Chemoenzymatic methods for site-specific protein modification

In the past decade, numerous chemical technologies have been developed to allow the site-specific post-translational modification of proteins. Traditionally covalent chemical protein modification has been accomplished by the attachment of synthetic groups to nucleophilic amino acids on protein surfaces. These chemistries, however, are rarely sufficiently selective to distinguish one residue within a literal sea of chemical functionality. One solution to this problem is to introduce a unique chemical handle into the target protein that is orthogonal to the remainder of the proteome. In practice, this handle can be a novel peptide sequence, which forms a 'tag' that is selectively and irreversibly modified by enzymes. Furthermore, if the enzymes can tolerate substrate analogs, it becomes possible to engineer chemically modified proteins in a site-specific fashion. This review details the significant progress in creating techniques for the chemoenzymatic generation of protein-small molecule constructs and provides examples of novel applications of these methodologies.     

Chemical modification of protein surfaces to improve their reversible enzyme immobilization on ionic exchangers

The enzyme penicillin G acylase (PGA) is not adsorbed at pH 7 on DEAE- or PEI-coated supports, neither is it adsorbed on carboxymethyl (CM)- or dextran sulfate (DS)-coated supports. The surface of the enzyme was chemically modified under controlled conditions: chemical amination of the protein surface of carboxylic groups (using soluble carbodiimide and ethylendiamine) and chemical succinylation (using succinic anhydride) of amino groups. The full chemical modification produced some negative effects on enzyme stability and activity, although partial modification (mainly succinylation) presented negligible effects on both enzyme features. The chemical amination of the protein surface permitted the immobilization of the enzyme on CM- and DS-coated support, while the chemical succinylation permitted the enzyme immobilization on DEAE- and PEI-coated supports. Immobilization was very strong on these supports, mainly in the polymeric ones, and dependent on the degree of modification, although the enzymes still can be desorbed after inactivation by incubation under drastic conditions. Moreover, the immobilization on ionic polymeric beds allowed a significant increase in enzyme stability against the inactivation and inhibitory effects of organic solvents, very likely by the promotion of a certain partition of the organic solvent out of the enzyme environment. These results suggest that the enrichment of the surface of proteins with ionic groups may be a good strategy to take advantage of the immobilization of industrial enzymes via ionic exchange on ionic polymeric beds.     

Improved stabilization of chemically aminated enzymes via multipoint covalent attachment on glyoxyl supports

The surface carboxylic groups of penicillin G acylase and glutaryl acylase were chemically aminated in a controlled way by reaction with ethylenediamine via the 1-ethyl-3-(dimethylamino-propyl) carbodiimide coupling method. Then, both proteins were immobilized on glyoxyl agarose. In both cases, the immobilization of the chemically modified enzymes improved the enzyme stability compared to the stability of the immobilized but non-modified enzyme (by a four-fold factor in the case of PGA and a 20-fold factor in the case of GA). The chemical modification presented a deleterious effect on soluble enzyme stability. Therefore, the improved stability should be related to a higher multipoint covalent attachment, involving both the lysine amino groups and also the new amino groups chemically introduced on the enzyme. Moreover, the lower pK(a) of the new amino groups permitted to immobilize the enzyme under milder conditions. In fact, the aminated proteins could be immobilized even at pH 9, while the non-modified enzymes could only be immobilized at pH over 10.     

CONVERSION OF TRYPSIN TO A COPPER ENZYME: TYROSINASE/CATECHOL OXIDASE BY CHEMICAL MODIFICATION

New active sites can be introduced into naturally occurring enzymes by the chemical modification of specific amino acid residues in concert with genetic techniques. Chemical strategies have had a significant impact in the field of enzyme design such as modifying the selectivity and catalytic activity which is very different from those of the corresponding native enzymes. Thus, chemical modification has been exploited for the incorporation of active site binding analogs onto protein templates and for atom replacement in order to generate new functionality such as the conversion of a hydrolase into a peroxidase. The introduction of a coordination complex into a substrate binding pocket of trypsin could probably also be extended to various enzymes of significant therapeutic and biotechnological importance.

