1
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Patil U, Goyal A, Vu B, Liu Y, Maranholkar V, Kourentzi K, Briggs JM, Willson RC. Antibody mix-and-read assays based on fluorescence intensity probes. MAbs 2021; 13:1980178. [PMID: 34662534 PMCID: PMC8525972 DOI: 10.1080/19420862.2021.1980178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Antibodies and Fc fusion proteins are a rapidly growing class of pharmaceuticals. Cell culture and purification process development and operation require frequent measurement of product concentrations, commonly by complex enzyme-linked immunosorbent assay and high-performance liquid chromatography methods. Here we report a fast (<30 s), and simple antibody Fc assay based on mix-and-read reporting by fluorescence emission. A soluble fluorescein-labeled Fc-affinity reporter produced by standard peptide synthesis is mixed with an Fc-containing sample to produce an immediate shift in both fluorescence polarization and intensity, compatible with on- and at-line measurements and microbioreactor monitoring. We observed significant shifts in fluorescence intensity in Chinese hamster ovary cell culture fluid spiked with IgG and detected an adalimumab biosimilar down to 100 ng/mL (10-4 g/L), despite the interferents in the complex sample matrix. Neither the fluorescence polarization nor the fluorescence intensity assay is significantly affected by the addition of clarified lysate of 2 million CHO-k1 cells/mL, suggesting applicability even to cultures of low viability. Biochemical and molecular docking approaches suggest that the fluorescence intensity enhancement is caused by changes in the fluorophore's local microenvironment upon binding to IgG Fc, especially by interactions with Fc His433.Abbreviations: CCF: Cell Culture Fluid; CHO: Chinese Hamster Ovary cells; ELISA: Enzyme Linked Immunosorbent Assay; Fc: Fragment Crystallizable of antibody; HPLC: High-Performance Liquid Chromatography; HPβCD: hydroxypropyl-β-cyclodextrin; IgG: ImmunoglobulinG; mAb: Monoclonal Antibody; PBS: Phosphate-Buffered Saline; PDB: Protein Data Bank; SpA: Staphylococcal protein A; SpG: Staphylococcal protein G.
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Affiliation(s)
- Ujwal Patil
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Atul Goyal
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Binh Vu
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Yanyun Liu
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Vijay Maranholkar
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Katerina Kourentzi
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - James M Briggs
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA.,William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Richard C Willson
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA.,William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA.,Escuela De Medicina Y Ciencias De La Salud TecSalud, Monterrey, Nuevo León, Mexico
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2
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Makasewicz K, Wennmalm S, Stenqvist B, Fornasier M, Andersson A, Jönsson P, Linse S, Sparr E. Cooperativity of α-Synuclein Binding to Lipid Membranes. ACS Chem Neurosci 2021; 12:2099-2109. [PMID: 34076426 PMCID: PMC8291482 DOI: 10.1021/acschemneuro.1c00006] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cooperative binding is a key feature of metabolic pathways, signaling, and transport processes. It provides tight regulation over a narrow concentration interval of a ligand, thus enabling switching to be triggered by small concentration variations. The data presented in this work reveal strong positive cooperativity of α-synuclein binding to phospholipid membranes. Fluorescence cross-correlation spectroscopy, confocal microscopy, and cryo-TEM results show that in excess of vesicles α-synuclein does not distribute randomly but binds only to a fraction of all available vesicles. Furthermore, α-synuclein binding to a supported lipid bilayer observed with total internal reflection fluorescence microscopy displays a much steeper dependence of bound protein on total protein concentration than expected for independent binding. The same phenomenon was observed in the case of α-synuclein binding to unilamellar vesicles of sizes in the nm and μm range as well as to flat supported lipid bilayers, ruling out that nonuniform binding of the protein is governed by differences in membrane curvature. Positive cooperativity of α-synuclein binding to lipid membranes means that the affinity of the protein to a membrane is higher where there is already protein bound compared to a bare membrane. The phenomenon described in this work may have implications for α-synuclein function in synaptic transmission and other membrane remodeling events.
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Affiliation(s)
- Katarzyna Makasewicz
- Division of Physical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Stefan Wennmalm
- Department of Applied Physics, Biophysics Group, SciLifeLab, Royal Institute of Technology-KTH, 171 65 Solna, Sweden
| | - Björn Stenqvist
- Division of Physical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Marco Fornasier
- Division of Physical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Alexandra Andersson
- Division of Physical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Peter Jönsson
- Division of Physical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Sara Linse
- Division of Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-22100 Lund, Sweden
| | - Emma Sparr
- Division of Physical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
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3
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Continuous Fc detection for protein A capture process control. Biosens Bioelectron 2020; 165:112327. [DOI: 10.1016/j.bios.2020.112327] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 05/16/2020] [Accepted: 05/23/2020] [Indexed: 11/19/2022]
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4
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Stadmiller SS, Aguilar JS, Waudby CA, Pielak GJ. Rapid Quantification of Protein-Ligand Binding via 19F NMR Lineshape Analysis. Biophys J 2020; 118:2537-2548. [PMID: 32348722 PMCID: PMC7231920 DOI: 10.1016/j.bpj.2020.03.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 03/19/2020] [Indexed: 12/14/2022] Open
Abstract
Fluorine incorporation is ideally suited to many NMR techniques, and incorporation of fluorine into proteins and fragment libraries for drug discovery has become increasingly common. Here, we use one-dimensional 19F NMR lineshape analysis to quantify the kinetics and equilibrium thermodynamics for the binding of a fluorine-labeled Src homology 3 (SH3) protein domain to four proline-rich peptides. SH3 domains are one of the largest and most well-characterized families of protein recognition domains and have a multitude of functions in eukaryotic cell signaling. First, we showe that fluorine incorporation into SH3 causes only minor structural changes to both the free and bound states using amide proton temperature coefficients. We then compare the results from lineshape analysis of one-dimensional 19F spectra to those from two-dimensional 1H-15N heteronuclear single quantum coherence spectra. Their agreement demonstrates that one-dimensional 19F lineshape analysis is a robust, low-cost, and fast alternative to traditional heteronuclear single quantum coherence-based experiments. The data show that binding is diffusion limited and indicate that the transition state is highly similar to the free state. We also measured binding as a function of temperature. At equilibrium, binding is enthalpically driven and arises from a highly positive activation enthalpy for association with small entropic contributions. Our results agree with those from studies using different techniques, providing additional evidence for the utility of 19F NMR lineshape analysis, and we anticipate that this analysis will be an effective tool for rapidly characterizing the energetics of protein interactions.
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Affiliation(s)
| | - Jhoan S Aguilar
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina
| | - Christopher A Waudby
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Gary J Pielak
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina; Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina; Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina.
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5
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Wang X, Hao Z, Olsen TR, Zhang W, Lin Q. Measurements of aptamer-protein binding kinetics using graphene field-effect transistors. NANOSCALE 2019; 11:12573-12581. [PMID: 31219127 DOI: 10.1039/c9nr02797a] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Quantifying interactions between biomolecules subject to various environmental conditions is essential for applications such as drug discovery and precision medicine. This paper presents an investigation of the kinetics of environmentally dependent biomolecular binding using an electrolyte-gated graphene field-effect transistor (GFET) nanosensor. In this approach, biomolecular binding occurring on and in the vicinity of a graphene surface induces a change in carrier concentration, whose resulting conductance change is measured. This allows a systematic study of the kinetic properties of the binding system. We apply this approach to the specific binding of human immunoglobulin E (IgE), an antibody involved in parasite immunity, with an aptamer at different ionic strengths (Na+ and Mg2+) and temperatures. Experimental results demonstrate increased-rate binding kinetics at higher salt-ion concentrations and temperatures. In particular, the divalent cation Mg2+ yields more pronounced changes in the conformational structure of the aptamer than the monovalent cation Na+. In addition, the dissociation of the aptamer-protein complex at room temperature is found to be characterized by large unfavorable changes in the activation enthalpy and entropy.
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Affiliation(s)
- Xuejun Wang
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA. and State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200438, China
| | - Zhuang Hao
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA.
| | - Timothy R Olsen
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA.
| | - Wenjun Zhang
- Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, S7N 5A9, Canada
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA.
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6
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Chen H, Hagström AEV, Kim J, Garvey G, Paterson A, Ruiz-Ruiz F, Raja B, Strych U, Rito-Palomares M, Kourentzi K, Conrad JC, Atmar RL, Willson RC. Flotation Immunoassay: Masking the Signal from Free Reporters in Sandwich Immunoassays. Sci Rep 2016; 6:24297. [PMID: 27075635 PMCID: PMC4830940 DOI: 10.1038/srep24297] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 03/23/2016] [Indexed: 12/04/2022] Open
Abstract
In this work, we demonstrate that signal-masking reagents together with appropriate capture antibody carriers can eliminate the washing steps in sandwich immunoassays. A flotation immunoassay (FI) platform was developed with horseradish peroxidase chemiluminescence as the reporter system, the dye Brilliant Blue FCF as the signal-masking reagent, and buoyant silica micro-bubbles as the capture antibody carriers. Only reporters captured on micro-bubbles float above the dye and become visible in an analyte-dependent manner. These FIs are capable of detecting proteins down to attomole levels and as few as 10(6) virus particles. This signal-masking strategy represents a novel approach to simple, sensitive and quantitative immunoassays in both laboratory and point-of-care settings.
