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Štěpánová S, Kašička V. Determination of physicochemical parameters of (bio)molecules and (bio)particles by capillary electromigration methods. J Sep Sci 2024; 47:e2400174. [PMID: 38867483 DOI: 10.1002/jssc.202400174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/03/2024] [Accepted: 05/10/2024] [Indexed: 06/14/2024]
Abstract
The review provides an overview of recent developments and applications of capillary electromigration (CE) methods for the determination of important physicochemical parameters of various (bio)molecules and (bio)particles. These parameters include actual and limiting (absolute) ionic mobilities, effective electrophoretic mobilities, effective charges, isoelectric points, electrokinetic potentials, hydrodynamic radii, diffusion coefficients, relative molecular masses, acidity (ionization) constants, binding constants and stoichiometry of (bio)molecular complexes, changes of Gibbs free energy, enthalpy and entropy and rate constants of chemical reactions and interactions, retention factors and partition and distribution coefficients. For the determination of these parameters, the following CE methods are employed: zone electrophoresis in a free solution or in sieving media, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography, and electrochromatography. In the individual sections, the procedures for the determination of the above parameters by the particular CE methods are described.
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Affiliation(s)
- Sille Štěpánová
- Electromigration methods, Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Prague, Czech Republic
| | - Václav Kašička
- Electromigration methods, Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Prague, Czech Republic
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2
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Sena-Torralba A, Banguera-Ordoñez YD, Mira-Pascual L, Maquieira Á, Morais S. Exploring the potential of paper-based electrokinetic phenomena in PoC biosensing. Trends Biotechnol 2023; 41:1299-1313. [PMID: 37150668 DOI: 10.1016/j.tibtech.2023.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/06/2023] [Accepted: 04/14/2023] [Indexed: 05/09/2023]
Abstract
In order to decentralize health care, the development of point-of-care (PoC) assays has gained significant attention in recent decades. The lateral flow immunoassay (LFIA) has emerged as a promising bioanalytical method due to its low cost and single-step detection process. However, its limited sensitivity and inability to detect disease biomarkers at clinically relevant levels have hindered its application for early diagnosis. This review explores the potential of merging different electrokinetic phenomena into paper-based assays to enhance their analytical performance, offering a versatile and affordable approach for PoC testing. The review exposes the challenges faced in integrating electrokinetic phenomena with paper-based biosensing and concludes by discussing the issues that need to be improved to maximize the potential of this technology for early diagnosis.
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Affiliation(s)
- Amadeo Sena-Torralba
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain; Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
| | - Yulieth D Banguera-Ordoñez
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - Laia Mira-Pascual
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - Ángel Maquieira
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain; Departamento de Química, Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - Sergi Morais
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain; Departamento de Química, Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain.
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3
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Sule R, Rivera G, Gomes AV. Western blotting (immunoblotting): history, theory, uses, protocol and problems. Biotechniques 2023; 75:99-114. [PMID: 36971113 DOI: 10.2144/btn-2022-0034] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Western blotting (immunoblotting) is a powerful and commonly used technique that is capable of detecting or semiquantifying an individual protein from complex mixtures of proteins extracted from cells or tissues. The history surrounding the origin of western blotting, the theory behind the western blotting technique, a comprehensive protocol and the uses of western blotting are presented. Lesser known and significant problems in the western blotting field and troubleshooting of common problems are highlighted and discussed. This work is a comprehensive primer and guide for new western blotting researchers and those interested in a better understanding of the technique or getting better results.
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Affiliation(s)
- Rasheed Sule
- Department of Neurobiology, Physiology & Behavior, University of California, Davis, Davis, CA 95616, USA
| | - Gabriela Rivera
- Department of Neurobiology, Physiology & Behavior, University of California, Davis, Davis, CA 95616, USA
| | - Aldrin V Gomes
- Department of Neurobiology, Physiology & Behavior, University of California, Davis, Davis, CA 95616, USA
- Department of Physiology & Membrane Biology, University of California, Davis, Davis, CA 95616, USA
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4
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Chen W, McCool EN, Sun L, Zang Y, Ning X, Liu X. Evaluation of Machine Learning Models for Proteoform Retention and Migration Time Prediction in Top-Down Mass Spectrometry. J Proteome Res 2022; 21:1736-1747. [PMID: 35616364 PMCID: PMC9250612 DOI: 10.1021/acs.jproteome.2c00124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Reversed-phase liquid
chromatography (RPLC) and capillary zone
electrophoresis (CZE) are two primary proteoform separation methods
in mass spectrometry (MS)-based top-down proteomics. Proteoform retention
time (RT) prediction in RPLC and migration time (MT) prediction in
CZE provide additional information for accurate proteoform identification
and quantification. While existing methods are mainly focused on peptide
RT and MT prediction in bottom-up MS, there is still a lack of methods
for proteoform RT and MT prediction in top-down MS. We systematically
evaluated eight machine learning models and a transfer learning method
for proteoform RT prediction and five models and the transfer learning
method for proteoform MT prediction. Experimental results showed that
a gated recurrent unit (GRU)-based model with transfer learning achieved
a high accuracy (R = 0.978) for proteoform RT prediction
and that the GRU-based model and a fully connected neural network
model obtained a high accuracy of R = 0.982 and 0.981
for proteoform MT prediction, respectively.
