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Lingg N, Öhlknecht C, Fischer A, Mozgovicz M, Scharl T, Oostenbrink C, Jungbauer A. Proteomics analysis of host cell proteins after immobilized metal affinity chromatography: Influence of ligand and metal ions. J Chromatogr A 2020; 1633:461649. [PMID: 33166743 DOI: 10.1016/j.chroma.2020.461649] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/20/2020] [Accepted: 10/26/2020] [Indexed: 01/03/2023]
Abstract
Different degrees of protein purity have been observed in immobilized metal affinity chromatography ranging from extremely high purity to moderate and low purity. It has been hypothesized that the host cell protein composition and the metal ligands are factors governing the purity of a protein obtained after immobilized metal affinity chromatography (IMAC). Ni nitrilotriacetic acid (NTA) has become the first choice for facile His-tagged protein purification, but alternative ligands such as iminodiacetic acid (IDA) with other immobilized metal ions such as Zn, Cu and Co are valuable options when the expected purity or binding capacity is not reached. Especially Cu and Zn are very attractive, due to their reduced environmental and safety concerns compared to Ni. Co and Zn are more selective than Ni and Cu. This increased selectivity comes at the cost of weaker binding. In this work, the influence of ligand choice on protein purity after IMAC was evaluated by several methods, including peptide mapping. His-tagged GFP was used as model protein. We found that host cell protein (HCP) content varies drastically between ligands, as IDA eluates generally showing higher HCP concentrations than NTA. The relative content of the key amino acids His, Cys and Trp in the sequence of the co-eluted protein does not suffice to explain co-eluting propensity. The co-elution of HCPs is mostly influenced by metal binding clusters on the protein surface and not by total content or surface concentration of metal interacting amino acids. Prediction of co-elution is not dependent on these clusters alone, due to protein-protein interactions, indicted by a relative low metal binding cluster score but high co-elution propensity and in a lot of cases these proteins are often part of complex such as ribosome and chaperones. The different co-eluting proteins were presented by a heatmap with a dendrogram. Ward's linkage method was used to calculate the distance between groups of co-eluting proteins. Clustering of co-eluting HCPs was observed according to ligand and by metal ions, with Zn and Co forming one cluster and Ni and Cu another. The co-elution of host cell proteins can be explained by clusters of metal interacting amino acids on the protein surface and by protein-protein interactions. While Ni NTA still appears to be highly advantageous, it might not be the cure-all for all applications.
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Affiliation(s)
- Nico Lingg
- Austrian Centre of Industrial Biotechnology, Muthgasse 18, A-1190 Vienna, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Christoph Öhlknecht
- Austrian Centre of Industrial Biotechnology, Muthgasse 18, A-1190 Vienna, Austria; Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Andreas Fischer
- Austrian Centre of Industrial Biotechnology, Muthgasse 18, A-1190 Vienna, Austria
| | - Markus Mozgovicz
- Austrian Centre of Industrial Biotechnology, Muthgasse 18, A-1190 Vienna, Austria
| | - Theresa Scharl
- Austrian Centre of Industrial Biotechnology, Muthgasse 18, A-1190 Vienna, Austria; Institute of Statistics, University of Natural Resources and Life Sciences, Vienna, Peter-Jordan-Straße 82, A-1190 Vienna, Austria
| | - Chris Oostenbrink
- Austrian Centre of Industrial Biotechnology, Muthgasse 18, A-1190 Vienna, Austria; Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Alois Jungbauer
- Austrian Centre of Industrial Biotechnology, Muthgasse 18, A-1190 Vienna, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria.
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Sun X, Chiu JF, He QY. Application of immobilized metal affinity chromatography in proteomics. Expert Rev Proteomics 2014; 2:649-57. [PMID: 16209645 DOI: 10.1586/14789450.2.5.649] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
It has been proved that the progress of proteomics is mostly determined by the development of advanced and sensitive protein separation technologies. Immobilized metal affinity chromatography (IMAC) is a powerful protein fractionation method used to enrich metal-associated proteins and peptides. In proteomics, IMAC has been widely employed as a prefractionation method to increase the resolution in protein separation. The combination of IMAC with other protein analytical technologies has been successfully utilized to characterize metalloproteome and post-translational modifications. In the near future, newly developed IMAC integrated with other proteomic methods will greatly contribute to the revolution of expression, cell-mapping and structural proteomics.
