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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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Sharmeen S, Kyei I, Hatch A, Hage DS. Analysis of drug interactions with serum proteins and related binding agents by affinity capillary electrophoresis: A review. Electrophoresis 2022; 43:2302-2323. [PMID: 36250426 PMCID: PMC10098505 DOI: 10.1002/elps.202200191] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/17/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022]
Abstract
Biomolecules such as serum proteins can interact with drugs in the body and influence their pharmaceutical effects. Specific and precise methods that analyze these interactions are critical for drug development or monitoring and for diagnostic purposes. Affinity capillary electrophoresis (ACE) is one technique that can be used to examine the binding between drugs and serum proteins, or other agents found in serum or blood. This article will review the basic principles of ACE, along with related affinity-based capillary electrophoresis (CE) methods, and examine recent developments that have occurred in this field as related to the characterization of drug-protein interactions. An overview will be given of the various formats that can be used in ACE and CE for such work, including the relative advantages or weaknesses of each approach. Various applications of ACE and affinity-based CE methods for the analysis of drug interactions with serum proteins and other binding agents will also be presented. Applications of ACE and related techniques that will be discussed include drug interaction studies with serum agents, chiral drug separations employing serum proteins, and the use of CE in hybrid methods to characterize drug binding with serum proteins.
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Affiliation(s)
- Sadia Sharmeen
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Isaac Kyei
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Arden Hatch
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - David S Hage
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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3
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Schwarz M, Eno RFM, Freitag-Pohl S, Coxon CR, Straker HE, Wortley DJ, Hughes DJ, Mitchell G, Moore J, Cummins I, Onkokesung N, Brazier-Hicks M, Edwards R, Pohl E, Steel PG. Flavonoid-based inhibitors of the Phi-class glutathione transferase from black-grass to combat multiple herbicide resistance. Org Biomol Chem 2021; 19:9211-9222. [PMID: 34643629 PMCID: PMC8564858 DOI: 10.1039/d1ob01802g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The evolution and growth of multiple-herbicide resistance (MHR) in grass weeds continues to threaten global cereal production. While various processes can contribute to resistance, earlier work has identified the phi class glutathione-S-transferase (AmGSTF1) as a functional biomarker of MHR in black-grass (Alopecurus myosuroides). This study provides further insights into the role of AmGSTF1 in MHR using a combination of chemical and structural biology. Crystal structures of wild-type AmGSTF1, together with two specifically designed variants that allowed the co-crystal structure determination with glutathione and a glutathione adduct of the AmGSTF1 inhibitor 4-chloro-7-nitro-benzofurazan (NBD-Cl) were obtained. These studies demonstrated that the inhibitory activity of NBD-Cl was associated with the occlusion of the active site and the impediment of substrate binding. A search for other selective inhibitors of AmGSTF1, using ligand-fishing experiments, identified a number of flavonoids as potential ligands. Subsequent experiments using black-grass extracts discovered a specific flavonoid as a natural ligand of the recombinant enzyme. A series of related synthetic flavonoids was prepared and their binding to AmGSTF1 was investigated showing a high affinity for derivatives bearing a O-5-decyl-α-carboxylate. Molecular modelling based on high-resolution crystal structures allowed a binding pose to be defined which explained flavonoid binding specificity. Crucially, high binding affinity was linked to a reversal of the herbicide resistance phenotype in MHR black-grass. Collectively, these results present a nature-inspired new lead for the development of herbicide synergists to counteract MHR in weeds. Nature inspired flavonoid derivatives bind to AmGSTF1 and overcome herbicide resistance in multiple herbicide resistant (MHR) Black Grass.![]()
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Affiliation(s)
- Maria Schwarz
- Department of Chemistry, University of Durham, Science Laboratories, South Road, Durham, DH1 3LE, UK.
| | - Rebecca F M Eno
- Department of Chemistry, University of Durham, Science Laboratories, South Road, Durham, DH1 3LE, UK.
| | - Stefanie Freitag-Pohl
- Department of Chemistry, University of Durham, Science Laboratories, South Road, Durham, DH1 3LE, UK.
| | - Christopher R Coxon
- Department of Chemistry, University of Durham, Science Laboratories, South Road, Durham, DH1 3LE, UK.
| | - Hannah E Straker
- Department of Chemistry, University of Durham, Science Laboratories, South Road, Durham, DH1 3LE, UK.
