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Wang TY, Rukundo JL, Mao Z, Krylov SN. Maximizing the Accuracy of Equilibrium Dissociation Constants for Affinity Complexes: From Theory to Practical Recommendations. ACS Chem Biol 2024. [PMID: 39121869 DOI: 10.1021/acschembio.4c00259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2024]
Abstract
The equilibrium dissociation constant (Kd) is a major characteristic of affinity complexes and one of the most frequently determined physicochemical parameters. Despite its significance, the values of Kd obtained for the same complex under similar conditions often exhibit considerable discrepancies and sometimes vary by orders of magnitude. These inconsistencies highlight the susceptibility of Kd determination to large systematic errors, even when random errors are small. It is imperative to both minimize and quantitatively assess the systematic errors inherent in Kd determination. Traditionally, Kd values are determined through nonlinear regression of binding isotherms. This analysis utilizes three variables: concentrations of two reactants and a fraction R of unbound limiting reactant. The systematic errors in Kd arise directly from systematic errors in these variables. Therefore, to maximize the accuracy of Kd, this study thoroughly analyzes the sources of systematic errors within the three variables, including (i) non-additive signals to calculate R, (ii) mis-calibrated experimental instruments, (iii) inaccurate calibration parameters, (iv) insufficient incubation time, (v) unsaturated binding isotherm, (vi) impurities in the reactants, and (vii) solute adsorption onto surfaces. Through this analysis, we illustrate how each source contributes to inaccuracies in the determination of Kd and propose strategies to minimize these contributions. Additionally, we introduce a method for quantitatively assessing the confidence intervals of systematic errors in concentrations, a crucial step toward quantitatively evaluating the accuracy of Kd. While presenting original findings, this paper also reiterates the fundamentals of Kd determination, hence guiding researchers across all proficiency levels. By shedding light on the sources of systematic errors and offering strategies for their mitigation, our work will help researchers enhance the accuracy of Kd determination, thereby making binding studies more reliable and the conclusions drawn from such studies more robust.
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Affiliation(s)
- Tong Ye Wang
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Jean-Luc Rukundo
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Zhiyuan Mao
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Sergey N Krylov
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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2
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Krait S, Salgado A, Villani C, Naumann L, Neusüß C, Chankvetadze B, Scriba GK. Unusual complexation behavior between daclatasvir and γ-Cyclodextrin. A multiplatform study. J Chromatogr A 2020; 1628:461448. [DOI: 10.1016/j.chroma.2020.461448] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/30/2020] [Accepted: 08/01/2020] [Indexed: 12/14/2022]
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3
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Zeidman Kalman T, Khalandovsky R, Tenenbaum Gonikman E, Bercovici M. Monitoring Dissociation Kinetics during Electrophoretic Focusing to Enable High-Specificity Nucleic Acid Detection. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201711673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tal Zeidman Kalman
- Russell Berrie Nanotechnology Institute; Technion-Israel Institute of Technology; Haifa 3200003 Israel
| | - Rebecca Khalandovsky
- Faculty of Mechanical Engineering; Technion-Israel Institute of Technology; Haifa 3200003 Israel
| | - Elena Tenenbaum Gonikman
- Faculty of Mechanical Engineering; Technion-Israel Institute of Technology; Haifa 3200003 Israel
| | - Moran Bercovici
- Faculty of Mechanical Engineering; Technion-Israel Institute of Technology; Haifa 3200003 Israel
- Russell Berrie Nanotechnology Institute; Technion-Israel Institute of Technology; Haifa 3200003 Israel
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4
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Zeidman Kalman T, Khalandovsky R, Tenenbaum Gonikman E, Bercovici M. Monitoring Dissociation Kinetics during Electrophoretic Focusing to Enable High-Specificity Nucleic Acid Detection. Angew Chem Int Ed Engl 2018; 57:3343-3348. [DOI: 10.1002/anie.201711673] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/31/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Tal Zeidman Kalman
