Evaluation of the interaction of protein alpha-amino groups with M(II) by immobilized metal ion affinity chromatography

Reflections on the evolution of the vertebrate tissue inhibitors of metalloproteinases

Jawed vertebrates (Gnathostomes) have 4 tissue inhibitors of metalloproteinases (TIMPs), multifunctional proteins that all inhibit members of the large matrix metalloproteinase (MMP) family but differ in their other roles, including the regulation of pro-MMP activation, cell growth, apoptosis and angiogenesis, and the structure of extracellular matrices (ECMs). Molecular phylogeny analyses indicate that vertebrate TIMP genes arose from an invertebrate ancestor through 3 successive duplications, possibly including 2 whole genome duplications, during early vertebrate phylogeny. TIMPs from invertebrates also inhibit metalloproteinases, bind to pro-MMPs, and contribute to ECM structures but are not orthologs of any particular vertebrate TIMP. The most ancient vertebrate superclass, the Agnatha (jawless fish), seems to provide a snapshot of a stage in TIMP evolution preceding the third gene duplication. This review examines the structures of TIMPs from different vertebrate orders using information relating to the structural basis of their various functions. Provisional conclusions are that during their evolutionary divergence, various TIMPs lost inhibitory activity toward some metalloproteinases, specialized in effects on different pro-MMPs, and developed new interactions with discrete targets (including integrins and receptors), while recapitulating a role in ECM structure. The analysis is limited by the sparse information available regarding the functional properties of nonmammalian TIMPs.-Brew, K. Reflections on the evolution of the vertebrate tissue inhibitors of metalloproteinases.

Selective biomineralization of Co3(PO4)2-sponges triggered by His-tagged proteins: efficient heterogeneous biocatalysts for redox processes

Heterogeneous redox biocatalyts fabricated by mineralization of cobalt phosphate triggered by His-tag enzymes.

Copper binding to prion octarepeat peptides, a combined metal chelate affinity and immunochemical approaches

Based on the hypothetical proposal of Sulkowski [E. Sulkowski, FEBS Lett. 307 (2) (1992) 129] for the implication of transition metal ions in the structural changes/oligomerisation of normal cellular prion protein (PrPc) resulting in the pathological isoform (PrPsc), we focused our study on the octarepat domain of this protein which has been supposed to be the metal binding site. We have studied the copper binding to synthetic prion octarepeat peptides (PHGGGWGQ)n (n=1, 3, 6) using metal chelate and size-exclusion modes of chromatographies. This copper binding induces oligomerisation resulting in multiple aggregates. Moreover, heterogeneity of metal bound octarepeat oligomers by ESI-MS has been demonstrated. In addition, anti prion antibodies specific to the octarepeat region were used to discriminate between metal free and copper, nickel and zinc bound hexamer octarepeat peptide. Differential recognition of Cu(II) and Zn(II) bound complexes has been observed which signify differences in exposed epitopes of aggregated peptides.

Evaluating immobilized metal affinity chromatography for the selection of histidine-containing peptides in comparative proteomics

Agarose based immobilized metal affinity chromatography (IMAC) columns loaded with copper (II) were evaluated for the selection of histidine-containing peptides in comparative proteomics. Recovery, binding specificity, and reproducibility were investigated with model proteins. Cu(II)-IMAC was found to be highly selective for histidine containing peptides; moreover, a low degree of nonspecific selection was observed. Acylation of the amino-terminus of peptides with either succinic anhydride, N-acetoxysuccinamide, or [3-(2,5)-dioxopyrrolidin-1-yloxycarbonyl)-propyl]-trimethylammonium (quaternary amine) reduced the number of histidine-containing peptides bound by the Cu(II)-IMAC columns. This provides an additional possibility for sample simplification in proteomic applications. The number of acylated peptides selected decreased in the order of quaternary amine > N-acetoxysuccinamide > succinic anhydride derivatization. Although the selection of N-terminally derivatized peptides is biased toward peptides that contain more than one histidine, it is not yet possible to predict selectivity.

