1
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Valente JFA, Queiroz JA, Sousa F. Dilemma on plasmid DNA purification: binding capacity vs selectivity. J Chromatogr A 2020; 1637:461848. [PMID: 33421679 DOI: 10.1016/j.chroma.2020.461848] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 10/22/2022]
Abstract
Plasmid DNA chromatography is a powerful field in constant development and evolution. The use of this technique is considered mandatory in the production of an efficient and safe formulation to be applied for plasmid-mediated gene therapy. Concerning this, the search for an ideal chromatographic support/ligand combination motivated scientist to pursue a continuous improvement on the plasmid chromatography performance, looking for a progression on the ligands and supports used. The present review explores the different approaches used over time to purify plasmid DNA, ambitioning both high recovery and high purity levels. Overall, it is presented a critical discussion relying on the relevance of the binding capacity versus selectivity of the supports.
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Affiliation(s)
- J F A Valente
- CICS-UBI - Health Sciences Research Centre, Universidade da Beira Interior, Avenida Infante D. Henrique, 6200-506Covilhã, Portugal; CDRSP-IPLEIRIA - Centre for Rapid and Sustainable Product Development, Instituto Politécnico de Leiria, Rua de Portugal - Zona Industrial, 2430-028Marinha Grande, Portugal
| | - J A Queiroz
- CICS-UBI - Health Sciences Research Centre, Universidade da Beira Interior, Avenida Infante D. Henrique, 6200-506Covilhã, Portugal
| | - F Sousa
- CICS-UBI - Health Sciences Research Centre, Universidade da Beira Interior, Avenida Infante D. Henrique, 6200-506Covilhã, Portugal.
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2
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Perret G, Boschetti E. Aptamer-Based Affinity Chromatography for Protein Extraction and Purification. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 174:93-139. [PMID: 31485702 DOI: 10.1007/10_2019_106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Aptamers are oligonucleotide molecules able to recognize very specifically proteins. Among the possible applications, aptamers have been used for affinity chromatography with effective results and advantages over most advanced protein separation technologies. This chapter first discusses the context of the affinity chromatography with aptamer ligands. With the adaptation of SELEX, the chemical modifications of aptamers to comply with the covalent coupling and the separation process are then extensively presented. A focus is then made about the most important applications for protein separation with real-life examples and the comparison with immunoaffinity chromatography. In spite of well-advanced demonstrations and the extraordinary potential developments, a significant optimization work is still due to deserve large-scale applications with all necessary validations. Graphical Abstract Aptamer-protein complexes by X-ray crystallography.
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3
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Matos MJB, Pina AS, Roque ACA. Rational design of affinity ligands for bioseparation. J Chromatogr A 2020; 1619:460871. [PMID: 32044126 DOI: 10.1016/j.chroma.2020.460871] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/05/2020] [Accepted: 01/08/2020] [Indexed: 11/25/2022]
Abstract
Affinity adsorbents have been the cornerstone in protein purification. The selective nature of the molecular recognition interactions established between an affinity ligands and its target provide the basis for efficient capture and isolation of proteins. The plethora of affinity adsorbents available in the market reflects the importance of affinity chromatography in the bioseparation industry. Ligand discovery relies on the implementation of rational design techniques, which provides the foundation for the engineering of novel affinity ligands. The main goal for the design of affinity ligands is to discover or improve functionality, such as increased stability or selectivity. However, the methodologies must adapt to the current needs, namely to the number and diversity of biologicals being developed, and the availability of new tools for big data analysis and artificial intelligence. In this review, we offer an overview on the development of affinity ligands for bioseparation, including the evolution of rational design techniques, dating back to the years of early discovery up to the current and future trends in the field.
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Affiliation(s)
- Manuel J B Matos
- UCIBIO, Chemistry Department, School of Sciences and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - Ana S Pina
- UCIBIO, Chemistry Department, School of Sciences and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal
| | - A C A Roque
- UCIBIO, Chemistry Department, School of Sciences and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal.