The aim of this study is the conversion of trypsin into a copper enzyme: tyrosinase by chemical modification. Tyrosinase is a biocatalyst (EC.1.14.18.1) containing two atoms of copper per active site with monooxygenase activity. The active site of trypsin (EC 3.4.21.4), a serine protease was chemically modified by copper (Cu⁺²) introduced p-aminobenzamidine (pABA- Cu⁺²: guanidine containing schiff base metal chelate) which exhibits affinity for the carboxylate group in the active site as trypsin-like inhibitor. Trypsin and the resultant semisynthetic enzyme preparation was analysed by means of its trypsin and catechol oxidase/tyrosinase activity. After chemical modification, trypsin-pABA-Cu⁺² preparation lost 63% of its trypsin activity and gained tyrosinase/catechol oxidase activity. The kinetic properties (K_cat, K_m, K_cat/K_m), optimum pH and temperature of the trypsin-pABA-Cu⁺² complex was also investigated.     

Protein tailoring of human granulocyte colony-stimulating factor

Summary Recombinant human granulocyte-colony stimulating factor (rhG-CSF) was modified by site-directed mutagenesis and chemical modification in order to improve its pharmacological activity and its thermostability. The mutant rhG CSF which 17th cysteine was substituted with alanine was chemically modified by activated polyethylene glycol. The chemically modified mutant rhG-CSF greatly increased both its biological activityin vivo and its thermostability. This is a successful example of protein tailoring in which site-directed mutagenesis and chemical modification were used at the same time.     

Conversion of cysteinyl residues to unnatural amino acid analogs. Examination in a model system

Improved and efficient techniques have led to an explosive growth in the application of site-directed mutagenesis to the study of enzymes. However, the limited availability of only those 20 amino acids that are translated by the genetic code has prevented the systematic variation of an amino acid's properties in order to define more precisely its role in the catalytic mechanism of an enzyme. An approach is being examined that combines the high specificity of site-directed mutagenesis with the flexibility of chemical modification to overcome these limitations. A set of reagents has been synthesized and reacted with a cysteine model to produce a series of amino acid structural analogs at appreciable rates and in good overall yields. The selective incorporation of these analogs in place of important functional amino acids in a protein will allow a more detailed examination of the role of that amino acid.     

ATP as effector of inorganic pyrophosphatase of <Emphasis Type="Italic">Escherichia coli</Emphasis>. Identification of the binding site for ATP

The interaction of Escherichia coli inorganic pyrophosphatase (E-PPase) with effector ATP has been studied. The E-PPase has been chemically modified with the dialdehyde derivative of ATP. It has been established that in the experiment only one molecule of effector ATP is bound to each subunit of the hexameric enzyme. Tryptic digestion of the adenylated protein followed by isolation of a modified peptide by HPLC and its mass-spectrometric identification has showed that it is an amino group of Lys146 that undergoes modification. Molecular docking of ATP to E-PPase indicates that the binding site for effector ATP is located in a cluster of positively charged amino acid residues proposed earlier on the basis of site-directed mutagenesis to participate in binding of effector pyrophosphate. Molecular docking also reveals several other amino acid residues probably involved in the interaction with effectors. Published in Russian in Biokhimiya, 2007, Vol. 72, No. 1, pp. 110–117.     

Tuning of Lecitase features via solid-phase chemical modification: Effect of the immobilization protocol

Lecitase Ultra (a quimeric fosfolipase commercialized by Novozymes) has been immobilized via two different strategies: mild covalent attachment on cyanogen bromide agarose beads and interfacial activation on octyl-agarose beads. Both immobilized preparations have been submitted to different individual or cascade chemical modifications (amination, glutaraldehyde or 2,4,6-trinitrobenzensulfonic acid (TNBS) modification) in order to check the effect of these modifications on the catalytic features of the immobilized enzymes (including stability and substrate specificity under different conditions). The first point to be remarked is that the immobilization strongly affects the enzyme catalytic features: octyl-Lecitase was more active versus p-nitrophenylbutyrate but less active versus methyl phenylacetate than the covalent preparations. Moreover, the effects of the chemical modifications strongly depend on the immobilization strategy used. For example, using one immobilization protocol a modification improves activity, while for the other immobiled enzyme is even negative. Most of the modifications presented a positive effect on some enzyme properties under certain conditions, although in certain cases that modification presented a negative effect under other conditions. For example, glutaraldehyde modification of immobilized or modified and aminated enzyme permitted to improve enzyme stability of both immobilized enzymes at pH 7 and 9 (around a 10-fold), but only the aminated enzyme improved the enzyme stability at pH 5 by glutaraldehyde treatment. This occurred even though some intermolecular crosslinking could be detected via SDS-PAGE. Amination improved the stability of octyl-Lecitase, while it reduced the stability of the covalent preparation. Modification with TNBS only improved enzyme stability of the covalent preparation at pH 9 (by a 10-fold factor).     