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Affiliation(s)
- Wenrong Chen
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United Staes
| | - Elijah N McCool
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United Staes
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United Staes
| | - Yong Zang
- Department of Biostatics and Health Data Sciences, Indiana University School of Medicine, Indianapolis, Indiana 46202, United Staes
| | - Xia Ning
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, United Staes.,Department of Computer Science and Engineering, The Ohio State University, Columbus, Ohio 43210, United Staes.,Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United Staes
| | - Xiaowen Liu
- Tulane Center for Biomedical Informatics and Genomics, Tulane University, New Orleans, Louisiana 70112, United Staes.,Deming Department of Medicine, Tulane University, New Orleans, Louisiana 70112, United Staes
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5
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Ramos Y, Almeida A, Carpio J, Rodríguez‐Ulloa A, Perera Y, González LJ, Wiśniewski JR, Besada V. Gel electrophoresis/electroelution sorting fractionator combined with filter aided sample preparation for deep proteomic analysis. J Sep Sci 2022; 45:1784-1796. [DOI: 10.1002/jssc.202100992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Yassel Ramos
- Proteomics Group System Biology Department Center for Genetic Engineering and Biotechnology Havana Cuba
| | - Alexis Almeida
- Proteomics Group System Biology Department Center for Genetic Engineering and Biotechnology Havana Cuba
| | - Jenis Carpio
- Proteomics Group System Biology Department Center for Genetic Engineering and Biotechnology Havana Cuba
| | - Arielis Rodríguez‐Ulloa
- Proteomics Group System Biology Department Center for Genetic Engineering and Biotechnology Havana Cuba
| | - Yasser Perera
- China‐Cuba Biotechnology Joint Innovation Center (CCBJIC) Yongzhou Zhong Gu Biotechnology Co., Ltd Hunan Province China
- Molecular Oncology Group Pharmacology Department, Center for Genetic Engineering and Biotechnology Havana Cuba
| | - Luis J. González
- Proteomics Group System Biology Department Center for Genetic Engineering and Biotechnology Havana Cuba
| | - Jacek R. Wiśniewski
- Biochemical Proteomics Group Department of Proteomics and Signal Transduction Max‐Planck‐Institute of Biochemistry Martinsried Germany
| | - Vladimir Besada
- Proteomics Group System Biology Department Center for Genetic Engineering and Biotechnology Havana Cuba
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6
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Microfluidic free-flow electrophoresis: a promising tool for protein purification and analysis in proteomics. J IND ENG CHEM 2022. [DOI: 10.1016/j.jiec.2022.02.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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7
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Sena-Torralba A, Alvarez-Diduk R, Parolo C, Torné-Morató H, Müller A, Merkoçi A. Paper-Based Electrophoretic Bioassay: Biosensing in Whole Blood Operating via Smartphone. Anal Chem 2021; 93:3112-3121. [PMID: 33534544 DOI: 10.1021/acs.analchem.0c04330] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Point-of-care (PoC) tests are practical and effective diagnostic solutions for major clinical problems, ranging from the monitoring of a pandemic to recurrent or simple measurements. Although, in recent years, a great improvement in the analytical performance of such sensors has been observed, there is still a major issue that has not been properly solved: the ability to perform adequate sample treatments. The main reason is that normally sample treatments require complicated or long procedures not adequate for deployment at the PoC. In response, a sensing platform, called paper-based electrophoretic bioassay (PEB), that combines the key characteristics of a lateral flow assay (LFA) with the sample treatment capabilities of electrophoresis is developed. In particular, the ability of PEB to separate different types of particles and to detect human antibodies in untreated spiked whole blood is demonstrated. Finally, to make the platform suitable for PoC, PEB is coupled with a smartphone that controls the electrophoresis and reads the optical signal generated. It is believed that the PEB platform represents a much-needed solution for the detection of low target concentrations in complex media, solving one of the major limitations of LFA and opening opportunities for point-of-care sensors.
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Affiliation(s)
- Amadeo Sena-Torralba
- Nanobioelectronics & Biosensors Group, Institut Català de Nanociència I Nanotecnologia (ICN2), CSIC and The Barcelona Institute of Science and Technology (BIST), Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Ruslan Alvarez-Diduk
- Nanobioelectronics & Biosensors Group, Institut Català de Nanociència I Nanotecnologia (ICN2), CSIC and The Barcelona Institute of Science and Technology (BIST), Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Claudio Parolo
- Nanobioelectronics & Biosensors Group, Institut Català de Nanociència I Nanotecnologia (ICN2), CSIC and The Barcelona Institute of Science and Technology (BIST), Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Helena Torné-Morató
- Nanobioelectronics & Biosensors Group, Institut Català de Nanociència I Nanotecnologia (ICN2), CSIC and The Barcelona Institute of Science and Technology (BIST), Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Alexander Müller
- Nanobioelectronics & Biosensors Group, Institut Català de Nanociència I Nanotecnologia (ICN2), CSIC and The Barcelona Institute of Science and Technology (BIST), Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Arben Merkoçi
- Nanobioelectronics & Biosensors Group, Institut Català de Nanociència I Nanotecnologia (ICN2), CSIC and The Barcelona Institute of Science and Technology (BIST), Campus UAB, Bellaterra, 08193 Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
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8
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Kadel S, Daigle G, Thibodeau J, Perreault V, Pellerin G, Lainé C, Bazinet L. How physicochemical properties of filtration membranes impact peptide migration and selectivity during electrodialysis with filtration membranes: Development of predictive statistical models and understanding of mechanisms involved. J Memb Sci 2021. [DOI: 10.1016/j.memsci.2020.118175] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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9
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Kolbanovskiy M, Shim Y, Min JH, Geacintov NE, Shafirovich V. Inhibition of Excision of Oxidatively Generated Hydantoin DNA Lesions by NEIL1 by the Competitive Binding of the Nucleotide Excision Repair Factor XPC-RAD23B. Biochemistry 2020; 59:1728-1736. [PMID: 32302101 DOI: 10.1021/acs.biochem.0c00080] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The interplay between nucleotide excision repair (NER) and base excision repair (BER) of nonbulky, oxidatively generated DNA lesions has long been a subject of significant interest. The hydantoin oxidation products of 8-oxoguanine, spiroiminodihydantoin (Sp) and 5-guanidinohydantoin (Gh), are substrates of both BER and NER in HeLa cell extracts and human cells [Shafirovich, V., et al. (2019) Chem. Res. Toxicol. 32, 753-761]. The primary factor that recognizes DNA lesions is the DNA damage-sensing factor XPC-RAD23B (XPC), while the glycosylase NEIL1 is known to remove Gh and Sp lesions from double-stranded DNA. It is shown here that in aqueous solutions containing nanomolar concentrations of proteins, XPC and NEIL1 compete for binding to 147-mer oligonucleotide duplexes that contain single Gh or Sp lesions under conditions of [protein] ≫ [DNA], thus inhibiting the rate of BER catalyzed by NEIL1. The non-covalently bound NEIL1 molecules can be displaced by XPC at concentration ratios R = [XPC]/[NEIL1] > 0.2, while full displacement of NEIL1 is observed at R ≥ 0.5. In the absence of XPC and under single-turnover conditions, only the burst phase is observable. However, with a progressive increase in the XPC concentration, the amplitude of the burst phase decreases gradually, and a slower time-dependent phase of incision product formation manifests itself with rate constants of 3.0 × 10-3 s-1 (Gh) and 0.90 × 10-3 s-1 (Sp). These slow kinetics are attributed to the dissociation of XPC-DNA complexes that allow for the rebinding of NEIL1 to the temporarily exposed Gh or Sp lesions, and the incisions observed under these steady-state conditions.
