Subsite mapping of enzymes. Double inhibition studies

Starch-Binding Domain Modulates the Specificity of Maltopentaose Production at Moderate Temperatures

Maltooligosaccharide-forming amylases (MFAs) hydrolyze starch into maltooligosaccharides with a defined degree of polymerization. However, the enzymatic mechanism underlying the product specificity remains partially understood. Here, we show that Saccharophagus degradans MFA (SdMFA) contains a noncatalytic starch-binding domain (SBD), which belongs to the carbohydrate-binding module family 20 and enables modulation of the product specificity. Removal of SBD from SdMFA resulted in a 3.5-fold lower production of the target maltopentaose. Conversely, appending SBD to another MFA from Bacillus megaterium improved the specificity for maltopentaose. SdMFA exhibited a higher level of exo-action and greater product specificity when reacting with amylopectin than with amylose. Our structural analysis and molecular dynamics simulation suggested that SBD could promote the recognition of nonreducing ends of substrates and delivery of the substrate chain to a groove end toward the active site in the catalytic domain. Furthermore, we demonstrate that a moderate temperature could mediate SBD to interact with the substrate with loose affinity, which facilitates the substrate to slide toward the active site. Together, our study reveals the structural and conditional bases for the specificity of MFAs, providing generalizable strategies to engineer MFAs and optimize the biosynthesis of maltooligosaccharides.

Modelling of enzyme kinetics: cellulose enzymatic hydrolysis case

Enzymes as industrial biocatalysts offer numerous advantages over traditional chemical processes resulting on improvements in process economy and environmental sustainability. Because enzymes are extensively used in different industrial areas, the enzyme kinetics is an important factor for industry as it is able to estimate the extent of substrate conversion under known conditions and evaluate reactor performance. Furthermore, kinetic modelling is useful in the analysis, prediction, and optimization of an enzymatic process. Thus, kinetic modelling is a powerful tool for biochemical reaction engineering. In addition to the aforementioned, in the industrial technology, modelling together with simulation play a key role because they help to understand how a system behaves under specific conditions, and thus they allow saving on costs and lead times. Enzymatic conversion of renewable cellulosic biomass into biofuels is at the heart of advanced bioethanol production. In the production of bioethanol from cellulosic biomass, enzymatic hydrolysis of cellulose to fermentable sugars accounts for a large portion (∼30%) of the total production costs. Therefore, a thorough understanding of enzymatic hydrolysis is necessary to create a robust model which helps designing optimal conditions and economical system. Nevertheless, it is a challenging task because cellulose is a highly complex substrate and its enzymatic hydrolysis is heterogeneous in nature, and thus the whole process of cellulose conversion to glucose involves more steps than classical enzyme kinetics. This chapter describes the bases of enzyme kinetic modelling, focussing on Michaelis-Menten kinetics, and presents the models classification based on the fundamental approach and methodology used. Furthermore, the modelling of cellulose enzymatic hydrolysis is described, also reviewing some model examples developed for cellulose hydrolysis over the years. Finally, the application of enzyme kinetics modelling in food, pharmaceutical and bioethanol industry is presented.

Kinetics and subsite mapping of a D-xylobiose- and D-xylose-producing Aspergillus niger endo-(1----4)-beta-D-xylanase

A previously described endo-(1----4)-beta-D-xylanase produced by Aspergillus niger was allowed to react with linear unlabeled and labeled D-xylo-oligosaccharides ranging from D-xylotriose to D-xylo-octaose. No evidence of multiple attack or of condensation and trans-D-xylosylation reactions was found. Maximum rates and Michaelis constants were measured at 40 degrees and pH 4.85. The former increased with increasing chain-length from D-xylotriose through D-xylohexaose to approximately 70% of that on soluble larchwood D-xylan, and then decreased slightly for D-xyloheptaose and D-xylo-octaose. Michaelis constants decreased monotonically with increasing chain-length. Bond-cleavage frequencies were highest near the reducing end of short substrates, with the locus of highest frequencies moving towards the middle of larger substrates. These data indicated that the endo-D-xylanase has five main subsites, with the catalytic site located between the third and fourth subsites, counting from the nonreducing end of the bound substrate. The subsite to the nonreducing side of the catalytic site strongly repels its corresponding D-xylosyl residue, while the two subsites farther towards the nonreducing end of the substrate strongly attract their corresponding residues. The subsite to the reducing side of the catalytic site moderately attracts D-xylosyl residues, while the next one towards the reducing end has a high affinity for them. The residual error of the numerical estimation was allocated largely to the Michaelis constants of the different D-xylo-oligosaccharides, whose calculated values were appreciably smaller than measured values, especially for shorter substrates. This suggests that the subsite model cannot fully account for the experimental data. Estimated and measured values of maximum rates, bond-cleavage frequencies, and dissociation constant when the active site is fully occupied by substrate agreed more closely with each other.

On porcine pancreatic alpha-amylase action: kinetic evidence for the binding of two maltooligosaccharide molecules (maltose, maltotriose and o-nitrophenylmaltoside) by inhibition studies. Correlation with the five-subsite energy profile

Hydrolysis of small substrates (maltose, maltotriose and o-nitrophenylmaltoside) catalysed by porcine pancreatic alpha-amylase was studied from a kinetic viewpoint over a wide range of substrate concentrations. Non-linear double-reciprocal plots are obtained at high maltose, maltotriose and o-nitrophenylmaltoside concentrations indicating typical substrate inhibition. These results are consistent with the successive binding of two molecules of substrate per enzyme molecule with dissociation constants Ks1 and Ks2. The Hill plot, log [v/(V-v)] versus log [S], is clearly biphasic and allows the dissociation constants of the ES1 and ES2 complexes to be calculated. Maltose and maltotriose are inhibitors of the amylase-catalysed amylose and o-nitrophenylmaltoside hydrolysis. The inhibition is of the competitive type. The (apparent) inhibition constant Kiapp varies with the inhibitor concentration. These results are also consistent with the successive binding of at least two molecules of maltose or maltotriose per amylase molecule with the dissociation constants Ki1 and Ki2. These inhibition studies show that small substrates and large polymeric ones are hydrolysed at the same catalytic site(s). The values of the dissociation constants Ks1 and Ki1 of the maltose-amylase complexes are identical. According to the five-subsite energy profile previously determined, at low concentration, maltose (as substrate and as inhibitor) binds to the same two sites (4,5) or (3,4), maltotriose (as substrate and as inhibitor) and o-nitrophenyl-maltoside (as substrate) bind to the same three subsites (3,4,5). The dissociation constants Ks2 and Ki2 determined at high substrate and inhibitor concentration are consistent with the binding of the second ligand molecule at a single subsite. The binding mode of the second molecule of maltose (substrate) and o-nitrophenylmaltoside remains uncertain, very likely because of the inaccuracy due to simplifications in the calculations of the subsite binding energies. No binding site(s) outside the catalytic one has been taken into account in this model.