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Affiliation(s)
- Hui Chen
- University of Houston, Department of Biology and Biochemistry, Houston, TX 77204, USA
| | - Anna E. V. Hagström
- University of Houston, Department of Chemical and Biomolecular Engineering, Houston, TX 77204, USA
| | - Jinsu Kim
- University of Houston, Department of Chemical and Biomolecular Engineering, Houston, TX 77204, USA
| | - Gavin Garvey
- University of Houston, Department of Chemical and Biomolecular Engineering, Houston, TX 77204, USA
| | - Andrew Paterson
- University of Houston, Department of Chemical and Biomolecular Engineering, Houston, TX 77204, USA
| | - Federico Ruiz-Ruiz
- Tecnológico de Monterrey, Departamento de Biotecnología e Ingeniería de Alimentos, Monterrey, Nuevo León 64849, Mexico
| | - Balakrishnan Raja
- University of Houston, Department of Chemical and Biomolecular Engineering, Houston, TX 77204, USA
| | - Ulrich Strych
- Baylor College of Medicine, Department of Pediatrics, Houston, TX 77030, USA
| | - Marco Rito-Palomares
- Tecnológico de Monterrey, Departamento de Biotecnología e Ingeniería de Alimentos, Monterrey, Nuevo León 64849, Mexico
| | - Katerina Kourentzi
- University of Houston, Department of Chemical and Biomolecular Engineering, Houston, TX 77204, USA
| | - Jacinta C. Conrad
- University of Houston, Department of Chemical and Biomolecular Engineering, Houston, TX 77204, USA
| | - Robert L. Atmar
- Baylor College of Medicine, Department of Medicine, Houston, TX 77030, USA
| | - Richard C. Willson
- University of Houston, Department of Biology and Biochemistry, Houston, TX 77204, USA
- University of Houston, Department of Chemical and Biomolecular Engineering, Houston, TX 77204, USA
- Tecnológico de Monterrey, Departamento de Biotecnología e Ingeniería de Alimentos, Monterrey, Nuevo León 64849, Mexico
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7
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Tauzin LJ, Shen H, Moringo NA, Roddy MH, Bothof CA, Griesgraber GW, McNulty AK, Rasmussen JK, Landes CF. Variable surface transport modalities on functionalized nylon films revealed with single molecule spectroscopy. RSC Adv 2016. [DOI: 10.1039/c5ra25592a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Functionalization of separation membranes with ion-exchange ligands allows control of the surface mobility of protein molecules facilitating optimized membrane design.
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Affiliation(s)
| | - Hao Shen
- Department of Chemistry
- Rice University
- Houston
- USA
| | | | | | - Cathy A. Bothof
- 3M Corporate Research Laboratories
- 3M Center 201-3E-03
- St. Paul
- USA
| | | | - Amy K. McNulty
- 3M Corporate Research Laboratories
- 3M Center 201-3E-03
- St. Paul
- USA
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8
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Adhikari M, Strych U, Kim J, Goux H, Dhamane S, Poongavanam MV, Hagström AEV, Kourentzi K, Conrad JC, Willson RC. Aptamer-Phage Reporters for Ultrasensitive Lateral Flow Assays. Anal Chem 2015; 87:11660-5. [PMID: 26456715 DOI: 10.1021/acs.analchem.5b00702] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We introduce the modification of bacteriophage particles with aptamers for use as bioanalytical reporters, and demonstrate the use of these particles in ultrasensitive lateral flow assays. M13 phage displaying an in vivo biotinylatable peptide (AviTag) genetically fused to the phage tail protein pIII were used as reporter particle scaffolds, with biotinylated aptamers attached via avidin-biotin linkages, and horseradish peroxidase (HRP) reporter enzymes covalently attached to the pVIII coat protein. These modified viral nanoparticles were used in immunochromatographic sandwich assays for the direct detection of IgE and of the penicillin-binding protein from Staphylococcus aureus (PBP2a). We also developed an additional lateral flow assay for IgE, in which the analyte is sandwiched between immobilized anti-IgE antibodies and aptamer-bearing reporter phage modified with HRP. The limit of detection of this LFA was 0.13 ng/mL IgE, ∼100 times lower than those of previously reported IgE assays.
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Affiliation(s)
- Meena Adhikari
- Department of Biology & Biochemistry, University of Houston , Houston, Texas 77004, United States
| | - Ulrich Strych
- Department of Biology & Biochemistry, University of Houston , Houston, Texas 77004, United States
| | - Jinsu Kim
- Department of Chemical & Biomolecular Engineering, University of Houston , Houston, Texas 77204, United States
| | - Heather Goux
- Department of Biology & Biochemistry, University of Houston , Houston, Texas 77004, United States
| | - Sagar Dhamane
- Department of Biology & Biochemistry, University of Houston , Houston, Texas 77004, United States
| | | | - Anna E V Hagström
- Department of Chemical & Biomolecular Engineering, University of Houston , Houston, Texas 77204, United States
| | - Katerina Kourentzi
- Department of Chemical & Biomolecular Engineering, University of Houston , Houston, Texas 77204, United States
| | - Jacinta C Conrad
- Department of Chemical & Biomolecular Engineering, University of Houston , Houston, Texas 77204, United States
| | - Richard C Willson
- Department of Biology & Biochemistry, University of Houston , Houston, Texas 77004, United States.,Department of Chemical & Biomolecular Engineering, University of Houston , Houston, Texas 77204, United States.,Centro de Biotecnología FEMSA, Tecnológico de Monterrey , Monterrey, Nuevo León, Mexico
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9
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Poongavanam MV, Kisley L, Kourentzi K, Landes CF, Willson RC. Ensemble and single-molecule biophysical characterization of D17.4 DNA aptamer-IgE interactions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:154-64. [PMID: 26307469 DOI: 10.1016/j.bbapap.2015.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 08/09/2015] [Accepted: 08/18/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND The IgE-binding DNA aptamer 17.4 is known to inhibit the interaction of IgE with the high-affinity IgE Fc receptor FcεRI. While this and other aptamers have been widely used and studied, there has been relatively little investigation of the kinetics and energetics of their interactions with their targets, by either single-molecule or ensemble methods. METHODS The dissociation kinetics of the D17.4/IgE complex and the effects of temperature and ionic strength were studied using fluorescence anisotropy and single-molecule spectroscopy, and activation parameters calculated. RESULTS The dissociation of D17.4/IgE complex showed a strong dependence on temperature and salt concentration. The koff of D17.4/IgE complex was calculated to be (2.92±0.18)×10(-3) s(-1) at 50 mM NaCl, and (1.44±0.02)×10(-2) s(-1) at 300 mM NaCl, both in 1 mM MgCl2 and 25°C. The dissociation activation energy for the D17.4/IgE complex, Ea, was 16.0±1.9 kcal mol(-1) at 50 mM NaCl and 1 mM MgCl2. Interestingly, we found that the C19A mutant of D17.4 with stabilized stem structure showed slower dissociation kinetics compared to D17.4. Single-molecule observations of surface-immobilized D17.4/IgE showed much faster dissociation kinetics, and heterogeneity not observable by ensemble techniques. CONCLUSIONS The increasing koff value with increasing salt concentration is attributed to the electrostatic interactions between D17.4/IgE. We found that both the changes in activation enthalpy and activation entropy are insignificant with increasing NaCl concentration. The slower dissociation of the mutant C19A/IgE complex is likely due to the enhanced stability of the aptamer. GENERAL SIGNIFICANCE The activation parameters obtained by applying transition state analysis to kinetic data can provide details on mechanisms of molecular recognition and have applications in drug design. Single-molecule dissociation kinetics showed greater kinetic complexity than was observed in the ensemble in-solution systems, potentially reflecting conformational heterogeneity of the aptamer. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.
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Affiliation(s)
| | - Lydia Kisley
- Department of Chemistry, Rice University, Houston, TX77005-1827, USA
| | - Katerina Kourentzi
- Department of Chemical and Biomolecular Engineering, University of Houston, TX 77204-4004, USA
| | - Christy F Landes
- Department of Chemistry, Rice University, Houston, TX77005-1827, USA; Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005-1827, USA.
| | - Richard C Willson
- Department of Biology and Biochemistry, University of Houston, TX 77204-5001, USA; Department of Chemical and Biomolecular Engineering, University of Houston, TX 77204-4004, USA; Houston Methodist Research Institute, Houston, TX 77030, USA; Centro de Biotecnología FEMSA, Departamento de Biotecnología e Ingeniería de Alimentos, Tecnológico de Monterrey, Monterrey 64849, Mexico.
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10
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Blake S, Amin S, Qi W, Majumdar M, Lewis EN. Colloidal Stability & Conformational Changes in β-Lactoglobulin: Unfolding to Self-Assembly. Int J Mol Sci 2015; 16:17719-33. [PMID: 26247930 PMCID: PMC4581217 DOI: 10.3390/ijms160817719] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 07/23/2015] [Accepted: 07/27/2015] [Indexed: 11/16/2022] Open
Abstract
A detailed understanding of the mechanism of unfolding, aggregation, and associated rheological changes is developed in this study for β-Lactoglobulin at different pH values through concomitant measurements utilizing dynamic light scattering (DLS), optical microrheology, Raman spectroscopy, and differential scanning calorimetry (DSC). The diffusion interaction parameter kD emerges as an accurate predictor of colloidal stability for this protein consistent with observed aggregation trends and rheology. Drastic aggregation and gelation were observed at pH 5.5. Under this condition, the protein's secondary and tertiary structures changed simultaneously. At higher pH (7.0 and 8.5), oligomerizaton with no gel formation occurred. For these solutions, tertiary structure and secondary structure transitions were sequential. The low frequency Raman data, which is a good indicator of hydrogen bonding and structuring in water, has been shown to exhibit a strong correlation with the rheological evolution with temperature. This study has, for the first time, demonstrated that this low frequency Raman data, in conjunction with the DSC endotherm, can be been utilized to deconvolve protein unfolding and aggregation/gelation. These findings can have important implications for the development of protein-based biotherapeutics, where the formulation viscosity, aggregation, and stability strongly affects efficacy or in foods where protein structuring is critical for functional and sensory performance.
