Three-dimensional spatial patterning of proteins in hydrogels

The ability to create three-dimensional biochemical environments that mimic those in vivo is valuable for the elucidation of fundamental biological phenomena and pathways. To this end, we designed a system in which proteins can be photochemically patterned in three dimensions within hydrogels under physiological conditions. Fibroblast growth factor-2 (FGF2) was immobilized within agarose hydrogels that were modified with two-photon labile 6-bromo-7-hydroxycoumarin-protected thiols. Two different methods were developed for FGF2 immobilization. The first procedure relies on the protein containing free cysteines for the formation of disulfide bonds with photoexposed agarose thiols. The second procedure takes advantage of the femtomolar binding partners, human serum albumin (HSA) and albumin binding domain (ABD), which have K(D) values of ~10(-14) M. Here HSA-maleimide was chemically bound to photoexposed agarose thiols, and then the FGF2-ABD fusion protein was added to form a stable complex with the immobilized HSA. The use of orthogonal, physical binding pairs allows protein immobilization under mild conditions and can be broadly applied to any protein expressed as an ABD fusion.     

Affinity chromatography of trypsin and related enzymes. IV. Quantitative comparison of affinity adsorbents containing various arginine peptides

In order to study the mechanism of substrate binding of trypsin by affinity chromatography, we synthesized various L-arginine-terminated oligopeptides having different chain length and amino acid sequences, and immobilized them on agarose gel. The interaction of beta-trypsin with these adsorbents was studied by a quantitative affinity chromatographic procedure which gave the dissociation constant (Kd) of the trypsin-immobilized ligand complex. This procedure proved to be very useful and to give information equivalent to that obtained by kinetic procedures. The contribution of the amino acid residue at P2 of the ligands to the affinity was studied by using tripeptide (Gly-X-Arg) Sepharoses, and alanine was found to be more effective than glycine or valine. This conclusion was supported by a kinetic experiment in which Ki values of the corresponding soluble tripeptides (Ac-Gly-X-Arg) were determined. A significant decrease in Kd was observed when the ligand was elongated from dipeptide to tripeptide. However, Kd decreased only slightly when the ligand was elongated further. This suggests that a tripeptide is sufficiently long as a ligand. On the basis of these results, the mode of substrate binding of trypsin is discussed.     

Purification and characterization of mouse interferon with novel affinity sorbents.

Several novel selective sorbents for mouse interferon are described that exploit the hydrophobic property and glycoprotein nature of this molecule. Low-molecular-weight ligands (hydrocarbons) and high-molecular-weight ligands (bovine serum albumin) immobilized on agarose bind selectively mouse L-cell interferon. The high selectivity of binding is due primarily to a hydrophobic effect, although electrostatic forces are also apparently involved. Mouse L-cell interferon binds to immobilized serum albumin and can be completely recovered by raising the ionic strength of the eluant. The specific activity of interferon preparations can be increased 2,000-fold to a value of 3 x 10(8) reference units per mg of protein in a single step with full recovery of the antiviral activity. A selective adsorption, although to a lesser degree, can be also obtained on hydrocarbon-coated agarose (Affi-Gel 202), resulting in 300-fold purification on desorption. The existence of two major components of mouse interferon was revealed upon its chromatography on the following sorbents: (i) bovine serum albumin-agarose, (ii) omega-carboxypentyl-agarose; and (iii) Bandeiraea simplicifolia lectin-agarose. This report thus provides for the first time a means for efficient and clear-cut separation of interferon components, thus enabling their further characterization.     

Synthesis and screening of a rationally designed combinatorial library of affinity ligands mimicking protein L from Peptostreptococcus magnus

Rational design and combinatorial chemistry were utilized to search for lead protein L (PpL) mimetics for application as affinity ligands for the purification of antibodies and small fragments, such as Fab and scFv, and as potential diagnostic or therapeutic agents. Inspection of the key structural features of the complex between PpL and human Fab prompted the de novo design and combinatorial synthesis of a 169-membered solid-phase ligand library, which was assessed for binding to human IgG and subsequent selectivity for the Fab fragment. Eight ligands were selected, chemically characterized and compared with a commercial PpL-adsorbent for binding pure immunoglobulin fractions. The most promising lead, ligand 8/7, when immobilized on an agarose support, behaved in a similar fashion to PpL in isolating Fab fragments from papain digests of human IgG to a final purity of 97%.     