Utilization of alkyne bioconjugations to modulate protein function

The ability to introduce or modify protein function has widespread application to multiple scientific disciplines. The introduction of unique unnatural amino acids represents an excellent mechanism to incorporate new functionality; however, this approach is limited by ability of the translational machinery to recognize and incorporate the chemical moiety. To overcome this potential limitation, we aimed to exploit the functionality of existing unnatural amino acids to perform bioorthogonal reactions to introduce the desired protein modification, altering its function. Specifically, via the introduction of a terminal alkyne containing unnatural amino acid, we demonstrated chemically programmable protein modification through the Glaser-Hay coupling to other terminal alkynes, altering the function of a protein. In a proof-of-concept experiment, this approach has been utilized to modify the fluorescence spectrum of green fluorescent protein.     

Improved activity and stability of alkaline phosphatases from psychrophilic and mesophilic organisms by chemically modifying aliphatic or amino groups using tetracarboxy-benzophenone derivatives.

The activity-stability-structure relationship of the cold-active alkaline phosphatase from Red Arctic shrimp, Pandalus borealis (SAP) was studied by chemically modifying aliphatic (C-H) or amino (NH2) groups using benzophenone tetracarboxylic derivatives in either a light (UV-A) or dark reaction. The response of the cold-adapted enzyme was compared to a similarly modified calf alkaline phosphatase (CAP). MALDI-TOF-MS was used to determine the extent and nature of the modifications in both SAP and CAP. On average 2 to 4 amino acid residues were linked to a BP-modifier, with up to 18 to 21 amino acids modified in a smaller portion of the material. The effect of the modifications on kinetic and thermodynamic properties varied with the enzyme and type of modification. The aliphatic-group modified SAP demonstrated typical characteristics of a mesophilic enzyme, consistent with an activity-stability trade-off where gain in thermostability was attained at the expense of decreased activity. In contrast, the activity of the amino-group modified SAP attained an even more psychrophilic character with respect to its kinetic (increase in kcat and Km) and thermodynamic (reduction in deltaH#) properties. Interestingly, the amino-group modified SAP also acquired higher thermostability, thus demonstrating that both activity and stability can be simultaneously enhanced using chemical modification. The study demonstrates the applicability of benzophenone chemical modification for improving the thermal properties of enzymes from psychrophiles and mesophiles.     

Relation between stabilization and rigidification of the three-dimensional structure of an enzyme

Purified cellobiase was coupled to periodate-oxidized dextran by reductive alkylation using sodium cyanoborohydride, sodium borohydride, and dimethylaminoborane for various reaction times. The thermal stability of the different conjugates obtained was studied and correlated to the number of links introduced between the enzyme and the soluble support. We observe that resistance to heat inactivation increases as a function of the number of modified lysines. Sodium cyanoborohydride was the most effective reducing agent. After 24 h reaction, the modification of 92% of the lysines gave a cellobiase-dextran conjugate that is a most stable enzyme. We conclude that the thermal stability observed for the chemically modified enzyme results from the rigidification of the three-dimensional structure of the protein. This rigidification increases with the number of links introduced between the enzyme and the polysaccharide. We also observe that chemical modification leads to a heterogeneous population of stabilized enzymes. Because of this heterogeneous population, it is necessary to develop a mathematical model of the kinetics of enzyme inactivation.     

Protein crosslinking: Uses in chemistry,biology and biotechnology

Abstract

Protein crosslinking is a part of many biological processes and is also carried out in vitro under several controllable conditions with the help of any of the commercially available bifunctional reagents. Many biotechnological applications utilize stable and/or reusable crosslinked enzymes such as soluble intramolecularly crosslinked enzymes; soluble bioconjugates of enzymes with other enzymes/proteins or polymers; chemically aggregated enzymes, chemically crosslinked enzyme aggregates and crosslinked enzyme crystals. The review after indicating how protein crosslinking is at the heart of such diverse processes/technology concludes with discussion of few applications which are currently drawing considerable attention.     