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Affiliation(s)
- Steven Blake
- Malvern Instruments, 7221 Lee Deforest Drive, Suite 300, Columbia, MD 21046, USA.
| | - Samiul Amin
- Malvern Instruments, 7221 Lee Deforest Drive, Suite 300, Columbia, MD 21046, USA.
| | - Wei Qi
- Malvern Instruments, 7221 Lee Deforest Drive, Suite 300, Columbia, MD 21046, USA.
| | - Madhabi Majumdar
- Malvern Instruments, 7221 Lee Deforest Drive, Suite 300, Columbia, MD 21046, USA.
| | - E Neil Lewis
- Malvern Instruments, 7221 Lee Deforest Drive, Suite 300, Columbia, MD 21046, USA.
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11
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Affiliation(s)
- Lydia Kisley
- Department of Chemistry and Department of Electrical and Computer
Engineering,
Rice Quantum Institute, Rice University, 6100 Main Street, MS-60, Houston, Texas 77005, United States
| | - Christy F. Landes
- Department of Chemistry and Department of Electrical and Computer
Engineering,
Rice Quantum Institute, Rice University, 6100 Main Street, MS-60, Houston, Texas 77005, United States
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12
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Paterson A, Raja B, Garvey G, Kolhatkar A, Hagström AEV, Kourentzi K, Lee TR, Willson RC. Persistent luminescence strontium aluminate nanoparticles as reporters in lateral flow assays. Anal Chem 2014; 86:9481-8. [PMID: 25247754 PMCID: PMC4188266 DOI: 10.1021/ac5012624] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 09/10/2014] [Indexed: 11/28/2022]
Abstract
Demand for highly sensitive, robust diagnostics and environmental monitoring methods has led to extensive research in improving reporter technologies. Inorganic phosphorescent materials exhibiting persistent luminescence are commonly found in electroluminescent displays and glowing paints but are not widely used as reporters in diagnostic assays. Persistent luminescence nanoparticles (PLNPs) offer advantages over conventional photoluminescent probes, including the potential for enhanced sensitivity by collecting time-resolved measurements or images with decreased background autofluorescence while eliminating the need for expensive optical hardware, superior resistance to photobleaching, amenability to quantitation, and facile bioconjugation schemes. We isolated rare-earth doped strontium aluminate PLNPs from larger-particle commercial materials by wet milling and differential sedimentation and water-stabilized the particles by silica encapsulation using a modified Stöber process. Surface treatment with aldehyde silane followed by reductive amination with heterobifunctional amine-poly(ethylene glycol)-carboxyl allowed covalent attachment of proteins to the particles using standard carbodiimide chemistry. NeutrAvidin PLNPs were used in lateral flow assays (LFAs) with biotinylated lysozyme as a model analyte in buffer and monoclonal anti-lysozyme HyHEL-5 antibodies at the test line. Preliminary experiments revealed a limit of detection below 100 pg/mL using the NeutrAvidin PLNPs, which was approximately an order of magnitude more sensitive than colloidal gold.
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Affiliation(s)
- Andrew
S. Paterson
- Department
of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77004, United States
| | - Balakrishnan Raja
- Department
of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77004, United States
| | - Gavin Garvey
- Department
of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77004, United States
| | - Arati Kolhatkar
- Department
of Chemistry, University of Houston, Houston, Texas 77004, United States
| | - Anna E. V. Hagström
- Department
of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77004, United States
| | - Katerina Kourentzi
- Department
of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77004, United States
| | - T. Randall Lee
- Department
of Chemistry, University of Houston, Houston, Texas 77004, United States
| | - Richard C. Willson
- Department
of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77004, United States
- Department
of Biology and Biochemistry, University
of Houston, Houston, Texas 77004, United
States
- Centro
de Biotecnología FEMSA, Tecnológico
de Monterrey, Campus Monterrey, Monterrey, Nuevo León 64849, Mexico
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13
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Cacao E, Sherlock T, Nasrullah A, Kemper S, Knoop J, Kourentzi K, Ruchhoeft P, Stein GE, Atmar RL, Willson RC. Helium beam shadowing for high spatial resolution patterning of antibodies on microstructured diagnostic surfaces. Biointerphases 2014; 8:9. [PMID: 24706125 PMCID: PMC4000555 DOI: 10.1186/1559-4106-8-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 03/11/2013] [Indexed: 11/10/2022] Open
Abstract
We have developed a technique for the high-resolution, self-aligning, and high-throughput patterning of antibody binding functionality on surfaces by selectively changing the reactivity of protein-coated surfaces in specific regions of a workpiece with a beam of energetic helium particles. The exposed areas are passivated with bovine serum albumin (BSA) and no longer bind the antigen. We demonstrate that patterns can be formed (1) by using a stencil mask with etched openings that forms a patterned exposure, or (2) by using angled exposure to cast shadows of existing raised microstructures on the surface to form self-aligned patterns. We demonstrate the efficacy of this process through the patterning of anti-lysozyme, anti-Norwalk virus, and anti-Escherichia coli antibodies and the subsequent detection of each of their targets by the enzyme-mediated formation of colored or silver deposits, and also by binding of gold nanoparticles. The process allows for the patterning of three-dimensional structures by inclining the sample relative to the beam so that the shadowed regions remain unaltered. We demonstrate that the resolution of the patterning process is of the order of hundreds of nanometers, and that the approach is well-suited for high throughput patterning.
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Affiliation(s)
- Eliedonna Cacao
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA,
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14
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Kisley L, Chen J, Mansur AP, Dominguez-Medina S, Kulla E, Kang MK, Shuang B, Kourentzi K, Poongavanam MV, Dhamane S, Willson RC, Landes CF. High ionic strength narrows the population of sites participating in protein ion-exchange adsorption: a single-molecule study. J Chromatogr A 2014; 1343:135-42. [PMID: 24751557 DOI: 10.1016/j.chroma.2014.03.075] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 03/27/2014] [Indexed: 11/19/2022]
Abstract
The retention and elution of proteins in ion-exchange chromatography is routinely controlled by adjusting the mobile phase salt concentration. It has repeatedly been observed, as judged from adsorption isotherms, that the apparent heterogeneity of adsorption is lower at more-eluting, higher ionic strength. Here, we present an investigation into the mechanism of this phenomenon using a single-molecule, super-resolution imaging technique called motion-blur Points Accumulation for Imaging in Nanoscale Topography (mbPAINT). We observed that the number of functional adsorption sites was smaller at high ionic strength and that these sites had reduced desorption kinetic heterogeneity, and thus narrower predicted elution profiles, for the anion-exchange adsorption of α-lactalbumin on an agarose-supported, clustered-charge ligand stationary phase. Explanations for the narrowing of the functional population such as inter-protein interactions and protein or support structural changes were investigated through kinetic analysis, circular dichroism spectroscopy, and microscopy of agarose microbeads, respectively. The results suggest the reduction of heterogeneity is due to both electrostatic screening between the protein and ligand and tuning the steric availability within the agarose support. Overall, we have shown that single molecule spectroscopy can aid in understanding the influence of ionic strength on the population of functional adsorbent sites participating in the ion-exchange chromatographic separation of proteins.
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Affiliation(s)
- Lydia Kisley
- Department of Chemistry, Rice University, Houston, TX 77251, USA.
| | - Jixin Chen
- Department of Chemistry, Rice University, Houston, TX 77251, USA.
| | - Andrea P Mansur
- Department of Chemistry, Rice University, Houston, TX 77251, USA.
| | | | - Eliona Kulla
- Department of Chemistry, Rice University, Houston, TX 77251, USA.
| | - Marci K Kang
- Department of Chemistry, Rice University, Houston, TX 77251, USA.
| | - Bo Shuang
- Department of Chemistry, Rice University, Houston, TX 77251, USA.
| | - Katerina Kourentzi
- Department of Chemical & Biomolecular Engineering, University of Houston, Houston, TX 77004, USA.
| | | | - Sagar Dhamane
- Department of Biology & Biochemistry, University of Houston, Houston, TX 77004, USA.
| | - Richard C Willson
- Department of Chemical & Biomolecular Engineering, University of Houston, Houston, TX 77004, USA; Department of Biology & Biochemistry, University of Houston, Houston, TX 77004, USA; Houston Methodist Research Institute, Houston, TX 77030, USA; Centro de Biotecnología FEMSA, Departamento de Biotecnología e Ingeniería de Alimentos, Tecnológico de Monterrey, Monterrey NL 64849, Mexico.
| | - Christy F Landes
- Department of Chemistry, Rice University, Houston, TX 77251, USA; Department of Electrical and Computer Engineering, Rice University, Houston, TX 77251, USA.
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15
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Kapil MA, Herr AE. Binding Kinetic Rates Measured via Electrophoretic Band Crossing in a Pseudohomogeneous Format. Anal Chem 2014; 86:2601-9. [DOI: 10.1021/ac403829z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Monica A. Kapil
- Department
of Bioengineering, University of California, Berkeley, California, 94706, United States
| | - Amy E. Herr
- Department
of Bioengineering, University of California, Berkeley, California, 94706, United States
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16
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Shammas S, Travis AJ, Clarke J. Remarkably fast coupled folding and binding of the intrinsically disordered transactivation domain of cMyb to CBP KIX. J Phys Chem B 2013; 117:13346-56. [PMID: 23875714 PMCID: PMC3807845 DOI: 10.1021/jp404267e] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 07/22/2013] [Indexed: 01/25/2023]
Abstract
Association rates for interactions between folded proteins have been investigated extensively, allowing the development of computational and theoretical prediction methods. Less is known about association rates for complexes where one or more partner is initially disordered, despite much speculation about how they may compare to those for folded proteins. We have attached a fluorophore to the N-terminus of the 25 amino acid cMyb peptide used previously in NMR and equilibrium studies (termed FITC-cMyb), and used this to monitor the kinetics of its interaction with the KIX protein. We have investigated the ionic strength and temperature dependence of the kinetics, and conclude that the association process is extremely fast, apparently exceeding the rates predicted by formulations applicable to interactions between pairs of folded proteins. This is despite the fact that not all collisions result in complex formation (there is an observable activation energy for the association process). We propose that this is partially a result of the disordered nature of the FITC-cMyb peptide itself.
