Lili Kandra

Two Secondary Carbohydrate Binding Sites on the Surface of Barley α-Amylase 1 Have Distinct Functions and Display Synergy in Hydrolysis of Starch Granules

Some polysaccharide processing enzymes possess secondary carbohydrate binding sites situated on the surface far from the active site. In barley alpha-amylase 1 (AMY1), two such sites, SBS1 and SBS2, are found on the catalytic (beta/alpha)(8)-barrel and the noncatalytic C-terminal domain, respectively. Site-directed mutagenesis of Trp(278) and Trp(279), stacking onto adjacent ligand glucosyl residues at SBS1, and of Tyr(380) and His(395), making numerous ligand contacts at SBS2, suggested that SBS1 and SBS2 act synergistically in degradation of starch granules. While SBS1 makes the major contribution to binding and hydrolysis of starch granules, SBS2 exhibits a higher affinity for the starch mimic beta-cyclodextrin. Compared to that of wild-type AMY1, the K(d) of starch granule binding by the SBS1 W278A, W279A, and W278A/W279A mutants thus increased 15-35 times; furthermore, the k(cat)/K(m) of W278A/W279A was 2%, whereas both affinity and activity for Y380A at SBS2 were 10% of the wild-type values. Dual site double and triple SBS1/SBS2 substitutions eliminated binding to starch granules, and the k(cat)/K(m) of W278A/W279A/Y380A AMY1 was only 0.4% of the wild-type value. Surface plasmon resonance analysis of mutants showed that beta-cyclodextrin binds to SBS2 and SBS1 with K(d,1) and K(d,2) values of 0.07 and 1.40 mM, respectively. A model that accounts for the observed synergy in starch hydrolysis, where SBS1 and SBS2 bind ordered and free alpha-glucan chains, respectively, thus targeting the enzyme to single alpha-glucan chains accessible for hydrolysis, is proposed. SBS1 and SBS2 also influence the kinetics of hydrolysis for amylose and maltooligosaccharides, the degree of multiple attack on amylose, and subsite binding energies.

Action pattern and subsite mapping of Bacillus licheniformis α-amylase (BLA) with modified maltooligosaccharide substrates

This study represents the first characterisation of the substrate‐binding site of Bacillus licheniformis α‐amylase (BLA). It describes the first subsite map, namely, number of subsites, apparent subsite energies and the dual product specificity of BLA. The product pattern and cleavage frequencies were determined by high‐performance liquid chromatography, utilising a homologous series of chromophore‐substituted maltooligosaccharides of degree of polymerisation 4–10 as model substrates. The binding region of BLA is composed of five glycone, three aglycone‐binding sites and a ‘barrier’ subsite. Comparison of the binding energies of subsites, which were calculated with a computer program, shows that BLA has similarity to the closely related Bacillus amyloliquefaciens α‐amylase.

Synthesis of chromogenic substrates of α-amylases on a cyclodextrin basis

Abstract One-pot acetylation and subsequent partial acetolysis of α-, β- and γ-cyclodextrins resulted in crystalline peracetylated malto-hexaose, -heptaose, and -octaose, respectively. Prolonged acetolysis of β-cyclodextrin gave a mixture of acetylated maltooligosaccharides, from which peracetylated malto-triose, -tetraose, and -pentaose were isolated. The acetylated oligosaccharides were converted into α-acetobromo derivatives, and then transformed into 4-nitrophenyl and 2-chloro-4-nitrophenyl β-glycosides. From the 4-nitrophenyl glycosides 4,6-O-benzylidene derivatives were prepared, which were used together with the free glycosides as substrates of porcine pancreatic α-amylase. One-pot acetylation and subsequent partial acetolysis of cyclodextrins resulted in the peracetylated maltooligomers (dp 3–8), which were transformed into 4-nitrophenyl and 2-chloro-4-nitrophenyl β-glycosides, the 4.6-O-benzylidene derivatives of NP-glycosides were also prepared