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Affiliation(s)
- Xuesong Sun
- Department of Chemistry, University of Hong Kong, Pokfulam, Hong Kong.
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Çam T, Osman B, Kara A, Demirbel E, Beşirli N, Irez G. Potentiometric, kinetic, and thermodynamic investigations into Cu2+ion binding properties of vinyl imidazole containing IMAC adsorbent. J Appl Polym Sci 2013. [DOI: 10.1002/app.39751] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Tülay Çam
- Department of Chemistry; Uludag University; Bursa Turkey
| | - Bilgen Osman
- Department of Chemistry; Uludag University; Bursa Turkey
| | - Ali Kara
- Department of Chemistry; Uludag University; Bursa Turkey
| | - Emel Demirbel
- Department of Chemistry; Uludag University; Bursa Turkey
| | - Necati Beşirli
- Department of Chemistry; Uludag University; Bursa Turkey
| | - Gazi Irez
- Department of Chemistry; Uludag University; Bursa Turkey
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Removal of PCR error products and unincorporated primers by metal-chelate affinity chromatography. PLoS One 2011; 6:e14512. [PMID: 21264292 PMCID: PMC3021510 DOI: 10.1371/journal.pone.0014512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Accepted: 12/11/2010] [Indexed: 12/02/2022] Open
Abstract
Immobilized Metal Affinity Chromatography (IMAC) has been used for decades to purify proteins on the basis of amino acid content, especially surface-exposed histidines and “histidine tags” genetically added to recombinant proteins. We and others have extended the use of IMAC to purification of nucleic acids via interactions with the nucleotide bases, especially purines, of single-stranded RNA and DNA. We also have demonstrated the purification of plasmid DNA from contaminating genomic DNA by IMAC capture of selectively-denatured genomic DNA. Here we describe an efficient method of purifying PCR products by specifically removing error products, excess primers, and unincorporated dNTPs from PCR product mixtures using flow-through metal-chelate affinity adsorption. By flowing a PCR product mixture through a Cu2+-iminodiacetic acid (IDA) agarose spin column, 94–99% of the dNTPs and nearly all the primers can be removed. Many of the error products commonly formed by Taq polymerase also are removed. Sequencing of the IMAC-processed PCR product gave base-calling accuracy comparable to that obtained with a commercial PCR product purification method. The results show that IMAC matrices (specifically Cu2+-IDA agarose) can be used for the purification of PCR products. Due to the generality of the base-specific mechanism of adsorption, IMAC matrices may also be used in the purification of oligonucleotides, cDNA, mRNA and micro RNAs.
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Kumar A, Galaev IY, Mattiasson B. Affinity precipitation of proteins using metal chelates. Methods Mol Biol 2008; 421:37-52. [PMID: 18826046 DOI: 10.1007/978-1-59745-582-4_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Metal affinity precipitation has been successfully developed as a simple purification process for the proteins that have affinity for the metal ions. The copolymers of vinylimidazole with N-isopropylacrylamide are easily synthesized by radical polymerization. When loaded with Cu(II) and Ni(II) ions, these copolymers are capable of selectively precipitating proteins with natural metal-binding groups or histidine-tagged recombinant proteins.
