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Deng L, Fu Q, Zhang Y, Shui F, Tang J, Wu J, Zeng J. Study of molecular interactions by nonequilibrium capillary electrophoresis of equilibrium mixtures: Originations, developments, and applications. Electrophoresis 2023; 44:1664-1673. [PMID: 37621032 DOI: 10.1002/elps.202300166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/16/2023] [Accepted: 08/18/2023] [Indexed: 08/26/2023]
Abstract
Molecular interactions play a vital role in regulating various physiological and biochemical processes in vivo. Kinetic capillary electrophoresis (KCE) is an analytical platform that offers significant advantages in studying the thermodynamic and kinetic parameters of molecular interactions. It enables the simultaneous analysis of these parameters within an interaction pattern and facilitates the screening of binding ligands with predetermined kinetic parameters. Nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) was the first proposed KCE method, and it has found widespread use in studying molecular interactions involving proteins/aptamers, proteins/small molecules, and peptides/small molecules. The successful applications of NECEEM have demonstrated its promising potential for further development and broader application. However, there has been a dearth of recent reviews on NECEEM. To address this gap, our study provides a comprehensive description of NECEEM, encompassing its origins, development, and applications from 2015 to 2022. The primary focus of the applications section is on aptamer selection and screening of small-molecule ligands. Furthermore, we discuss important considerations in NECEEM experimental design, such as buffer suitability, detector selection, and protein adsorption. By offering this thorough review, we aim to contribute to the understanding, advancement, and wider utilization of NECEEM as a valuable tool for studying molecular interactions and facilitating the identification of potential ligands and targets.
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Affiliation(s)
- Li Deng
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, P. R. China
| | - Qifeng Fu
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, P. R. China
| | - Yujie Zhang
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, P. R. China
| | - Fan Shui
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, P. R. China
| | - Jia Tang
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, P. R. China
| | - Jianming Wu
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, P. R. China
- School of Basic Medical Science, Southwest Medical University, Luzhou, Sichuan, P. R. China
| | - Jing Zeng
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, P. R. China
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2
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Sázelová P, Koval D, Severa L, Teplý F, Vigh G, Kašička V. Determination of binding constants of multiple charged cyclodextrin complexes by ACE using uncorrected and ionic strength corrected actual mobilities of the species involved. Electrophoresis 2020; 41:523-535. [DOI: 10.1002/elps.201900352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/06/2019] [Accepted: 11/21/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Petra Sázelová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague 6 Czechia
| | - Dušan Koval
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague 6 Czechia
| | - Lukáš Severa
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague 6 Czechia
| | - Filip Teplý
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague 6 Czechia
| | - Gyula Vigh
- Texas A&M UniversityDepartment Chemistry College Station TX USA
| | - Václav Kašička
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague 6 Czechia
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3
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Sisavath N, Rukundo JL, Le Blanc JCY, Galievsky VA, Bao J, Kochmann S, Stasheuski AS, Krylov SN. Transient Incomplete Separation Facilitates Finding Accurate Equilibrium Dissociation Constant of Protein-Small Molecule Complex. Angew Chem Int Ed Engl 2019; 58:6635-6639. [PMID: 30901510 DOI: 10.1002/anie.201901345] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/21/2019] [Indexed: 01/18/2023]
Abstract
Current practical methods for finding the equilibrium dissociation constant, Kd , of protein-small molecule complexes have inherent sources of inaccuracy. Introduced here is "accurate constant via transient incomplete separation" (ACTIS), which appears to be free of inherent sources of inaccuracy. Conceptually, a short plug of the pre-equilibrated protein-small molecule mixture is pressure-propagated in a capillary, causing fast transient incomplete separation of the complex from the unbound small molecule. A superposition of signals from these two components is measured near the capillary exit and used to calculate a fraction of unbound small molecule, which, in turn, is used to calculate Kd . Herein the validity of ACTIS is proven theoretically, its accuracy is verified by computer simulation, and its practical use is demonstrated. ACTIS has the potential to become a reference-standard method for determining Kd values of protein-small molecule complexes.