Affinity chromatography of plasma proteins (guanidinobenzoatase): use of mimetic matrices and mimetic soluble ligands to prevent the binding of albumin on target affinity matrices

Serum albumin is the most abundant protein in plasma and it has a high capacity to bind many small compounds and macromolecules. In this way, albumin may promote important interferences during affinity chromatography of plasma proteins. Guanidinobenzoatase (GB) is a very relevant plasma protease that seems to be related to tumoral processes. This enzyme may be adsorbed on tailor-made agmatine-amide-agarose (CH-A) supports (e.g., the ones having 2 μmol of guanidino groups per ml of agarose attached to the support, through a 6 C aliphatic chain). Such tailor-made supports containing a very low concentration of ionized groups are hardly able to adsorb any protein by anion-exchange. However, they are able to strongly adsorb albumin. In order to solve this problem new mimetic affinity matrices have been designed: (i) by using the same ligand immobilized through a different chemical linkage [guanidino groups attached via secondary amino bonds, (AEA)] or (ii) by using slightly different ligands (e.g., 1,8-octanediamine containing a primary amino group instead of a guanidino one) also attached to the support via amido bonds (CH-DAO). Albumin adsorbs on the target and on the two mimetic matrices while GB is mainly adsorbed on the target one. Moreover, the adsorption of albumin on the affinity matrix (CH-A) is very strongly inhibited by the presence of low concentrations of soluble ligands (e.g., 1,8-octanediamine containing two ionized primary amino groups). On the contrary, the adsorption of GB on CH-A is hardly inhibited by the presence of such mimetic soluble ligand. In this way, the former offering of crude GB samples to AEA plus the use of mimetic inhibitors during adsorption of the extract on CH-A completely prevent the undesirable adsorption of albumin. In a such way, an extremely selective adsorption of GB can be performed. Such an improved chromatography procedure allows a very easy affinity purification and detection of GB.     

Physico-Chemical Characterization of Hamster Interferon

The glycoprotein nature of Syrian hamster interferon was tested on several immobilized lectins. The specific retention of small portion (20%) of interferon activity was observed only on concanavalin A-agarose; Component I of the interferon (not retained) has an apparent molecular weight of 23,500 whereas Component II (retained) is larger, 31,500. The apparent hydrophobicity of Syrian hamster interferon was probed by its chromatography on: (a) straight chain hydrocarbons of varied length; (b) aromatic ligands (aminobenzene, benzylamine, β-phenylethylamine, γ-phenyl-propylamine); ligands listed in (a) and (b) were immobilized to cyanogen bromide-activated agarose (isoure linkage); and (c) phenyl-agarose (Phenyl-Sepharose CL-4B), an aromatic ligand immobilized vi 2-hydroxypropyl arm to the agarose (ether linkage).

For a hydrophobic interaction to occur under physiological solvent conditions, the hydrocarbon arm (isourea 1inkage) must be C₉ to C₁₀ carbon atoms long, whereas the aromatic ligand (isourea linkage) must be removed from the agarose matrix by a molecular arm of C₃ carbon atoms. There is no significant binding of hamster interferon to phenyl-agarose (ether linkage) near neutral pH.

The apparent hydrophobicity of Syrian hamster interferon can be profoundly influenced by the pH of the solvent. At lower pH values, interferon binds to both octyl-agarose and phenyl-agarose. The midpoint of transition between binding of interferon and its release from these ligands is about the same, pH 6.0, suggesting the identity of the binding site on the interferon molecule for both aliphatic and aromatic hydrocarbons.     

