Pig Pancreatic Alpha-amylase Research Articles

Phytochemical investigation of Mezoneuron benthamianum Baill, isolation, in vitro antioxidant, alpha-amylase inhibition, and in silico modelling studies

Mezoneuron benthamianum (Leguminosae-caesalpinioideae family), is widely used across West Africa for the treatment of bacterial, fungal, and inflammatory diseases. This study is aimed at investigating the antioxidant and antidiabetic activities of extracts and isolated compounds from Mezoneuron benthamianum leaf and root. The pulverized leaf (1 kg) was extracted by maceration with dichloromethane and methanol to give the dichloromethane (MBLD) and methanol (MBLM) extracts, while the root (2 kg) samples were extracted using dichloromethane and methanol (1:1) to give the dichloromethane-methanol extract (MBRDM) which was further partitioned to give the hexane (MBRH), ethyl acetate (MBRE) and methanol (MBRM) extracts respectively. The leaf methanol extract (MBLM) was fractionated using column chromatography (70–230 mesh size) which led to the isolation of compound 1. The extracts and isolated compounds were subjected to in-vitro antioxidant assay with 1,1-diphenyl-2-picrylhydrazyl (DPPH) and α-amylase inhibitory assay using porcine pancreatic α-amylase respectively. FT-IR spectroscopic analysis compound 1 showed strong peaks at 1678 and 1612 cm−1 suggesting the presence of a carbonyl and an aromatic group respectively. 1H NMR spectroscopic analysis of compound 1 showed two peaks at 3.80 (3H, s) and 7.04 ppm (2H, s) indicating methoxy and aromatic protons respectively. 13C NMR also confirmed the presence of the methoxy peak at 50.8 ppm, four aromatic peaks at 108.76, 120.19, 131.25, 145.14 ppm indicating a para-disubstituted benzene ring, and a carbonyl peak at 167.80 ppm, this led to the elucidation of compound 1 known as methyl gallate. The antioxidant activities of the extracts and compounds showed that MBLM (IC50 = 112.0 μg/ml) and MBRE (IC50 = 91.84 μg/ml) had the highest activity of the leaf and root extracts respectively while methyl gallate (IC50 = 91.84 μg/ml) had lower activity than gallic acid (IC50 = 27.4 μg/ml), ascorbic acid (IC50 = 43.94 μg/ml) and BHT (68.94 μg/ml). The α-amylase inhibitory activities showed that MBLD (IC50 = 27.4 μg/ml), MBRE (IC50 = 72.2 μg/ml), gallic acid (IC50 = 27.4 μg/ml) and methyl gallate (IC50 = 43.9 μg/ml) had higher activity than the standard drug acarbose (IC50 = 378.2 μg/ml). For the In silico study, methyl gallate was docked into the active site of the targeted diabetic proteins; human pancreatic alpha-amylase, pig pancreatic alpha-amylase, and tetrameric IIB-HSDI. The results showed that methyl gallate had good interactions with the proteins, with binding affinities of −4.8, −4.8 and −6.5 kcal/mol respectively. Furthermore, in silico pharmacokinetics and toxicology properties of methyl gallate using the AdmetSAR and SwissADME software showed that the compound has good pharmacokinetic properties and it is generally non-toixc. This research has revealed detailed chemical and biological studies on Mezoneuron benthamianum and its isolated compound as an antioxidant and antidiabetic.

