A support for affinity chromatography that covalently binds amino groups via a cleavable connector arm.

The preparation of a new succinimidyl ester agarose derivative (SEPE-Agarose) is described. This agarose derivative can be used for covalently linking proteins and other ligands containing amino groups to agarose via phenyl ester linkages that can later be broken under mild conditions which should not alter other groups which may be present in proteins such as cystinyl residues and glycosyl residues. SEPE-Agarose is prepared by the reaction of bis[4-[2-(N-succinimidoxycarbonyl)ethyl]phenyl]succinate with an aminoethylcarbamylmethyl derivative of agarose. Studies of the covalent binding and release of trypsin and myoglobin to SEPE-Agarose indicate that gels containing 0.1 to 0.6 μmol protein/ml of gel are obtained by reacting protein (0.5–5 mg/ml) with the N-succinimidyl ester groups in SEPE-Agarose. Protein-linked gel is reasonably stable in dilute phosphate buffers (pH ≤ 7.4, ≤ 25 °C). Protein is released from the gel, however, by treatment at 25 °C with solutions containing nucleophiles such as 1 m imidazole-glycine, pH 7.4, for 4 h, or 1 m hydroxylamine, pH 7, for 10 min. Protein is also released from the gel by treatment with 1 m Tris pH 8.2 for 24 h. SEPE-Agarose should prove useful in affinity chromatography and immunoabsorption when it is difficult or impractical to elute material bound to conventional affinity supports.     

Facile preparation and some applications of an affinity matrix with a cleavable connector arm containing a disulfide bond

A versatile affinity matrix in which the ligand of interest is linked to the matrix through a connector arm containing a disulfide bond is described. It can be synthesized from any amino-substituted matrix by successive reaction with 2-imino-thiolane, 5,5'-dithiobis(2-nitrobenzoic acid), and a thiol derivative of the ligand of choice. The repertoire of ligands can be significantly increased by the appropriate use of avidin-biotin bridges. After adsorption of the material to be fractionated, elution can be effected by reducing the disulfide bond in the connector arm with dithiothreitol. Examples of the preparation and use of various affinity matrices based on amino-substituted Sepharose 6MB are given. One involves the immobilization of the Fab' fragment of a monoclonal antibody against Aspergillus oryzae beta-galactosidase and the specific binding of that enzyme to the resulting immunoaffinity matrix. Another involves the immobilization of N-biotinyl-2-thioethylamine followed by complex formation with avidin. The resulting avidin-substituted matrix was used for the selective adsorption and subsequent recovery of mouse hybridoma cells producing anti-avidin antibodies. By further complexing the avidin-substituted matrix with appropriate biotinylated antigens, it should be possible to fractionate cells producing antibodies against a variety of antigens.     

A highly selective Hsp90 affinity chromatography resin with a cleavable linker

Over 200 proteins have been identified that interact with the protein chaperone Hsp90, a recognized therapeutic target thought to participate in non-oncogene addiction in a variety of human cancers. However, defining Hsp90 clients is challenging because interactions between Hsp90 and its physiologically relevant targets involve low affinity binding and are thought to be transient. Using a chemo-proteomic strategy, we have developed a novel orthogonally cleavable Hsp90 affinity resin that allows purification of the native protein and is quite selective for Hsp90 over its immediate family members, GRP94 and TRAP 1. We show that the resin can be used under low stringency conditions for the rapid, unambiguous capture of native Hsp90 in complex with a native client. We also show that the choice of linker used to tether the ligand to the insoluble support can have a dramatic effect on the selectivity of the affinity media.     

Use of commercial anion-exchange resins as solid support for peptide synthesis and affinity chromatography

This report demonstrates that due to the presence of residual reactive sites in their matrices, classical diethylaminoethyl-attaching commercial anion-exchanger resins such as DEAE-MacroPrep and DEAE-Sephadex A50 supports can be used for peptide synthesis. Moreover, due to the high stability of the peptide-resin bond in the final cleavage treatments, desired peptidyl-resins free of side-chain protecting groups, which enables them to be further used as solid support for affinity chromatography, can be obtained. To demonstrate this potentiality, a fragment corresponding to the antigenic and immunodominant epitope of sporozoites of the Plasmodium falciparum malaria parasite was synthesized in these traditional resins and antibody molecules generated against the peptide sequence were successfully retained in these peptidyl supports. Due to the maintenance of their original anion-exchange capacities, the present findings open the unique possibility of applying, simultaneously, dual anion-exchange and affinity procedures for purification of a variety of macromolecules.     