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Affiliation(s)
- Ashok Kumar
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, India
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Nastasijevic B, Becker NA, Wurster SE, Maher LJ. Sequence-specific binding of DNA and RNA to immobilized Nickel ions. Biochem Biophys Res Commun 2007; 366:420-5. [PMID: 18068116 DOI: 10.1016/j.bbrc.2007.11.169] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2007] [Accepted: 11/23/2007] [Indexed: 10/22/2022]
Abstract
Immobilization of divalent Nickel cations provides a tool for affinity purification of proteins containing hexahistidine tags. During experiments to generate single-stranded DNA aptamers to immobilized proteins we inadvertently identified DNA sequences with affinity for Nickel-nitrilotriacetic acid (Ni(2+)-NTA) magnetic beads. Analysis of these aptamers revealed that affinity for the Ni(2+)-NTA support requires only single-stranded sequences with multiple adenosine residues. Bound nucleic acids can be eluted with imidazole. A single-stranded dA(20) affinity tag (but not other homopolymer sequences) is sufficient for immobilization of double-stranded DNA PCR products on Ni(2+)-NTA magnetic beads. Addition of an rA(20) sequence to an RNA transcript allowed its affinity capture on Ni(2+)-NTA magnetic beads, suggesting an approach for purification of poly(A) mRNA.
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Affiliation(s)
- Branislav Nastasijevic
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
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Fu JY, Potty ASR, Fox GE, Willson RC. Water-elutability of nucleic acids from metal-chelate affinity adsorbents: enhancement by control of surface charge density. J Mol Recognit 2006; 19:348-53. [PMID: 16865664 DOI: 10.1002/jmr.789] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Immobilized metal affinity chromatography (IMAC) is widely used for purification of proteins, especially "hexahistidine-tagged" recombinant proteins. We previously demonstrated the application of IMAC to selective capture of nucleic acids, including RNA, selectively-denatured genomic DNA, and PCR primers through interactions with purine bases exposed in single-stranded regions. We also found that the binding affinity of nucleic acids for IMAC adsorbents can be increased several-fold by addition of 20 volume% of neutral additives such as ethanol or DMSO. In the present work, it is demonstrated that bound nucleic acids can be effectively eluted with water instead of the usual imidazole-containing competitive eluants, when the surface density of negative charges is enhanced by operation at alkaline pH, or by deliberate metal-underloading of the anionic chelating ligands. With enhanced negative surface charge density, nucleic acid adsorption can be made strongly dependent on the presence of adsorption-promoting additives and/or repulsion-shielding salts, and removal of these induces elution. Complete water-elutability is demonstrated for baker's yeast RNA bound to 10% Cu(II)- underloaded IDA Chelating Sepharose in a binding buffer of 20 mM HEPES, 240 mM NaCl, pH 7. Water elutability will significantly enhance the utility of IMAC in nucleic acid separations.
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Affiliation(s)
- Joseph Y Fu
- Department of Chemical Engineering, University of Houston, Houston, TX 77204-4004, USA
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Potty ASR, Fu JY, Balan S, Haymore BL, Hill DJ, Fox GE, Willson RC. Neutral additives enhance the metal-chelate affinity adsorption of nucleic acids: Role of water activity. J Chromatogr A 2006; 1115:88-92. [PMID: 16600263 DOI: 10.1016/j.chroma.2006.02.077] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2005] [Revised: 02/20/2006] [Accepted: 02/24/2006] [Indexed: 10/24/2022]
Abstract
Immobilized metal-chelate affinity chromatography has been widely used in the purification of proteins, and we have recently found that it can also be applied to purification of nucleic acids through interactions involving exposed bases, especially purines. Here we report that the inclusion of moderate quantities of neutral solutes in the buffer substantially enhances the binding affinity of nucleic acids for immobilized metal-chelate affinity adsorbents. Addition of 20% (v/v) of solutes such as ethanol, methanol, isopropanol, n-propanol, and dimethyl sulfoxide enhances the initial affinity of binding of total yeast RNA by 4.4-, 3.8-, 3.7-, 3.0-, and 2.8-fold, respectively for Cu(II)-iminodiacetic acid (IDA) agarose adsorbent, and the weaker adsorption by Cu(II)-nitrilotriacetic acid (NTA) agarose was even more strongly enhanced. The adsorption affinities of the smaller oligodeoxynucleotide molecules A20, G20, C20 and T20 also increase with the addition of ethanol, suggesting that the effect is not significantly mediated by conformational changes. Binding enhancement generally correlates with reduction of water activity by the various solutes, as predicted by several models of solution thermodynamics, consistent with an entropic contribution by displacement of waters from the metal-chelate. Interestingly, the enhancement was not seen with the proteins bovine serum albumin and lysozyme.