Interactions of proteins with immobilized metal ions: a comparative analysis using various isotherm models

Immobilized metal ion affinity chromatography (IMAC) is now a widely accepted technique for the purification of natural and recombinant therapeutic products and is beginning to find industrial applications. The design, optimization, and scale-up of a chromatographic process using IMAC demands a thorough understanding to be developed regarding the fundamental factors governing the various interactions between immobilized metal ions and proteins. Consequently, there is an immediate need to find out a theory that is able to account for these interactions most efficiently in a qualitative as well as a quantitative manner. In view of this requirement, the interactions of several model proteins (lysozyme, ovalbumin, bovine serum albumin, conalbumin, and wheat germ agglutinin) with metal (Cu(II), Ni(II))-chelated IDA (iminodiacetate) and tris(2-aminoethyl)amine were investigated. The adsorption data were analyzed using four isotherm models, viz., the general affinity interaction theory/Langmuir model, the Freundlich model, the Temkin model, and the Langmuir-Freundlich model, and the sorption parameters were computed. Although the first three models were applicable to some protein-IMA-M(II) systems, the Langmuir-Freundlich model appeared to be the most efficient model for explaining the interactions of proteins with IMA-M(II) gels. Also, this model was able to explain cooperativity and binding heterogeneity in quantitative terms. It is envisaged that this analysis would be useful in developing an improved understanding of protein-immobilized metal ion interactions and providing guidelines for designing preparative-scale separations using IMAC.

Histidine mapping of serine protease: a synergic study by IMAC and molecular modelling

The immobilized metal ion affinity (IMA) interaction of different serine proteases, namely porcine and bovine trypsins and BPN' and Carlsberg subtilisins, was studied on Sepharose-IDA-CuII. Both trypsins were resolved into their different subspecies, whereas the subtilisins appeared as only one species. The use of diethyl pyrocarbonate-modified enzymes demonstrated the contribution of histidine(s) as the sole interacting site(s). The use of different peptidic and chemical inhibitors complexed to the enzymes confirmed the contribution of histidine(s) as the interacting site(s) and further resulted in different chromatographic patterns for the free and complexed serine proteases. Comparison of the chromatographic data for each enzyme with the accessible surface area calculation by molecular modelling on the available crystallographic structure allowed us to hypothesize a map of the surface-accessible histidine on each enzyme.

Immobilised metal ion affinity chromatography purification of alcohol dehydrogenase from baker's yeast using an expanded bed adsorption system

Alcohol dehydrogenase (ADH) from solutions of homogenised packed bakers' yeast has been successfully purified using immobilised metal-ion affinity chromatography in an expanded bed. Method scouting carried out using pure ADH solutions loaded onto 5-ml HiTrap columns charged with Zn2+, Ni2+ and Cu2+ and eluted using 0-50 mM EDTA gradient found that charging with Zn2+ gave the highest recovery and the lowest EDTA concentration required for elution. These results were used to develop a protocol for the expanded bed system and further tested using clarified yeast homogenate loaded onto XK16/20 packed beds (approximately 30 ml) packed with Chelating Sepharose FastFlow matrix in order to determine the optimum elution conditions using EDTA. The ADH was found to elute at 5 mM EDTA and the dynamic and total binding capacities of Streamline chelating for ADH were found to be 235 U/ml and 1075 U/ml matrix, respectively. Expanded bed work based on a step EDTA elution protocol demonstrated that ADH could be successfully eluted from unclarified homogenised bakers' yeast diluted to 10 mg/ml total protein content with a recovery of 80-100% that was maintained over five consecutive runs with a vigorous clean-in-place procedure between each run.

Protein selectivity with immobilized metal ion-tacn sorbents: chromatographic studies with human serum proteins and several other globular proteins

The chromatographic selectivity of the immobilized chelate system, 1,4,7-triazocyclononane (tacn), complexed with the borderline metal ions Cu2+, Cr3+, Mn2+, Co2+, Zn2+, and Ni2+ has been investigated with hen egg white lysozyme, horse heart cytochrome c, and horse skeletal muscle myoglobin, as well as proteins present in partially fractionated preparations of human plasma. The effects of ionic strength and pH of the loading and elution buffers on protein selectivities of these new immobilized metal ion affinity chromatographic (IMAC) systems have been examined. The results confirm that immobilized Mn;pl-tacn sorbents exhibit a novel type of IMAC behavior with proteins. In particular, the chromatographic properties of these immobilized M(n+)-tacn ligand systems were significantly different compared to the IMAC behavior observed with other types of immobilized tri- and tetradentate chelating ligands, such as iminodiacetic acid, O-phosphoserine, or nitrilotriacetic acid, when complexed with borderline metal ions. The experimental results have consequently been evaluated in terms of the additional contributions to the interactive processes mediated by effects other than solely the conventional lone pair Lewis soft acid-Lewis soft base coordination interactions, typically found for the IMAC of proteins with borderline and soft metal ions, such as Cu2+ or Ni2+.