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Affiliation(s)
- Sarah
L. Shammas
- Department of Chemistry, University of
Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Alexandra J. Travis
- Department of Chemistry, University of
Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Jane Clarke
- Department of Chemistry, University of
Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
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17
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Bates JT, Keefer CJ, Utley TJ, Correia BE, Schief WR, Crowe JE. Reversion of somatic mutations of the respiratory syncytial virus-specific human monoclonal antibody Fab19 reveal a direct relationship between association rate and neutralizing potency. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2013; 190:3732-9. [PMID: 23455501 PMCID: PMC3608519 DOI: 10.4049/jimmunol.1202964] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The role of affinity in determining neutralizing potency of mAbs directed against viruses is not well understood. We investigated the kinetic, structural, and functional advantage conferred by individual naturally occurring somatic mutations in the Ab H chain V region of Fab19, a well-described neutralizing human mAb directed to respiratory syncytial virus. Comparison of the affinity-matured Ab Fab19 with recombinant Fab19 Abs that were variants containing reverted amino acids from the inferred unmutated ancestor sequence revealed the molecular basis for affinity maturation of this Ab. Enhanced binding was achieved through mutations in the third H chain CDR (HCDR3) that conferred a markedly faster on-rate and a desirable increase in antiviral neutralizing activity. In contrast, most somatic mutations in the HCDR1 and HCDR2 regions did not significantly enhance Ag binding or antiviral activity. We observed a direct relationship between the measured association rate (Kon) for F protein and antiviral activity. Modeling studies of the structure of the Ag-Ab complex suggested the HCDR3 loop interacts with the antigenic site A surface loop of the respiratory syncytial virus F protein, previously shown to contain the epitope for this Ab by experimentation. These studies define a direct relationship of affinity and neutralizing activity for a viral glycoprotein-specific human mAb.
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Affiliation(s)
- John T. Bates
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center,
Nashville, TN
| | | | - Thomas J. Utley
- Department of Pathology, Microbiology, and Immunology,
Vanderbilt University Medical Center, Nashville, TN
| | - Bruno E. Correia
- Department of Chemical Physiology, The Scripps Research
Institute, La Jolla, CA
| | - William R. Schief
- Department of Immunology and Microbial Science, The Scripps
Research Institute, La Jolla, CA
| | - James E. Crowe
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center,
Nashville, TN
- Department of Pediatrics, Vanderbilt University Medical
Center, Nashville, TN
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18
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Jaeger IS, Kretzschmar I, Körner J, Weiser AA, Mahrenholz CC, Potty A, Kourentzi K, Willson RC, Volkmer R, Preissner R. Mapping discontinuous protein-binding sites via structure-based peptide libraries: combiningin silicoandin vitroapproaches. J Mol Recognit 2012; 26:23-31. [DOI: 10.1002/jmr.2237] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 08/23/2012] [Accepted: 08/24/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Ines S. Jaeger
- Institute for Physiology, Structural Bioinformatics Group; Charité-Universitätsmedizin Berlin; Lindenberger Weg 80; 13125; Berlin; Germany
| | - Ines Kretzschmar
- Institut für Medizinische Immunologie, Molecular Libraries and Recognition Group; Charité-Universitätsmedizin Berlin; Hessische Strasse 3-4; 10115; Berlin; Germany
| | - Jana Körner
- Leibniz-Institut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP); R.-Rössle-Strasse 10; 13125; Berlin; Germany
| | | | - Carsten C. Mahrenholz
- Institut für Medizinische Immunologie, Molecular Libraries and Recognition Group; Charité-Universitätsmedizin Berlin; Hessische Strasse 3-4; 10115; Berlin; Germany
| | | | - Katerina Kourentzi
- University of Houston; Department of Chemical and Biomolecular Engineering; Houston; TX; 77204-4004; USA
| | - Richard C. Willson
- University of Houston; Department of Chemical and Biomolecular Engineering; Houston; TX; 77204-4004; USA
| | - Rudolf Volkmer
- Institut für Medizinische Immunologie, Molecular Libraries and Recognition Group; Charité-Universitätsmedizin Berlin; Hessische Strasse 3-4; 10115; Berlin; Germany
| | - Robert Preissner
- Institute for Physiology, Structural Bioinformatics Group; Charité-Universitätsmedizin Berlin; Lindenberger Weg 80; 13125; Berlin; Germany
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19
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Khan HU, Jang J, Kim JJ, Knoll W. In Situ Antibody Detection and Charge Discrimination Using Aqueous Stable Pentacene Transistor Biosensors. J Am Chem Soc 2011; 133:2170-6. [DOI: 10.1021/ja107088m] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Hadayat Ullah Khan
- Material Science Group, Max-Planck Institute for Polymer Research, Ackermannweg-10, D-55128 Mainz, Germany
| | - Junhyuk Jang
- OLED Center, Department of Materials Science and Engineering, Seoul National University, Seoul 151-744, Korea
| | - Jang-Joo Kim
- OLED Center, Department of Materials Science and Engineering, Seoul National University, Seoul 151-744, Korea
| | - Wolfgang Knoll
- Material Science Group, Max-Planck Institute for Polymer Research, Ackermannweg-10, D-55128 Mainz, Germany
- AIT Austrian Institute of Technology GmbH, Donau-City-Strasse 1, 1220 Vienna, Austria
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20
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Potty ASR, Kourentzi K, Fang H, Schuck P, Willson RC. Biophysical characterization of DNA and RNA aptamer interactions with hen egg lysozyme. Int J Biol Macromol 2010; 48:392-7. [PMID: 21167858 DOI: 10.1016/j.ijbiomac.2010.12.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 12/03/2010] [Accepted: 12/08/2010] [Indexed: 01/24/2023]
Abstract
This work characterized the binding of an RNA aptamer recognizing hen egg white lysozyme, as well as a literature-reported single-stranded DNA analog of sequence identical to the original RNA aptamer, using fluorescence anisotropy, isothermal titration calorimetry (ITC) and analytical ultracentrifugation. The polyanionic DNA aptamer analog is selective for lysozyme even over cationic cytochrome c and has been reported to be successfully used in biosensing applications. The association however, is predominantly of electrostatic character, strongly salt-sensitive and entropically-driven, in contrast to previously described enthalpically-driven antibody-lysozyme and DNA aptamer-VEGF interactions. With a moderate selectivity for their target, high salt-sensitivity along with fast association and dissociation behavior, these molecules might serve as pseudo-affinity ligands for biomolecular separations.
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Affiliation(s)
- Ajish S R Potty
- Department of Chemical & Biomolecular Engineering, University of Houston, 4800 Calhoun Rd, Houston, TX 77204-4004, USA
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21
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Singhal A, Haynes CA, Hansen CL. Microfluidic Measurement of Antibody−Antigen Binding Kinetics from Low-Abundance Samples and Single Cells. Anal Chem 2010; 82:8671-9. [DOI: 10.1021/ac101956e] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Anupam Singhal
- Department of Chemical and Biological Engineering, University of British Columbia, 2360 East Mall; Vancouver, British Columbia, Canada V6T 1Z3, Michael Smith Laboratories, University of British Columbia, 2185 East Mall #301, Vancouver, British Columbia, Canada V6T 1Z4, Department of Physics and Astronomy, University of British Columbia, 6224 Agricultural Road, Vancouver, British Columbia, Canada V6T 1Z1, and Centre for High-Throughput Biology, University of British Columbia, 2125 East Mall, Vancouver,
| | - Charles A. Haynes
- Department of Chemical and Biological Engineering, University of British Columbia, 2360 East Mall; Vancouver, British Columbia, Canada V6T 1Z3, Michael Smith Laboratories, University of British Columbia, 2185 East Mall #301, Vancouver, British Columbia, Canada V6T 1Z4, Department of Physics and Astronomy, University of British Columbia, 6224 Agricultural Road, Vancouver, British Columbia, Canada V6T 1Z1, and Centre for High-Throughput Biology, University of British Columbia, 2125 East Mall, Vancouver,
| | - Carl L. Hansen
- Department of Chemical and Biological Engineering, University of British Columbia, 2360 East Mall; Vancouver, British Columbia, Canada V6T 1Z3, Michael Smith Laboratories, University of British Columbia, 2185 East Mall #301, Vancouver, British Columbia, Canada V6T 1Z4, Department of Physics and Astronomy, University of British Columbia, 6224 Agricultural Road, Vancouver, British Columbia, Canada V6T 1Z1, and Centre for High-Throughput Biology, University of British Columbia, 2125 East Mall, Vancouver,
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22
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Długosz M, Antosiewicz JM, Trylska J. pH-dependent association of proteins. The test case of monoclonal antibody HyHEL-5 and its antigen hen egg white lysozyme. J Phys Chem B 2010; 113:15662-9. [PMID: 19883097 DOI: 10.1021/jp906829z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We describe a method for determining diffusion-controlled rate constants for protein-protein association that explicitly includes the solution pH. The method combines the transient-complex theory for computing electrostatically enhanced association rates with an approach based on a rigorous thermodynamic cycle and partition functions for energy levels characterizing protonation states of associating proteins and their complexes. To test our method, we determine the pH-dependent kinetics of association of the HyHEL-5 antibody with its antigen hen egg white lysozyme. It was shown experimentally that their association rate constant depends on pH, increasing linearly in the pH range 6-8 and saturating or even exhibiting a flat maximum in the pH range 8-10. The presented methodology leads to a qualitative agreement with the experimental data. Our approach allows one to study diffusion-controlled protein-protein association under different pH conditions by taking into account the ensembles of protonation states rather than just the most probable protonation state of each protein.
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Affiliation(s)
- Maciej Długosz
- Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Zwirki i Wigury 93, Warsaw 02-089, Poland.