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Affiliation(s)
- Nicolas Sisavath
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Jean-Luc Rukundo
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
| | | | - Victor A Galievsky
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Jiayin Bao
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Sven Kochmann
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Alexander S Stasheuski
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Sergey N Krylov
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
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4
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Sisavath N, Rukundo J, Le Blanc JCY, Galievsky VA, Bao J, Kochmann S, Stasheuski AS, Krylov SN. Transient Incomplete Separation Facilitates Finding Accurate Equilibrium Dissociation Constant of Protein–Small Molecule Complex. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Nicolas Sisavath
- Centre for Research on Biomolecular InteractionsYork University Toronto Ontario M3J 1P3 Canada
| | - Jean‐Luc Rukundo
- Centre for Research on Biomolecular InteractionsYork University Toronto Ontario M3J 1P3 Canada
| | | | - Victor A. Galievsky
- Centre for Research on Biomolecular InteractionsYork University Toronto Ontario M3J 1P3 Canada
| | - Jiayin Bao
- Centre for Research on Biomolecular InteractionsYork University Toronto Ontario M3J 1P3 Canada
| | - Sven Kochmann
- Centre for Research on Biomolecular InteractionsYork University Toronto Ontario M3J 1P3 Canada
| | - Alexander S. Stasheuski
- Centre for Research on Biomolecular InteractionsYork University Toronto Ontario M3J 1P3 Canada
| | - Sergey N. Krylov
- Centre for Research on Biomolecular InteractionsYork University Toronto Ontario M3J 1P3 Canada
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5
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Nevídalová H, Michalcová L, Glatz Z. Capillary electrophoresis-based approaches for the study of affinity interactions combined with various sensitive and nontraditional detection techniques. Electrophoresis 2019; 40:625-642. [PMID: 30600537 DOI: 10.1002/elps.201800367] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/20/2018] [Accepted: 12/20/2018] [Indexed: 12/17/2022]
Abstract
Nearly all processes in living organisms are controlled and regulated by the synergy of many biomolecule interactions involving proteins, peptides, nucleic acids, nucleotides, saccharides, and small molecular weight ligands. There is growing interest in understanding them, not only for the purposes of interactomics as an essential part of system biology, but also in their further elucidation in disease pathology, diagnostics, and treatment. The necessity of detailed investigation of these interactions leads to the requirement of laboratory methods characterized by high efficiency and sensitivity. As a result, many instrumental approaches differing in their fundamental principles have been developed, including those based on capillary electrophoresis. Although capillary electrophoresis offers numerous advantages for such studies, it still has one serious limitation, its poor concentration sensitivity with the most commonly used detection method-ultraviolet-visible spectrometry. However, coupling capillary electrophoresis with a more sensitive detector fulfils the above-mentioned requirement. In this review, capillary electrophoresis combined with fluorescence, mass spectrometry, and several nontraditional detection techniques in affinity interaction studies are summarized and discussed, together with the possibility of conducting these measurements in microchip format.
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Affiliation(s)
- Hana Nevídalová
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lenka Michalcová
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zdeněk Glatz
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
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6
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Domínguez-Vega E, Haselberg R, Somsen GW, de Jong GJ. Simultaneous Assessment of Protein Heterogeneity and Affinity by Capillary Electrophoresis–Mass Spectrometry. Anal Chem 2015. [DOI: 10.1021/acs.analchem.5b01701] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- E. Domínguez-Vega
- Division
of BioAnalytical Chemistry, VU University Amsterdam, de Boelelaan
1083, 1081 HV Amsterdam, The Netherlands
| | - R. Haselberg
- Division
of BioAnalytical Chemistry, VU University Amsterdam, de Boelelaan
1083, 1081 HV Amsterdam, The Netherlands
| | - G. W. Somsen
- Division
of BioAnalytical Chemistry, VU University Amsterdam, de Boelelaan
1083, 1081 HV Amsterdam, The Netherlands
| | - G. J. de Jong
- Biomolecular
Analysis, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
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Stephan M, Kramer C, Steinem C, Janshoff A. Binding assay for low molecular weight analytes based on reflectometry of absorbing molecules in porous substrates. Analyst 2015; 139:1987-92. [PMID: 24599267 DOI: 10.1039/c4an00009a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Small molecule sensing is of great importance in pharmaceutical research. While there exist well established screening methods such as EMSA (electrophoretic motility shift assay) or biointeraction chromatography to report on successful binding interactions, there are only a few techniques that allow studying and quantifying the interaction of low molecular weight analytes with a binding partner directly. We report on a binding assay for small molecules based on the reflectivity change of a porous transparent film upon immobilisation of an absorbing substance on the pore walls. The porous matrix acts as a thin optical transparent film to produce interference fringes and accumulates molecules at the inner wall to amplify the sensor response. The benefits and limits of the assay are demonstrated by investigating the binding of biotin labelled with an atto dye to avidin physisorbed within an anodic aluminium oxide membrane.