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Affiliation(s)
- Ajish S R Potty
- Department of Chemical Engineering, University of Houston, 4800 Calhoun, Houston, TX 77204-4004, USA
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Chaga GS. Twenty-five years of immobilized metal ion affinity chromatography: past, present and future. JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS 2001; 49:313-34. [PMID: 11694287 DOI: 10.1016/s0165-022x(01)00206-8] [Citation(s) in RCA: 261] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- G S Chaga
- BD Clontech Laboratories, Inc., 1020 E. Meadow Circle, Palo Alto, CA 94303, USA
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Millot MC, Hervé F, Sébille B. Retention behaviour of proteins on poly(vinylimidazole)-copper(II) complexes supported on silica: application to the fractionation of desialylated human alpha 1-acid glycoprotein variants. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL APPLICATIONS 1995; 664:55-67. [PMID: 7757241 DOI: 10.1016/0378-4347(94)00352-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The retention behaviour of various amino acids, peptides and proteins on poly(vinylimidazole)-Cu(II) complexes supported on silica was investigated. Free amino acids and peptides containing one histidine and in some instances one additional tryptophan residue in their primary structure were found to elute from the supports only after addition of a competing complexing agent to the mobile phase. However, the results obtained the proteins containing metal binding groups suggested that, in addition to the presence of donor-acceptor interactions between the macromolecules and the immobilized metal, other additional (essentially ionic and/or hydrophobic) interactions took place between the proteins and the surrounding of the metal. When donor-acceptor interactions were predominant, proteins were strongly adsorbed on the stationary phase and their elution required the addition of a competing complexing agent in the mobile phase. However, when the binding between the proteins and the supports via donor-acceptor interactions was less favourable, proteins were eluted from the columns without the addition of a competing agent in the mobile phase. With respect to the binding of these proteins, ionic and/or hydrophobic interactions were no longer negligible during the chromatographic process and the retention of the macromolecules by the stationary phase depended on the elution conditions (ionic strength, pH, etc.). These supports were used in the fractionation of the three main genetic variants of desialylated alpha 1-acid glycoprotein.
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Affiliation(s)
- M C Millot
- Laboratoire de Physico-Chimie des Biopolymères, Université Paris XII Val de Marne, Créteil, France
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Freitag R, Horváth C. Chromatography in the downstream processing of biotechnological products. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 1995; 53:17-59. [PMID: 8578972 DOI: 10.1007/bfb0102324] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Chromatography techniques are essential for the isolation and purification of most of the high value products of modern biotechnology. The economically sensible and technically satisfactory downstream processing of a therapeutic protein, usually involves a number of chromatographic steps. Its development and optimization require considerable knowledge of the various physico-chemical and engineering aspects of biochemical chromatography. This review addresses the various modes of chromatography and the design of chromatographic separation processes from a biotechnologist's point of view. Strategies for optimizing the structure of the downstream process are outlined and scaling up consideration are discussed. The importance of the different chromatographic methods in research and development is estimated in an analysis of protein purification schemes recently published in the literature. Finally, examples of the application of chromatographic procedures for process scale product purification in the biotechnological industry are given.