An agarose derivative containing an arsenical for affinity chromatography of thiol compounds

An adsorbent for affinity chromatography of thiol compounds was prepared by covalently linking p-aminophenylarsine oxide to CNBr-activated Sepharose 6B. The adsorbent retained mono- and dithiols from acid and neutral solutions. Monothiols and 1,4-dithiols were eluted at pH 12, whereas more alkaline conditions were necessary for elution of 1,2- and 1,3-dithiols. The latter could also be eluted at pH 12 by 0.01 m phenylarsine oxide. Alternatively, thiol compounds may be eluted at neutral or acid conditions by other thiol compounds. Monothiols and 1,4-dithiols were thus eluted by cysteine, whereas 1,2- and 1,3-dithiols required dithiopropylamine for elution.     

A cleavable affinity biotinylating agent reveals a retinoid binding role for RPE65

Retinal pigment epithelial (RPE) membranes contain the full biochemical apparatus capable of processing all-trans-retinol (vitamin A) into 11-cis-retinal, the visual chromophore. As many of these proteins are integral membrane proteins and resistant to traditional methods of identification, alternate methods of identifying these proteins are sought. The approach described here involves affinity biotinylation with alkali cleavable linkers. A vitamin A containing affinity-labeling haloacetate is described which facilitates the identification of retinoid binding proteins (RBPs). Treatment of crude bovine RPE membranes with (3R)-3-[boc-lys(biotinyl)-O]-all-trans-retinol chloroacetate 1 in the low micromolar range led to the specific labeling of RPE65 and lecithin retinol acyltransferase (LRAT). Only RPE65 is labeled at 5 microM 1 at 4 degrees C. Labeled RPE65 was readily isolated by binding the labeled protein to avidin-containing beads, followed by cleavage of the protein from the beads at pH 11. Trypsin digestion of RPE65 modified by 1, followed by mass spectrometry, demonstrates that C231 and C448 are alkylated by 1. These studies validate the approach that was used, and furthermore demonstrate that RPE65, a major membrane-associated protein of the RPE, is a RBP.     

Silica containing primary hydroxyl groups for high-performance affinity chromatography

Primary hydroxyl groups were incorporated into silica by a four-step reaction procedure which includes modification of the silica surface with gamma-glycidoxypropyltrimethoxysilane, leading to an epoxide silica; hydrolysis with acid to yield a diol silica; oxidation of the diol silica with periodate to yield a silica resin with aldehyde functions; and reduction with sodium borohydride to obtain the primary hydroxyl-containing silica. The hydroxyl groups were activated with chloroformates or carbodiimidazole. Proteins were coupled under mild conditions in high yield to these activated silica resins. Columns containing these newly developed silica derivatives were used for the fast and efficient purification of antibodies on antigen-containing silica, as well as for the purification of trypsin on a trypsin inhibitor column (or vice-versa). The effect of pressure on association and dissociation of the affinity complex is discussed.     

Phosphorus 31 solid state NMR characterization of oligonucleotides covalently bound to a solid support.

31P cross polarization (CP) magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectra were acquired for various linear and branched di- and tri-nucleotides attached to a controlled pore glass (CPG) solid support. The technique readily distinguishes the oxidation state of the phosphorus atom (phosphate versus phosphate), the presence or absence of a protecting group attached directly to phosphorus (cyanoethyl), and other large changes in the phosphorus chemistry (phosphate versus phosphorothioate). However, differences in configurational details remote from the phosphorus atom, such as the attachment position of the ribose sugar (2'5' versus 3'5'), or the particulars of the nucleotide bases (adenine versus uridine versus thymine), could not be resolved. When different stages of the oligonucleotide synthetic cycle were examined, 31P CPMAS NMR revealed that the cyanoethyl protecting group is removed during the course of chain assembly.     