Subsite mapping of human salivary α-amylase and the mutant Y151M

This study characterizes the substrate‐binding sites of human salivary α‐amylase (HSA) and its Y151M mutant. It describes the first subsite maps, namely, the number of subsites, the position of cleavage sites and apparent subsite energies. The product pattern and cleavage frequencies were determined by high‐performance liquid chromatography, utilizing a homologous series of chromophore‐substituted maltooligosaccharides of degree of polymerization 3–10 as model substrates. The binding region of HSA is composed of four glycone and three aglycone‐binding sites, while that of Tyr151Met is composed of four glycone and two aglycone‐binding sites. The subsite maps show that Y151M has strikingly decreased binding energy at subsite (+2), where the mutation has occurred (−2.6 kJ/mol), compared to the binding energy at subsite (+2) of HSA (−12.0 kJ/mol).

Examination of the active sites of human salivary α-amylase (HSA)

The action pattern of human salivary amylase (HSA) was examined by utilising as model substrates 2-chloro-4-nitrophenyl (CNP) β-glycosides of maltooligosaccharides of dp 4–8 and some 4-nitrophenyl (NP) derivatives modified at the nonreducing end with a 4,6-O-benzylidene (Bnl) group. The product pattern and cleavage frequency were investigated by product analysis using HPLC. The results revealed that the binding region in HSA is longer than five subsites usually considered in the literature and suggested the presence of at least six subsites; four glycone binding sites (−4, −3, −2, −1) and two aglycone binding sites (+1, +2). In the ideal arrangement, the six subsites are filled by a glucosyl unit and the release of maltotetraose (G4) from the nonreducing end is dominant. The benzylidene group was also recognisable by subsites (−3) and (−4). The binding modes of the benzylidene derivatives indicated a favourable interaction between the Bnl group and subsite (−3) and an unfavourable one with subsite (−4). Thus, subsite (−4) must be more hydrophylic than hydrophobic. As compared with the action of porcine pancreatic α-amylase (PPA) on the same substrates, the results showed differences in the three-dimensional structure of active sites of HSA and PPA.

Evidence for pentagalloyl glucose binding to human salivary α-amylase through aromatic amino acid residues

We demonstrate here that pentagalloyl glucose (PGG), a main component of gallotannins, was an effective inhibitor of HSA and it exerted similar inhibitory potency to Aleppo tannin used in this study. The inhibition of HSA by PGG was found to be non-competitive and inhibitory constants of K(EI)=2.6 microM and K(ESI)=3.9 microM were determined from Lineweaver-Burk secondary plots. PGG as a model compound for gallotannins was selected to study the inhibitory mechanism and to characterize the interaction of HSA with this type of molecules. Surface plasmon resonance (SPR) binding experiments confirmed the direct interaction of HSA and PGG, and it also established similar binding of Aleppo tannin to HSA. Saturation transfer difference (STD) experiment by NMR clearly demonstrated the aromatic rings of PGG may be involved in the interaction suggesting a possible stacking with the aromatic side chains of HSA. The role of aromatic amino acids of HSA in PGG binding was reinforced by kinetic studies with the W58L and Y151M mutants of HSA: the replacement of the active site aromatic amino acids with aliphatic ones decreased the PGG inhibition dramatically, which justified the importance of these residues in the interaction.

Mapping of barley α-amylases and outer subsite mutants reveals dynamic high-affinity subsites and barriers in the long substrate binding cleft

Subsite affinity maps of long substrate binding clefts in barley α‐amylases, obtained using a series of maltooligosaccharides of degree of polymerization of 3–12, revealed unfavorable binding energies at the internal subsites −3 and −5 and at subsites −8 and +3/+4 defining these subsites as binding barriers. Barley α‐amylase 1 mutants Y105A and T212Y at subsite −6 and +4 resulted in release or anchoring of bound substrate, thus modifying the affinities of other high‐affinity subsites (−2 and +2) and barriers. The double mutant Y105A‐T212Y displayed a hybrid subsite affinity profile, converting barriers to binding areas. These findings highlight the dynamic binding energy distribution and the versatility of long maltooligosaccharide derivatives in mapping extended binding clefts in α‐amylases.