- Russell Berrie Nanotechnology Institute; Technion-Israel Institute of Technology; Haifa 3200003 Israel
| | - Rebecca Khalandovsky
- Faculty of Mechanical Engineering; Technion-Israel Institute of Technology; Haifa 3200003 Israel
| | - Elena Tenenbaum Gonikman
- Faculty of Mechanical Engineering; Technion-Israel Institute of Technology; Haifa 3200003 Israel
| | - Moran Bercovici
- Faculty of Mechanical Engineering; Technion-Israel Institute of Technology; Haifa 3200003 Israel
- Russell Berrie Nanotechnology Institute; Technion-Israel Institute of Technology; Haifa 3200003 Israel
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5
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Miyabe K, Suzuki N, Shimazaki Y. Determination of Association and Dissociation Rate Constants in an Inclusion Complex System between Thymol and Sulfated-β-cyclodextrin by Moment Analysis - Affinity Capillary Electrophoresis. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2016. [DOI: 10.1246/bcsj.20160193] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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6
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Miyabe K, Shimazaki Y. Moment Analysis of Affinity Kinetics in Inclusion Complex System between Thymol and Sulfated-β-cyclodextrin by Chromatographic Capillary Electrophoresis (CCE). BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2015. [DOI: 10.1246/bcsj.20150203] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Kanji Miyabe
- Department of Chemistry, Faculty of Science, Rikkyo University
| | - Youki Shimazaki
- Department of Chemistry, Faculty of Science, Rikkyo University
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Zheng X, Bi C, Li Z, Podariu M, Hage DS. Analytical methods for kinetic studies of biological interactions: A review. J Pharm Biomed Anal 2015; 113:163-80. [PMID: 25700721 PMCID: PMC4516701 DOI: 10.1016/j.jpba.2015.01.042] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/16/2015] [Accepted: 01/19/2015] [Indexed: 01/13/2023]
Abstract
The rates at which biological interactions occur can provide important information concerning the mechanism and behavior of these processes in living systems. This review discusses several analytical methods that can be used to examine the kinetics of biological interactions. These techniques include common or traditional methods such as stopped-flow analysis and surface plasmon resonance spectroscopy, as well as alternative methods based on affinity chromatography and capillary electrophoresis. The general principles and theory behind these approaches are examined, and it is shown how each technique can be utilized to provide information on the kinetics of biological interactions. Examples of applications are also given for each method. In addition, a discussion is provided on the relative advantages or potential limitations of each technique regarding its use in kinetic studies.
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Affiliation(s)
- Xiwei Zheng
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Cong Bi
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Zhao Li
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Maria Podariu
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - David S Hage
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA.
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8
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Whitty EG, Maniego AR, Bentwitch SA, Guillaneuf Y, Jones MR, Gaborieau M, Castignolles P. Cellular Response to Linear and Branched Poly(acrylic acid). Macromol Biosci 2015; 15:1724-34. [PMID: 26257305 DOI: 10.1002/mabi.201500153] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/29/2015] [Indexed: 12/14/2022]
Abstract
Poly(acrylic acid-co-sodium acrylate) (PNaA) is a pH-responsive polymer with potential in anticancer drug delivery. The cytotoxicity and intracellular effects of 3-arm star, hyperbranched and linear PNaA were investigated with L1210 progenitor leukemia cells and L6 myoblast cells. Free solution capillary electrophoresis demonstrated interactions of PNaA with serum proteins. In a 72 h MTT assay most PNaAs exhibited a IC50 between 7 and 14 mmol L(-1), showing that precipitation may be a sufficient purification for PNaA dilute solutions. Dialyzed 3-arm star and hyperbranched PNaA caused an increase in L6 cell viability, challenging the suitability of MTT as cytotoxicity assay for PNaA. Fluorescent confocal microscopy revealed merging of cellular lipids after exposure to PNaA, likely caused by serum starvation.