Affinity chromatography of mitochondrial nicotinamide nucleotide transhydrogenase

The binding of mitochondrial nicotinamide nucleotide transhydrogenase to NAD+ and NADP+ immobilized to agarose through different parts of the nicotinamide nucleotide molecule was investigated. NADP+ bound at the C8 atom in the adenine moiety proved to be the most efficient ligand whereas that bound at the C3 atom of the ribose moiety was relatively inefficient. NAD+ ligands were generally inactive independently of the site of attachment. Previous results suggest, however, that binding to immobilized NAD+ may be influenced by the detergent in which transhydrogenase is dispersed. Binding to neither ligand was affected by the presence of the second substrate.     

Assay development and data analysis of receptor-ligand binding based on scintillation proximity assay

In this paper, we described the optimization of a generic binding assay to measure ligand-receptor interactions for peroxisome proliferator-activated receptors (PPARs). The assay is based on scintillation proximity assay, in which a protein is coated on scintillant-incorporated beads, and a radiolabeled ligand stimulates the beads to emit a signal by binding to the immobilized protein. An intrinsic binding affinity of unlabeled ligands is determined by competitive displacement of the radioligand. The protein coating and ligand binding are achieved in one step by simply mixing ligands, protein and beads in sequence. No additional steps of pre-coating and washing of beads are required. Protein is captured on beads effectively by electrostatic interactions, thus no affinity labeling of protein is required. In data analysis, ligands are grouped into two classes based on their binding affinities. For tight binding ligands, an equation is derived to accurately determine the binding affinity. Otherwise a general equation applies. This quantitative and high throughput assay provides a tool to screen a large library of molecules in search of potent ligands.     

Selective adsorption of proteins to their ligands covalently immobilized onto microfibers

Following ozone oxidation of polyester microfibers of 3.5 mum average diameter and 0.83 m(2)/g specific area, the fiber surface was subjected to graft polymerization of acrylic acid and subsequently immobilized with serologically active proteins including Staphylococcus aureus protein A, a specific antigen, and a specific antibody. The immobilization reaction was mediated by a watersoluble carbodiimide, which allowed formation of a co-valent linkage between the ligand proteins and the grafted poly(acrylic acid)chains. The yields of the immobilized ligand proteins were of the order of 1 mg/g fiber. Their binding affinity and capacity to respective specific proteins were studied in vitro from a buffered solution and serum. It was found that the specific proteins were selectively adsorbed with dissociation constants as low as 1x 10(-6) M, suggesting the adsorption to take place through highly specific protein-protein interaction. An addition of serum albumin did not significantly affect the specific binding, regardless of the ligand proteins. The binding capacity ranged from 1 x 10(-13) to 1x 10(-11) mol/cm(2) primarily depending on the surface density of the immobilized ligands and the number of their binding sites per molecule. (c) 1995 John Wiley & Sons Inc.     

Comparative studies of the binding of some ligands to human serum albumin non-covalently attached to immobilized Cibacron Blue, or covalently immobilized on Sepharose, by column affinity chromatography.

A comparative study of the ligand-binding properties of human serum albumin was performed by the technique of affinity chromatography with the protein attached to immobilized Cibacron Blue F3GA (Blue Sepharose), or covalently immobilized on Sepharose. The binding strength of octanoate, decanoate and dodecanoate is much weaker when human serum albumin is attached to immobilized Cibacron Blue, indicating that the binding sites for fatty acids are involved in the attachment of human serum albumin to immobilized Cibacron Blue. The results revealed additional alterations of the ligand binding when human serum albumin was attached to immobilized Cibacron Blue, involving sites outside of the binding domains of fatty acids. Thus the stereoselective binding of L-tryptophan was abolished, and the resolution of the warfarin enantiomers was impaired. However, the binding strength of warfarin and salicylic acid was rather close to the values observed with human serum albumin covalently immobilized on Sepharose. It is suggested that the availability of the binding sites for L-tryptophan, warfarin and salicylic acid is partially blocked by the complex between albumin and the dye without direct participation in the complex-formation. An alternative interpretation involves an allosteric mechanism brought about by complex-formation between serum albumin and the immobilized Cibacron Blue.     