Chemical amination of lipase B from Candida antarctica is an efficient solution for the preparation of crosslinked enzyme aggregates

Lipase B from Candida antarctica (CALB) is not very adequate to prepare crosslinked enzyme aggregates (CLEAs). Although the precipitation step is easy using different precipitants, the crosslinking step becomes a problem due to the low amount of Lys residues in this enzyme. In this paper, we have enriched the enzyme in amino groups by chemical amination of the enzyme using ethylenediamine and carbodiimide. The modification was performed using a solid phase strategy modifying the enzyme adsorbed on octyl-Sepharose. After desorption from the support, the enzyme was more active at pH 7.0 than the unmodified enzyme. This modified enzyme showed to be suitable to produce CLEAs. Using this modified enzyme, precipitation is also effective but the crosslinking step did not fail in giving an intense intermolecular crosslinking. This way, the CLEA did not release enzyme molecules even if boiled in SDS. Stability of this CLEA was higher in both thermal and cosolvent inactivation experiments than that of the coCLEA produced by coagregation of BSA and CALB; another alternative to produce a CLEA of this interesting enzyme.The strategy may be of high interest for many other enzymes as a way to both permit the production of CLEAs and to improve enzyme stability during CLEA production.     

Chemical modification of papain for use in alkaline medium

Chemical modification is a useful method to recognize and modify functional determinants of enzymes. Papain, an endolytic cysteine protease (EC3.4.22.2) from Carica papaya latex has been chemically modified using different dicarboxylic anhydrides of citraconic, phthalic, maleic and succinic acids. These anhydrides reacted with five to six amino groups of the lysine residues in the enzyme, thereby changing the net charge of the enzyme from positive to negative. The resultant enzyme had its optimum pH shifted from 7 to 9 and change in temperature optima from 60 to 80 °C. The modified papain also had a higher thermostability. Stability of the modified papain was further increased by immobilization of the enzyme either by adsorption onto inert matrix or by entrapment in polysaccharide polymeric gels. Entrapment in starch gel showed better retention of enzyme activity. Incorporation of modified and immobilized enzymes to branded domestic detergent powders was found to have very good activity retention. The papain entrapped in starch gel showed better stability and activity retention than in other carbohydrate polymers when added to domestic detergent powders.     

Cross-linked enzyme crystals

The active site of cross-linked enzyme crystals can be further modified by chemical means, yielding a new type of chemically engineered enzyme. In the past year, the characteristics of cross-linked protein crystals as microporous materials have been studied and used as stationary phases in chromatographic separations.     

Incorporation of non-natural modules into proteins: structural features beyond the genetic code

The biotechnological application of enzymes necessitates a permanent quest for new biocatalysts. Among others, improvement of catalytic activity, modification of substrate specificity, or increase in stability of the enzymes are desirable goals. The exploration of homologous enzymes from various sources or DNA-based methods, like site-directed mutagenesis or directed evolution, yield an incredible variety of biocatalysts but they all rely on the restricted number of canonical amino acids. Chemistry offers an almost unlimited palette of additional modifications which can endow the proteins with improved or even completely new properties. Numerous techniques to furnish proteins with non-natural amino acids or non-proteinogenic modules have been introduced and are reviewed with special focus on expressed protein ligation, a method that combines the potential of protein biosynthesis and chemical synthesis. An erratum to this article can be found at     

Regulation of catalytic activity of a multifunctional polyketide biosynthetic enzyme, 6-hydroxymellein synthase, by interaction between NADPH and phenylglyoxal-sensitive amino acid residue at the reaction center