| | - David J Wortley
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - David J Hughes
- Syngenta, Jealott's Hill International Research Station, Bracknell, Berks RG42 6EY, UK
| | - Glynn Mitchell
- Syngenta, Jealott's Hill International Research Station, Bracknell, Berks RG42 6EY, UK
| | - Jenny Moore
- Syngenta, Jealott's Hill International Research Station, Bracknell, Berks RG42 6EY, UK
| | - Ian Cummins
- Department of Biosciences, University of Durham, Science Laboratories, South Road, Durham, DH1 3LE, UK
| | - Nawaporn Onkokesung
- Agriculture, School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Melissa Brazier-Hicks
- Agriculture, School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Robert Edwards
- Agriculture, School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Ehmke Pohl
- Department of Chemistry, University of Durham, Science Laboratories, South Road, Durham, DH1 3LE, UK. .,Department of Biosciences, University of Durham, Science Laboratories, South Road, Durham, DH1 3LE, UK
| | - Patrick G Steel
- Department of Chemistry, University of Durham, Science Laboratories, South Road, Durham, DH1 3LE, UK.
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4
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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: 7] [Impact Index Per Article: 1.4] [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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5
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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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6
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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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7
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Wang B, Qin Q, Chang M, Li S, Shi X, Xu G. Molecular interaction study of flavonoids with human serum albumin using native mass spectrometry and molecular modeling. Anal Bioanal Chem 2017; 410:827-837. [PMID: 28840311 DOI: 10.1007/s00216-017-0564-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/30/2017] [Accepted: 08/02/2017] [Indexed: 11/29/2022]
Abstract
Noncovalent interactions between proteins and small-molecule ligands widely exist in biological bodies and play significant roles in many physiological and pathological processes. Native mass spectrometry (MS) has emerged as a new powerful tool to study noncovalent interactions by directly analyzing the ligand-protein complexes. In this work, an ultrahigh-resolution native MS method based on a 15-T SolariX XR Fourier transform ion cyclotron resonance mass spectrometer was firstly used to investigate the interaction between human serum albumin (HSA) and flavonoids. Various flavonoids with similar structure were selected to unravel the relationship between the structure of flavonoids and their binding affinity for HSA. It was found that the position of the hydroxyl groups and double bond of flavonoids could influence the noncovalent interaction. Through a competitive experiment between HSA binding site markers and apigenin, the subdomain IIA (site 1) of HSA was determined as the binding site for flavonoids. Moreover, a cooperative allosteric interaction between apigenin and ibuprofen was found from their different HSA binding sites, which was further verified by circular dichroism spectroscopy and molecular docking studies. These results show that native MS is a useful tool to investigate the molecular interaction between a protein and its ligands. Graphical abstract Unravel the relationship between the structure of flavonoids and their binding affinity to HSA by native MS.
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Affiliation(s)
- Bohong Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qian Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mengmeng Chang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuyan Li
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Xianzhe Shi
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China.
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China.
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8
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Bao J, Krylova SM, Cherney LT, Le Blanc JCY, Pribil P, Johnson PE, Wilson DJ, Krylov SN. Pre-equilibration kinetic size-exclusion chromatography with mass spectrometry detection (peKSEC-MS) for label-free solution-based kinetic analysis of protein-small molecule interactions. Analyst 2015; 140:990-4. [PMID: 25611307 DOI: 10.1039/c4an02232g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we introduce pre-equilibration kinetic size-exclusion chromatography with mass-spectrometry detection (peKSEC-MS), which is a label-free solution-based kinetic approach for characterizing non-covalent protein-small molecule interactions. In this method, a protein and a small molecule are mixed outside the column and incubated to approach equilibrium. The equilibrium mixture is then introduced into the SEC column to initiate the dissociation process by separating small molecules from the complex inside the column. A numerical model of a 1-dimensional separation was constructed to simulate mass chromatograms of the small molecule for varying rate constants of binding.
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Affiliation(s)
- Jiayin Bao
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada.
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9
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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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10
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Bao J, Krylova SM, Cherney LT, Hale RL, Belyanskaya SL, Chiu CH, Arico-Muendel CC, Krylov SN. Prediction of Protein–DNA Complex Mobility in Gel-Free Capillary Electrophoresis. Anal Chem 2015; 87:2474-9. [DOI: 10.1021/ac504504c] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jiayin Bao
- Department of Chemistry
and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Svetlana M. Krylova
- Department of Chemistry
and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Leonid T. Cherney
- Department of Chemistry
and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Robert L. Hale
- GlaxoSmithKline, 343 Winter Street, Waltham, Mississippi 02451-8714, United States
| | | | - Cynthia H. Chiu
- GlaxoSmithKline, 343 Winter Street, Waltham, Mississippi 02451-8714, United States
| | | | - Sergey N. Krylov
- 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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Bao J, Krylova SM, Cherney LT, LeBlanc JCY, Pribil P, Johnson PE, Wilson DJ, Krylov SN. Kinetic size-exclusion chromatography with mass spectrometry detection: an approach for solution-based label-free kinetic analysis of protein-small molecule interactions. Anal Chem 2014; 86:10016-20. [PMID: 25275785 DOI: 10.1021/ac503391c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Studying the kinetics of reversible protein-small molecule binding is a major challenge. The available approaches require that either the small molecule or the protein be modified by labeling or immobilization on a surface. Not only can such modifications be difficult to do but also they can drastically affect the kinetic parameters of the interaction. To solve this problem, we present kinetic size-exclusion chromatography with mass spectrometry detection (KSEC-MS), a solution-based label-free approach. KSEC-MS utilizes the ability of size-exclusion chromatography (SEC) to separate any small molecule from any protein-small molecule complex without immobilization and the ability of mass spectrometry (MS) to detect a small molecule without a label. The rate constants of complex formation and dissociation are deconvoluted from the temporal pattern of small molecule elution measured with MS at the exit from the SEC column. This work describes the concept of KSEC-MS and proves it in principle by measuring the rate constants of interaction between carbonic anhydrase and acetazolamide.