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Affiliation(s)
- Marina Kolbanovskiy
- Chemistry Department, New York University, 31 Washington Place, New York, New York 10003-5180, United States
| | - Yoonjung Shim
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Jung-Hyun Min
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Nicholas E Geacintov
- Chemistry Department, New York University, 31 Washington Place, New York, New York 10003-5180, United States
| | - Vladimir Shafirovich
- Chemistry Department, New York University, 31 Washington Place, New York, New York 10003-5180, United States
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10
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Chen D, Lubeckyj RA, Yang Z, McCool EN, Shen X, Wang Q, Xu T, Sun L. Predicting Electrophoretic Mobility of Proteoforms for Large-Scale Top-Down Proteomics. Anal Chem 2020; 92:3503-3507. [PMID: 32043875 PMCID: PMC7543059 DOI: 10.1021/acs.analchem.9b05578] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Large-scale top-down proteomics characterizes proteoforms in cells globally with high confidence and high throughput using reversed-phase liquid chromatography (RPLC)-tandem mass spectrometry (MS/MS) or capillary zone electrophoresis (CZE)-MS/MS. The false discovery rate (FDR) from the target-decoy database search is typically deployed to filter identified proteoforms to ensure high-confidence identifications (IDs). It has been demonstrated that the FDRs in top-down proteomics can be drastically underestimated. An alternative approach to the FDR can be useful for further evaluating the confidence of proteoform IDs after the database search. We argue that predicting retention/migration time of proteoforms from the RPLC/CZE separation accurately and comparing their predicted and experimental separation time could be a useful and practical approach. Based on our knowledge, there is still no report in the literature about predicting separation time of proteoforms using large top-down proteomics data sets. In this pilot study, for the first time, we evaluated various semiempirical models for predicting proteoforms' electrophoretic mobility (μef) using large-scale top-down proteomics data sets from CZE-MS/MS. We achieved a linear correlation between experimental and predicted μef of E. coli proteoforms (R2 = 0.98) with a simple semiempirical model, which utilizes the number of charges and molecular mass of each proteoform as the parameters. Our modeling data suggest that the complete unfolding of proteoforms during CZE separation benefits the prediction of their μef. Our results also indicate that N-terminal acetylation and phosphorylation both decrease the proteoforms' charge by roughly one charge unit.
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Affiliation(s)
- Daoyang Chen
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Rachele A Lubeckyj
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Zhichang Yang
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Elijah N McCool
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Xiaojing Shen
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Qianjie Wang
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Tian Xu
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
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11
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Pero-Gascon R, Tascon M, Sanz-Nebot V, Gagliardi LG, Benavente F. Improving separation optimization in capillary electrophoresis by using a general quality criterion. Talanta 2020; 208:120399. [DOI: 10.1016/j.talanta.2019.120399] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 10/25/2022]
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12
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Kadel S, Pellerin G, Thibodeau J, Perreault V, Lainé C, Bazinet L. How Molecular Weight Cut-Offs and Physicochemical Properties of Polyether Sulfone Membranes Affect Peptide Migration and Selectivity during Electrodialysis with Filtration Membranes. MEMBRANES 2019; 9:membranes9110153. [PMID: 31766261 PMCID: PMC6918500 DOI: 10.3390/membranes9110153] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 11/26/2022]
Abstract
Filtration membranes (FMs) are an integral part of electrodialysis with filtration membranes (EDFM), a green and promising technology for bioactive peptide fractionation. Therefore, it is paramount to understand how physicochemical properties of FMs impact global and selective peptide migration to anionic (A−RC) and cationic (C+RC) peptide recovery compartments during their simultaneous separation by EDFM. In this context, six polyether sulfone (PES) membranes with molecular weight cut-offs (MWCO) of 5, 10, 20, 50, 100 and 300 kDa were characterized and used during EDFM to separate peptides from a complex whey protein hydrolysate. Surface charge, roughness, thickness and surface/pores nature of studied PES membranes were similar with small differences in conductivity, porosity and pore size distribution. Interestingly, global peptides migration to both recovery compartments increased linearly as a function of MWCO. However, peptide selectivity changed according to the recovery compartments and/or the peptide’s charge and MW with an increase in MWCO of FMs. Indeed, in A−RC, the relative abundance (RA) of peptides having low negative charge and MW (IDALNENK and VLVLDTDYK) decreased (45% to 19%) with an increase in MWCO, while the opposite for peptides having high negative charge and MW (TPEVDDEALEK, TPEVDDEALEKFDK & VYVEELKPTPEGDLEILLQK) (increased from 16% to 43%). Concurrently, in C+RC, regardless of MWCO used, the highest RA was observed for peptides having low positive charge and MW (IPAVFK & ALPMHIR). It was the first time that the significant impact of charge, MWCO and pore size distribution of PES membranes on a wide range of MWCO was demonstrated on EDFM performances.
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Affiliation(s)
- Sabita Kadel
- Institute of Nutrition and Functional Foods (INAF), Dairy Science and Technology Research Centre and Department of Food Sciences, Université Laval, Québec, QC G1V 0A6, Canada; (S.K.); (G.P.); (J.T.); (V.P.)
- Laboratory of Food Processing and ElectroMembrane Processes (LTAPEM), Université Laval, Québec, QC G1V 0A6, Canada
| | - Geneviève Pellerin
- Institute of Nutrition and Functional Foods (INAF), Dairy Science and Technology Research Centre and Department of Food Sciences, Université Laval, Québec, QC G1V 0A6, Canada; (S.K.); (G.P.); (J.T.); (V.P.)
- Laboratory of Food Processing and ElectroMembrane Processes (LTAPEM), Université Laval, Québec, QC G1V 0A6, Canada
| | - Jacinthe Thibodeau
- Institute of Nutrition and Functional Foods (INAF), Dairy Science and Technology Research Centre and Department of Food Sciences, Université Laval, Québec, QC G1V 0A6, Canada; (S.K.); (G.P.); (J.T.); (V.P.)
- Laboratory of Food Processing and ElectroMembrane Processes (LTAPEM), Université Laval, Québec, QC G1V 0A6, Canada
| | - Véronique Perreault
- Institute of Nutrition and Functional Foods (INAF), Dairy Science and Technology Research Centre and Department of Food Sciences, Université Laval, Québec, QC G1V 0A6, Canada; (S.K.); (G.P.); (J.T.); (V.P.)
- Laboratory of Food Processing and ElectroMembrane Processes (LTAPEM), Université Laval, Québec, QC G1V 0A6, Canada
| | | | - Laurent Bazinet
- Institute of Nutrition and Functional Foods (INAF), Dairy Science and Technology Research Centre and Department of Food Sciences, Université Laval, Québec, QC G1V 0A6, Canada; (S.K.); (G.P.); (J.T.); (V.P.)
