The role of tryptophan residues in substrate binding to catalytic domains A and B of xylanase C from Fibrobacter succinogenes S85

Establishing the oxidative tolerance of Thermomyces lanuginosus xylanase

AIMS

This work aims to determine the tolerance of xylanase towards enzyme-generated oxidative conditions, such as those produced by the peroxidase or laccase mediator systems (LMS).

METHODS AND RESULTS

The activity of Thermomyces lanuginosus xylanase was measured after incubation with lignin peroxidase, manganese peroxidase or laccase plus various mediators. The laccase system, using mediators such as 1-hydroxybenzotriazole and violuric acid, resulted in complete loss of xylanase activity, accompanied by an increase in the solution potential. However, an increase in solution potential alone was not sufficient to inactivate xylanase, nor was loss of xylanase activity always accompanied by a significant increase in solution potential, as observed with N-hydroxyphthalimide as the mediator. Neither lignin peroxidase nor manganese peroxidase impacted xylanase activity; only extended treatment with elevated hydrogen peroxide concentration promoted modest xylanase activity loss. The mechanism of inactivation as determined by the tryptophan-modifying reagent N-bromosuccinimide (NBS) indicated that oxidation of just one of the eight tryptophan residues of T. lanuginosus xylanase would be sufficient to result in complete loss of xylanase activity, since xylanase is completely inactivated at 1 : 1 molar ratio of NBS to xylanase.

CONCLUSIONS

While showing tolerance to peroxidase-based enzyme systems, T. lanuginosus xylanase is readily inactivated in the presence of the LMS. Based upon treatment with NBS as the oxidant, inactivation can be attributed to modification of a single tryptophan residue.

SIGNIFICANCE AND IMPACT OF THE STUDY

The simultaneous application of mixed hydrolytic and oxidative enzyme systems is of importance to biomass processing industries. Understanding the tolerance of xylanase to oxidative conditions will facilitate the design of reaction conditions or enzyme variants to maximize the impact of mixed enzyme systems.

C(1)-/C(2)-aromatic-imino-glyco-conjugates: experimental and computational studies of binding, inhibition and docking aspects towards glycosidases isolated from soybean and jack bean

Several C(1)-imino conjugates of D: -galactose, D: -lactose and D: -ribose, where the nitrogen center was substituted by the salicylidene or naphthylidene, were synthesized and characterized. Similar C(2)-imino conjugates of D: -glucose have also been synthesized. All the glyco-imino-conjugates, which are transition state analogues, exhibited 100% inhibition of the activity towards glycosidases extracted from soybean and jack bean meal. Among these, a galactosyl-napthyl-imine-conjugate (1c) showed 50% inhibition of the activity of pure alpha-mannosidase from jack bean at 22 +/- 2.5 microM, and a ribosyl-naphthyl-imine-conjugate (3c) showed at 31 +/- 5.5 microM and hence these conjugates are potent inhibitors of glycosidases. The kinetic studies suggested non-competitive inhibition by these conjugates. The studies are also suggestive of the involvement of aromatic, imine and carbohydrate moieties of the glyco-imino-conjugates in the effective inhibition. The binding of glyco-imino-conjugate has been established by extensive studies carried out using fluorescence emission and isothermal titration calorimetry. The conformational changes resulted in the enzyme upon interaction of these derivatives has been established by studying the fluorescence quench of the enzyme by KI as well as from the secondary structural changes noticed in CD spectra. All these studies revealed the difference in the binding strengths of the naphthylidene vs. salicylidene as well as galactosyl vs. lactosyl moieties present in these conjugates. The differential inhibition of these glyco-conjugates has been addressed by quantifying the specific interactions present between the glyco-conjugates and the enzyme by using rigid docking studies.

Identifying residues in antigenic determinants by chemical modification

Chemical modification of the side chains of amino acid residues was one of the first methods developed to investigate epitopes in protein antigens. The principle of the method is that alteration of the structure of a key residue of an epitope by a chemical modification will alter reactivity with antibody by affecting either specificity or avidity or both. Chemical modification has the advantage that it can be applied to discontinuous as well as continuous epitopes and may be of value in identifying cryptic epitopes. We consider here the several recent studies that have applied site-specific chemical modification to the identification of epitopes on antigens, including the use of formaldehyde, glutaraldehyde, and acid anhydrides, to produce allergoids where determinants important to reaction with IgE are modified but the ability to elicit an IgG response is retained. It is noteworthy that modification of amino groups with charge reversal appears to be the most useful approach. The approach to the use of site-specific chemical modification as a tool for the study of protein function is discussed, and emphasis is placed on the necessity to (1) validate the specificity of modification and (2) assess potential conformational change that may occur secondary to modification. Finally, a list of chemical reagents used for protein modification is presented, together with properties and references to use.

Catalytically important amino acid residues in endoglucanases from a mutant strain Trichoderma sp. M7

Two endoglucanases, EG-III (49.7 kD) and EG-IV (47.5 kD), from a mutant strain Trichoderma sp. M7 were modified with several specific reagents. Water-soluble carbodiimide completely inactivated only one of the purified endoglucanases and kinetic analysis indicated that at least two molecules of carbodiimide bind to EG-IV for inactivation. The reaction followed pseudo-first-order kinetics with a second-order rate constant of 3.57 x 10(-5) mM(-1) x in(-1). Both endoglucanases were inhibited by iodoacetamide, but the absence of substrate protection excluded direct involvement of cysteine residues in the catalysis. N-Bromosuccinimide (NBS) showed a strong inhibitory effect on both endoglucanases, suggesting that tryptophan residues are essential for the activity and binding to the substrate, since the presence of substrates or analogs prior to NBS modification protected the enzymes against inactivation.

Mutagenesis of Trp(54) and Trp(203) residues on Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase significantly affects catalytic activities of the enzyme

The possible structural and catalytic functions of the nine tryptophan amino acid residues, including Trp(54), Trp(105), Trp(112), Trp(141), Trp(148), Trp(165), Trp(186), Trp(198), and Trp(203) in Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase (Fs beta-glucanase), were characterized using site-directed mutagenesis, initial rate kinetics, fluorescence spectrometry, and structural modeling analysis. Kinetic studies showed that a 5-7-fold increase in K(m) value for lichenan was observed for W141F, W141H, and W203R mutant Fs beta-glucanases, and approximately 72-, 56-, 30-, 29.5-, 4.9-, and 4.3-fold decreases in k(cat) relative to that for the wild-type enzyme were observed for the W54F, W54Y, W141H, W203R, W141F, and W148F mutants, respectively. In contrast, W186F and W203F, unlike the other 12 mutants, exhibited a 1.4- and 4.2-fold increase in k(cat), respectively. W165F and W203R were the only two mutants that exhibited a 4-7-fold higher activity relative to the wild-type enzyme after they were incubated at pH 3.0 for 1 h. Fluorescence spectrometry indicated that all of the mutations on the nine tryptophan amino acid residues retained a folding similar to that of the wild-type enzyme. Structural modeling and kinetic studies suggest that Trp(54), Trp(141), Trp(148), and Trp(203) play important roles in maintaining structural integrity in the substrate-binding cleft and the catalytic efficiency of the enzyme.