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23
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Dimitrov JD, Roumenina LT, Andre S, Repesse Y, Atanasov BP, Jacquemin M, Saint-Remy JM, Bayry J, Kaveri SV, Lacroix-Desmazes S. Kinetics and thermodynamics of interaction of coagulation factor VIII with a pathogenic human antibody. Mol Immunol 2009; 47:290-7. [DOI: 10.1016/j.molimm.2009.09.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 09/06/2009] [Accepted: 09/08/2009] [Indexed: 10/20/2022]
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24
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Demers JP, Mittermaier A. Binding mechanism of an SH3 domain studied by NMR and ITC. J Am Chem Soc 2009; 131:4355-67. [PMID: 19267471 DOI: 10.1021/ja808255d] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Complexes between Src-homology 3 domains and proline-rich target peptides can have lifetimes on the order of milliseconds, making them too short-lived for kinetic characterization by conventional methods. Nuclear magnetic resonance (NMR) dynamics experiments are ideally suited to study such rapid binding equilibria, and additionally provide information on partly bound intermediate states. We used NMR together with isothermal titration calorimetry (ITC) to characterize the interaction of the SH3 domain from the Fyn tyrosine kinase with a 12-residue peptide at temperatures between 10 and 50 degrees C. NMR data at all temperatures are consistent with an effectively two-state binding reaction, such that any intermediates are either very weakly populated or exchange extremely rapidly with the free or bound forms. Dissociation rate constants, determined by CPMG and ZZ-exchange NMR experiments, range from k(off)(10 degrees C) = 4.5 s(-1) to k(off)(50 degrees C) = 331 s(-1). ITC data at all temperatures follow a simple two-state interaction model. Binding is favored enthalpically, with a dissociation enthalpy, DeltaH(D)(30 degrees C) = 15.4 kcal mol(-1), and disfavored entropically, with a dissociation entropy, DeltaS(D)(30 degrees C) = 20.0 cal mol(-1) K(-1). The free protein and peptide have significantly higher heat capacity than the bound complex, DeltaC(p) = 352 cal mol(-1) K(-1), which is consistent with the largely hydrophobic character of the binding interface. An Eyring plot of k(off) values gives an activation enthalpy of dissociation, DeltaH(D)(double dagger)(30 degrees C) = 19.3 kcal mol(-1) and exhibits slight curvature consistent with the ITC-derived value of DeltaC(p). The curvature suggests that nonpolar residues of the hydrophobic interface are solvated in the transition state for dissociation. Association rate constants were calculated as k(on) = k(off)/K(D), and range from k(on)(10 degrees C) = 1.03 x 10(8) M(-1) s(-1) to k(on)(50 degrees C) = 2.0 x 10(8) M(-1) s(-1), with an apparent activation enthalpy, DeltaH(A)(double dagger) = 3.4 kcal mol(-1). Both the magnitudes and temperature dependence of k(on) values are consistent with a diffusion-limited association mechanism. The combination of NMR and ITC data sheds light on how the Fyn tyrosine kinase is activated by binding to proline-rich targets, and represents a powerful approach for characterizing transient protein/ligand interactions.
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Affiliation(s)
- Jean-Philippe Demers
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada, H3A 2K6
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25
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Mohan S, Kourentzi K, Schick KA, Uehara C, Lipschultz CA, Acchione M, Desantis ME, Smith-Gill SJ, Willson RC. Association energetics of cross-reactive and specific antibodies. Biochemistry 2009; 48:1390-8. [PMID: 19166328 DOI: 10.1021/bi801901d] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
HyHEL-8, HyHEL-10, and HyHEL-26 (HH8, HH10, and HH26, respectively) are murine monoclonal IgG(1) antibodies which share over 90% variable-region amino acid sequence identity and recognize identical structurally characterized epitopes on hen egg white lysozyme (HEL). Previous immunochemical and surface plasmon resonance-based studies have shown that these antibodies differ widely in their tolerance of mutations in the epitope. While HH8 is the most cross-reactive, HH26 is rigidified by a more extensive network of intramolecular salt links and is highly specific, with both association and dissociation rates strongly affected by epitope mutations. HH10 is of intermediate specificity, and epitope mutations produce changes primarily in the dissociation rate. Calorimetric characterization of the association energetics of these three antibodies with the native antigen HEL and with Japanese quail egg white lysozyme (JQL), a naturally occurring avian variant, shows that the energetics of interaction correlate with cross-reactivity and specificity. These results suggest that the greater cross-reactivity of HH8 may be mediated by a combination of conformational flexibility and less specific intermolecular interactions. Thermodynamic calculations suggest that upon association HH8 incurs the largest configurational entropic penalty and also the smallest loss of enthalpic driving force with variant antigen. Much smaller structural perturbations are expected in the formation of the less flexible HH26 complex, and the large loss of enthalpic driving force observed with variant antigen reflects its specificity. The observed thermodynamic parameters correlate well with the observed functional behavior of the antibodies and illustrate fundamental differences in thermodynamic characteristics between cross-reactive and specific molecular recognition.
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Affiliation(s)
- S Mohan
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204-4004, USA
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26
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Potty ASR, Kourentzi K, Fang H, Jackson GW, Zhang X, Legge GB, Willson RC. Biophysical characterization of DNA aptamer interactions with vascular endothelial growth factor. Biopolymers 2009; 91:145-56. [PMID: 19025993 DOI: 10.1002/bip.21097] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The binding of a DNA aptamer (5'-CCGTCTTCCAGACAAGAGTGCAGGG-3') to recombinant human vascular endothelial growth factor (VEGF(165)) was characterized using surface plasmon resonance (SPR), fluorescence anisotropy and isothermal titration calorimetry (ITC). Results from both fluorescence anisotropy and ITC indicated that a single aptamer molecule binds to each VEGF homodimer, unlike other VEGF inhibitors that exhibit 2(ligand):1(VEGF homodimer) stoichiometry. In addition, ITC revealed that the association of the aptamer to VEGF at 20 degrees C is enthalpically driven, with an unfavorable entropy contribution. SPR kinetic studies, with careful control of possible mass transfer effects, demonstrated that the aptamer binds to VEGF with an association rate constant k(on) = 4.79 +/- 0.03 x 10(4) M(-1) s(-1) and a dissociation rate constant k(off) = 5.21 +/- 0.02 x 10(-4) s(-1) at 25 degrees C. Key recognition hot-spots were determined by a combination of aptamer sequence substitutions, truncations, and extensions. Most single-nucleotide substitutions, particularly within an mfold-predicted stem, suppress binding, whereas those within a predicted loop have a minimal effect. The 5'-end of the aptamer plays a key role in VEGF recognition, as a single-nucleotide truncation abolished VEGF binding. Conversely, an 11-fold increase in the association rate (and affinity) is observed with a single cytosine nucleotide extension, due to pairing of the 3'-GGG with 5'-CCC in the extended aptamer. Our approach effectively maps the secondary structural elements in the free aptamer, which present the unpaired interface for high affinity VEGF recognition. These data demonstrate that a directed binding analysis can be used in concert with library screening to characterize and improve aptamer/ligand recognition.
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27
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Levy M, Ellington AD. Directed evolution of streptavidin variants using in vitro compartmentalization. ACTA ACUST UNITED AC 2008; 15:979-89. [PMID: 18804035 DOI: 10.1016/j.chembiol.2008.07.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Revised: 07/14/2008] [Accepted: 07/18/2008] [Indexed: 10/21/2022]
Abstract
We have developed and implemented an in vitro compartmentalization (IVC) selection scheme for the identification of streptavidin (SA) variants with altered specificities for the biotin analog desthiobiotin. Wild-type SA and selected variants bind desthiobiotin with similar affinities (approximately 10(-13) M), but the variants have off rates almost 50 times slower and a half-life for dissociation of 24 hr at 25 degrees C. The utility of streptavidin variants with altered specificities and kinetic properties was shown by constructing protein microarrays that could be used to differentially organize and immobilize DNAs bearing these ligands. The methods we have developed should prove to be generally useful for generating a variety of novel SA reagents and for evolving other extremely high-affinity protein:ligand couples.
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Affiliation(s)
- Matthew Levy
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
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28
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Influence of macromolecular crowding on protein-protein association rates--a Brownian dynamics study. Biophys J 2008; 95:5030-6. [PMID: 18757562 DOI: 10.1529/biophysj.108.136291] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The high total concentration of macromolecules, often referred to as macromolecular crowding, is one of the characteristic features of living cells. Macromolecular crowding influences interactions between many types of macromolecules, with consequent effects on, among others, the rates of reactions occurring in the cell. Simulations to study the influence of crowding on macromolecular association rate were performed using a modified Brownian dynamics protocol. The calculated values of the time-dependent self-diffusion coefficients in different crowding conditions are in a very good agreement with those obtained by other authors. Simulations of the complex formation between the monoclonal antibody HyHEL-5 and its antigen hen egg lysozyme, both represented at atomic level detail, show that the calculated association rates strongly depend on the volume excluded by crowding. The rate obtained for the highest concentration of crowding particles is greater than twofold higher than the rate for proteins without crowding.