Essential role of the concentration of immobilized ligands in affinity chromatography:: Purification of guanidinobenzoatase on an ionized ligand

Guanidinobenzoatase, a plasma protein with possible application as a ‘tumor marker’, has been fully purified by one-step affinity chromatography. The affinity matrix was prepared by ‘controlled’ immobilization of an enzyme inhibitor (agmatine) onto commercial agarose gels containing carboxyl moieties activated as N-hydroxysuccinimide esters. In this way, agmatine becomes immobilized through an amido bond and preserves an ionized guanidino moiety. Different matrices with different concentration of ligands were prepared in order to evaluate their properties as affinity supports. Interestingly, matrices with a very low concentration of immobilized ligands (2 μmol/ml, corresponding to the modification of only 5% of active groups in the commercial resins) exhibited a low capacity for unspecific adsorption of proteins (as anion-exchange resins) and displayed also a high capacity for specific adsorption of our target protein. On the other hand, when affinity matrices possessed a moderate concentration of agmatine (10 μmol/ml of gel or higher), two undesirable phenomena were observed: (a) the matrix behaves as a very good anionic exchange support able to non-specifically adsorb most of plasma proteins and (b) the specific adsorption of our target protein becomes much lower. The latter phenomenon could be due to steric hindrances promoted by the interaction between each individual immobilized ligand and the corresponding binding pocket in the target protein. These hindrances could also be promoted by the presence of a fairly dense layer of immobilized ligands covering the support surface, thus preventing interactions between immobilized ligands and partially buried protein-binding pockets. In this way, a successful affinity purification (23.5% yield, ×220 purification factor, a unique electrophoretic band) could be achieved by combination of three approaches: (i) the use of affinity matrices possessing a very low density of immobilized ligands, (ii) performing affinity adsorption at high ionic strength and (iii) performing specific desorption with substrates or substrate analogues.     

Quantitative affinity chromatography of alpha-chymotrypsin

Affinity chromatography on a column of 4-phenylbutylamine, immobilized on succinylated polyacrylic hydrazide agarose, has been employed to study binding of ligands to α-chymotrypsin. In contrast to earlier studies of competitive elution phenomena, where an added soluble ligand interferes with enzyme binding to an affinity matrix, benzyloxycarbonyl derivatives of aromatic acids have been shown to facilitate binding of chymotrypsin to this matrix. This behavior has been analyzed in terms of an expanded binding scheme for affinity chromatography including the formation of a ternary complex (α-chymotrypsin · benzyloxycarbonyl-amino acid · 4-phenylbutylamine · matrix) where the soluble ligand and immobilized ligand bind to different sites. Equations to describe the phenonema have been derived and utilized to quantitate equilibrium constants for dissociation of the binary and ternary complexes. Benzyloxycarbonyl-Ala-Ala was found to promote earlier elution of the enzyme from its affinity matrix. Other ligands known to bind to the active site do not alter the binding to the 4-phenylbutylamine affinity matrix. These results illustrate the conclusion that binding of a small molecule can alter affinity retention in positive, negative, or neutral modes. This suggests that affinity chromatography could be “fine-tuned” by appropriate selection of cosolutes and illustrates the value of relatively weakly binding affinity matrices in enzyme studies.     

Hydrophobic interaction of human, mouse, and rabbit interferons with immobilized hydrocarbons.

Interferons of human, mouse, and rabbit origin bind to straight chain hydrocarbons immobilized on agarose. The hydrophobic nature of binding is established by the following observations: (a) a positive correlation between the length of hydrocarbon ligand and the strength of interaction; (b) a stronger interaction with hydrocarbon ligands terminated with apolar rather than polar head groups; (c) a lack of dependence of binding on ionic strength and pH of the solvent; (d) a reversal of binding by ethylene glycol, a hydrophobic solute; (e) an increasing eluting efficacy of tetraalkylammonium ions with the length of their alkyl substituents. The hydrophobic interactions of human interferon underlie the efficiency of two-step chromatographic procedures. For example, human embryo kidney interferon can be purified about 3,600-fold by sequential chromatography on (a) concanavalin A-agarose, (b) octyl-agarose. Another two-step procedure: (a) concanavalin A-agarose, (b) L-tryptophan-agarose, gives about 10,000-fold purification. The overall recovery of interferon in both cases in close to 90%.     