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Affiliation(s)
- Elizabeth G Whitty
- University of Western Sydney, Molecular Medicine Research Group, Locked Bag 1797, Penrith, New South Wales, 2751, Australia.,University of Western Sydney, Australian Centre for Research on Separation Science (ACROSS), Locked Bag 1797, Penrith, New South Wales, 2751, Australia.,University of Western Sydney, School of Science and Health, Locked Bag 1797, Penrith, New South Wales, 2751, Australia
| | - Alison R Maniego
- University of Western Sydney, Molecular Medicine Research Group, Locked Bag 1797, Penrith, New South Wales, 2751, Australia.,University of Western Sydney, Australian Centre for Research on Separation Science (ACROSS), Locked Bag 1797, Penrith, New South Wales, 2751, Australia.,University of Western Sydney, School of Science and Health, Locked Bag 1797, Penrith, New South Wales, 2751, Australia
| | - Sharon A Bentwitch
- University of Western Sydney, Molecular Medicine Research Group, Locked Bag 1797, Penrith, New South Wales, 2751, Australia.,University of Western Sydney, Australian Centre for Research on Separation Science (ACROSS), Locked Bag 1797, Penrith, New South Wales, 2751, Australia.,University of Western Sydney, School of Science and Health, Locked Bag 1797, Penrith, New South Wales, 2751, Australia
| | - Yohann Guillaneuf
- CNRS, Institut de Chimie Radicalaire, Aix-Marseille Université, UMR 7273, 13397, Marseille, France
| | - Mark R Jones
- University of Western Sydney, School of Science and Health, Locked Bag 1797, Penrith, New South Wales, 2751, Australia
| | - Marianne Gaborieau
- University of Western Sydney, Molecular Medicine Research Group, Locked Bag 1797, Penrith, New South Wales, 2751, Australia. .,University of Western Sydney, Australian Centre for Research on Separation Science (ACROSS), Locked Bag 1797, Penrith, New South Wales, 2751, Australia. .,University of Western Sydney, School of Science and Health, Locked Bag 1797, Penrith, New South Wales, 2751, Australia.
| | - Patrice Castignolles
- University of Western Sydney, Australian Centre for Research on Separation Science (ACROSS), Locked Bag 1797, Penrith, New South Wales, 2751, Australia.,University of Western Sydney, School of Science and Health, Locked Bag 1797, Penrith, New South Wales, 2751, Australia
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Durney BC, Crihfield CL, Holland LA. Capillary electrophoresis applied to DNA: determining and harnessing sequence and structure to advance bioanalyses (2009-2014). Anal Bioanal Chem 2015; 407:6923-38. [PMID: 25935677 PMCID: PMC4551542 DOI: 10.1007/s00216-015-8703-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/09/2015] [Accepted: 04/13/2015] [Indexed: 12/17/2022]
Abstract
This review of capillary electrophoresis methods for DNA analyses covers critical advances from 2009 to 2014, referencing 184 citations. Separation mechanisms based on free-zone capillary electrophoresis, Ogston sieving, and reptation are described. Two prevalent gel matrices for gel-facilitated sieving, which are linear polyacrylamide and polydimethylacrylamide, are compared in terms of performance, cost, viscosity, and passivation of electroosmotic flow. The role of capillary electrophoresis in the discovery, design, and characterization of DNA aptamers for molecular recognition is discussed. Expanding and emerging techniques in the field are also highlighted.