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4
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Jose L, Lee C, Hwang A, Park JH, Song JK, Paik HJ. Magnetically steerable Fe3O4@Ni2+-NTA-polystyrene nanoparticles for the immobilization and separation of his6-protein. Eur Polym J 2019. [DOI: 10.1016/j.eurpolymj.2019.01.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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5
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Kumar R, Ghosh AK, Pal P. Sustainable Production of Biofuels through Membrane-Integrated Systems. SEPARATION & PURIFICATION REVIEWS 2019. [DOI: 10.1080/15422119.2018.1562942] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- Ramesh Kumar
- Department of Chemistry, The University of Burdwan, Bardhaman, West Bengal, India
| | - Alak Kumar Ghosh
- Department of Chemistry, The University of Burdwan, Bardhaman, West Bengal, India
| | - Parimal Pal
- Environment and Membrane Technology Laboratory, Department of Chemical Engineering, National Institute of Technology, Durgapur, West Bengal, India
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6
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Development of a metal/chelate polyhydroxyethylmethacrylate monolith capillary for selective depletion of immunoglobulin G from human plasma for proteomics. J Chromatogr A 2017; 1517:117-125. [DOI: 10.1016/j.chroma.2017.08.047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 07/17/2017] [Accepted: 08/17/2017] [Indexed: 02/03/2023]
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7
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Jacob SI, Khogeer B, Bampos N, Sheppard T, Schwartz R, Lowe CR. Development and Application of Synthetic Affinity Ligands for the Purification of Ferritin-Based Influenza Antigens. Bioconjug Chem 2017; 28:1931-1943. [DOI: 10.1021/acs.bioconjchem.7b00253] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Shaleem I. Jacob
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, United Kingdom
| | - Basmah Khogeer
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, United Kingdom
| | - Nick Bampos
- Department
of Chemistry, University of Cambridge, Cambridge, CB2 1EW, United Kingdom
| | - Tom Sheppard
- Department
of Chemistry, University College London, London, WC1H 0AJ, United Kingdom
| | - Richard Schwartz
- Vaccine
Production Program Laboratory, National Institute of Health, Gaithersburg, Maryland 20878, United States
| | - Christopher R. Lowe
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, United Kingdom
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8
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Petasis-Ugi ligands: New affinity tools for the enrichment of phosphorylated peptides. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1031:86-93. [DOI: 10.1016/j.jchromb.2016.07.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 07/15/2016] [Accepted: 07/18/2016] [Indexed: 01/07/2023]
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9
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Batalha IL, Zhou H, Lilley K, Lowe CR, Roque ACA. Mimicking nature: Phosphopeptide enrichment using combinatorial libraries of affinity ligands. J Chromatogr A 2016; 1457:76-87. [PMID: 27345211 DOI: 10.1016/j.chroma.2016.06.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 06/08/2016] [Accepted: 06/09/2016] [Indexed: 12/11/2022]
Abstract
Phosphorylation is a reversible post-translational modification of proteins that controls a plethora of cellular processes and triggers specific physiological responses, for which there is a need to develop tools to characterize phosphorylated targets efficiently. Here, a combinatorial library of triazine-based synthetic ligands comprising 64 small molecules has been rationally designed, synthesized and screened for the enrichment of phosphorylated peptides. The lead candidate (coined A8A3), composed of histidine and phenylalanine mimetic components, showed high binding capacity and selectivity for binding mono- and multi-phosphorylated peptides at pH 3. Ligand A8A3 was coupled onto both cross-linked agarose and magnetic nanoparticles, presenting higher binding capacities (100-fold higher) when immobilized on the magnetic support. The magnetic adsorbent was further screened against a tryptic digest of two phosphorylated proteins (α- and β-caseins) and one non-phosphorylated protein (bovine serum albumin, BSA). The MALDI-TOF mass spectra of the eluted peptides allowed the identification of nine phosphopeptides, comprising both mono- and multi-phosphorylated peptides.