Treatment of 6-hydroxymellein synthase, a multifunctional polyketide biosynthetic enzyme in carrot cells, with phenylglyoxal yielded a chemically modified protein in which approximately two moles of the reagent were covalently attached to each subunit of the enzyme. Only NADH- but not NADPH-associated form of native 6-hydroxymellein synthase was inhibited by cerulenin; however, the NADPH-synthase complex lost the insensitivity by the chemical modification of the enzyme protein with phenylglyoxal. Appreciable differences in K(m) values observed between the NADPH- and NADH-associated enzymes were greatly reduced by the treatment with phenylglyoxal. Although the catalytic activity of the NADPH-associated synthase was enhanced by the addition of free CoA, the compound exhibited a significant inhibitory activity to the phenylglyoxal-modified enzyme. A marked deuterium isotope effect in the catalytic reaction of the native synthase-NADPH complex was appreciably decreased in the chemically modified enzyme. These results strongly suggest that an electrostatic interaction between the phosphate group attached to the 2'-position of adenosyl moiety of NADPH and the phenylglyoxal-sensitive amino acid residue, probably arginine, at the reaction center of 6-hydroxymellein synthase regulates several biochemical properties of this multifunctional enzyme.     

Stabilization of collagen through bioconversion: An insight in protein–protein interaction

Collagen is a natural protein, which is used as a vital biomaterial in tissue engineering. The major concern about native collagen is lack of its thermal stability and weak resistance to proteolytic degradation. In this scenario, the crosslinking compounds used for stabilization of collagen are mostly of chemical nature and exhibit toxicity. The enzyme mediated crosslinking of collagen provides a novel alternative, nontoxic method for stabilization. In this study, aldehyde forming enzyme (AFE) is used in the bioconversion of hydroxylmethyl groups of collagen to formyl groups that results in the formation of peptidyl aldehyde. The resulted peptidyl aldehyde interacts with bipolar ions of basic amino acid residues of collagen. Further interaction leads to the formation of conjugated double bonds (aldol condensation involving the aldehyde group of peptidyl aldehyde) within the collagen. The enzyme modified collagen matrices have shown an increase in the denaturation temperature, when compared with native collagen. Enzyme modified collagen membranes exhibit resistance toward collagenolytic activity. Moreover, they exhibited a nontoxic nature. The catalytic activity of AFE on collagen as a substrate establishes an efficient modification, which enhances the structural stability of collagen. This finds new avenues in the context of protein–protein stabilization and discovers paramount application in tissue engineering. © 2014 Wiley Periodicals, Inc. Biopolymers 101: 903–911, 2014.     

Microenvironmental effects on enzyme catalysis. A kinetic study of hydrophobic derivatives of chymotrypsin

The aim of this work was to study the role of hydrophobic interactions in the enzymic activity of chymotrypsin. The amino groups of chymotrypsin were chemically modified by aliphatic aldehydes of various chain lengths - acetaldehyde, butyraldehyde, hexanal - and with two aldehydes of different steric hindrance - benzaldehyde and trimethyl acetaldehyde. After a rapid study of the derivated enzymes, the hexylchymotrypsin has been chosen for its new catalytic properties: the Michaelis constant is not modified and the maximal velocity with N-glutaryl-L-phenylalanine-4-nitroaniline is increased to 164%. The increase is due to the increase of the acylation constant, k2, by 230%. The value of k3 is not modified or less modified. In the modified enzyme, 85% of free amino acids are still able to react with trinitrobenzenesulphonic acid. The optimum pH is shifted by one pH unit towards the alkaline pH. The thermodynamic study shows that the catalytic process itself is not modified. The increase in Vm could be a simple increase of k2 linked to a modification of the site or of the protein. The phenomenon described is very specific and obtained only with one modification, hexanal, and with one enzyme, alpha-chymotrypsin.     

Chemical modification of chloroperoxidase for enhanced stability and activity

Chloroperoxidase from Caldariomyces fumago (CPO, EC 1.11.1.10) is one of the most interesting enzymes from the group of heme peroxidases and has been extensively applied in synthetic processes. Nevertheless, the practical application of CPO is limited due to its very low operational stability, especially in the presence of peroxidative compounds. For this reason, effect of chemical modifications of CPO in the stability of the enzyme was studied. Side-chain selective modifications of amino groups of Lys residues, and carboxyl groups of Asp and Glu residues, as well as crosslinking and periodate oxidation of sugar moiety were carried out. The stability of modified CPOs was evaluated at elevated pH and temperature, and in the presence of tert-butyl hydroperoxide. Effect of modification of CPO on the performance of the reaction of Cbz-ethanolamine oxidation was studied as well. Those modifications that involved carboxyl groups via carbodiimide coupled method and the periodate oxidation of the sugar moiety produced better catalysts than native CPO in terms of stability and activity at elevated pH values and temperatures.