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29
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Díez Montoro R, Salabert Salvador M, Moreno Frigols J. Prediction of calibration curves in ria of digoxin. J Pharm Biomed Anal 2008; 47:435-41. [DOI: 10.1016/j.jpba.2008.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2007] [Revised: 01/08/2008] [Accepted: 01/14/2008] [Indexed: 10/22/2022]
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30
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Hantgan RR, Stahle MC, Horita DA. Entropy Drives Integrin αIIbβ3:Echistatin Binding—Evidence from Surface Plasmon Resonance Spectroscopy. Biochemistry 2008; 47:2884-92. [DOI: 10.1021/bi701877a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Roy R. Hantgan
- Department of Biochemistry, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, North Carolina 27157-1016
| | - Mary C. Stahle
- Department of Biochemistry, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, North Carolina 27157-1016
| | - David A. Horita
- Department of Biochemistry, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, North Carolina 27157-1016
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31
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Kourentzi K, Srinivasan M, Smith-Gill SJ, Willson RC. Conformational flexibility and kinetic complexity in antibody–antigen interactions. J Mol Recognit 2008; 21:114-21. [DOI: 10.1002/jmr.874] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Svitel J, Boukari H, Van Ryk D, Willson RC, Schuck P. Probing the functional heterogeneity of surface binding sites by analysis of experimental binding traces and the effect of mass transport limitation. Biophys J 2007; 92:1742-58. [PMID: 17158569 PMCID: PMC1796841 DOI: 10.1529/biophysj.106.094615] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Accepted: 11/16/2006] [Indexed: 11/18/2022] Open
Abstract
Many techniques rely on the binding activity of surface-immobilized proteins, including antibody-based affinity biosensors for the detection of analytes, immunoassays, protein arrays, and surface plasmon resonance biosensors for the study of thermodynamic and kinetic aspects of protein interactions. To study the functional homogeneity of the surface sites and to characterize their binding properties, we have recently proposed a computational tool to determine the distribution of affinity and kinetic rate constants from surface binding progress curves. It is based on modeling the experimentally measured binding signal as a superposition of signals from binding to sites spanning a range of rate and equilibrium constants, with regularization providing the most parsimonious distribution consistent with the data. In the present work, we have expanded the scope of this approach to include a compartment-like transport step, which can describe competitive binding to different surface sites in a zone of depleted analyte close to the sensor surface. This approach addresses a major difficulty in the analysis of surface binding where both transport limitation as well as unknown surface site heterogeneity may be present. In addition to the kinetic binding parameters of the ensemble of surface sites, it can provide estimates for effective transport rate constants. Using antibody-antigen interactions as experimental model systems, we studied the effects of the immobilization matrix and of the analyte flow-rate on the effective transport rate constant. Both were experimentally observed to influence mass transport. The approximate description of mass transport by a compartment model becomes critical when applied to strongly transport-controlled data, and we examined the limitations of this model. In the presence of only moderate mass transport limitation the compartment model provides a good description, but this approximation breaks down for strongly transport-limited surface binding. In the latter regime, we report experimental evidence for the formation of gradients within the sensing volume of the evanescent field biosensor used.
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Affiliation(s)
- Juraj Svitel
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
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33
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Díez Montoro R, Salabert Salvador MT, Moreno Frigols JL. Biexponential model for the kinetics of the substitution reaction in the radioimmunoassay of triiodothyronine. Scand J Clin Lab Invest 2007; 67:848-58. [PMID: 17852821 DOI: 10.1080/00365510701408541] [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: 05/17/2023]
Abstract
The influence of initial concentrations, ionic strength, viscosity and temperature on the substitution reaction of 125I-triiodothyronine (T3) (M) by unlabelled T3 (Q) in the immunocomplex PM (P = anti-T3 antibody) has been studied, and a kinetic model is proposed. The apparent rate constant is dependent on the initial concentration of labelled and unlabelled T3, viscosity and temperature, and independent of ionic strength. The reaction is endothermic and is not controlled by diffusion. The results obtained are in line with the proposed model. We propose some modifications for optimizing the technique.
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Affiliation(s)
- R Díez Montoro
- Department of Physical Chemistry, Faculty of Pharmacy, Valencia, Spainb Radioisotope Service, Valencia Hospital Clínico, Valencia, Spain
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34
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Sohn J, Rudolph J. Temperature dependence of binding and catalysis for the Cdc25B phosphatase. Biophys Chem 2006; 125:549-55. [PMID: 17174465 PMCID: PMC1849978 DOI: 10.1016/j.bpc.2006.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Revised: 11/21/2006] [Accepted: 11/21/2006] [Indexed: 11/28/2022]
Abstract
Using a combination of steady-state and single-turnover kinetics, we probe the temperature dependence of substrate association and chemistry for the reaction of Cdc25B phosphatase with its Cdk2-pTpY/CycA protein substrate. The transition state for substrate association is dominated by an enthalpic barrier (DeltaH(++) of 13 kcal/mol) and has a favorable entropic contribution of 4 kcal/mol at 298 K. Phosphate transfer from Cdk2-pTpY/CycA to enzyme (DeltaH(++) of 12 kcal/mol) is enthalpically more favorable than for the small molecule substrate p-nitrophenyl phosphate (DeltaH(++) of 18 kcal/mol), yet entropically less favorable (TDeltaS(++) of 2 vs. -6 kcal/mol at 298 K, respectively). By measuring the temperature dependence of binding and catalysis for several hotspot mutants involved in binding of protein substrate, we determine the enthalpy-entropy compensations for changes in rates of association and phosphate transfer compared to the wild type system. We conclude that the transition state for enzyme-substrate association involves tight and specific contacts at the remote docking site and that phospho-transfer from Cdk2-pTpY/CycA to the pre-organized active site of the enzyme is accompanied by unfavorable entropic rearrangements that promote rapid product dissociation.
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Affiliation(s)
| | - Johannes Rudolph
- * To whom correspondence should be addressed, phone: (919) 668-6188, fax: (919) 613-8642, e-mail:
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35
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Riechmann L, Winter G. Early Protein Evolution: Building Domains from Ligand-binding Polypeptide Segments. J Mol Biol 2006; 363:460-8. [PMID: 16978646 DOI: 10.1016/j.jmb.2006.08.031] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Revised: 08/09/2006] [Accepted: 08/11/2006] [Indexed: 11/30/2022]
Abstract
It has been suggested that in the early evolution of proteins, segments of polypeptide, unable to fold in isolation, may have collapsed together to form folded proto-domains. We wondered whether the incorporation of segments with a pre-existing binding activity into a folded domain could, by fixing the ligand binding conformation and/or providing additional contacts, lead to large affinity improvements and provide an evolutionary advantage. As a model, we took a segment of polypeptide from hen egg lysozyme that in the native protein forms the binding interface with the monoclonal antibodies HyHEL5 and F10 (KD=60 pM). When expressed in bacteria the isolated segment was unfolded, readily proteolysed and only bound weakly to the antibodies (KD>1 microM). We then combined the segment with random genomic segments to create a repertoire of chimaeric polypeptides displayed on filamentous bacteriophage. By use of proteolysis (to select folded polypeptide) and anti-lysozyme antibodies (to select an active conformation) we isolated a folded dimeric protein with an enhanced antibody affinity (KD=400 pM). Unexpectedly the dimer also incorporated a single heme molecule (KD=33 nM) that stabilised the dimer (Tm=59 degrees C with heme, 35 degrees C without heme). These results show that the binding affinities of flexible polypeptide segments can be greatly enhanced on protein folding, and that the folding can be stabilised by prosthetic groups. This supports the hypothesis that sub-domain polypeptide segments with functional activities may have contributed to domain creation in early evolution.
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Affiliation(s)
- Lutz Riechmann
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
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36
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Madeo J, Gunner MR. Modeling binding kinetics at the Q(A) site in bacterial reaction centers. Biochemistry 2005; 44:10994-1004. [PMID: 16101283 PMCID: PMC2727067 DOI: 10.1021/bi050544j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacterial reaction centers (RCs) catalyze a series of electron-transfer reactions reducing a neutral quinone to a bound, anionic semiquinone. The dissociation constants and association rates of 13 tailless neutral and anionic benzo- and naphthoquinones for the Q(A) site were measured and compared. The K(d) values for these quinones range from 0.08 to 90 microM. For the eight neutral quinones, including duroquinone (DQ) and 2,3-dimethoxy-5-methyl-1,4-benzoquinone (UQ(0)), the quinone concentration and solvent viscosity dependence of the association rate indicate a second-order rate-determining step. The association rate constants (k(on)) range from 10(5) to 10(7) M(-)(1) s(-)(1). Association and dissociation rate constants were determined at pH values above the hydroxyl pK(a) for five hydroxyl naphthoquinones. These negatively charged compounds are competitive inhibitors for the Q(A) site. While the neutral quinones reach equilibrium in milliseconds, anionic hydroxyl quinones with similar K(d) values take minutes to bind or dissociate. These slow rates are independent of ionic strength, solvent viscosity, and quinone concentration, indicating a first-order rate-limiting step. The anionic semiquinone, formed by forward electron transfer at the Q(A) site, also dissociates slowly. It is not possible to measure the association rate of the unstable semiquinone. However, as the protein creates kinetic barriers for binding and releasing anionic hydroxyl quinones without greatly increasing the affinity relative to neutral quinones, it is suggested that the Q(A) site may do the same for anionic semiquinone. Thus, the slow semiquinone dissociation may not indicate significant thermodynamic stabilization of the reduced species in the Q(A) site.