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Affiliation(s)
- Iris L Batalha
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Houjiang Zhou
- Cambridge Centre for Proteomics, Cambridge, CB2 1QR, UK
| | | | - Christopher R Lowe
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Tennis Court Road, CB2 1QT, Cambridge, UK
| | - Ana C A Roque
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
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10
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Lin CP, Boysen RI, Campi EM, Saito K, Hearn MTW. Studies on the binding sites of IgG2 monoclonal antibodies recognized by terpyridine-based affinity ligands. J Mol Recognit 2016; 29:334-42. [PMID: 26842829 DOI: 10.1002/jmr.2535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 12/16/2015] [Indexed: 11/09/2022]
Abstract
This investigation has examined the origin of the molecular recognition associated with the interaction of monoclonal IgG2's with terpyridine-based ligands immobilized onto agarose-derived chromatographic adsorbents. Isothermal titration calorimetric (ITC) methods have been employed to acquire thermodynamic data associated with the IgG2-ligand binding. These ITC investigations have documented that different enthalpic and entropic processes are involved depending on the nature of the chemical substituents in the core structure of the terpyridinyl moiety. In addition, molecular docking studies have been carried out with IgG2 structures with the objective to identify possible ligand binding sites and key interacting amino acid residues. These molecular docking experiments with the different terpyridine-based ligands have shown that all of the examined ligands can potentially undergo favorable interactions with a site located within the Fab region of the IgG2. However, another favorable binding site was also identified from the docking poses to exist within the Fc region of the IgG2 for some, but not all, of the ligands studied. These investigations have provided a basis to elucidate the unique binding properties and chromatographic behaviors shown by several substituted terpyridine ligands in their interaction with IgGs of different isotype. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Chih-Pei Lin
- School of Chemistry, Monash University, Melbourne, VIC, 3800, Australia
| | - Reinhard I Boysen
- School of Chemistry, Monash University, Melbourne, VIC, 3800, Australia
| | - Eva M Campi
- School of Chemistry, Monash University, Melbourne, VIC, 3800, Australia
| | - Kei Saito
- School of Chemistry, Monash University, Melbourne, VIC, 3800, Australia
| | - Milton T W Hearn
- School of Chemistry, Monash University, Melbourne, VIC, 3800, Australia
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11
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Mild and cost-effective green fluorescent protein purification employing small synthetic ligands. J Chromatogr A 2015; 1418:83-93. [DOI: 10.1016/j.chroma.2015.09.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 09/09/2015] [Accepted: 09/12/2015] [Indexed: 11/24/2022]
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12
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Salvalaglio M, Paloni M, Guelat B, Morbidelli M, Cavallotti C. A two level hierarchical model of protein retention in ion exchange chromatography. J Chromatogr A 2015; 1411:50-62. [DOI: 10.1016/j.chroma.2015.07.101] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/23/2015] [Accepted: 07/27/2015] [Indexed: 10/23/2022]
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13
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Perret G, Santambien P, Boschetti E. The quest for affinity chromatography ligands: are the molecular libraries the right source? J Sep Sci 2015; 38:2559-72. [DOI: 10.1002/jssc.201500285] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 04/26/2015] [Accepted: 05/10/2015] [Indexed: 12/15/2022]
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14
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Zeinali Sehrig F, Majidi S, Nikzamir N, Nikzamir N, Nikzamir M, Akbarzadeh A. Magnetic nanoparticles as potential candidates for biomedical and biological applications. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2015; 44:918-27. [PMID: 25613027 DOI: 10.3109/21691401.2014.998832] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Magnetic iron oxide nanoparticles have become the main candidates for biomedical and biological applications, and the application of small iron oxide nanoparticles in in vitro diagnostics has been practiced for about half a century. Magnetic nanoparticles (MNPs), in combination with an external magnetic field and/or magnetizable grafts, allow the delivery of particles to the chosen target area, fix them at the local site while the medication is released, and act locally. In this review, we focus mostly on the potential use of MNPs for biomedical and biotechnological applications, and the improvements made in using these nanoparticles (NPs) in biological applications.