- Laboratory of Food Processing and ElectroMembrane Processes (LTAPEM), Université Laval, Québec, QC G1V 0A6, Canada
- Correspondence:
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13
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Ramos Y, González A, Sosa‐Acosta P, Perez‐Riverol Y, García Y, Castellanos‐Serra L, Gil J, Sánchez A, González LJ, Besada V. Sodium dodecyl sulfate free gel electrophoresis/electroelution sorting for peptide fractionation. J Sep Sci 2019; 42:3712-3717. [DOI: 10.1002/jssc.201900495] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Yassel Ramos
- Department of ProteomicsCenter for Genetic Engineering and Biotechnology La Habana Cuba
| | - Annia González
- Department of ProteomicsCenter for Genetic Engineering and Biotechnology La Habana Cuba
| | - Patricia Sosa‐Acosta
- Department of ProteomicsCenter for Genetic Engineering and Biotechnology La Habana Cuba
| | - Yasset Perez‐Riverol
- European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL‐EBI)Wellcome Trust Genome Campus Hinxton Cambridge United Kingdom
| | - Yairet García
- Department of ProteomicsCenter for Genetic Engineering and Biotechnology La Habana Cuba
| | | | - Jeovanis Gil
- Clinical Protein Science & Imaging, Biomedical CentreDepartment of Biomedical EngineeringLund University, Lund Lund Sweden
| | - Aniel Sánchez
- Section for Clinical ChemistryDepartment of Translational MedicineLund UniversitySkåne University Hospital Malmö Malmö Sweden
| | - Luis J. González
- Department of ProteomicsCenter for Genetic Engineering and Biotechnology La Habana Cuba
| | - Vladimir Besada
- Department of ProteomicsCenter for Genetic Engineering and Biotechnology La Habana Cuba
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14
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Stounbjerg L, Vestergaard C, Andreasen B, Ipsen R. Associative phase separation of potato protein and anionic polysaccharides. Colloids Surf A Physicochem Eng Asp 2019. [DOI: 10.1016/j.colsurfa.2019.01.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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15
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Kubota Y, Fujioka K, Takekawa M. WGA-based lectin affinity gel electrophoresis: A novel method for the detection of O-GlcNAc-modified proteins. PLoS One 2017; 12:e0180714. [PMID: 28686627 PMCID: PMC5501588 DOI: 10.1371/journal.pone.0180714] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 06/20/2017] [Indexed: 11/29/2022] Open
Abstract
Post-translational modification with O-linked β-N-acetylglucosamine (O-GlcNAc) occurs selectively on serine and/or threonine residues of cytoplasmic and nuclear proteins, and dynamically regulates their molecular functions. Since conventional strategies to evaluate the O-GlcNAcylation level of a specific protein require time-consuming steps, the development of a rapid and easy method for the detection and quantification of an O-GlcNAcylated protein has been a challenging issue. Here, we describe a novel method in which O-GlcNAcylated and non-O-GlcNAcylated forms of proteins are separated by lectin affinity gel electrophoresis using wheat germ agglutinin (WGA), which primarily binds to N-acetylglucosamine residues. Electrophoresis of cell lysates through a gel containing copolymerized WGA selectively induced retardation of the mobility of O-GlcNAcylated proteins, thereby allowing the simultaneous visualization of both the O-GlcNAcylated and the unmodified forms of proteins. This method is therefore useful for the quantitative detection of O-GlcNAcylated proteins.
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Affiliation(s)
- Yuji Kubota
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Ko Fujioka
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Mutsuhiro Takekawa
- Division of Cell Signaling and Molecular Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
- * E-mail:
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16
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Peró-Gascón R, Benavente F, Barbosa J, Sanz-Nebot V. Determination of acidity constants and prediction of electrophoretic separation of amyloid beta peptides. J Chromatogr A 2017; 1508:148-157. [DOI: 10.1016/j.chroma.2017.05.069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/16/2017] [Accepted: 05/31/2017] [Indexed: 11/29/2022]
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17
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Tůmová T, Monincová L, Nešuta O, Čeřovský V, Kašička V. Determination of effective charges and ionic mobilities of polycationic antimicrobial peptides by capillary isotachophoresis and capillary zone electrophoresis. Electrophoresis 2017; 38:2018-2024. [DOI: 10.1002/elps.201700092] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/14/2017] [Accepted: 04/21/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Tereza Tůmová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Prague Czech Republic
- Faculty of Food and Biochemical Technology; University of Chemistry and Technology Prague; Prague Czech Republic
| | - Lenka Monincová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Prague Czech Republic
| | - Ondřej Nešuta
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Prague Czech Republic
- Faculty of Food and Biochemical Technology; University of Chemistry and Technology Prague; Prague Czech Republic
| | - Václav Čeřovský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Prague Czech Republic
| | - Václav Kašička
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Prague Czech Republic
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Craig DB, King SD, Reinfelds G, Henderson AR, Wood TE. Electrophoretic mobility, catalytic rate, and activation energy of catalysis of single molecules of the enzyme β-glucuronidase from Escherichia coli. Int J Biol Macromol 2017; 96:669-674. [DOI: 10.1016/j.ijbiomac.2016.12.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 10/12/2016] [Accepted: 12/12/2016] [Indexed: 12/28/2022]
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Krokhin OV, Anderson G, Spicer V, Sun L, Dovichi NJ. Predicting Electrophoretic Mobility of Tryptic Peptides for High-Throughput CZE-MS Analysis. Anal Chem 2017; 89:2000-2008. [PMID: 28208305 DOI: 10.1021/acs.analchem.6b04544] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A multiparametric sequence-specific model for predicting peptide electrophoretic mobility has been developed using large-scale bottom-up proteomic CE-MS data (5% (∼0.8M) acetic acid as background electrolyte). Peptide charge (Z) and size (molecular mass, M) are the two major factors determining electrophoretic mobility, in complete agreement with previous studies. The extended size of the data set (>4000 peptides) permits access to many sequence-specific factors that impact peptide mobility. The presence of acidic residues Asp and Glu near the peptide N-terminus is by far the most prominent among them. The induction effect of the side chain of N-terminal Asp reduces the basicity of the N-terminal amino group and, as hence, its charge, by ∼0.27 units, lowering mobility. The correlation of the model (R2 ∼ 0.995) indicates that the peptide separation process in CZE is relatively simple and can be predicted to a much higher precision than current RP-HPLC models. Similar to RP-HPLC prediction studies, we anticipate future developments that introduce peptide migration standards, collect larger data sets for modeling through the alignment of multiple CZE-MS acquisitions, and study of the behavior of peptides carrying post-translational modifications. The increased size of data sets will also permit investigation of the fine-scale effects of peptide secondary structure on peptide mobility. We observed that peptides with higher helical propensity tend to have higher than predicted electrophoretic mobility; the incorporation of these features into CZE migration models will require significantly larger data sets.
