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Chahine Z, Le Roch KG. Decrypting the complexity of the human malaria parasite biology through systems biology approaches. FRONTIERS IN SYSTEMS BIOLOGY 2022; 2:940321. [PMID: 37200864 PMCID: PMC10191146 DOI: 10.3389/fsysb.2022.940321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The human malaria parasite, Plasmodium falciparum, is a unicellular protozoan responsible for over half a million deaths annually. With a complex life cycle alternating between human and invertebrate hosts, this apicomplexan is notoriously adept at evading host immune responses and developing resistance to all clinically administered treatments. Advances in omics-based technologies, increased sensitivity of sequencing platforms and enhanced CRISPR based gene editing tools, have given researchers access to more in-depth and untapped information about this enigmatic micro-organism, a feat thought to be infeasible in the past decade. Here we discuss some of the most important scientific achievements made over the past few years with a focus on novel technologies and platforms that set the stage for subsequent discoveries. We also describe some of the systems-based methods applied to uncover gaps of knowledge left through single-omics applications with the hope that we will soon be able to overcome the spread of this life-threatening disease.
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Katimba HA, Wang R, Cheng C. Current findings support the potential use of bioactive peptides in enhancing zinc absorption in humans. Crit Rev Food Sci Nutr 2021:1-21. [PMID: 34708681 DOI: 10.1080/10408398.2021.1996328] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
More than two billion people around the world are affected by zinc deficiency, mainly due to the inadequate intake and absorption of zinc. Based on recent research findings, the bioactive peptides could potentially be used to combat zinc deficiency particularly due to their Zinc chelating ability. The main aim of this review was to present current findings, supporting the potential use of bioactive peptides based on their ability to enhance zinc absorption. In-vivo, in-vitro, and ex-vivo studies have demonstrated that zinc chelating peptides can enhance the retention, transportation, and absorption of zinc. Comparative studies on zinc bioavailability from protein hydrolysates and zinc salts have demonstrated that the protein hydrolysates-zinc complexes are more bioavailable than the zinc salts. Data from the structure-function relationship of zinc chelating peptides suggest that the zinc chelating capacities of peptides increase in the following order; the position of zinc chelator > zinc chelator strength > abundance of zinc chelators > net charge > molecular weight. In addition, the transport mechanism of peptide-zinc complex is hypothesized, and the potential use of bioactive peptides based on their safety and taste and limitations to their commercialization are also discussed.
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Affiliation(s)
- Hija Athman Katimba
- Department of Food Science and Engineering, Harbin Institute of Technology, Harbin, China.,Department of Food Science and Engineering, School of Agriculture & Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Rongchun Wang
- Department of Food Science and Engineering, Harbin Institute of Technology, Harbin, China
| | - Cuilin Cheng
- Department of Food Science and Engineering, Harbin Institute of Technology, Harbin, China
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3
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Wright P, Noirel J, Ow SY, Fazeli A. A review of current proteomics technologies with a survey on their widespread use in reproductive biology investigations. Theriogenology 2012; 77:738-765.e52. [DOI: 10.1016/j.theriogenology.2011.11.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 11/08/2011] [Accepted: 11/11/2011] [Indexed: 12/27/2022]
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4
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Tichy A, Salovska B, Rehulka P, Klimentova J, Vavrova J, Stulik J, Hernychova L. Phosphoproteomics: Searching for a needle in a haystack. J Proteomics 2011; 74:2786-97. [DOI: 10.1016/j.jprot.2011.07.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 07/13/2011] [Accepted: 07/22/2011] [Indexed: 11/27/2022]
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5
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Spencer KA, Osorio FA, Hiscox JA. Recombinant viral proteins for use in diagnostic ELISAs to detect virus infection. Vaccine 2007; 25:5653-9. [PMID: 17478017 PMCID: PMC7130988 DOI: 10.1016/j.vaccine.2007.02.053] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Revised: 02/15/2007] [Accepted: 02/19/2007] [Indexed: 12/22/2022]
Abstract
ELISAs provide a valuable tool in the detection and diagnosis of virus infection. The ability to produce recombinant viral proteins will ensure that future ELISAs are safe, specific and rapid. This latter point being the most crucial advantage in that even if a virus cannot be cultured, provided gene sequence is available, it is possible to rapidly respond to emerging viruses and new viral strains of existing pathogens. Indeed, ELISAs based on peptides (corresponding to epitopes) also hold great promise, as in this case no cloning or expression of a recombinant protein is required. Both recombinant protein and peptide based systems lend themselves to large scale production and purification. These approaches can also be used to distinguish recombinant vaccines from parental or wild type viruses.