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Affiliation(s)
| | - Sima Majidi
- b Biotechnology Research Center, Tabriz University of Medical Sciences , Tabriz , Iran
| | - Nasrin Nikzamir
- a Drug Applied Research Center, Tabriz University of Medical Sciences , Tabriz , Iran
| | - Nasim Nikzamir
- a Drug Applied Research Center, Tabriz University of Medical Sciences , Tabriz , Iran
| | - Mohammad Nikzamir
- a Drug Applied Research Center, Tabriz University of Medical Sciences , Tabriz , Iran
| | - Abolfazl Akbarzadeh
- a Drug Applied Research Center, Tabriz University of Medical Sciences , Tabriz , Iran.,b Biotechnology Research Center, Tabriz University of Medical Sciences , Tabriz , Iran.,c Hematology and Oncology Research Center, Tabriz University of Medical Sciences , Tabriz , Iran.,d Department of Medical Nanotechnology , Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences , Tabriz , Iran
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15
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Fernandes CS, Pina AS, Dias AM, Branco RJ, Roque ACA. A theoretical and experimental approach toward the development of affinity adsorbents for GFP and GFP-fusion proteins purification. J Biotechnol 2014; 186:13-20. [DOI: 10.1016/j.jbiotec.2014.06.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 06/12/2014] [Accepted: 06/16/2014] [Indexed: 11/27/2022]
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16
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Pina AS, Guilherme M, Pereira AS, Fernandes CSM, Branco RJF, El Khoury G, Lowe CR, Roque ACA. A Tailor-Made “Tag-Receptor” Affinity Pair for the Purification of Fusion Proteins. Chembiochem 2014; 15:1423-35. [DOI: 10.1002/cbic.201400018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Indexed: 11/11/2022]
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17
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Pina AS, Lowe CR, Roque ACA. Challenges and opportunities in the purification of recombinant tagged proteins. Biotechnol Adv 2014; 32:366-81. [PMID: 24334194 PMCID: PMC7125906 DOI: 10.1016/j.biotechadv.2013.12.001] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 12/04/2013] [Accepted: 12/08/2013] [Indexed: 01/05/2023]
Abstract
The purification of recombinant proteins by affinity chromatography is one of the most efficient strategies due to the high recovery yields and purity achieved. However, this is dependent on the availability of specific affinity adsorbents for each particular target protein. The diversity of proteins to be purified augments the complexity and number of specific affinity adsorbents needed, and therefore generic platforms for the purification of recombinant proteins are appealing strategies. This justifies why genetically encoded affinity tags became so popular for recombinant protein purification, as these systems only require specific ligands for the capture of the fusion protein through a pre-defined affinity tag tail. There is a wide range of available affinity pairs "tag-ligand" combining biological or structural affinity ligands with the respective binding tags. This review gives a general overview of the well-established "tag-ligand" systems available for fusion protein purification and also explores current unconventional strategies under development.
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Affiliation(s)
- Ana Sofia Pina
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; IBET-Instituto de Biologia Experimental Tecnológica, Oeiras, Portugal
| | - Christopher R Lowe
- Institute of Biotechnology, Department of Chemical Engineering and Biotechnology, University of Cambridge, Tennis Court Road, CB2 1QT Cambridge, UK
| | - Ana Cecília A Roque
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
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18
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Tippkötter N, Al-Kaidy H, Wollny S, Ulber R. Functionalized Magnetizable Particles for Downstream Processing in Single-Use Systems. CHEM-ING-TECH 2012. [DOI: 10.1002/cite.201200130] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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19
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Salvalaglio M, Cavallotti C. Molecular modeling to rationalize ligand-support interactions in affinity chromatography. J Sep Sci 2011; 35:7-19. [DOI: 10.1002/jssc.201100595] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 09/26/2011] [Accepted: 09/30/2011] [Indexed: 11/09/2022]
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20
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Ye L, Xu A, Cheng C, Zhang L, Huo C, Huang F, Xu H, Li R. Design and synthesis of affinity ligands and relation of their structure with adsorption of proteins. J Sep Sci 2011; 34:3145-50. [DOI: 10.1002/jssc.201100606] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 08/12/2011] [Accepted: 08/24/2011] [Indexed: 11/11/2022]
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21
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Dias AMGC, Hussain A, Marcos AS, Roque ACA. A biotechnological perspective on the application of iron oxide magnetic colloids modified with polysaccharides. Biotechnol Adv 2010; 29:142-55. [PMID: 20959138 DOI: 10.1016/j.biotechadv.2010.10.003] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 09/29/2010] [Accepted: 10/11/2010] [Indexed: 11/27/2022]
Abstract
Iron oxide magnetic nanoparticles (MNPs) alone are suitable for a broad spectrum of applications, but the low stability and heterogeneous size distribution in aqueous medium represent major setbacks. These setbacks can however be reduced or diminished through the coating of MNPs with various polymers, especially biopolymers such as polysaccharides. Polysaccharides are biocompatible, non-toxic and renewable; in addition, they possess chemical groups that permit further functionalization of the MNPs. Multifunctional entities can be created through decoration with specific molecules e.g. proteins, peptides, drugs, antibodies, biomimetic ligands, transfection agents, cells, and other ligands. This development opens a whole range of applications for iron oxide nanoparticles. In this review the properties of magnetic structures composed of MNPs and several polysaccharides (Agarose, Alginate, Carrageenan, Chitosan, Dextran, Heparin, Gum Arabic, Pullulan and Starch) will be discussed, in view of their recent and future biomedical and biotechnological applications.