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Affiliation(s)
| | | | | | - Liangliang Sun
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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20
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Zhang C, Hage DS. Glycoform analysis of alpha 1-acid glycoprotein by capillary electrophoresis. J Chromatogr A 2016; 1475:102-109. [PMID: 27863712 PMCID: PMC5147584 DOI: 10.1016/j.chroma.2016.11.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/09/2016] [Accepted: 11/10/2016] [Indexed: 11/25/2022]
Abstract
A relatively fast and reproducible CE separation was developed for the glycoform analysis of α1-acid glycoprotein (AGP). Factors that were considered included the pH for this separation and various techniques for coating the capillary and/or to minimize electroosmotic flow and protein adsorption. Optimum resolution of the AGP glycoforms was obtained at pH 4.2 with a running buffer containing 0.1% Brij 35 and by using static and dynamic coatings of PEO on the capillary. These conditions made it possible to separate nine AGP glycoform bands in about 20min. The limit of detection (based on absorbance measurements) ranged from 0.09 to 0.38μM for these AGP glycoform bands, and the linear range extended up to a total AGP concentration of at least 240μM. The migration times for the glycoform bands had typical within-day and day-to-day precisions of ±0.16-0.23% or less, respectively, on a single treated capillary and the variation between capillaries was ±0.56% or less. A charge ladder approach was employed to examine the mass or charge differences in the glycoforms that made up these bands, giving a good fit to a model in which the neighboring bands differed by one charge (e.g., from a sialic acid residue) and had an average mass difference of approximately 0.7-0.9kDa. The approaches used to develop this separation method are not limited to AGP but could be extended to the analysis of other glycoproteins by CE.
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Affiliation(s)
- Chenhua Zhang
- 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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21
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Tůmová T, Monincová L, Čeřovský V, Kašička V. Estimation of acidity constants, ionic mobilities and charges of antimicrobial peptides by capillary electrophoresis. Electrophoresis 2016; 37:3186-3195. [DOI: 10.1002/elps.201600342] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Revised: 08/25/2016] [Accepted: 09/18/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Tereza Tůmová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Prague Czech Republic
- Faculty of Food and Biochemical Technology; University of Chemistry and Technology Prague; Prague Czech Republic
| | - Lenka Monincová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Prague Czech Republic
| | - Václav Čeřovský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Prague Czech Republic
| | - Václav Kašička
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Prague Czech Republic
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Crawford JJ, Itzkow F, MacLean J, Craig DB. Conformational change in individual enzyme molecules. Biochem Cell Biol 2015; 93:611-8. [PMID: 26529308 DOI: 10.1139/bcb-2015-0099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Single β-galactosidase molecule assays were performed using a capillary electrophoresis based protocol, employing post-column laser-induced fluorescence detection. In a first set of experiments, the distribution of single β-galactosidase molecule catalytic rates and electrophoretic mobilities were determined from lysates of Escherichia coli strains containing deletions for different heat shock proteins and grown under normal and heat shock conditions. There was no clear observed pattern of effect of heat shock protein expression on these distributions. In a second set of experiments, individual enzyme molecule catalytic rates were determined at 21 °C before and after 2 sequential brief periods of incubation at 50, 28, and 10 °C. The brief incubations at 50 °C caused a change in the enzyme molecules resulting in a different catalytic rate. Any given molecule was just as likely to show an increase in rate as a decrease, resulting in no significant difference in the average rate of the population. The average change in individual molecule rate was dependent upon the temperature of the brief incubation period, with a lesser average change occurring at 28 °C and negligible change at 10 °C. A third set of experiments was similar to that of the second with the exception that it was electrophoretic mobility that was considered. This provided a similar result. Incubation at higher temperature resulted in a change in electrophoretic mobility. The probability of an individual molecules switching to a higher mobility was approximately equal to that of switching to a lower mobility, resulting in no net average change in the population. The magnitude of the changes in electrophoretic mobilities suggest that the associated conformational changes are subtle.
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Affiliation(s)
- Jeremie J Crawford
- a Department of Chemistry, 360 Parker Building, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Frannie Itzkow
- b Department of Chemistry, 599 Portage Avenue, University of Winnipeg, Winnipeg, MB R3B 2G3, Canada
| | - Joanna MacLean
- b Department of Chemistry, 599 Portage Avenue, University of Winnipeg, Winnipeg, MB R3B 2G3, Canada
| | - Douglas B Craig
- b Department of Chemistry, 599 Portage Avenue, University of Winnipeg, Winnipeg, MB R3B 2G3, Canada
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Wu H, Truncali K, Ritchie J, Kroe-Barrett R, Singh S, Robinson AS, Roberts CJ. Weak protein interactions and pH- and temperature-dependent aggregation of human Fc1. MAbs 2015; 7:1072-83. [PMID: 26267255 PMCID: PMC4966490 DOI: 10.1080/19420862.2015.1079678] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/21/2015] [Accepted: 07/27/2015] [Indexed: 01/29/2023] Open
Abstract
The Fc (fragment crystallizable) is a common structural region in immunoglobulin gamma (IgG) proteins, IgG-based multi-specific platforms, and Fc-fusion platform technologies. Changes in conformational stability, protein-protein interactions, and aggregation of NS0-produced human Fc1 were quantified experimentally as a function of pH (4 to 6) and temperature (30 to 77 °C), using a combination of differential scanning calorimetry, laser light scattering, size-exclusion chromatography, and capillary electrophoresis. The Fc1 was O-glycosylated at position 3 (threonine), and confirmed to correspond to the intact IgG1 by comparison with Fc1 produced by cleavage of the parent IgG1. Changing the pH caused large effects for thermal unfolding transitions, but it caused surprisingly smaller effects for electrostatic protein-protein interactions. The aggregation behavior was qualitatively similar across different solution conditions, with soluble dimers and larger oligomers formed in most cases. Aggregation rates spanned approximately 5 orders of magnitude and could be divided into 2 regimes: (i) Arrhenius, unfolding-limited aggregation at temperatures near or above the midpoint-unfolding temperature of the CH2 domain; (ii) a non-Arrhenius regime at lower temperatures, presumably as a result of the temperature dependence of the unfolding enthalpy for the CH2 domain. The non-Arrhenius regime was most pronounced for lower temperatures. Together with the weak protein-protein repulsions, these highlight challenges that are expected for maintaining long-term stability of biotechnology products that are based on human Fc constructs.