X-ray Crystallographic Analyses of Pig Pancreatic α-Amylase with Limit Dextrin, Oligosaccharide, and α-Cyclodextrin,

Further refinement of the model using maximum likelihood procedures and reevaluation of the native electron density map has shown that crystals of pig pancreatic alpha-amylase, whose structure we reported more than 15 years ago, in fact contain a substantial amount of carbohydrate. The carbohydrate fragments are the products of glycogen digestion carried out as an essential step of the protein's purification procedure. In particular, the substrate-binding cleft contains a limit dextrin of six glucose residues, one of which contains both alpha-(1,4) and alpha-(1,6) linkages to contiguous residues. The disaccharide in the original model, shared between two amylase molecules in the crystal lattice, but also occupying a portion of the substrate-binding cleft, is now seen to be a tetrasaccharide. There are, in addition, several other probable monosaccharide binding sites. Furthermore, we have further reviewed our X-ray diffraction analysis of alpha-amylase complexed with alpha-cyclodextrin. alpha-Amylase binds three cyclodextrin molecules. Glucose residues of two of the rings superimpose upon the limit dextrin and the tetrasaccharide. The limit dextrin superimposes in large part upon linear oligosaccharide inhibitors visualized by other investigators. By comprehensive integration of these complexes we have constructed a model for the binding of polysaccharides having the helical character known to be present in natural substrates such as starch and glycogen.

Crystal Structure of the Pig Pancreatic α-Amylase Complexed with ρ-Nitrophenyl-α-D-Maltoside-Flexibility in the Active Site

The X-ray structure analysis of a crystal of pig pancreatic alpha-amylase soaked with a rho-nitrophenyl-alpha-D-maltoside (pNPG2) substrate showed a pattern of electron density corresponding to the binding of a rho-nitrophenol unit at subsite -2 of the active site. Binding of the product to subsite -2 after hydrolysis of the pNPG2 molecules, may explain the low catalytic efficiency of the hydrolysis of pNPG2 by PPA. Except a small movement of the segment from residues 304-305 the typical conformational changes of the "flexible loop" (303-309), that constitutes the surface edge of the substrate binding cleft, were not observed in the present complex structure. This result supports the hypothesis that significant movement of the loop may depend on aglycone site being filled (Payan and Qian, J. Protein Chen. 22: 275, 2003). Structural analyses have shown that pancreatic alpha-amylases undergo an induced conformational change of the catalytic residue Asp300 upon substrate binding; in the present complex the catalytic residue is observed in its unliganded orientation. The results suggest that the induced reorientation is likely due to the presence of a sugar unit at subsite -1 and not linked to the closure of the flexible surface loop. The crystal structure was refined at 2.4 A resolution to an R factor of 17.55% (Rfree factor of 23.32%).

Crystal structure of the pig pancreatic alpha-amylase complexed with malto-oligosaccharides.

The structural X-ray map of a pig pancreatic alpha-amylase crystal soaked (and flash-frozen) with a maltopentaose substrate showed a pattern of electron density corresponding to the binding of oligosaccharides at the active site and at three surface binding sites. The electron density region observed at the active site, filling subsites-3 through-1, was interpreted in terms of the process of enzyme-catalyzed hydrolysis undergone by maltopentaose. Because the expected conformational changes in the "flexible loop" that constitutes the surface edge of the active site were not observed, the movement of the loop may depend on aglycone site being filled. The crystal structure was refined at 2.01 A resolution to an R factor of 17.0% ( R(free) factor of 19.8%). The final model consists of 3910 protein atoms, one calcium ion, two chloride ions, 103 oligosaccharide atoms, 761 atoms of water molecules, and 23 ethylene glycol atoms.

Identification of catalytic and substrate-binding site residues in Bacillus cereus ATCC7064 oligo-1,6-glucosidase.