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Affiliation(s)
- A M G C Dias
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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22
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Pina AS, Lowe CR, Roque ACA. Comparison of Fluorescence Labelling Techniques for the Selection of Affinity Ligands from Solid-Phase Combinatorial Libraries. SEP SCI TECHNOL 2010. [DOI: 10.1080/01496395.2010.507447] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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23
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Rasmussen JE, Schiødt CB, Christensen SF, Nørskov-Lauritsen L, Meldal M, St Hilaire PM, Jensen KJ. Small-molecule affinity ligands for protein purification: combined computational enrichment and automated in-line screening of an optically encoded library. Angew Chem Int Ed Engl 2010; 49:3477-80. [PMID: 20301150 DOI: 10.1002/anie.200906602] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jakob E Rasmussen
- Protein Engineering, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark.
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Rasmussen J, Schiødt C, Christensen S, Nørskov-Lauritsen L, Meldal M, St. Hilaire P, Jensen K. Small-Molecule Affinity Ligands for Protein Purification: Combined Computational Enrichment and Automated In-line Screening of an Optically Encoded Library. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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25
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Preparation and characterization of a cellulose affinity membrane for human immunoglobulin G (IgG) purification. J Memb Sci 2010. [DOI: 10.1016/j.memsci.2009.11.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Batalha IL, Hussain A, Roque ACA. Gum Arabic coated magnetic nanoparticles with affinity ligands specific for antibodies. J Mol Recognit 2010; 23:462-71. [DOI: 10.1002/jmr.1013] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Dedieu A, Bérenguer F, Basset C, Prat O, Quéméneur E, Pible O, Vidaud C. Identification of uranyl binding proteins from human kidney-2 cell extracts by immobilized uranyl affinity chromatography and mass spectrometry. J Chromatogr A 2009; 1216:5365-76. [PMID: 19501829 DOI: 10.1016/j.chroma.2009.05.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Revised: 05/06/2009] [Accepted: 05/11/2009] [Indexed: 11/17/2022]
Abstract
To improve our knowledge on protein targets of uranyl ion (UO(2)(2+)), we set up a proteomic strategy based on immobilized metal-affinity chromatography (IMAC). The successful enrichment of UO(2)(2+)-interacting proteins from human kidney-2 (HK-2) soluble cell extracts was obtained using an ion-exchange chromatography followed by a dedicated IMAC process previously described and designed for the uranyl ion. By mass spectrometry analysis we identified 64 proteins displaying varied functions. The use of a computational screening algorithm along with the particular ligand-based properties of the UO(2)(2+) ion allowed the analysis and categorization of the protein collection. This profitable approach demonstrated that most of these proteins fulfill criteria which could rationalize their binding to the UO(2)(2+)-loaded phase. The obtained results enable us to focus on some targets for more in-depth studies and open new insights on its toxicity mechanisms at molecular level.
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Callesen AK, Madsen JS, Vach W, Kruse TA, Mogensen O, Jensen ON. Serum protein profiling by solid phase extraction and mass spectrometry: A future diagnostics tool? Proteomics 2009; 9:1428-41. [DOI: 10.1002/pmic.200800382] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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29
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Brne P, Lim YP, Podgornik A, Barut M, Pihlar B, Štrancar A. Development and characterization of methacrylate-based hydrazide monoliths for oriented immobilization of antibodies. J Chromatogr A 2009; 1216:2658-63. [DOI: 10.1016/j.chroma.2008.11.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2008] [Revised: 10/29/2008] [Accepted: 11/03/2008] [Indexed: 10/21/2022]
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30
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31
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Sun Y, Liu FF, Shi QH. Approaches to high-performance preparative chromatography of proteins. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2009; 113:217-254. [PMID: 19373447 DOI: 10.1007/10_2008_32] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Preparative liquid chromatography is widely used for the purification of chemical and biological substances. Different from high-performance liquid chromatography for the analysis of many different components at minimized sample loading, high-performance preparative chromatography is of much larger scale and should be of high resolution and high capacity at high operation speed and low to moderate pressure drop. There are various approaches to this end. For biochemical engineers, the traditional way is to model and optimize a purification process to make it exert its maximum capability. For high-performance separations, however, we need to improve chromatographic technology itself. We herein discuss four approaches in this review, mainly based on the recent studies in our group. The first is the development of high-performance matrices, because packing material is the central component of chromatography. Progress in the fabrication of superporous materials in both beaded and monolithic forms are reviewed. The second topic is the discovery and design of affinity ligands for proteins. In most chromatographic methods, proteins are separated based on their interactions with the ligands attached to the surface of porous media. A target-specific ligand can offer selective purification of desired proteins. Third, electrochromatography is discussed. An electric field applied to a chromatographic column can induce additional separation mechanisms besides chromatography, and result in electrokinetic transport of protein molecules and/or the fluid inside pores, thus leading to high-performance separations. Finally, expanded-bed adsorption is described for process integration to reduce separation steps and process time.