Hydrazide as a ligand moiety in immobilized metal ion affinity chromatography. Separation of BO-IMI and BODIPY-hydrazide

BODIPY hydrazide (BO-HZ, a commercially available fluorescent dye) and BO-IMI (obtained by coupling the hydrazide moiety of BODIPY to the carboxyl group of N-acetylhistidine) were separated on three forms of a Sepharose-iminodiacetic acid column: Cu(II), Ni(II) and Zn(II). Whereas BO-IMI eluted first on the Cu(II) and Ni(II) columns (a pH gradient from 7.0 to 2.0 was applied), it eluted last on the Zn(II) column. BO-HZ eluted from the Zn(II) column without displacing this metal. The explanation suggested for these results is that BODIPY hydrazide undergoes strong, bidendate binding only to the Cu(II) and Ni(II) columns.

Chromatographic method involving inductively coupled plasma atomic emission spectrometric detection for the study of metal-protein complexes

A chromatographic method has been used to study metal ion-protein complexes. It involves successively a gel filtration technique to separate and distinguish the complexed from the free metallic ions, and a spectrometric technique, inductively coupled plasma atomic emission spectrometry (ICP-AES), which allows us to calculate accurately the concentration of ionic metallic species in solution. In the chromatographic step, we applied a large-zone Hummel and Dreyer method. Thus, fractions can be collected throughout the chromatographic experiment and their metal concentration measured by ICP-AES, at constant and known protein concentration. This method has been tested on the copper complex of bovine serum albumin. Results of our study are in good agreement with previous studies on this complex.

Residue accessibility, hydrogen bonding, and molecular recognition: metal-chelate probing of active site histidines in chymotrypsins

Subspecies defining the maturation pathway of bovine chymotrypsinogen to alpha-chymotrypsin have been separated in a single chromatographic run by affinity to iminodiacetic acid-Cu(II) [IDA-Cu(II)] immobilized onto Novarose. A major highlight of the elution pattern is that, as maturation proceeds, these subspecies exhibit a correlated increase in affinity toward IDA-Cu(II). This behavior is analyzed by a combination of physicochemical and molecular modeling techniques to assess the contribution of the two histidines present in chymotrypsins, at positions 40 and 57 on the protein surface. Catalytic His-57 features adequate surface accessibility to serve as a ligand to IDA-Cu(II), but its participation is clearly ruled out by specific chemical modification. In contrast, His-40, whose side chain is buried in the crystal structures of both zymogen and mature enzyme, surprisingly proves the most plausible candidate as an electron donor to IDA-Cu(II). This apparent conflict between histidine accessibility and their implication in IDA-Cu(II) recognition has been rationalized on the basis of their flexibility and/or hydrogen-bonding status, with the following outcome. First, histidine constitutes a useful reporter group for subtle protein conformational fluctuations. Second, static accessibility computation alone provides no unequivocal guideline as to whether a protein residue can serve as a ligand. Third, this study is the first to document the occurrence of a screening effect due to hydrogen bonding of an otherwise "accessible" histidine. A significant corollary to this finding would be that the catalytic histidine is rigidly entrapped in a remarkably strong hydrogen-bonding network, a situation that may pertain to mechanistic aspects of catalysis.

Multipoint binding in metal-affinity chromatography II. Effect of pH and imidazole on chromatographic retention of engineered histidine-containing cytochromes c

Protein binding in immobilized metal affinity chromatography (IMAC) was studied using a set of Saccharomyces cerevisiae iso-1-cytochrome c variants which differed only in their histidine content and placement. Elution with an imidazole gradient enabled separation of cytochrome c variants based on their histidine multiplicity. Millimolar concentrations of imidazole dramatically decreased protein partitioning to the IMAC support as measured by the chromatographic capacity factors under isocratic conditions. Fitting the partitioning data to the "stoichiometric displacement" model indicates that cytochrome c variants containing from one to four surface histidines each displaced approximately three equivalents of imidazole upon adsorption. Therefore even a protein with a single surface histidine appears to coordinate to multiple copper sites on the IMAC support at neutral pH. The effect of pH on the capacity factors of these variants measured in the absence of imidazole further supports this interpretation. Although the presence of a surface histidine was required for retention at neutral pH, a variant with no surface histidines still partitioned strongly to the IMAC support at higher pH (pH > 7.5). These results indicate the contribution of additional protein-metal-coordinating groups, presumably surface amines, to chromatographic retention in IMAC.