Physico-chemical characterization of hamster interferon.

The glycoprotein nature of Syrian hamster interferon was tested on several immobilized lectins. The specific retention of a small portion (20%) of interferon activity was observed only on concanavalin A-agarose; Component I of the interferon (not retained) has an apparent molecular weight of 23,500 whereas Component II (retained) is larger, 31,500. The apparent hydrophobicity of Syrian hamster interferon was probed by its chromatography on: (a) straight chain hydrocarbons of varied length; (b) aromatic ligands (aminobenzene, benzylamine, beta-phenylethylamine, gamma-phenyl-propylamine); ligands listed in (a) and (b) were immobilized to cyanogen bromide-activated agarose (isourea linkage); and (c) phenyl-agarose (Phenyl-Sepharose CL-4B), an aromatic ligand immobilized via a 2-hydroxypropyl arm to the agarose (ether linkage).     

Frontal gel chromatographic analysis of the interaction of a protein with self-associating ligands: aberrant saturation in the binding of flavins to bovine serum albumin

Frontal gel chromatography is an accurate method to obtain the total free ligand concentration of a protein-ligand mixture in which ligands self-associate. The average number of bound ligands per protein molecule is obtained as a function of the total free ligand concentration. The method was applied to the interaction of bovine serum albumin with self-associating flavins. The binding curves for FMN and FAD leveled off at about 0.7 and 0.5, respectively. These data were simulated well by a binding model where flavins undergo isodesmic indefinite self-association and the monomer alone binds to a single binding site of albumin. The isodesmic association constants of FMN and FAD were (1.7 +/- 0.1) x 10(2) and (2.2 +/- 0.3) x 10(2) M(-1), respectively. The binding constants of the monomer of FMN and FAD were (7.6 +/- 0.2) x 10(2) and (3.5 +/- 0.2) x 10(2) M(-1), respectively. FMN competitively inhibited the binding of FAD to albumin. The affinity to flavins was in the following order at pH 5.8: lumiflavin, FMN, riboflavin, and FAD. The SH modification and the binding of palmitate did not affect the FMN binding to bovine albumin at pH 5.8. As pH increased from 5.8 to 9.0, the affinity to FMN of bovine albumin decreased 3-fold, whereas that of human albumin increased about 80-fold. The present study clearly showed how isodesmic self-association of a ligand can cause apparent saturation of the interaction of a protein with the ligand at levels lower than 1.     

Drug affinity to immobilized target bio-polymers by high-performance liquid chromatography and capillary electrophoresis

This review addresses the use of high-performance liquid chromatography (HPLC) and capillary electrophoresis (CE) as affinity separation methods to characterise drugs or potential drugs-bio-polymer interactions. Targets for the development of new drugs such as enzymes (IMERs), receptors, and membrane proteins were immobilized on solid supports. After the insertion in the HPLC system, these immobilized bio-polymers were used for the determination of binding constants of specific ligands, substrates and inhibitors of pharmaceutical interest, by frontal analyses and zonal elution methods. The most used bio-polymer immobilization techniques and methods for assessing the amount of active immobilized protein are reported. Examples of increased stability of immobilized enzymes with reduced amount of used protein were shown and the advantages in terms of recovery for reuse, reproducibility and on-line high-throughput screening for potential ligands are evidenced. Dealing with the acquisition of relevant pharmacokinetic data, examples concerning human serum albumin binding studies are reviewed. In particular, papers are reported in which the serum carrier has been studied to monitor the enantioselective binding of chiral drugs and the mutual interaction between co-administered drugs by CE and HPLC. Finally CE, as merging techniques with very promising and interesting application of microscale analysis of drugs' binding parameters to immobilized bio-polymers is examined.     