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Affiliation(s)
- R Freitag
- Institut für Technische Chemie, Universität Hannover, Germany
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Birger Anspach F. Silica-based metal chelate affinity sorbents I. Preparation and characterization of iminodiacetic acid affinity sorbents prepared via different immobilization techniques. J Chromatogr A 1994. [DOI: 10.1016/0021-9673(94)80592-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Reif OW, Nier V, Bahr U, Freitag R. Immobilized metal affinity membrane adsorbers as stationary phases for metal interaction protein separation. J Chromatogr A 1994. [DOI: 10.1016/0021-9673(94)80623-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Serafica GC, Belfort G, Pimbley J. Protein fractionation using fast flow immobilized metal chelate affinity membranes. Biotechnol Bioeng 1994; 43:21-36. [DOI: 10.1002/bit.260430105] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Abstract
The introduction of immobilized metal ion affinity chromatography, directed toward specific protein side chains, has opened a new dimension in protein purification. This review covers the principles and practice of IMAC that can be performed under very mild, nondenaturing conditions. IMAC is particularly suitable for preparative group fractionation of complex extracts and biofluids, but can also be used in high-performance mode: "HP-IMAC." Single-step purifications of 1000-fold or more may allow isolation of a particular protein from crude extracts on a milligram or gram scale. With respect to separation efficiency, IMAC compares well with biospecific affinity chromatography, and the immobilized metal ion ligand complexes are more likely to withstand wear and tear than are antibodies or enzymes. The enormous potential of IMAC and related metal affinity techniques is only in the initial stages of being explored and exploited. Synthesis of IMA adsorbents, and various modes of performing IMAC are discussed and exemplified with selected applications. Advantages and disadvantages are listed. Effective means of counteracting the few undesirable effects that can occur are suggested.
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Affiliation(s)
- J Porath
- Division of Biotechnology, University of Arizona, Tucson 85721
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Li-Chan E, Kwan L, Nakai S. Isolation of Immunoglobulins by Competitive Displacement of Cheese Whey Proteins During Metal Chelate Interaction Chromatography. J Dairy Sci 1990. [DOI: 10.3168/jds.s0022-0302(90)78887-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Gauthier J, Amiot J, Vijayalakshmi MA. Preparative separation of small molecular weight peptides from casein hydrolysate using gel filtration and immobilized metal ion affinity chromatography. PREPARATIVE BIOCHEMISTRY 1990; 20:23-50. [PMID: 2367347 DOI: 10.1080/00327489008050175] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A two step method consisting of a gel filtration step, followed by a Immobilized Metal Affinity Chromatography (IMAC) step using a IDA-Cu coupled Sephadex G-25 column, on a preparative scale is described for the group separation of peptides from a casein hydrolysate. The 48 groups of peptides thus separated are further characterised by RP-HPLC and amino acid analysis. Some peptides after the analytical RP-HPLC step are further characterised by sequencing. An insight into the mechanism of retention on IMAC of the peptides is attempted. In such complex mixtures as casein hydrolysate, the peptide-peptide interaction can mask the potential sites of interactions in a single peptide. The results obtained using volatile buffers as eluents show the possibility of using IMAC step as an alternative to obtain gram quantities of group of peptides free of salts from complex protein hydrolysates.
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Affiliation(s)
- J Gauthier
- Département de Sciences et Technologie des Aliments, Université Laval, Sté-Foy, Québec
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el Rassi Z, Horváth C. Metal chelate-interaction chromatography of proteins with iminodiacetic acid-bonded stationary phases on silica support. J Chromatogr A 1986; 359:241-53. [PMID: 3015996 DOI: 10.1016/0021-9673(86)80078-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
An iminodiacetic acid (IDA)-bonded stationary phase on a wide-pore microparticulate silica support was used for the chromatography of amino acids and proteins at pH 5.0 and 6.0. Without chelated metal the retention behavior of the stationary phase parallelled that of other silica-bound cation exchangers used in high-performance liquid chromatography of proteins. In metal chelate-interaction chromatography (MCIC) with IDA, chelated by Cu(II), Zn(II), Ni(II), Fe(II), or Fe(III), amino acids were most strongly retained on Cu(II)-IDA, whereas all metal chelates separated the proteins under investigation but with different selectivity. The effect of salt concentration in the eluent on protein retention was investigated and the pertinent electrostatic and hydrophobic interaction parameters were evaluated. The proteins were separated by MCIC with increasing salt gradient and, using the same column, by hydrophobic-interaction chromatography with decreasing salt gradient. In MCIC the addition of methanol to the mobile phase had disparate effect on protein retention, whereas addition of histidine or glycine, which acted as competing ligands, reduced the retention.
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