Purification of cysteine-containing synthetic peptides via selective binding of the alpha-amino group to immobilised Cu2+ and Ni2+ ions

Peptides containing a cysteine residue but lacking histidine and tryptophan were synthesised by the solid-phase method. Their retention behaviour on Cu2+ - and Ni2+ -loaded immobilised metal ion affinity chromatography (IMAC) supports at pH 5-11 was studied and compared with that observed for the corresponding compounds without the free alpha-amino group and/or the thiol function. Unexpectedly, it was found that neither a cysteine side-chain nor a cysteine disulphide affects the retention of the peptides. A free alpha-amino group is required for binding; no retention is observed in its absence. At pH 9 substantial amounts of metal ions were transferred from the chromatographic support to an alpha-amino-protected cysteine-containing peptide. However, at pH 7 no such transfer occurred. Therefore, the lack of retention observed for peptides with a blocked alpha-amino function over the entire pH range is not solely caused by metal ion scavenging by the thiol group. Partial dimerisation may occur upon chromatography; the dimers formed are retained strongly due to the presence of two free alpha-amino groups. It seems that IMAC on a Cu2+ - or Ni2+ -loaded support can be used for the purification of cysteine-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.

The affinity technology in downstream processing

The quality criteria imposed on several biochemicals are stringent, thus, high-separation purification technology is important to downstream processing. Affinity-based purification technologies are regarded as the finest available, and each one differs in its purifying ability, economy, processing speed and capacity. The most widely used affinity technology is classical affinity chromatography, however, other chromatography-based approaches have also been developed, for example, perfusion affinity chromatography, hyperdiffusion affinity chromatography, high-performance affinity chromatography, centrifugal affinity chromatography, affinity repulsion chromatography, heterobifunctional ligand affinity chromatography and the various chromatographic applications of 'affinity tails'. On the other hand, non-chromatographic affinity technologies aim at high throughput and seek to circumvent problems associated with diffusion limitations experienced with most chromatographic packings. Continuous affinity recycle extraction, aqueous two-phase affinity partitioning, membrane affinity filtration, affinity cross-flow ultrafiltration, reversible soluble affinity polymer separation and affinity precipitation are all non-chromatographic technologies. Several types of affinity ligands are used to different extents; antibodies and their fragments, receptors and their binding substances, avidin/biotin systems, textile and biomimetic dyes, (oligo)peptides, antisense peptides, chelated metal cations, lectins and phenylboronates, protein A and G, calmodulin, DNA, sequence-specific DNA, (oligo)nucleotides and heparin. Likewise, there are several support types developed and used; natural, synthetic, inorganic and composite materials.

Purification of tryptophan containing synthetic peptides by selective binding of the alpha-amino group to immobilised metal ions

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.

Chromatography in analytical biotechnology

Recent advances in biochromatography have focused on improvements in the design of stationary supports for liquid chromatography. During the past year, the innovative use of columns packed with small non-porous particles has significantly improved the efficiency of chromatographic separations. Bioseparations that previously took hours are now possible in only a few minutes.

High-performance liquid chromatography of amino acids, peptides and proteins. CXXXI. O-phosphoserine as a new chelating ligand for use with hard Lewis metal ions in the immobilized-metal affinity chromatography of proteins

Conditions for the immobilization of O-phosphoserine (OPS) to epoxy-activated Sepharose CL-4B are described. The binding behaviour of OPS and iminodiacetic acid (IDA) immobilized onto Sepharose CL-4B, toward the hard Lewis metal ions Al3+, Fe3+, Ca2+ and Yb3+, and Cu2+ ion as a borderline metal ion control, over the pH range pH 4.0 to pH 8.0, was examined. Immobilized OPS shows a stronger affinity for Fe3+ and Al3+ ions but a lower affinity for Cu2+ and Yb3+ ions, compared to immobilized iminodiacetic acid (IDA), over the equilibrating range examined. Immobilized OPS-Mn+ was screened for protein binding using as model proteins tuna heart cytochrome c (THCC), horse myoglobin (HMYO) and hen egg while lysozyme (HEWL) over the pH range 5.5 to 8.0. Immobilized OPS-Fe3+ bound THCC under all the examined equilibrating conditions, bound HMYO between pH 5.5 and pH 7.0 and did not bind HEWL under any condition examined. Immobilized OPS thus presents an additional mode of metal ion and protein selectivity in immobilized-metal affinity chromatography.

Immobilized metal ion affinity chromatography of synthetic peptides. Binding via the alpha-amino group

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.