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Affiliation(s)
- Kelly-Anne Spencer
- Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, UK
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6
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Rais-Beghdadi C, Roggero MA, Fasel N, Reymond CD. Purification of recombinant proteins by chemical removal of the affinity tag. Appl Biochem Biotechnol 1998; 74:95-103. [PMID: 9885186 DOI: 10.1007/bf02787176] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The efficient removal of a N- or C-terminal purification tag from a fusion protein is necessary to obtain a protein in a pure and active form, ready for use in human or animal medicine. Current techniques based on enzymatic cleavage are expensive and result in the presence of additional amino acids at either end of the proteins, as well as contaminating proteases in the preparation. Here we evaluate an alternative method to the one-step affinity/protease purification process for large-scale purification. It is based upon the cyanogen bromide (CNBr) cleavage at a single methionine placed in between a histidine tag and a Plasmodium falciparum antigen. The C-terminal segment of the circumsporozoite polypeptide was expressed as a fusion protein with a histidine tag in Escherichia coli purified by Ni-NAT agarose column chromatography and subsequently cleaved by CNBr to obtain a polypeptide without any extraneous amino acids derived from the cleavage site or from the affinity purification tag. Thus, a recombinant protein is produced without the need for further purification, demonstrating that CNBr cleavage is a precise, efficient, and low-cost alternative to enzymatic digestion, and can be applied to large-scale preparations of recombinant proteins.
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Affiliation(s)
- C Rais-Beghdadi
- Institut de Biochimie, Université de Lausanne, Epalinges, Switzerland
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7
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Schmidt B, Ehlert DK. Preparation of N-Boc-(2,6-bis-(ethoxycarbonyl)pyridin-4-yl)-L-alanines as tridentate ligands. Tetrahedron Lett 1998. [DOI: 10.1016/s0040-4039(98)00711-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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8
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Selective purification of synthetic proteins by the use of FMOC- and biotin-based reversible chromatographic probes. Anal Chim Acta 1997. [DOI: 10.1016/s0003-2670(97)00361-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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9
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Roggero MA, Servis C, Corradin G. A simple and rapid procedure for the purification of synthetic polypeptides by a combination of affinity chromatography and methionine chemistry. FEBS Lett 1997; 408:285-8. [PMID: 9188777 DOI: 10.1016/s0014-5793(97)00441-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Chemical synthesis of bioactive peptides has become a widespread and rapidly growing technique due to automated and efficient protocols for chain assembly. For most applications, the crude synthetic product must be purified to remove residual reactants, failure sequences and chemically modified peptide species. We propose here a method of universal applicability based on immobilized metal ion affinity chromatography, CNBr cleavage and use of reversible Met-sulfoxide protection. With this method we were able to purify to homogeneity in high yield the PbCS 242-310 polypeptide corresponding to the C-terminal region of Plasmodium berghei CS protein.
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Affiliation(s)
- M A Roggero
- Institute of Biochemistry, University of Lausanne, Epalinges, Switzerland
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10
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Mattinen ML, Linder M, Teleman A, Annila A. Interaction between cellohexaose and cellulose binding domains from Trichoderma reesei cellulases. FEBS Lett 1997; 407:291-6. [PMID: 9175871 DOI: 10.1016/s0014-5793(97)00356-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Most Trichoderma reesei cellulases consist of a catalytic and a cellulose binding domain (CBD) joined by a linker. We have used cellohexaose as a model compound for the glucose chain to investigate the interaction between the soluble enzyme and cellulose. The binding of cellohexaose to family I CBDs was studied by NMR spectroscopy. CBDs cause line broadening effects and decreasing T2 relaxation times for certain cellohexaose resonances, whereas there are no effects in the presence of a mutant which binds weakly to cellulose. Yet it remains uncertain how well the soluble cellooligosaccharide mimics the binding of CBD to the cellulose.
