence in drug resistance. With the availability of structural data, in silico experiments have been instrumental in exploiting and improving interactions between drugs and viral targets, such as HIV protease, reverse transcriptase, and integrase. Issues such as viral target dynamics and mutational variability, as well as the role of water and estimates of binding free energy in characterizing ligand interactions, are areas of active computational research. Ever-increasing computational resources and theoretical and algorithmic advances have played a significant role in progress to date, and we envision a continually expanding role for computational methods in our understanding of HIV biology and SBDD in the future.
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Affiliation(s)
- Stefano Forli
- MGL, Department of Integrative Structural and Computational Biology and HIV Interaction and Viral Evolution Center, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
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Abstract
In a fluorescence polarization screen for the MYC-MAX interaction, we have identified a novel small-molecule inhibitor of MYC, KJ-Pyr-9, from a Kröhnke pyridine library. The Kd of KJ-Pyr-9 for MYC in vitro is 6.5 ± 1.0 nM, as determined by backscattering interferometry; KJ-Pyr-9 also interferes with MYC-MAX complex formation in the cell, as shown in a protein fragment complementation assay. KJ-Pyr-9 specifically inhibits MYC-induced oncogenic transformation in cell culture; it has no or only weak effects on the oncogenic activity of several unrelated oncoproteins. KJ-Pyr-9 preferentially interferes with the proliferation of MYC-overexpressing human and avian cells and specifically reduces the MYC-driven transcriptional signature. In vivo, KJ-Pyr-9 effectively blocks the growth of a xenotransplant of MYC-amplified human cancer cells.
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