Three active site residues (Asp199, Glu255, Asp329) and two substrate-binding site residues (His103, His328) of oligo-1,6-glucosidase (EC 3.2.1.10) from Bacillus cereus ATCC7064 were identified by site-directed mutagenesis. These residues were deduced from the X-ray crystallographic analysis and the comparison of the primary structure of the oligo-1,6-glucosidase with those of Saccharomyces carlsbergensis alpha-glucosidase, Aspergillus oryzae alpha-amylase and pig pancreatic alpha-amylase which act on alpha-1,4-glucosidic linkages. The distances between these putative residues of B. cereus oligo-1,6-glucosidase calculated from the X-ray analysis data closely resemble those of A. oryzae alpha-amylase and pig pancreatic alpha-amylase. A single mutation of Asp199-->Asn, Glu255-->Gln, or Asp329-->Asn resulted in drastic reduction in activity, confirming that three residues are crucial for the reaction process of alpha-1,6-glucosidic bond cleavage. Thus, it is identified that the basic mechanism of oligo-1,6-glucosidase for the hydrolysis of alpha-1,6-glucosidic linkage is essentially the same as those of other amylolytic enzymes belonging to Family 13 (alpha-amylase family). On the other hand, mutations of histidine residues His103 and His328 resulted in pronounced dissimilarity in catalytic function. The mutation His328-->Asn caused the essential loss in activity, while the mutation His103-->Asn yielded a mutant enzyme that retained 59% of the k0/Km of that for the wild-type enzyme. Since mutants of other alpha-amylases acting on alpha-1,4-glucosidic bond linkage lost most of their activity by the site-directed mutagenesis at their equivalent residues to His103 and His328, the retaining of activity by His103-->Asn mutation in B. cereus oligo-1,6-glucosidase revealed the distinguished role of His103 for the hydrolysis of alpha-1,6-glucosidic bond linkage.

A plant-seed inhibitor of two classes of alpha-amylases: X-ray analysis of Tenebrio molitor larvae alpha-amylase in complex with the bean Phaseolus vulgaris inhibitor.

The alpha-amylase from Tenebrio molitor larvae (TMA) has been crystallized in complex with the alpha-amylase inhibitor (alpha-AI) from the bean Phaseolus vulgaris. A molecular-replacement solution of the structure was obtained using the refined pig pancreatic alpha-amylase (PPA) and alpha-AI atomic coordinates as starting models. The structural analysis showed that although TMA has the typical structure common to alpha-amylases, large deviations from the mammalian alpha-amylase models occur in the loops. Despite these differences in the interacting loops, the bean inhibitor is still able to inhibit both the insect and mammalian alpha-amylase.

Crystallization and preliminary X-ray diffraction studies of alpha-amylase from the antarctic psychrophile Alteromonas haloplanctis A23.

A cold-active alpha-amylase was purified from culture supernatants of the antarctic psychrophile Alteromonas haloplanctis A23 grown at 4 degrees C. In order to contribute to the understanding of the molecular basis of cold adaptations, crystallographic studies of this cold-adapted enzyme have been initiated because a three-dimensional structure of a mesophilic counterpart, pig pancreatic alpha-amylase, already exists. alpha-Amylase from A. haloplanctis, which shares 53% sequence identity with pig pancreatic alpha-amylase, has been crystallized and data to 1.85 A have been collected. The space group is found to be C222(1) with a = 71.40 A, b = 138.88 A, and c = 115.66 A. Until now, a three-dimensional structure of a psychrophilic enzyme is lacking.

Crystal Structure of Pig Pancreatic α‐amylase Isoenzyme II, in Complex with the Carbohydrate Inhibitor Acarbose

Two different crystal forms of pig pancreatic alpha-amylase isoenzyme II (PPAII), free and complexed to a carbohydrate inhibitor (acarbose), have been compared together and to previously reported structures of PPAI. A crystal form obtained at 4 degrees C, containing nearly 72% solvent, made it possible to obtain a new complex with acarbose, different from a previous one obtained at 20 degrees C [Qian, M., Buisson, G., Duée, E., Haser, H. & Payan, F. (1994) Biochemistry 33, 6284-6294]. In the present form, six contiguous subsites of the enzyme active site are occupied by the carbohydrate ligand; the structural data indicate that the binding site is capable of holding more than the five glucose units of the scheme proposed through kinetic studies. A monosaccharide ring bridging two protein molecules related by the crystal packing is located on the surface, at a distance of 2.0 nm from the reducing end of the inhibitor ligand; the symmetry-related glucose ring in the crystal lattice is found 1.5 nm away from the non-reducing end of the inhibitor ligand.