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Affiliation(s)
- Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China,
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Priego Capote F, Sanchez JC. Strategies for proteomic analysis of non-enzymatically glycated proteins. MASS SPECTROMETRY REVIEWS 2009; 28:135-146. [PMID: 18949816 DOI: 10.1002/mas.20187] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Among post-translational modifications of proteins, non-enzymatic glycation is one of the less frequently studied by experts in proteomics. However, the relevance of protein glycation has been widely shown up in several pathological conditions. In fact, non-enzymatic glycation has been strongly related to hyperglycemic conditions and, thus, to chronic complications associated to diabetes mellitus and renal failure as well as degenerative changes occurring in the course of aging. Two different glycation levels are distinguished whether the structure of the protein is seriously damaged or not. The biochemical and clinical significance of both glycations have been already described. Several reasons have contributed to the lack of highly sensitive and selective methods for identification and quantitation of glycated proteins. These are mainly (1) the low concentration of glycated proteins in humans due to the low efficiency of the glycation process, (2) the modification of enzymatic digestion patterns, (3) the low ionization efficiency of glycated peptides, and (4) the lack of software including tools to identify this post-translational modification. The aim of this review is to provide the analytical guidelines required to succeed in the analysis of glycated proteins. For this purpose, different analytical approaches are considered to solve the main drawbacks derived from this gap in the proteomics field. Some challenges are finally proposed to be taken into account in future research.
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Affiliation(s)
- Feliciano Priego Capote
- Biomedical Proteomics Research Group, Département de Biologie Structurale et Bioinformatique, Centre Médical Universitaire, 1 Rue Michel Servet, 1211 Geneva 14, Switzerland
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Integrated process for the purification of antibodies combining aqueous two-phase extraction, hydrophobic interaction chromatography and size-exclusion chromatography. J Chromatogr A 2008; 1213:154-61. [DOI: 10.1016/j.chroma.2008.09.115] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Revised: 09/18/2008] [Accepted: 09/30/2008] [Indexed: 11/21/2022]
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Chromatographic purification of equine immunoglobulin G F(ab)2 from plasma. J Chromatogr B Analyt Technol Biomed Life Sci 2008; 876:109-15. [DOI: 10.1016/j.jchromb.2008.10.030] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2008] [Revised: 09/09/2008] [Accepted: 10/17/2008] [Indexed: 11/18/2022]
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Dong D, Gui Y, Chen D, Li R. Utilizing a library of synthetic affinity ligands for the enrichment, depletion and one-step purification of leech proteins. J Mol Recognit 2008; 21:163-8. [DOI: 10.1002/jmr.879] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Viljanen J, Larsson J, Broo KS. Orthogonal protein purification--expanding the repertoire of GST fusion systems. Protein Expr Purif 2007; 57:17-26. [PMID: 17964806 DOI: 10.1016/j.pep.2007.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Revised: 08/17/2007] [Accepted: 09/04/2007] [Indexed: 11/27/2022]
Abstract
We have previously developed a labeling scheme that can be used to site-specifically link human glutathione transferases (hGSTs) from the alpha class to chemical entities such as fluorophores and aldehydes. The reagents are in-house synthesized derivatives of glutathione (GS-derivatives). We have focused on a lysine mutant of hGST A1:A216K. In this study, we wanted to utilize these findings and improve on protein purification schemes that are using GSTs as fusion partners. We have used random mutagenesis to scramble the hydrophobic binding site of A216K through mutations at position M208 and isolated a library of 11 A216K/M208X mutants. All mutants were easily expressed and purified and retained all or parts of the catalytic properties of the parent GST. The mutants were stable over several days at room temperature. The A216K/M208X mutants could be site-specifically labeled using our designed fluorescent reagents. Furthermore, reaction with an aldehyde-containing reagent termed GS-Al results in site-specific introduction of an orthogonal handle for subsequent conjugation with aldehyde-reactive probes. Labeling with coumarin results in a fluorescent protein-conjugate that can bind glutathione (GSH) derivatives for subsequent affinity purification. The K(d) for S-hexyl-GSH of coumarin-labeled A216K was measured to be 2.5 microM. The candidate proteins A216K and A216K/M208F could be purified in high yield in a one-step procedure through affinity chromatography (Glutathione Sepharose 4B). The proteins can readily be perceived as improved GST fusion partners.