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Affiliation(s)
- Milena Stephan
- Department of Physical Chemistry, Georg-August University, Göttingen, Germany.
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8
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Štěpánová S, Kašička V. Capillary electrophoretic methods applied to the investigation of peptide complexes. J Sep Sci 2015; 38:2708-21. [DOI: 10.1002/jssc.201500399] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/01/2015] [Accepted: 05/01/2015] [Indexed: 01/18/2023]
Affiliation(s)
- Sille Štěpánová
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Prague Czech Republic
| | - Václav Kašička
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Prague Czech Republic
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9
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Galievsky VA, Stasheuski AS, Krylov SN. Capillary Electrophoresis for Quantitative Studies of Biomolecular Interactions. Anal Chem 2014; 87:157-71. [DOI: 10.1021/ac504219r] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Victor A. Galievsky
- Department
of Chemistry and
Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Alexander S. Stasheuski
- Department
of Chemistry and
Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Sergey N. Krylov
- Department
of Chemistry and
Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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10
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Terminal protection of small molecule-linked DNA for small molecule-protein interaction assays. Int J Mol Sci 2014; 15:5221-32. [PMID: 24670475 PMCID: PMC4013559 DOI: 10.3390/ijms15045221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 03/15/2014] [Accepted: 03/17/2014] [Indexed: 01/24/2023] Open
Abstract
Methods for the detection of specific interactions between diverse proteins and various small-molecule ligands are of significant importance in understanding the mechanisms of many critical physiological processes of organisms. The techniques also represent a major avenue to drug screening, molecular diagnostics, and public safety monitoring. Terminal protection assay of small molecule-linked DNA is a demonstrated novel methodology which has exhibited great potential for the development of simple, sensitive, specific and high-throughput methods for the detection of small molecule–protein interactions. Herein, we review the basic principle of terminal protection assay, the development of associated methods, and the signal amplification strategies adopted for performance improving in small molecule–protein interaction assay.
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Kašička V. Recent developments in capillary and microchip electroseparations of peptides (2011-2013). Electrophoresis 2013; 35:69-95. [PMID: 24255019 DOI: 10.1002/elps.201300331] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/10/2013] [Accepted: 09/10/2013] [Indexed: 01/15/2023]
Abstract
The review presents a comprehensive survey of recent developments and applications of capillary and microchip electroseparation methods (zone electrophoresis, ITP, IEF, affinity electrophoresis, EKC, and electrochromatography) for analysis, isolation, purification, and physicochemical and biochemical characterization of peptides. Advances in the investigation of electromigration properties of peptides, in the methodology of their analysis, including sample preseparation, preconcentration and derivatization, adsorption suppression and EOF control, as well as in detection of peptides, are presented. New developments in particular CE and CEC modes are reported and several types of their applications to peptide analysis are described: conventional qualitative and quantitative analysis, determination in complex (bio)matrices, monitoring of chemical and enzymatical reactions and physical changes, amino acid, sequence and chiral analysis, and peptide mapping of proteins. Some micropreparative peptide separations are shown and capabilities of CE and CEC techniques to provide relevant physicochemical characteristics of peptides are demonstrated.
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Affiliation(s)
- Václav Kašička
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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12
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Ji H, Li M, Guo L, Yuan H, Wang C, Xiao D. Design and evaluation of capillary coupled with optical fiber light-emitting diode induced fluorescence detection for capillary electrophoresis. Electrophoresis 2013; 34:2546-52. [DOI: 10.1002/elps.201300125] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Revised: 05/06/2013] [Accepted: 05/30/2013] [Indexed: 12/17/2022]
Affiliation(s)
- Hongyun Ji
- College of Chemistry; Sichuan University; Chengdu P. R. China
| | - Meng Li
- College of Chemistry; Sichuan University; Chengdu P. R. China
| | - Lihong Guo
- College of Chemistry; Sichuan University; Chengdu P. R. China
| | - Hongyan Yuan
- College of Chemical Engineering; Sichuan University; Chengdu P. R. China
| | - Chunling Wang
- College of Chemical Engineering; Sichuan University; Chengdu P. R. China
| | - Dan Xiao
- College of Chemistry; Sichuan University; Chengdu P. R. China
- College of Chemical Engineering; Sichuan University; Chengdu P. R. China
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