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Affiliation(s)
- Jennifer Madeo
- Physics Department J-419 City College of New York 138th Street and Convent Avenue, New York, New York 10031
| | - M. R. Gunner
- Physics Department J-419 City College of New York 138th Street and Convent Avenue, New York, New York 10031
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37
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Vigdorovich V, Strong RK, Miller AD. Expression and characterization of a soluble, active form of the jaagsiekte sheep retrovirus receptor, Hyal2. J Virol 2005; 79:79-86. [PMID: 15596803 PMCID: PMC538683 DOI: 10.1128/jvi.79.1.79-86.2005] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Retrovirus entry into cells is mediated by specific interactions between virus envelope glycoproteins and cell surface receptors. Many of these receptors contain multiple membrane-spanning regions, making their purification and study difficult. The jaagsiekte sheep retrovirus (JSRV) receptor, hyaluronidase 2 (Hyal2), is a glycosylphosphatidylinositol (GPI)-anchored molecule containing no peptide transmembrane regions, making it an attractive candidate for study of retrovirus entry. Further, the hyaluronidase activity reported for human Hyal2, combined with its broad expression pattern, may point to a critical function of Hyal2 in the turnover of hyaluronan, a major extracellular matrix component. Here we describe the properties of a soluble form of human Hyal2 (sHyal2) purified from a baculoviral expression system. sHyal2 is a 54-kDa monomer with weak hyaluronidase activity compared to that of the known hyaluronidase Spam1. In contrast to a previous report indicating that Hyal2 cleaved hyaluronan to a limit product of 20 kDa and was active only at acidic pH, we find that sHyal2 is capable of further degradation of hyaluronan and is active over a broad pH range, consistent with Hyal2 being active at the cell surface where it is normally localized. Interaction of sHyal2 with the JSRV envelope glycoprotein was analyzed by viral inhibition assays, showing >90% inhibition of transduction at 28 nM sHyal2, and by surface plasmon resonance, revealing a remarkably tight specific interaction with a dissociation constant (KD) of 32 +/- 1 pM. In contrast to results obtained with avian retroviruses, purified receptor was not capable of promoting transduction of cells that do not express the virus receptor.
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Affiliation(s)
- Vladimir Vigdorovich
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA
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38
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Stewart RC, Van Bruggen R. Association and dissociation kinetics for CheY interacting with the P2 domain of CheA. J Mol Biol 2004; 336:287-301. [PMID: 14741223 DOI: 10.1016/j.jmb.2003.11.059] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The chemotaxis system of Escherichia coli makes use of an extended two-component sensory response pathway in which CheA, an autophosphorylating protein histidine kinase (PHK) rapidly passes its phosphoryl group to CheY, a phospho-accepting response regulator protein (RR). The CheA-->CheY phospho-transfer reaction is 100-1000 times faster than the His-->Asp phospho-relays that operate in other (non-chemotaxis) two-component regulatory systems, suggesting that CheA and CheY have unique features that enhance His-->Asp phospho-transfer kinetics. One such feature could be the P2 domain of CheA. P2 encompasses a binding site for CheY, but an analogous RR-binding domain is not found in other PHKs. In previous work, we removed P2 from CheA, and this decreased the catalytic efficiency of CheA-->CheY phospho-transfer by a factor of 50-100. Here we examined the kinetics of the binding interactions between CheY and P2. The rapid association reaction (k(assn) approximately 10(8)M(-1)s(-1) at 25 degrees C and micro=0.03 M) exhibited a simple first-order dependence on P2 concentration and appeared to be largely diffusion-limited. Ionic strength (micro) had a moderate effect on k(assn) in a manner predictable based on the calculated electrostatic interaction energy of the protein binding surfaces and the expected Debye-Hückel shielding. The speed of binding reflects, in part, electrostatic interactions, but there is also an important contribution from the inherent plasticity of the complex and the resulting flexibility that this allows during the process of complex formation. Our results support the idea that the P2 domain of CheA contributes to the overall speed of phospho-transfer by promoting rapid association between CheY and CheA. However, this alone does not account for the ability of the chemotaxis system to operate much more rapidly than other two-component systems: k(cat) differences indicate that CheA and CheY also achieve the chemical events of phospho-transfer more rapidly than do PHK-RR pairs of slower systems.
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Affiliation(s)
- Richard C Stewart
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
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39
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Kozer N, Schreiber G. Effect of Crowding on Protein–Protein Association Rates: Fundamental Differences between Low and High Mass Crowding Agents. J Mol Biol 2004; 336:763-74. [PMID: 15095986 DOI: 10.1016/j.jmb.2003.12.008] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2003] [Revised: 11/28/2003] [Accepted: 12/03/2003] [Indexed: 11/16/2022]
Abstract
Physiological media constitutes a crowded environment that serves as the field of action for protein-protein interaction in vivo. Measuring protein-protein interaction in crowded solutions can mimic this environment. In this work we follow the process of protein-protein association and its rate constants (k(on)) of the beta-lactamase (TEM)-beta-lactamase inhibitor protein (BLIP) complex in crowded solution using both low and high molecular mass crowding agents. In all crowded solutions (0-40% (w/w) of ethylene glycol (EG), poly(ethylene glycol) (PEG) 200, 1000, 3350, 8000 Da Ficoll-70 and Haemaccel the measured absolute k(on), but not k(off) values, were found to be slower as compared to buffer. However, there is a fundamental difference between low and high mass crowding agents. In the presence of low mass crowding agents and Haemaccel k(on) depends inversely on the solution viscosity. In high mass polymer solutions k(on) changes only slightly, even at viscosities 12-fold higher than water. The border between low and high molecular mass polymers is sharp and is dictated by the ratio between the polymer length (L) and its persistence length (Lp). Polymers that are long enough to form a flexible coil (L/Lp > 2) behave as high molecular mass polymers and those who are unable to do so (L/Lp < 2) behave as low molecular mass polymers. We concluded that although polymers solution are crowded, this property is not uniform; i.e. there are areas in the solution that contain bulk water, and in these areas proteins can diffuse and associate almost as if they were in diluted environment. This porous medium may be taken as mimicking some aspects of the cellular environment, where many of the macromolecules are organized along membranes and the cytoskeleton. To determine the contribution of electrostatic attraction between proteins in crowded milieu, we followed k(on) of wt-TEM and three BLIP analogs with up to 100-fold increased values of k(on) due to electrostatic steering. Faster associating BLIP variants keep their relative advantage in all crowded solutions, including Haemaccel. This result suggests that faster associating protein complexes keep their advantage also in complex environment.
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Affiliation(s)
- Noga Kozer
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100 Israel
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40
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García Gómez J, Moreno Frigols JL. Comparison between mono- and bi-exponential models for reaction kinetics in the immunoradiometric assay of neuron-specific enolase. J Pharm Biomed Anal 2003; 33:891-901. [PMID: 14656580 DOI: 10.1016/s0731-7085(03)00418-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
This paper studies the kinetics of the antigen-antibody reactions involved in the analytical determination of neuron-specific enolase (NSE) by means of radiometric immunoassay (IRMA). For the global process, kinetics were found to be dependent on analyte and labelled antibody concentrations, such dependence fitting with the models described in previous papers. Viscosity results clearly indicate its negative influence on the direct reaction rate. Ionic strength shows noticeable but not too relevant effects, which suggests that the variation caused by the glycerol addition is not due to the influence of the dielectric constant of the solutions used. The effect of temperature shows activation parameters similar to the viscous flow energy of water, which suggests diffusion control for the global process. The analysis of the kinetic data of the experiences conducted can be explained by admitting that the antigen-antibody binding takes place through two different binding site types.
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Affiliation(s)
- J García Gómez
- Department of Physical Chemistry, Valencia Pharmacy Faculty, Radioisotope Service, Valencia University Hospital, Avda. Vicent Andrés Estellés s/n, 46110 Burjassot (Valencia), Spain
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41
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Garcia Gomez J, Moreno Frigols JL. Kinetics and equilibrium in the immunoradiometric assay (IRMA) of thyroglobuline. J Immunoassay Immunochem 2003; 23:347-67. [PMID: 12227420 DOI: 10.1081/ias-120013033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
This paper studies the kinetics of the thyroglobuline reaction with its specific antibody immobilised on the inner wall of the reaction tube, and the subsequent binding of the immunocomplex formed with a second 125I-labelled antibody. These reactions are used in the immunoradiometric determination of thyroglobuline. Independent variables were analyte and labelled antibody, temperature, viscosity, and the medium's ionic strength. For the global process, mono-exponential kinetics were found to be dependent on the concentrations, such dependence fitting with the models discussed in the paper. Viscosity results clearly indicate its negative influence on the direct reaction rate. Ionic strength shows noticeable, but not too relevant, effects, which suggests that the variation caused by the glycerol addition is not due to the influence of the dielectric constant of the solutions used. The effect of temperature shows activation parameters similar to the viscous flow energy of water, which suggests diffusion control for the global process.
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Affiliation(s)
- J Garcia Gomez
- Department of Physical Chemistry, Faculty of Pharmacy, Valencia University Hospital, Spain
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42
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Olivas Arroyo C, Duart Duart MJ, Moreno Frígols JL. Kinetics and equilibrium in insulin radioimmunoassay. J Immunoassay Immunochem 2003; 23:407-28. [PMID: 12458725 DOI: 10.1081/ias-120015473] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The kinetics of insulin reaction has been studied with its specific antibody immobilized on the inner wall of the reaction tube; the radioimmunoanalytical determination of such a substance is based on the reaction. Independent variables were labelled and unlabelled insulin concentrations, temperature, viscosity, and the medium's ionic strength. Biexponential kinetics was found to be dependent on the concentrations fitted to the models discussed in the paper. The effect of temperature shows activation parameters similar to the viscous flow energy of water, which suggests that the reaction is diffusion-controlled. The results of the viscosity analysis points at the clearly negative influence of viscosity upon the direct reaction rate. Ionic strength has a noticeable, though not relevant, effect which seems to indicate that the variation resulting from the glycerol addition is not due to the influence of the dielectric constant in the solutions used.
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Affiliation(s)
- C Olivas Arroyo
- Department of Physical Chemistry, Faculty of Pharmacy, University of Valencia, Avda. Vicent Andrés Estellés s/n, 46110 Burjassot, Valencia, Spain
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43
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Duart Duart MJ, Arroyo CO, Moreno Frígols JL. Validation of a kinetic model for the reactions in RIA. Clin Chem Lab Med 2002; 40:1161-7. [PMID: 12521236 DOI: 10.1515/cclm.2002.203] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The goal of this work was to check the validity of a model previously described for the study of kinetics of the processes taking place during the immuno-analytical measurement of insulin. The antibody was immobilized on the suface wall of the reaction tube. Tracer and insulin concentration, temperature, viscosity and ionic strength in the reaction medium were taken as independent variables. Biexponential kinetics depending on the concentration was observed. The results of the viscosity study show a clear negative influence of this parameter on the direct reaction velocity. Ionic strength had a slight effect, which suggests that the observed variation due to the addition of glycerol is not induced by the influence of the dielectric constant of the solution used. The effect of the temperature shows activation parameters similar to water flow-viscosity energy, which suggests a diffusion control for the reaction. The proposed model correctly interprets the influence of the studied variables.