Demonstration of the pH sensitive binding of multivalent carbohydrate ligands to immobilized Shiga-like toxin 1 B subunits.

The cytotoxic effects of Shiga-like toxins from enterohemorrhagic Escherichia coli O157:H7 depend on the recognition of carbohydrate determinants by B subunits. As a specific carbohydrate ligand, globotriaosylceramide has been characterized. We developed an alternative binding assay using multivalent carbohydrate ligands. We prepared globotriose-conjugated poly-lysine, and measured their binding to immobilized recombinant B subunits by an ELISA format. The signals representing ligand binding were dependent on the amount of immobilized B subunits as well as on the concentration of the ligands. The ligand binding activity was lost in an acidic environment, in which changes in the local conformation of the B subunits have been reported. Furthermore, pH dependent dissociation of the ligands from the B subunits was observed. We also demonstrate that antiserum from mice immunized with the B subunits specifically interferes with ligand binding. This suggests further potential for an assay to screen for blocking antibodies that could inhibit toxin internalization into host cells.     

Galactosyl-mimodye ligands for Pseudomonas fluorescens beta-galactose dehydrogenase.

Protein molecular modelling and ligand docking were employed for the design of anthraquinone galactosyl-biomimetic dye ligands (galactosyl-mimodyes) for the target enzyme galactose dehydrogenase (GaDH). Using appropriate modelling methodology, a GaDH model was build based on a glucose-fructose oxidoreductase (GFO) protein template. Subsequent computational analysis predicted chimaeric mimodye-ligands comprising a NAD-pseudomimetic moiety (anthraquinone diaminobenzosulfonic acid) and a galactosyl-mimetic moiety (2-amino-2-deoxygalactose or shikimic acid) bearing an aliphatic 'linker' molecule. In addition, the designed mimodye ligands had an appropriate in length and chemical nature 'spacer' molecule via which they can be attached onto a chromatographic support without steric clashes upon interaction with GaDH. Following their synthesis, purification and analysis, the ligands were immobilized to agarose. The respective affinity adsorbents, compared to other conventional adsorbents, were shown to be superior affinity chromatography materials for the target enzyme, Pseudomonas fluorescensbeta-galactose dehydrogenase. In addition, these mimodye affinity adsorbents displayed good selectivity, binding low amounts of enzymes other than GaDH. Further immobilized dye-ligands, comprising different linker and/or spacer molecules, or not having a biomimetic moiety, had inferior chromatographic behavior. Therefore, these new mimodyes suggested by computational analysis, are candidates for application in affinity labeling and structural studies as well as for purification of galactose dehydrogenase.     

Expression of multivalency in the affinity chromatography of antibodies. Appendix: Derivation and evaluation of equations for independent bivalent interacting systems in quantitative affinity chromatography.

The expression of multivalency in the interaction of antibody with immobilized antigen was evaluated by quantitative affinity chromatography. Zones of radioisotopically labeled bivalent immunoglobulin A monomer derived from the myeloma protein TEPC 15 were eluted from columns of phosphorylcholine-Sepharose both in the absence and presence of competing soluble phosphorylcholine. At sufficient immobilized phosphorylcholine concentration, the variation of elution volume of bivalent monomer with soluble ligand was found to deviate from that observed for the univalent binding of the corresponding Fab fragment. In addition, the apparent binding affinity of the bivalent monomer increased with immobilized antigen density. Use of equations relating the variation of elution volume with free ligand concentration for a bivalent binding protein allowed calculation of microscopic single-site binding parameters for the bivalent monomeric antibody to both immobilized and soluble phosphorylcholine. The chromatographic data not only demonstrate the effect of multivalency on apparent binding affinity but also offer a relatively simple means to measure microscopic dissociation constants for proteins participating in bivalent interactions with their ligands.