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Affiliation(s)
- Haixia Wu
- Department of Chemistry and Biochemistry; University of Delaware; Newark, DE USA
- Department of Biotherapeutics; Boehringer Ingelheim Pharmaceuticals Inc.; Ridgefield, CT USA
| | - Kristopher Truncali
- Department of Biotherapeutics; Boehringer Ingelheim Pharmaceuticals Inc.; Ridgefield, CT USA
| | - Julie Ritchie
- Department of Biotherapeutics; Boehringer Ingelheim Pharmaceuticals Inc.; Ridgefield, CT USA
| | - Rachel Kroe-Barrett
- Department of Biotherapeutics; Boehringer Ingelheim Pharmaceuticals Inc.; Ridgefield, CT USA
| | - Sanjaya Singh
- Department of Biotherapeutics; Boehringer Ingelheim Pharmaceuticals Inc.; Ridgefield, CT USA
| | - Anne S Robinson
- Department of Chemical and Biomolecular Engineering; Tulane University; New Orleans, LA USA
- Department of Chemical and Biomolecular Engineering; University of Delaware; Newark, DE USA
| | - Christopher J Roberts
- Department of Chemical and Biomolecular Engineering; University of Delaware; Newark, DE USA
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Singh S, Kroe-Barrett RR, Canada KA, Zhu X, Sepulveda E, Wu H, He Y, Raymond EL, Ahlberg J, Frego LE, Amodeo LM, Catron KM, Presky DH, Hanke JH. Selective targeting of the IL23 pathway: Generation and characterization of a novel high-affinity humanized anti-IL23A antibody. MAbs 2015; 7:778-91. [PMID: 25905918 PMCID: PMC4622456 DOI: 10.1080/19420862.2015.1032491] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Herein, we describe the generation and characterization of BI 655066, a novel, highly potent neutralizing anti-interleukin-23 (IL23) monoclonal antibody in clinical development for autoimmune conditions, including psoriasis and Crohn's disease. IL23 is a key driver of the differentiation, maintenance, and activity of a number of immune cell subsets, including T helper 17 (Th17) cells, which are believed to mediate the pathogenesis of several immune-mediated disorders. Thus, IL23 neutralization is an attractive therapeutic approach. Designing an antibody for clinical activity and convenience for the patient requires certain properties, such as high affinity, specificity, and solubility. These properties were achieved by directed design of the immunization, lead identification, and humanization procedures. Favorable substance and pharmacokinetic properties were established by biophysical assessments and studies in cynomolgus monkeys.
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Key Words
- ADCC, antibody-dependent cell-mediated cytotoxicity
- AUC, analytical ultracentrifugation
- BI 655066
- CCG, Chemical Computing Group
- CDRs, complementarity-determining regions
- CH, constant region
- Cκ, constant kappa
- DMF, dimethylformamide
- EOF, electro-osmotic flow
- ESI, electrospray ionization
- F, phenylalanine
- G, glycine
- GAHA, goat anti-human IgG gamma antibody
- HCLF, high concentration liquid formulation
- IL12, Interleukin 12
- IL12RB1, IL12 receptor subunit beta 1
- IL23, Interleukin-23
- IL23R, IL23 receptor
- JAK2, Janus kinase 2
- PBS, phosphate-buffered saline
- PK, pharmacokinetic
- RU, resonance units
- SEC, size-exclusion chromatography
- SPR, surface plasmon resonance
- Th17, T helper 17 cells
- UV, ultraviolet
- V, variable
- VH, variable heavy
- Vκ, variable kappa
- Y, tyrosine
- biophysical assessment
- humanization
- immunogen design
- pharmacokinetic profile
- tyk2, tyrosine kinase 2
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Affiliation(s)
- Sanjaya Singh
- a Department of Biotherapeutics Research; Boehringer Ingelheim Pharmaceuticals Inc. ; Ridgefield , CT , USA
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Barroso A, Giménez E, Benavente F, Barbosa J, Sanz-Nebot V. Modelling the electrophoretic migration behaviour of peptides and glycopeptides from glycoprotein digests in capillary electrophoresis-mass spectrometry. Anal Chim Acta 2014; 854:169-77. [PMID: 25479881 DOI: 10.1016/j.aca.2014.10.038] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 10/08/2014] [Accepted: 10/26/2014] [Indexed: 10/24/2022]
Abstract
In this study, the classical semiempirical relationships between the electrophoretic mobility and the charge-to-mass ratio (me vs. q/M(α)) were used to model the migration behaviour of peptides and glycopeptides originated from the digestion of recombinant human erythropoietin (rhEPO), a biologically and therapeutically relevant glycoprotein. The Stoke's law (α=1/3), the classical polymer model (α=1/2) and the Offord's surface law (α=2/3) were evaluated to predict migration of peptides and glycopeptides, with and without sialic acids (SiA), in rhEPO digested with trypsin and trypsin-neuraminidase. The Stoke's law resulted in better correlations for the set of peptides used to evaluate the models, while glycopeptides fitted better with the classical polymer model. Once predicted migration times with both models, it was easy to simulate their separation electropherogram. Results were later validated predicting migration and simulating separation of a different set of rhEPO glycopeptides and also human transferrin (Tf) peptides and glycopeptides. The excellent agreement between the experimental and the simulated electropherograms with rhEPO and Tf digests confirmed the potential applicability of this simple strategy to predict, in general, the peptide-glycopeptide electrophoretic map of any digested glycoprotein.
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Affiliation(s)
- Albert Barroso
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Estela Giménez
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Fernando Benavente
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - José Barbosa
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Victoria Sanz-Nebot
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain.
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Giesler L, Linke D, Rabe S, Appel D, Berger RG. Hydrolysis of wheat gluten by combining peptidases of Flammulina velutipes and electrodialysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:8641-8649. [PMID: 23947566 DOI: 10.1021/jf401716m] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Wheat gluten hydrolysis, used to generate seasonings, was studied using peptidases from Flammulina velutipes or commercial Flavourzyme. L-amino acids were added in a range from 0.5 to 75.0 mM, and L-isoleucine, L-leucine, L-valine, and L-phenylalanine were identified as the strongest inhibitors for both enzyme mixtures. L-serine inhibited Flammulina velutipes peptidases only, while L-histidine and L-glutamine inhibited Flavourzyme peptidases only. To reduce product inhibition by released L-amino acids, electrodialysis was explored. An increase of the degree of hydrolysis of up to 60% for Flammulina velutipes peptidases and 31% for Flavourzyme compared to that for the best control batch was observed after applying an electrodialysis unit equipped with an ultrafiltration membrane for two times 1 h during the 20 h of hydrolysis. The total transfer of free L-amino acids into the concentrate reached 25-30% per hour. Peptides passed the membrane less easily, although the nominal cutoff was 4 kDa.