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Affiliation(s)
- Jiayin Bao
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University , Toronto, Ontario M3J 1P3, Canada
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12
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Capillary electrophoresis-based assessment of nanobody affinity and purity. Anal Chim Acta 2014; 818:1-6. [DOI: 10.1016/j.aca.2014.01.048] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 01/15/2014] [Accepted: 01/21/2014] [Indexed: 12/17/2022]
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13
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Liyanage R, Krylova SM, Krylov SN. Minimizing adsorption of histidine-tagged proteins for the study of protein–deoxyribonucleic acid interactions by kinetic capillary electrophoresis. J Chromatogr A 2013; 1322:90-6. [DOI: 10.1016/j.chroma.2013.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/31/2013] [Accepted: 11/01/2013] [Indexed: 01/24/2023]
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14
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Berezovski MV, Mironov GG. Utility of kinetic capillary electrophoresis-mass spectrometry to study protein dynamics and affinity interactions. Expert Rev Proteomics 2012. [PMID: 23194262 DOI: 10.1586/epr.12.45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Seidel SAI, Wienken CJ, Geissler S, Jerabek-Willemsen M, Duhr S, Reiter A, Trauner D, Braun D, Baaske P. Label-free microscale thermophoresis discriminates sites and affinity of protein-ligand binding. Angew Chem Int Ed Engl 2012; 51:10656-9. [PMID: 23001866 PMCID: PMC3588113 DOI: 10.1002/anie.201204268] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Indexed: 01/04/2023]
Affiliation(s)
- Susanne A I Seidel
- Systems Biophysics and Functional Nanosystems, Ludwig-Maximilians-Universität München, Amalienstrasse 54, 80799 Munich, Germany
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16
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Seidel SAI, Wienken CJ, Geissler S, Jerabek-Willemsen M, Duhr S, Reiter A, Trauner D, Braun D, Baaske P. Markierungsfreie “Microscale Thermophoresis” zur Bestimmung von Bindestellen und Affinitäten bei Protein-Liganden-Wechselwirkungen. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204268] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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17
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Bao J, Krylov SN. Volatile kinetic capillary electrophoresis for studies of protein-small molecule interactions. Anal Chem 2012; 84:6944-7. [PMID: 22823518 DOI: 10.1021/ac301829t] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Kinetic capillary electrophoresis (KCE) is a toolset of homogeneous affinity methods for studying kinetics of noncovalent binding. Sensitive KCE measurements are typically done with fluorescence detection and require a fluorescent label on a smaller-sized binding partner. KCE with fluorescence detection is difficult to use for study of protein-small molecule interactions since labeling small molecules is cumbersome and can affect binding. A combination of KCE with mass-spectrometry (KCE-MS) has been recently suggested for label-free studies of protein-small molecule interactions. The major obstacle for studies by KCE-MS is a buffer mismatch between KCE and MS; MS requires volatile buffers while KCE of protein-ligand interactions is always run in near-physiological buffers. Here we asked a simple question: can protein-ligand interactions be studied with KCE in a volatile buffer? We compared three volatile buffers (ammonium acetate, ammonium bicarbonate, and ammonium formate) with a near-physiological buffer (Tris-acetate) for three protein-ligand pairs. The volatile buffers were found not to significantly affect protein-ligand complex stability; moreover, when used as CE run buffers, they facilitated good-quality separation of free ligands from the protein-ligand complexes. The use of volatile buffers instead of Tris-acetate in detection of small molecules by MS improved the detection limit by approximately 2 orders of magnitude. These findings prove the principle of "volatile" KCE, which can be easily coupled with MS to facilitate label-free kinetic studies of protein-small molecule interactions.
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Affiliation(s)
- Jiayin Bao
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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