Chemoenzymatic synthesis of 2-chloro-4-nitrophenyl β-maltoheptaoside acceptor-products using glycogen phosphorylase b

In the present work, we aimed at developing a chemoenzymatic procedure for the synthesis of beta-maltooligosaccharide glycosides. The primer in the enzymatic reaction was 2-chloro-4-nitrophenyl beta-maltoheptaoside (G(7)-CNP), synthesised from beta-cyclodextrin using a convenient chemical method. CNP-maltooligosaccharides of longer chain length, in the range of DP 8-11, were obtained by a transglycosylation reaction using alpha-D-glucopyranosyl-phosphate (G-1-P) as a donor. Detailed enzymological studies revealed that the conversion of G(7)-CNP catalysed by rabbit skeletal muscle glycogen phosphorylase b (EC 2.4.1.1) could be controlled by acarbose and was highly dependent on the conditions of transglycosylation. More than 90% conversion of G(7)-CNP was achieved through a 10:1 donor-acceptor ratio. Tranglycosylation at 37 degrees C for 30 min with 10 U enzyme resulted in G(8-->12)-CNP oligomers in the ratio of 22.8, 26.6, 23.2, 16.5, and 6.8%, respectively. The reaction pattern was investigated using an HPLC system. The preparative scale isolation of G(8-->11)-CNP glycosides was achieved on a semipreparative HPLC column. The productivity of the synthesis was improved by yields up to 70-75%. The structures of the oligomers were confirmed by their chromatographic behaviours and MALDI-TOF MS data.

Action pattern of porcine pancreatic alpha-amylase on three different series of β-maltooligosaccharide glycosides

A technique for the investigation of the action pattern of porcine pancreatic amylase (PPA) has been developed by utilising as model substrates 2-chloro-4-nitrophenyl (CNP) and 4-nitrophenyl (NP) beta-glycosides of maltooligosaccharides of dp 4-8 and some NP derivatives modified at the nonreducing end with a 4,6-O-benzylidene (Bnl) group. The action pattern was investigated by the method of product analysis, using an HPLC method. The product pattern and cleavage frequency was very similar in the CNP- and NP-oligomers and showed that the glucopyranose residue could be replaced by the aglycon group. Modification of the nonreducing end of NP glycosides to give a 4,6-O-benzylidene-D-glucopyranosyl group indicated a favourable interaction between the Bnl group and the subsites (-3) and (-5) but an unfavourable one with subsite (-4), which resulted in a clear shift in the product pattern. The results obtained with the digestion of the benzylidene-protected substrates confirm a multiple attack mechanism for PPA.

Model for β-1,6-N-acetylglucosamine oligomer hydrolysis catalysed by DispersinB, a biofilm degrading enzyme

DispersinB (DspB), a member of β-1,6-N-acetylglucosaminidase group of GH 20 glycoside hydrolases, catalyses the biofilm degradation of several human pathogenic microorganisms. DspB is a (β/α)(8) barrel protein, showing retaining cleavage mechanism towards oligomer and polymer substrates. A chromophore containing oligomer substrate series was used to study the DspBs mode of action. The hydrolysis reaction of β(1,6)-linked N-acetylglucosamine thiophenyl glycosides with degree of polymerisation of 2, 3, 4 and 5 was followed by reversed phase HPLC and progress curves were determined and analysed. Based on the analysis of process curves obtained from prolonged hydrolysis we assumed the presence of more productive binding modes resulting in parallel reactions followed by consecutive reaction steps. Strictly nonreducing-end specificity was observed, the presence of monomer, dimer and trimer nonreducing-end products was verified by MALDI-TOF MS. Another cleavage was suggested after the first glycosidic attack in the case of trimer, while two and three consecutive steps were possible in tetramer and pentamer hydrolyses, respectively. Chain lengthening increased catalytic efficiency (2.1→8.6M(-1)s(-1)) and calculated kinetic constants showed a similarly increasing tendency (1.0→6.7 × 10(-3) min(-1)).