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Affiliation(s)
- Lucienne Giesler
- Leibniz Universität Hannover, Institut für Lebensmittelchemie , Callinstraβe 5, 30167 Hannover, Germany
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Craig DB, Bayaraa B, Lee D, Charleton J. EFFECT OF INDUCTION TEMPERATURE AND PARTIAL THERMAL DENATURATION ON THE CATALYTIC AND ELECTROPHORETIC HETEROGENEITY OF β-GALACTOSIDASE FROM TWO ESCHERICHIA COLI STRAINS. J LIQ CHROMATOGR R T 2013. [DOI: 10.1080/10826076.2012.731672] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Douglas B Craig
- a Chemistry Department , University of Winnipeg , Winnipeg , Manitoba , Canada
| | - Bayasgalan Bayaraa
- a Chemistry Department , University of Winnipeg , Winnipeg , Manitoba , Canada
| | - Dorice Lee
- a Chemistry Department , University of Winnipeg , Winnipeg , Manitoba , Canada
| | - Justin Charleton
- a Chemistry Department , University of Winnipeg , Winnipeg , Manitoba , Canada
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Deiber JA, Piaggio MV, Peirotti MB. Evaluation of the slip length in the slipping friction between background electrolytes and peptides through the modeling of their capillary zone electrophoretic mobilities. Electrophoresis 2013; 34:2648-54. [DOI: 10.1002/elps.201300102] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 03/30/2013] [Accepted: 04/02/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Julio A. Deiber
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC); UNL, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Santa Fe; Argentina
| | - Maria V. Piaggio
- Cátedra de Bioquímica Básica de Macromoléculas; Facultad de Bioquímica y Ciencias Biológicas; Universidad Nacional del Litoral (UNL); Santa Fe; Argentina
| | - Marta B. Peirotti
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC); UNL, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Santa Fe; Argentina
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30
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Doyen A, Roblet C, Beaulieu L, Saucier L, Pouliot Y, Bazinet L. Impact of water splitting phenomenon during electrodialysis with ultrafiltration membranes on peptide selectivity and migration. J Memb Sci 2013. [DOI: 10.1016/j.memsci.2012.10.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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31
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Deiber JA, Piaggio MV, Peirotti MB. Determination of electrokinetic and hydrodynamic parameters of proteins by modeling their electrophoretic mobilities through the electrically charged spherical soft particle. Electrophoresis 2013; 34:708-15. [DOI: 10.1002/elps.201200463] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/03/2012] [Accepted: 10/17/2012] [Indexed: 01/23/2023]
Affiliation(s)
- Julio A. Deiber
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC); Universidad Nacional del Litoral (UNL); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Santa Fe; Argentina
| | - María V. Piaggio
- Cátedra de Bioquímica Básica de Macromoléculas; Facultad de Bioquímica y Ciencias Biológicas; UNL; Santa Fe; Argentina
| | - Marta B. Peirotti
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC); Universidad Nacional del Litoral (UNL); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Santa Fe; Argentina
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Craig DB, Schwab T, Sterner R. Random mutagenesis suggests that sequence errors are not a major cause of variation in the activity of individual molecules of β-galactosidase. Biochem Cell Biol 2012; 90:540-7. [DOI: 10.1139/o2012-006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Wild-type Escherichia coli lacZ was subjected to error-prone PCR to generate two plasmid-encoded gene libraries containing approximately 2.6 (SD 1.9) nucleotide exchanges resulting in 1.8 (SD 1.4) amino-acid substitutions. The libraries were used, along with a plasmid containing wild-type lacZ, to transform E. coli lacking genomic lacZ. Cells expressing functional β-galactosidase were identified by blue/white screening. Cell lysates containing the populations of heterogeneously mutagenized β-galactosidase were subjected to single molecule assays using a capillary electrophoresis laser-induced fluorescence-based protocol. There was no significant difference in the average catalytic rate between the random mutagenized and wild-type enzyme populations. Furthermore, there was no clear pattern between error rates and the variances in the population catalytic rates. This suggests that random sequence errors are not a substantial source of the catalytic heterogeneity of this enzyme.
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Affiliation(s)
- Douglas B. Craig
- Chemistry Department, University of Winnipeg, 515 Portage Avenue, Winnipeg, MB, Canada
| | - Thomas Schwab
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Universitätsstraße 31, D-93053, Regensburg, Germany
| | - Reinhard Sterner
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Universitätsstraße 31, D-93053, Regensburg, Germany
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Doyen A, Saucier L, Beaulieu L, Pouliot Y, Bazinet L. Electroseparation of an antibacterial peptide fraction from snow crab by-products hydrolysate by electrodialysis with ultrafiltration membranes. Food Chem 2012; 132:1177-1184. [DOI: 10.1016/j.foodchem.2011.11.059] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 08/17/2011] [Accepted: 11/07/2011] [Indexed: 11/29/2022]
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34
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Deiber JA, Peirotti MB, Piaggio MV. Interplay between electrophoretic mobility and intrinsic viscosity of polypeptide chains. Electrophoresis 2012; 33:990-9. [DOI: 10.1002/elps.201100637] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Julio A. Deiber
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC); Universidad Nacional del Litoral (UNL); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Santa Fe; Argentina
| | - Marta B. Peirotti
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC); Universidad Nacional del Litoral (UNL); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Santa Fe; Argentina
| | - María V. Piaggio
- Cátedra de Bioquímica Básica de Macromoléculas,; Facultad de Bioquímica y Ciencias Biológicas; UNL; Santa Fe; Argentina
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Mean net charge of intrinsically disordered proteins: experimental determination of protein valence by electrophoretic mobility measurements. Methods Mol Biol 2012; 896:331-49. [PMID: 22821535 DOI: 10.1007/978-1-4614-3704-8_22] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Under physiological conditions, intrinsically disordered proteins (IDPs) are unfolded, mainly because of their low hydrophobicity and the strong electrostatic repulsion between charged residues of the same sign within the protein. Softwares have been designed to facilitate the computation of the mean net charge of proteins (formally protein valence) from their amino acid sequences. Nevertheless, discrepancies between experimental and computed valence values for several proteins have been reported in the literature. Hence, experimental approaches are required to obtain accurate estimation of protein valence in solution. Moreover, ligand-induced disorder-to-order transition is involved in the folding of numerous IDPs. Some of the ligands are cations or anions, which, upon protein binding, decrease the mean net charge of the protein, favoring its folding via a charge reduction effect. An accurate determination of the mean net charge of protein in both its ligand-free intrinsically disordered state and in its folded, ligand-bound state allows one to estimate the number of ligands bound to the protein in the holo-state. Here, we describe an experimental protocol to determine the mean net charge of protein, from its electrophoretic mobility, its molecular mass and its hydrodynamic radius.