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Linder M, Lindeberg G, Reinikainen T, Teeri TT, Pettersson G. The difference in affinity between two fungal cellulose-binding domains is dominated by a single amino acid substitution. FEBS Lett 1995; 372:96-8. [PMID: 7556652 DOI: 10.1016/0014-5793(95)00961-8] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Cellulose-binding domains (CBDs) form distinct functional units of most cellulolytic enzymes. We have compared the cellulose-binding affinities of the CBDs of cellobiohydrolase I (CBHI) and endoglucanase I (EGI) from the fungus Trichoderma reesei. The CBD of EGI had significantly higher affinity than that of CBHI. Four variants of the CBHI CBD were made in order to identify the residues responsible for the increased affinity in EGI. Most of the difference could be ascribed to a replacement of a tyrosine by a tryptophan on the flat cellulose-binding face.
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Affiliation(s)
- M Linder
- VTT Biotechnology and Food Research, Espoo, Finland
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13
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Ball HL, Bertolini G, Mascagni P. Affinity purification of 101 residue rat cpn10 using a reversible biotinylated probe. J Pept Sci 1995; 1:288-94. [PMID: 9223007 DOI: 10.1002/psc.310010503] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The purification of large synthetic peptides using conventional separation techniques often results in poor yields and homogeneity due to the accumulation of chromatographically similar deletion and truncated impurities. We have developed a highly effective synthetic strategy and one-step purification procedure that is based on (i) the application of single coupling using HBTU/HOBt activation to reduce incomplete couplings, (ii) the use of N-(2-chlorobenzyloxycarbonyloxy)succinimide as a capping agent to terminate deletion sequences and (iii) the N-terminal derivatization of the complete peptidyl-resin with a reversible Fmoc-based chromatographic probe possessing enhanced physico-chemical properties (i.e. hydrophobicity, charge or affinity label). We report the application of a biotinylated probe, activated as the succinimidyl carbonate, for the purification of a 101 residue chaperonin protein from Rattus norvegicus (rat cpn10), previously synthesized using an optimized synthetic protocol. Biotinylated rat cpn10 was separated from underivatized impurities on an immobilized monomeric avidin column. Free rat cpn10 was released from avidin-agarose column with 5% aqueous triethylamine and after desalting by RP-HPLC gave 9.9% recovery. Characterization and assessment of homogeneity was achieved using ESI-MS, CZE and RP-HPLC.
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Affiliation(s)
- H L Ball
- Italfarmaco Research Centre, Milan, Italy
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14
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Linder M, Mattinen ML, Kontteli M, Lindeberg G, Ståhlberg J, Drakenberg T, Reinikainen T, Pettersson G, Annila A. Identification of functionally important amino acids in the cellulose-binding domain of Trichoderma reesei cellobiohydrolase I. Protein Sci 1995; 4:1056-64. [PMID: 7549870 PMCID: PMC2143141 DOI: 10.1002/pro.5560040604] [Citation(s) in RCA: 158] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Cellobiohydrolase I (CBHI) of Trichoderma reesei has two functional domains, a catalytic core domain and a cellulose binding domain (CBD). The structure of the CBD reveals two distinct faces, one of which is flat and the other rough. Several other fungal cellulolytic enzymes have similar two-domain structures, in which the CBDs show a conserved primary structure. Here we have evaluated the contributions of conserved amino acids in CBHI CBD to its binding to cellulose. Binding isotherms were determined for a set of six synthetic analogues in which conserved amino acids were substituted. Two-dimensional NMR spectroscopy was used to assess the structural effects of the substitutions by comparing chemical shifts, coupling constants, and NOEs of the backbone protons between the wild-type CBD and the analogues. In general, the structural effects of the substitutions were minor, although in some cases decreased binding could clearly be ascribed to conformational perturbations. We found that at least two tyrosine residues and a glutamine residue on the flat face were essential for tight binding of the CBD to cellulose. A change on the rough face had only a small effect on the binding and it is unlikely that this face interacts with cellulose directly.