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Affiliation(s)
- Brandon C Durney
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
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10
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Kanoatov M, Galievsky VA, Krylova SM, Cherney LT, Jankowski HK, Krylov SN. Using nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) for simultaneous determination of concentration and equilibrium constant. Anal Chem 2015; 87:3099-106. [PMID: 25668425 DOI: 10.1021/acs.analchem.5b00171] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) is a versatile tool for studying affinity binding. Here we describe a NECEEM-based approach for simultaneous determination of both the equilibrium constant, K(d), and the unknown concentration of a binder that we call a target, T. In essence, NECEEM is used to measure the unbound equilibrium fraction, R, for the binder with a known concentration that we call a ligand, L. The first set of experiments is performed at varying concentrations of T, prepared by serial dilution of the stock solution, but at a constant concentration of L, which is as low as its reliable quantitation allows. The value of R is plotted as a function of the dilution coefficient, and dilution corresponding to R = 0.5 is determined. This dilution of T is used in the second set of experiments in which the concentration of T is fixed but the concentration of L is varied. The experimental dependence of R on the concentration of L is fitted with a function describing their theoretical dependence. Both K(d) and the concentration of T are used as fitting parameters, and their sought values are determined as the ones that generate the best fit. We have fully validated this approach in silico by using computer-simulated NECEEM electropherograms and then applied it to experimental determination of the unknown concentration of MutS protein and K(d) of its interactions with a DNA aptamer. The general approach described here is applicable not only to NECEEM but also to any other method that can determine a fraction of unbound molecules at equilibrium.
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Affiliation(s)
- Mirzo Kanoatov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University , Toronto, Ontario M3J 1P3, Canada
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11
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Wynne TM, McCallum C, Del Bonis-O’Donnell JT, Crisalli P, Pennathur S. Hybridization Thermodynamics of DNA Oligonucleotides during Microchip Capillary Electrophoresis. Anal Chem 2015; 87:2811-8. [DOI: 10.1021/ac504209m] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Thomas M. Wynne
- Department
of Mechanical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Christopher McCallum
- Department
of Mechanical Engineering, University of California, Santa Barbara, California 93106, United States
| | | | - Pete Crisalli
- Department
of Mechanical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Sumita Pennathur
- Department
of Mechanical Engineering, University of California, Santa Barbara, California 93106, United States
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12
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Yufa R, Krylova SM, Bruce C, Bagg EA, Schofield CJ, Krylov SN. Emulsion PCR significantly improves nonequilibrium capillary electrophoresis of equilibrium mixtures-based aptamer selection: allowing for efficient and rapid selection of aptamer to unmodified ABH2 protein. Anal Chem 2014; 87:1411-9. [PMID: 25495441 DOI: 10.1021/ac5044187] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM), a homogeneous approach to select DNA aptamers, is among the most efficient partitioning techniques. In contrast with surface-based systematic evolution of ligands by exponential enrichment (SELEX) approaches, the ability of NECEEM to select aptamers to unmodified proteins in solution is preferable for identifying aptamers for eventual in vivo use. The high stringency and low sample volumes of NECEEM, although generally beneficial, can result in binding of very few aptamers, requiring highly efficient amplification to propagate them. When amplified with standard PCR, detectable library enrichment can fail due to the fast conversion of the aptamers into byproducts and preferential amplification of nonbinders. As an alternative, we proposed the use of emulsion PCR (ePCR), which is known to reduce byproduct formation, as a PCR mode for coupling with NECEEM partitioning. For the first time, we tested the advantages of ePCR in NECEEM-based aptamer selection to a medically relevant DNA repair enzyme, ABH2. We report that the combination of ePCR with NECEEM allowed for the selection of aptamers in the first three rounds of SELEX, while SELEX with conventional PCR failed in a number of attempts. Selected aptamers to an unmodified ABH2 protein have potential use in diagnostics and as leads for anticancer cotherapies, used as enhancements of alkylating agents in chemotherapy.