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Deiber JA, Piaggio MV, Peirotti MB. Global conformations of proteins as predicted from the modeling of their CZE mobility data. Electrophoresis 2011; 32:2779-87. [DOI: 10.1002/elps.201100016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 02/07/2011] [Accepted: 02/10/2011] [Indexed: 11/11/2022]
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Taichrib A, Scriba GKE, Neusüß C. Identification and characterization of impurities of tetracosactide by capillary electrophoresis and liquid chromatography coupled to time-of-flight mass spectrometry. Anal Bioanal Chem 2011; 401:1365-75. [DOI: 10.1007/s00216-011-5183-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 06/09/2011] [Accepted: 06/13/2011] [Indexed: 12/19/2022]
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Brummitt RK, Nesta DP, Chang L, Chase SF, Laue TM, Roberts CJ. Nonnative Aggregation of an IgG1 Antibody in Acidic Conditions: Part 1. Unfolding, Colloidal Interactions, and Formation of High-Molecular-Weight Aggregates. J Pharm Sci 2011; 100:2087-103. [DOI: 10.1002/jps.22448] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2010] [Revised: 10/09/2010] [Accepted: 11/17/2010] [Indexed: 01/26/2023]
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Brummitt RK, Nesta DP, Chang L, Kroetsch AM, Roberts CJ. Nonnative Aggregation of an IgG1 Antibody in Acidic Conditions, Part 2: Nucleation and Growth Kinetics with Competing Growth Mechanisms. J Pharm Sci 2011; 100:2104-19. [DOI: 10.1002/jps.22447] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2010] [Revised: 10/09/2010] [Accepted: 11/17/2010] [Indexed: 01/22/2023]
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Conductivity and electrophoretic mobility of dilute ionic solutions. J Colloid Interface Sci 2010; 352:1-10. [DOI: 10.1016/j.jcis.2010.08.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 07/30/2010] [Accepted: 08/02/2010] [Indexed: 11/23/2022]
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Sugimoto M, Hirayama A, Robert M, Abe S, Soga T, Tomita M. Prediction of metabolite identity from accurate mass, migration time prediction and isotopic pattern information in CE-TOFMS data. Electrophoresis 2010; 31:2311-8. [PMID: 20568260 DOI: 10.1002/elps.200900584] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
CE-TOFMS is a powerful method for profiling charged metabolites. However, the limited availability of metabolite standards hinders the process of identifying compounds from detected features in CE-TOFMS data sets. To overcome this problem, we developed a method to identify unknown peaks based on the predicted migration time (t(m)) and accurate m/z values. We developed a predictive model using 375 standard cationic metabolites and support vector regression. The model yielded good correlations between the predicted and measured t(m) (R=0.952 and 0.905 using complete and cross-validation data sets, respectively). Using the trained model, we subsequently predicted the t(m) for 2938 metabolites available from the public databases and assigned tentative identities to noise-filtered features in human urine samples. While 38.9% of the peaks were assigned metabolite names by matching with the standard library alone, the proportion increased to 52.2%. The proposed methodology increases the value of metabolomic data sets obtained from CE-TOFMS profiling.
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Affiliation(s)
- Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan.
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Piaggio MV, Peirotti MB, Deiber JA. Estimation of global structural and transport properties of peptides through the modeling of their CZE mobility data. J Sep Sci 2010; 33:2423-9. [DOI: 10.1002/jssc.201000134] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Sharma GM, Mundoma C, Seavy M, Roux KH, Sathe SK. Purification and biochemical characterization of Brazil nut (Bertholletia excelsa L.) seed storage proteins. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2010; 58:5714-5723. [PMID: 20405841 DOI: 10.1021/jf9036326] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Brazil nut storage proteins, 2S albumin, 7S vicilin, and an 11S legumin, were purified using column chromatography. Analytical ultracentrifugation of the purified albumin, vicilin, and legumin proteins, respectively, registered sedimentation coefficients of 1.8, 7.1, and 11.8 S. Under reducing conditions, the major polypeptide bands in 2S albumin were observed at 6.4, 10-11, and 15.2 kDa. The 7S globulin was composed of one 12.6 kDa, two approximately 38-42 kDa, and two approximately 54-57 kDa polypeptides, whereas the 11S globulin contained two major classes of polypeptides: approximately 30-32 and approximately 20-21 kDa. The 7S globulin stained positive when reacted with Schiff reagent, indicating that it is a glycoprotein. The estimated molecular mass and Stokes radius for 2S albumin and 7S and 11S globulins were 19.2 kDa and 20.1 A, 114.8 kDa and 41.1 A, and 289.4 kDa and 56.6 A, respectively. Circular dichroism spectroscopic analysis indicated the secondary structure of the three proteins to be mainly beta-sheets and turns. Emission fluorescence spectra of the native proteins registered a lambda(max) at 337, 345, and 328 nm for 2S albumin and 7S and 11S globulins, respectively. When probed with anti-Brazil nut seed protein rabbit polyclonal antibodies, 7S globulin exhibited higher immunoreactivity than 2S albumin and 11S globulin.
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Affiliation(s)
- Girdhari M Sharma
- Department of Nutrition, Food and Exercise Sciences, College of Human Sciences, The Florida State University, Tallahassee, Florida 32306-1493, USA
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Benavente F, Giménez E, Barrón D, Barbosa J, Sanz-Nebot V. Modeling the electrophoretic behavior of quinolones in aqueous and hydroorganic media. Electrophoresis 2010; 31:965-72. [DOI: 10.1002/elps.200900344] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Allison SA, Pei H, Baek S, Brown J, Lee MY, Nguyen V, Twahir UT, Wu H. The dependence of the electrophoretic mobility of small organic ions on ionic strength and complex formation. Electrophoresis 2010; 31:920-32. [DOI: 10.1002/elps.200900625] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Piaggio MV, Peirotti MB, Deiber JA. Analysis of the interplay among charge, hydration and shape of proteins through the modeling of their CZE mobility data. Electrophoresis 2009; 30:2328-36. [DOI: 10.1002/elps.200800743] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Ahmed FE. The role of capillary electrophoresis–mass spectrometry to proteome analysis and biomarker discovery. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:1963-81. [DOI: 10.1016/j.jchromb.2009.05.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2008] [Revised: 04/24/2009] [Accepted: 05/10/2009] [Indexed: 01/25/2023]
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Nichols ER, Shadabi E, Craig DB. Effect of alteration of translation error rate on enzyme microheterogeneity as assessed by variation in single molecule electrophoretic mobility and catalytic activity. Biochem Cell Biol 2009; 87:517-29. [DOI: 10.1139/o09-010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The role of translation error for Escherichia coli individual β-galactosidase molecule catalytic and electrophoretic heterogeneity was investigated using CE-LIF. An E. coli rpsL mutant with a hyperaccurate translation phenotype produced enzyme molecules that exhibited significantly less catalytic heterogeneity but no reduction of electrophoretic heterogeneity. Enzyme expressed with streptomycin-induced translation error had increased thermolability, lower activity, and no significant change to catalytic or electrophoretic heterogeneity. Modeling of the electrophoretic behaviour of β-galactosidase suggested that variation of the hydrodynamic radius may be the most significant contributor to electrophoretic heterogeneity.
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Affiliation(s)
- Ellert R. Nichols
- Chemistry Department, University of Winnipeg, 515 Portage Ave, Winnipeg, MB R3B 2E9, Canada
- Registered as a graduate student at the Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Elnaz Shadabi
- Chemistry Department, University of Winnipeg, 515 Portage Ave, Winnipeg, MB R3B 2E9, Canada
- Registered as a graduate student at the Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Douglas B. Craig
- Chemistry Department, University of Winnipeg, 515 Portage Ave, Winnipeg, MB R3B 2E9, Canada
- Registered as a graduate student at the Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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Jing J, Liang G, Mei H, Xiao S, Xia Z, Li Z. Quantitative structure–mobility relationship studies of dipeptides in capillary zone electrophoresis using three-dimensional holographic vector of atomic interaction field. MOLECULAR SIMULATION 2009. [DOI: 10.1080/08927020802512203] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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