Biliverdin binds covalently to agrobacterium phytochrome Agp1 via its ring A vinyl side chain

The widely distributed phytochrome photoreceptors carry a bilin chromophore, which is covalently attached to the protein during a lyase reaction. In plant phytochromes, the natural chromophore is coupled by a thioether bond between its ring A ethylidene side chain and a conserved cysteine residue within the so-called GAF domain of the protein. Many bacterial phytochromes carry biliverdin as natural chromophore, which is coupled in a different manner to the protein. In phytochrome Agp1 of Agrobacterium tumefaciens, biliverdin is covalently attached to a cysteine residue close to the N terminus (position 20). By testing different natural and synthetic biliverdin derivatives, it was found that the ring A vinyl side chain is used for chromophore attachment. Only those bilins that have ring A vinyl side chain were covalently attached, whereas bilins with an ethylidene or ethyl side chain were bound in a noncovalent manner. Phycocyanobilin, which belongs to the latter group, was however covalently attached to a mutant in which a cysteine was introduced into the GAF domain of Agp1 (position 249). It is proposed that the regions around positions 20 and 249 are in close contact and contribute both to the chromophore pocket. In competition experiments it was found that phycocyanobilin and biliverdin bind with similar strength to the wild type protein. However, in the V249C mutant, phycocyanobilin bound much more strongly than biliverdin. This finding could explain why during phytochrome evolution in cyanobacteria, the chromophore-binding site swapped from the N terminus into the GAF domain.     

A designed four-alpha-helix bundle that binds the volatile general anesthetic halothane with high affinity

The structural features of volatile anesthetic binding sites on proteins are being examined with the use of a defined model system consisting of a four-alpha-helix bundle scaffold with a hydrophobic core. Previous work has suggested that introducing a cavity into the hydrophobic core improves anesthetic binding affinity. The more polarizable methionine side chain was substituted for a leucine, in an attempt to enhance the dispersion forces between the ligand and the protein. The resulting bundle variant has an improved affinity (K(d) = 0.20 +/- 0.01 mM) for halothane binding, compared with the leucine-containing bundle (K(d) = 0.69 +/- 0.06 mM). Photoaffinity labeling with (14)C-halothane reveals preferential labeling of the W15 residue in both peptides, supporting the view that fluorescence quenching by bound anesthetic reports both the binding energetics and the location of the ligand in the hydrophobic core. The rates of amide hydrogen exchange were similar for the two bundles, suggesting that differences in binding affinity were not due to changes in protein stability. Binding of halothane to both four-alpha-helix bundle proteins stabilized the native folded conformations. Molecular dynamics simulations of the bundles illustrate the existence of the hydrophobic core, containing both W15 residues. These results suggest that in addition to packing defects, enhanced dispersion forces may be important in providing higher affinity anesthetic binding sites. Alternatively, the effect of the methionine substitution on halothane binding energetics may reflect either improved access to the binding site or allosteric optimization of the dimensions of the binding pocket. Finally, preferential stabilization of folded protein conformations may represent a fundamental mechanism of inhaled anesthetic action.     

A high-throughput assay shows that DNase-I binds actin monomers and polymers with similar affinity

Previous conflicting reports suggest that DNase-I binds F-actin with either equal or drastically different K(D) values compared to G-actin. We developed a high-throughput DNase-I inhibition assay to determine the K(D) of DNase-I for F-actin. We confirmed that phalloidin-stabilized F-actin is protected from depolymerization by DNase-I and that the critical concentration at the pointed end of phalloidin-F-actin is 45.5+/-13.9 nM. We found that DNase-I inhibition by actin follows ultrasensitive mechanics. Using varying lengths of gelsolin-capped phalloidin-F-actin, we concluded that the affinities of DNase-I for G- and the pointed end subunits of F-actin are almost indistinguishable, such that DNase-I may not distinguish between G- and F-actin conformations.     

Purification of a form of protease nexin 1 that binds heparin with a low affinity

A form of protease nexin 1 (PN-1) that binds heparin with a low affinity (L-PN-1) was purified and studies since altered interactions with glycosaminoglycans could affect its inhibition of certain serine proteases. Purification of L-PN-1 and PN-1 was achieved by fractionating serum-free conditioned culture medium from human fibroblasts over dextran sulfate-Sepharose followed by immunoaffinity fractionation over a PN-1 monoclonal antibody-Sepharose column. The first step separated L-PN-1 from PN-1, and the second step resulted in apparently homogeneous L-PN-1 and PN-1. Comparisons of the two proteins showed that they could not be distinguished by the following properties: (a) molecular weight; (b) proteases complexed; (c) molecular weights of protease-L-PN-1 and protease-PN-1 complexes; (d) CNBr peptide maps; and (e) immunological cross-reactivity. Studies on activities that depend on the heparin binding domain revealed that heparin equally accelerated the rate of formation of 125I-thrombin-L-PN-1 and 125I-thrombin-PN-1 complexes even when the ratio of heparin to L-PN-1 or PN-1 was varied from 0.01 to 100. A functional difference, however, between L-PN-1 and PN-1 was observed in studies on the ability of the fibroblast surface to accelerate their reactions. Fixed fibroblasts accelerated the formation of 125I-thrombin-L-PN-1 complexes 2-fold, whereas they accelerated the formation of 125I-thrombin-PN-1 complexes 5-fold. The availability of purified L-PN-1 will permit studies on its functional relationship to PN-1.     