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Affiliation(s)
- Roman Yufa
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University , Toronto, Ontario M3J 1P3, Canada
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13
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Ashby J, Pan S, Zhong W. Size and surface functionalization of iron oxide nanoparticles influence the composition and dynamic nature of their protein corona. ACS APPLIED MATERIALS & INTERFACES 2014; 6:15412-9. [PMID: 25144382 PMCID: PMC4160264 DOI: 10.1021/am503909q] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Nanoparticles (NPs) adsorb proteins when in the biological matrix, and the resulted protein corona could affect NP-cell interactions. The corona has a dynamic nature with the adsorbed proteins constantly exchanging with the free proteins in the matrix at various rates. The rapidly exchanging proteins compose the soft corona, which responds more dynamically to environment changes than the hard corona established by the ones with slow exchange rates. In the present study, the corona formed on the superparamagnetic iron oxide NPs (SPIONs) in human serum was studied by flow field-flow fractionation and ultracentrifugation, which rapidly differentiated the corona proteins based on their exchange rates. By varying the surface hydrophobicity of the SPIONs with a core size around 10 nm, we found out that, the more hydrophobic surface ligand attracted proteins with higher surface hydrophobicity and formed a more dynamic corona with a larger portion of the involved proteins with fast exchange rates. Increasing the core diameter of the SPIONs but keeping the surface ligand the same could also result in a more dynamic corona. A brief investigation of the effect on the cellular uptake of SPIONs using one selected corona protein, transferrin, was conducted. The result showed that, only the stably bound transferrin could significantly enhance cellular uptake, while transferrin bound in a dynamic nature had negligible impact. Our study has led to a better understanding of the relationship between the particle properties and the dynamic nature of the corona, which can help with design of nanomaterials with higher biocompatibility and higher efficacy in biosystems for biomedical applications.
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Affiliation(s)
- Jonathan Ashby
- Department of Chemistry and Institute for Integrative Genome Biology, University of California, Riverside, California 92521, United States
| | - Songqin Pan
- Department of Chemistry and Institute for Integrative Genome Biology, University of California, Riverside, California 92521, United States
| | - Wenwan Zhong
- Department of Chemistry and Institute for Integrative Genome Biology, University of California, Riverside, California 92521, United States
- E-mail:
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Ashby J, Schachermeyer S, Pan S, Zhong W. Dissociation-based screening of nanoparticle-protein interaction via flow field-flow fractionation. Anal Chem 2013; 85:7494-501. [PMID: 23859073 PMCID: PMC3815437 DOI: 10.1021/ac401485j] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A protein corona will be formed on nanoparticles (NPs) entering a biological matrix, which can influence particles' subsequent behaviors inside the biological systems. For proteins bound stably to the NPs, they can exhibit different association/dissociation rates. The binding kinetics could affect interaction of the NPs with cell surface receptors and possibly contribute to the outcomes of NPs uptake. In the present study, a method to differentiate the corona proteins based on their relative dissociation rates from the NPs was developed, employing flow field-flow fraction (F4) in combination with centrifugation. The proteins bound to the superparamagnetic iron oxide NPs (SPION) present in an IgG/albumin depleted serum were isolated via collection of the SPIONs by either F4 or centrifugation. They were subsequently analyzed by LC-MS/MS and identified. Because the SPION-protein complexes injected to F4 dissociated continuously under the nonequilibrium separation condition, only the proteins with slow enough dissociation rates would be collected with the NPs in the eluent of F4. However, in centrifugation, proteins with good affinity to the SPIONs were collected regardless of the dissociation rates of the complexes. In both cases, the nonbinding ones were washed off. Capillary electrophoresis and circular dichroism were employed to verify the binding situations of a few SPION-protein interactions, confirming the effectiveness of our method. Our results support that our method can screen for proteins binding to NPs with fast on-and-off rates, which should be the ones quickly exchanging with the free matrix proteins when the NPs are exposed to a new biological media. Thus, our method will be useful for investigation of the temporal profile of protein corona and its evolution in biological matrices as well as for high-throughput analysis of the dynamic feature of protein corona related to particle properties.
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Affiliation(s)
- Jonathan Ashby
- Department of Chemistry, University of California, Riverside
| | | | - Songqin Pan
- Institute for Integrative Genome Biology, University of California, Riverside
| | - Wenwan Zhong
- Department of Chemistry, University of California, Riverside
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