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Affiliation(s)
- Maria J Duart Duart
- Departamento Química Física, Facultad de Farmacia de Valencia, Hospital Clinico Universitario de Valencia, Spain
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44
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Jarrett NM, Djavadi-Ohaniance L, Willson RC, Tachibana H, Goldberg ME. Immunochemical pulsed-labeling characterization of intermediates during hen lysozyme oxidative folding. Protein Sci 2002; 11:2584-95. [PMID: 12381842 PMCID: PMC2373722 DOI: 10.1110/ps.0221802] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2002] [Revised: 08/13/2002] [Accepted: 08/15/2002] [Indexed: 10/27/2022]
Abstract
Previous studies have shown that reduced hen egg white lysozyme refolds and oxidizes according to a linear model, in which the number of disulfide bonds increases sequentially. In this study, we describe the kinetics of native tertiary structure formation during the oxidative-renaturation of reduced hen egg white lysozyme, as monitored using an immunochemical pulsed-labeling method based on enzyme-linked immunosorbent assay (ELISA) in conjunction with two monoclonal antibodies (mAb). Each of these antibodies recognizes a separate face of the native lysozyme surface and, more importantly, each epitope is composed of discontinuous regions of the polypeptide chain. Renaturation kinetics were studied under the same refolding conditions as previous investigations of the kinetics of the regain of far-UV CD, fluorescence, enzymatic activity, and disulfide bonds. Comparison of our results with the results from those studies showed that the immunoreactivity (i.e., the native fold) of the alpha-domain appeared in intermediates containing two SS bonds only (C6-C127 and C30-C115), while the immunoreactivity of the beta-domain appeared together with the formation of the third SS bond (C64-C80). Thus, the alpha-domain folds before the beta-domain during the oxidative folding of reduced lysozyme.
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Affiliation(s)
- Nicole M Jarrett
- Unité de Repliement et Modélisation des Protéines (CNRS URA 2185), Institut Pasteur, 75254 Paris Cedex 15, France
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45
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García Gómez J, Porcar Pons M, Moreno Frigols JL. Some kinetic aspects in the immunoradiometric assay of insulin-like growth factor binding protein-3. J Pharm Biomed Anal 2002; 29:307-15. [PMID: 12062691 DOI: 10.1016/s0731-7085(02)00090-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In this article the kinetics of the insulin-like growth factor binding protein-3 (IGFBP-3) reaction with its specific antibody immobilised on the inner wall of the reaction tube, and the subsequent binding of the immunocomplex formed with a second (125)I-labelled antibody are described. These reactions are used in the immunoradiometric determination of IGFBP-3. Independent variables were analyte and labelled antibody, temperature, viscosity, and the ionic strength of the medium. For the global process mono-exponential kinetics were found to be dependent on the concentrations, such dependence fitting with the models discussed in this paper. Viscosity results clearly indicate its negative influence on the direct reaction rate. Ionic strength shows noticeable but not too relevant effects, which suggests that the variation caused by the glycerol addition is not due to the influence of the dielectric constant of the solutions used. The effect of temperature shows activation parameters similar to the viscous flow energy of water, which suggests diffusion control for the global process.
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Affiliation(s)
- J García Gómez
- Department of Physical Chemistry, Faculty of Pharmacy, Radioisotope Service, Valencia University Hospital, Avenida Vicent Andrés Estellés s/n, 46110 Burjassot, Valencia, Spain
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46
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Abstract
The structure of a protein-protein interaction, its affinity and thermodynamic characteristics depict a 'frozen' state of a complex. This picture ignores the kinetic nature of complex formation and dissociation, which are of major biological and biophysical interest. This review highlights recent advances in deciphering the kinetic pathway of protein-protein complexation, the nature of the encounter complex, transition state and intermediate along the reaction, and the effects of mutation, viscosity, pH and salt on association.
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Affiliation(s)
- Gideon Schreiber
- Department of Biological Chemistry, Weizmann Institute of Science, 76100, Rehovot, Israel.
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47
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Banerjee A, Srilatha NS, Murthy GS. Real-time kinetic analysis of hCG-monoclonal antibody interaction using radiolabeled hCG probe: presence of two forms of Ag-mAb complex as revealed by solid phase dissociation studies. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1569:21-30. [PMID: 11853953 DOI: 10.1016/s0304-4165(01)00228-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Real-time kinetics of ligand-ligate interaction has predominantly been studied by either fluorescence or surface plasmon resonance based methods. Almost all such studies are based on association between the ligand and the ligate. This paper reports our analysis of dissociation data of monoclonal antibody-antigen (hCG) system using radio-iodinated hCG as a probe and nitrocellulose as a solid support to immobilize mAb. The data was analyzed quantitatively for a one-step and a two-step model. The data fits well into the two-step model. We also found that a fraction of what is bound is non-dissociable (tight-binding portion (TBP)). The TBP was neither an artifact of immobilization nor does it interfere with analysis. It was present when the reaction was carried out in homogeneous solution in liquid phase. The rate constants obtained from the two methods were comparable. The work reported here shows that real-time kinetics of other ligand-ligate interaction can be studied using nitrocellulose as a solid support.
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Affiliation(s)
- Ashish Banerjee
- Primate Research Laboratory, Department of Molecular Reproduction Development and Genetics, Indian Institute of Science, Bangalore 560 012, India
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48
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Olivas Arroyo C, Moreno Frígols JL. Influence of viscosity and ionic strength on the reaction kinetics of aldosterone and androstendione and their specific antibodies. J Pharm Biomed Anal 2001; 26:547-62. [PMID: 11516905 DOI: 10.1016/s0731-7085(01)00454-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This paper analyses the influence of viscosity and ionic strength on the kinetics and equilibrium of the reactions of (125)I labelled androstendione and aldosterone with their specific antibodies used in the radioactive immunoassay determination of such hormones. Bi-exponential and irreversible kinetics is found for androstendione, and single-exponential and reversible ones for aldosterone. The results of the viscosity analysis reflect clear negative influence on direct reaction rate. Ionic strength excerpts some influence but not in a significant way, which suggests that the variation resulting from the effect of the glycerol addition is not due to the influence of the dielectric constant of the solutions used. The apparent product of the electrical charges is 0.228 for aldosterone, and 0.230 and -0.230 for androstendione. Results show diffusive control for both cases.
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Affiliation(s)
- C Olivas Arroyo
- Department of Physical Chemistry, Faculty of Pharmacy, Avda. Vicent Andrés Estellés s/n 46110 Burjassot Valencia, Spain
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49
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Abstract
A free energy decomposition scheme has been developed and tested on antibody-antigen and protease-inhibitor binding for which accurate experimental structures were available for both free and bound proteins. Using the x-ray coordinates of the free and bound proteins, the absolute binding free energy was computed assuming additivity of three well-defined, physical processes: desolvation of the x-ray structures, isomerization of the x-ray conformation to a nearby local minimum in the gas-phase, and subsequent noncovalent complex formation in the gas phase. This free energy scheme, together with the Generalized Born model for computing the electrostatic solvation free energy, yielded binding free energies in remarkable agreement with experimental data. Two assumptions commonly used in theoretical treatments; viz., the rigid-binding approximation (which assumes no conformational change upon complexation) and the neglect of vdW interactions, were found to yield large errors in the binding free energy. Protein-protein vdW and electrostatic interactions between complementary surfaces over a relatively large area (1400--1700 A(2)) were found to drive antibody-antigen and protease-inhibitor binding.
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Affiliation(s)
- S Y Noskov
- Institute of Biomedical Sciences, Academia Sinica, 11529 Taipei, Taiwan
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50
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Shiroishi M, Yokota A, Tsumoto K, Kondo H, Nishimiya Y, Horii K, Matsushima M, Ogasahara K, Yutani K, Kumagai I. Structural evidence for entropic contribution of salt bridge formation to a protein antigen-antibody interaction: the case of hen lysozyme-HyHEL-10 Fv complex. J Biol Chem 2001; 276:23042-50. [PMID: 11297547 DOI: 10.1074/jbc.m100480200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A structural and thermodynamic study of the entropic contribution of salt bridge formation to the interaction between hen egg white lysozyme (HEL) and the variable domain fragment (Fv) of anti-HEL antibody, HyHEL-10, was carried out. Three Fv mutants (HD32A, HD96A, and HD32AD96A) were prepared, and the interactions between the mutant Fvs and HEL were investigated. Crystallography revealed that the overall structures of these mutant complexes were almost identical to that of wild-type Fv. Little structural changes were observed in the HD32AD96A mutant-HEL complex, and two water molecules were introduced into the mutation site, indicating that the two water molecules structurally compensated for the complete removal of the salt bridges. This result suggests that the entropic contribution of the salt bridge originates from dehydration. In the singly mutated complexes, one water molecule was also introduced into the mutated site, bridging the antigen-antibody interface. However, a local structural difference was observed in the HD32A Fv-HEL complex, and conformational changes occurred due to changes in the relative orientation of the heavy chain to the light chain upon complexation in HD96A Fv-HEL complexes. The reduced affinity of these single mutants for the antigen originates from the increase in entropy loss, indicating that these structural changes also introduced an increase in entropy loss. These results suggest that salt bridge formation makes an entropic contribution to the protein antigen-antibody interaction through reduction of entropy loss due to dehydration and structural changes.
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Affiliation(s)
- M Shiroishi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba-yama 07, Aoba-ku, Sendai 980-8579, Japan
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