Development of support matrices for affinity chromatography of thyroid hormone receptors

Certain cellular responses to thyroid hormones appear to be mediated by non-histone chromatin protein receptors. Purification of these proteins is important for an investigation of the detailed mechanisms of their regulatory role. In the present studies, we report the development of an affinity chromatographic system that can be used to purify thyroid hormone receptors solubilized from nuclei. Amine-substituted hormone analogs were prepared with D and L isomers of T3; these bind to the receptor. This finding supports the hypothesis that thyroid hormones fit into the receptor with the amino groups accessible from outside the binding site. Although L-triiodothyronine (LT3) (the naturally occurring isomer) binds more tightly (relative Kd = 1.0 nM) to the nuclear receptor than D-triiodothyronine (DT3) (relative Kd = 2.0 nM), the amine-substituted analog of DT3 binds more tightly than the LT3 analog (DT3 analog, relative Kd = 40 nM; LT3 analog, relative Kd = 1500 nM). Agarose-based gels containing DT3 and LT3 covalently coupled by their amino groups were also prepared. Binding of receptor to these gels was biospecific in that it could be inhibited by prior incubation of the receptors with LT3. In addition, as predicted by the analog studies, the DT3 affinity gels were more effective than LT3 gels in adsorbing receptor. Elution of receptor from the LT3-derived gels was achieved in a predicted volume and concentration of counter-ligand in elution buffer. These results suggest that affinity chromatography can be applied to the purification of thyroid hormone receptors.     

A new covalently modified support for gas-liquid phase sequencing

A new method for activation of glass fiber supports for immobilisation of proteins and peptides in gas-liquid phase sequencing is described. The new support offers several advantages over the presently used carrier polybrene: no precycling is required, initial yields are improved and background contamination is lower. This leads to an overall increase in detection sensitivity. The derivatisation method includes acid activation and subsequent covalent coating of glass fibers with quaternary ammonium groups thereby giving the glass surface a high binding capacity for both proteins and peptides. The activated glass has been successfully used for sequencing proteins and peptides isolated by HPLC as well as by electroelution from polyacrylamide gels.     

The solid phase in affinity chromatography: strategies for antibody attachment.

Antibodies (Ab) are commonly used in affinity chromatography (AC) as a versatile and specific means of isolating target molecules from complex mixtures. A number of procedures have been developed to immobilize antibodies on the solid matrix. Some of these methods couple the antibody via chemical groups that may be important for specific recognition of antigen, resulting in loss of functionality in a proportion of the antibodies. In other methods, the outcome of immobilization is coupling via unique sites in the Fc region of the antibody molecule, ensuring orientation of the antibody combining sites (Fab) towards the mobile phase. This review discusses the advantages and disadvantages of the various methods available for immobilization and outlines protocols for site-directed, covalent coupling of the antibody to the solid phase that essentially retains the activity of the antibody.     

A metalloantibody that irreversibly binds a protein antigen

Antibody affinity is critically important in therapeutic applications, as well as steady state diagnostic assays. Picomolar affinity antibodies, approaching the association limit of protein-protein interactions, have been discovered for highly potent antigens, but even such high-affinity binders have off-rates sufficient to negate therapeutic efficacy. To cross this affinity threshold, antibodies that tether their targets in a manner other than reversible non-covalent interaction will be required. Here we report the design and construction of an antibody that forms an irreversible complex with a protein antigen in a metal-dependent reaction. The complex resists thermal and chemical denaturation, as well as attempts to remove the coordinating metal ion. Such irreversibly binding antibodies could facilitate the development of next generation "reactive antibody" therapeutics and diagnostics.