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Affiliation(s)
- M Linder
- Department of Biochemistry, University of Uppsala, Sweden
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15
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Hansen P, Lindeberg G. Importance of the alpha-amino group in the selective purification of synthetic histidine peptides by immobilised metal ion affinity chromatography. J Chromatogr A 1995; 690:155-9. [PMID: 7889169 DOI: 10.1016/0021-9673(94)01100-s] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The retention behaviour of some histidine containing peptides on Cu2(+)- and Ni2(+)-loaded immobilised metal ion affinity chromatography (IMAC) supports has been investigated and compared with that observed for the corresponding compounds lacking the free alpha-amino group and/or the imidazole function. On immobilised Cu2+ all histidine-containing peptides, including those with a blocked alpha-amino function, were strongly retained above pH 5. The presence of a free alpha-amino group increased the retention marginally. On immobilised Ni2+ histidine peptides with a free alpha-amino group were strongly bound with a maximal retention at pH 8.5. Blocking of the amino group or removal of the imidazole moiety reduced the maximal retention by a factor 5 to 10, with no retention observed for peptides lacking both histidine and a free alpha-amino group. These observations indicate the involvement of two equipotent attachment points in the binding. It seems that IMAC on a Ni2(+)-loaded support can be used for the purification of histidine containing peptides synthesised by the solid-phase method. Inclusion of a capping protocol in the synthesis ensures that a free alpha-amino group, which can be used as an affinity handle, will be present only on the target peptide.
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Affiliation(s)
- P Hansen
- Department of Immunology, University of Uppsala, Sweden
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16
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Silica-based metal chelate affinity sorbents II. Adsorption and elution behaviour of proteins on iminodiacetic acid affinity sorbents prepared via different immobilization techniques. J Chromatogr A 1994. [DOI: 10.1016/0021-9673(94)80425-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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17
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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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18
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Hansen P, Lindeberg G. Purification of tryptophan containing synthetic peptides by selective binding of the alpha-amino group to immobilised metal ions. J Chromatogr A 1994; 662:235-41. [PMID: 8143027 DOI: 10.1016/0021-9673(94)80510-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Immobilised metal ion affinity chromatography (IMAC) based on selective binding via the alpha-amino group to Cu2+ and Ni2+ ions has been used to purify tryptophan containing synthetic peptides. A free alpha-amino group, serving as an affinity handle, is present only in the target peptide when the peptides are synthesised by the solid-phase method and remaining amino groups after each coupling step are blocked by acetylation. A free alpha-amino group is necessary to retain the peptide on the column. The tryptophan residue may contribute to the binding only if the peptide is simultaneously anchored via the alpha-amino group.
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Affiliation(s)
- P Hansen
- Department of Immunology, University of Uppsala, Sweden
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19
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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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20
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Hansen P, Lindeberg G, Andersson L. Immobilized metal ion affinity chromatography of synthetic peptides. Binding via the alpha-amino group. J Chromatogr A 1992; 627:125-35. [PMID: 1487524 DOI: 10.1016/0021-9673(92)87192-b] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Peptides synthesized by the solid-phase method can be efficiently purified in a single immobilized metal affinity chromatography step based on interaction with the alpha-amino group if, after coupling of each amino acid residue, unreacted amino groups are irreversibly blocked by acetylation and if no strongly metal-binding amino acids (His, Trp, Cys) are present in the sequence. A difference in basicity for alpha- and epsilon-amino functions of ca. 2 pH units is sufficiently large to allow selective binding of peptides to immobilized metal ions via the unprotonated alpha-amino group. The binding is pH-dependent: on Cu(2+)- and Ni(2+)-loaded supports most peptides are maximally retarded at pH values around 7.5 and 8.5, respectively. The decreased binding strength at lower pH values is due to protonation of the alpha-amino function, whereas the reduced affinity at higher pH is caused by metal ion transfer from the matrix to the peptide. The metal ion is captured in a multidentate chelate where, in addition to the alpha-amino group, up to three adjacent deprotonated amide nitrogens are coordinated to the metal. If the pH is raised further, additional metal ions may be bound in biuret-like structures. Immobilized Ni2+, owing to its higher selectivity and affinity, is the preferred chromatographic support if slightly basic conditions can be tolerated.
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Affiliation(s)
- P Hansen
- Department of Immunology, University of Uppsala, Sweden
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