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Azarkan M, Huet J, Baeyens-Volant D, Looze Y, Vandenbussche G. Affinity chromatography: A useful tool in proteomics studies. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 849:81-90. [PMID: 17113368 DOI: 10.1016/j.jchromb.2006.10.056] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2006] [Revised: 09/26/2006] [Accepted: 10/27/2006] [Indexed: 11/22/2022]
Abstract
Separation or fractionation of a biological sample in order to reduce its complexity is often a prerequisite to qualitative or quantitative proteomic approaches. Affinity chromatography is an efficient protein separation method based on the interaction between target proteins and specific immobilized ligands. The large range of available ligands allows to separate a complex biological extract in different protein classes or to isolate the low abundance species such as post-translationally modified proteins. This method plays an essential role in the isolation of protein complexes and in the identification of protein-protein interaction networks. Affinity chromatography is also required for quantification of protein expression by using isotope-coded affinity tags.
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Affiliation(s)
- Mohamed Azarkan
- Laboratoire de Chimie Générale (CP: 609), Faculté de Médecine, Université Libre de Bruxelles, Campus Erasme, 808, route de Lennik, B-1070 Bruxelles, Belgium
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Roy I, Mondal K, Gupta MN. Leveraging protein purification strategies in proteomics. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 849:32-42. [PMID: 17141589 DOI: 10.1016/j.jchromb.2006.11.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2006] [Revised: 11/03/2006] [Accepted: 11/09/2006] [Indexed: 11/25/2022]
Abstract
The proteomic studies, although, tend to be analytical in nature, yet many strategies of preparative protein purification can be usefully employed in such studies. This review points out the importance of purification techniques which are capable of dealing with samples which are suspensions rather than clear solution, e.g. aqueous two phase partitioning, three phase partitioning, expanded bed chromatography, etc. The review also outlines the potential of non-chromatographic techniques in dealing with fractionation of proteomes. Separation protocols which can deal with post-translationally modified (PTM) proteins are also considered.
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Affiliation(s)
- Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, SAS Nagar, Punjab 160062, India
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Ljunglöf A, Lacki KM, Mueller J, Harinarayan C, van Reis R, Fahrner R, Van Alstine JM. Ion exchange chromatography of antibody fragments. Biotechnol Bioeng 2007; 96:515-24. [PMID: 17096387 DOI: 10.1002/bit.21124] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Effects of pH and conductivity on the ion exchange chromatographic purification of an antigen-binding antibody fragment (Fab) of pI 8.0 were investigated. Normal sulfopropyl (SP) group modified agarose particles (SP Sepharosetrade mark Fast Flow) and dextran modified particles (SP Sepharose XL) were studied. Chromatographic measurements including adsorption isotherms and dynamic breakthrough binding capacities, were complemented with laser scanning confocal microscopy. As expected static equilibrium and dynamic binding capacities were generally reduced by increasing mobile phase conductivity (1-25 mS/cm). However at pH 4 on SP Sepharose XL, Fab dynamic binding capacity increased from 130 to 160 (mg/mL media) as mobile phase conductivity changed from 1 to 5 mS/cm. Decreasing protein net charge by increasing pH from 4 to 5 at 1.3 mS/cm caused dynamic binding capacity to increase from 130 to 180 mg/mL. Confocal scanning laser microscopy studies indicate such increases were due to faster intra-particle mass transport and hence greater utilization of the media's available binding capacity. Such results are in agreement with recent studies related to ion exchange of whole antibody molecules under similar conditions.
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Dalakouras T, Smith BJ, Platis D, Cox MMJ, Labrou NE. Development of recombinant protein-based influenza vaccine. Expression and affinity purification of H1N1 influenza virus neuraminidase. J Chromatogr A 2006; 1136:48-56. [PMID: 17046775 DOI: 10.1016/j.chroma.2006.09.067] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2006] [Revised: 09/14/2006] [Accepted: 09/19/2006] [Indexed: 11/18/2022]
Abstract
The influenza virus surface glycoprotein antigen neuraminidase (NA) is a crucial viral enzyme with many potential medical applications; therefore, the development of efficient upstream and downstream processing strategy for the expression and purification of NA is of high importance. In the present work the NA gene from the H1N1 influenza virus strain A/Beijing/262/95 was cloned from viral RNA and expressed in expresSF+ insect cells using the baculovirus expression vector system (BVES). A limited affinity-ligand library was synthesized and evaluated for its ability to bind and purify the recombinant H1N1 neuraminidase. Affinity-ligand design was based on mimicking the interactions of the lock-and-key (LAK) motif (Phe-Gly-Gln), a common structural moiety found in the subunit interface of glutathione S-transferase I (GST I), and plays an important structural role in subunit-subunit recognition. Solid-phase combinatorial chemistry was used to synthesize 13 variants of the lock-and-key lead ligand (Phe-Trz-X, where X was selected alpha-amino acid) using the 1,3,5-triazine moiety (Trz) as the scaffold for assembly. One immobilized ligand, bearing phenylalanine and isoleucine linked on the chlorotriazine ring (Phe-Trz-Ile), displayed high affinity for NA. Absorption equilibrium and molecular modeling studies were carried out to provide a detailed picture of Phe-Trz-Ile interaction with NA. This LAK-mimetic affinity adsorbent was exploited in the development of a facile purification protocol for NA, which led to 335-fold purification in a single-step. The present purification procedure is the most efficient reported so far for recombinant NA.
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Affiliation(s)
- Thanasis Dalakouras
- Laboratory of Enzyme Technology, Department of Agricultural Biotechnology, Agricultural University of Athens, 75 Iera Odos, GR 118 55 Athens, Greece
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Mondal K, Gupta MN. The affinity concept in bioseparation: Evolving paradigms and expanding range of applications. ACTA ACUST UNITED AC 2006; 23:59-76. [PMID: 16527537 DOI: 10.1016/j.bioeng.2006.01.004] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Revised: 01/26/2006] [Accepted: 01/30/2006] [Indexed: 11/19/2022]
Abstract
The meaning of the word affinity in the context of protein separation has undergone evolutionary changes over the years. The exploitation of molecular recognition phenomenon is no longer limited to affinity chromatography modes. Affinity based separations today include precipitation, membrane based purification and two-phase/three-phase extractions. Apart from the affinity ligands, which have biological relationship (in vivo) with the target protein, a variety of other ligands are now used in the affinity based separations. These include dyes, chelated metal ions, peptides obtained by phage display technology, combinatorial synthesis, ribosome display methods and by systematic evolution of ligands by exponential enrichment (SELEX). Molecular modeling techniques have also facilitated the designing of biomimetic ligands. Fusion proteins obtained by recombinatorial methods have emerged as a powerful approach in bioseparation. Overexpression in E. coli often result in inactive and insoluble inclusion bodies. A number of interesting approaches are used for simultaneous refolding and purification in such cases. Proteomics also needs affinity chromatography to reduce the complexity of the system before analysis by electrophoresis and mass spectrometry are made. At industrial level, validation, biosafety and process hygiene are also important aspects. This overview looks at these evolving paradigms and various strategies which utilize affinity phenomenon for protein separations.
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Affiliation(s)
- Kalyani Mondal
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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Abstract
It has now become apparent that a full understanding of a biological process (e.g. a disease state) is only possible if all biomolecular interactions are taken into account. Systems biology works towards understanding the intricacies of cellular life through the collaborative efforts of biologists, chemists, mathematicians and computer scientists and recently, a number of laboratories around the world have embarked upon such research agendas. The fields of genomics and proteomics are foundational in systems biology studies and a great deal of research is currently being conducted in each worldwide. Moreover, many technological advances (particularly in mass spectrometry) have led to a dramatic rise in the number of proteomic studies over the past two decades. This short review summarizes a selection of technological innovations in proteomics that contribute to systems biology studies.
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Affiliation(s)
- Jeffrey C Smith
- Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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