Crystallization and preliminary X-ray analysis of pig pancreatic alpha-amylase in complex with a bean lectin-like inhibitor.

Pig pancreatic alpha-amylase (PPA, E.C. 3.2. 1. 17, 496 amino-acid residues) has been crystallized as a complex with a lectin-like inhibitor from bean Phaseolus vulgaris (224 amino-acid residues for the inhibitor monomer). The hanging-drop vapour-diffusion method was used to grow crystals from solutions containing 2-methyl-2,4-pentanediol as precipitant. The crystals belong to monoclinic space group C2 with a = 152.5, b = 80.3, c = 68.8 A, beta = 91.4 and diffract to 2.9 A resolution. A molecular-replacement solution of the structure has been obtained using the refined PPA and LoLl (Lathyrus ochrus isolectin I) atomic coordinates as starting models. Low-resolution refinement of the model is underway. The analysis reveals that the functional inhibitor molecule is dimeric and interacts with two molecules of enzyme.

Molecular modelling of the interaction between the catalytic site of pig pancreatic alpha-amylase and amylose fragments.

A stereo chemical refinement of the crystalline complex between porcine pancreatic alpha-amylase and a pseudopentasaccharide from the amylostatin family has been performed through molecular mechanics calculations, using a set of parameters appropriate for protein and protein-carbohydrate interactions. The refinement provided a starting point for docking a maltopentaose moiety within the catalytic site, in the absence of water. A thorough exploration of the different orientations and conformations of maltopentaose established the sense of binding of the amylosic substrate in the amylase cleft. After optimising the geometry of the binding site, the conformations adopted by the four contiguous linkages could be rationalised by considering the environment, either hydrophobic or hydrophilic, of the different glucose moieties. Seemingly, details of the non-bonded interactions (hydrogen bonds, van der Waals and stacking interactions) that underlie this molecular recognition have been established. In particular, it was confirmed that the three acidic amino acids of the catalytic site (Asp197, Asp300 and Glu233) are close to their glucosidic target, and that there is no steric reason to propose an alteration of the 4C1 conformation of the glucose residue prior to hydrolysis. However, in the absence of water molecules, it is difficult to elucidate the details of the catalysis. Additional macroscopic information has been gained, such as the impossibility to fit a double-helical arrangement of amylose chains in the amylasic cleft. This explains why some native starches containing such motifs resist amylolytic enzymes. Tentative models involving longer amylosic chains have been elaborated, which extend our knowledge of the interaction and orientation of starch fragments in the vicinity of the hydrolytic sites.

Carbohydrate binding sites in a pancreatic alpha-amylase-substrate complex, derived from X-ray structure analysis at 2.1 A resolution.

The X-ray structure analysis of a crystal of pig pancreatic alpha-amylase (PPA, EC 3.2.1.1.) that was soaked with the substrate maltopentaose showed electron density corresponding to two independent carbohydrate recognition sites on the surface of the molecule. Both binding sites are distinct from the active site described in detail in our previous high-resolution study of a complex between PPA and a carbohydrate inhibitor (Qian M, Buisson G, Duée E, Haser H, Payan F, 1994, Biochemistry 33:6284-6294). One of the binding sites previously identified in a 5-A-resolution electron density map, lies at a distance of 20 A from the active site cleft and can accommodate two glucose units. The second affinity site for sugar units is located close to the calcium binding site. The crystal structure of the maltopentaose complex was refined at 2.1 A resolution, to an R-factor of 17.5%, with an RMS deviation in bond distances of 0.007 A. The model includes all 496 residues of the enzyme, 1 calcium ion, 1 chloride ion, 425 water molecules, and 3 bound sugar rings. The binding sites are characterized and described in detail. The present complex structure provides the evidence of an increased stability of the structure upon interaction with the substrate and allows identification of an N-terminal pyrrolidonecarboxylic acid in PPA.

The active center of a mammalian alpha-amylase. Structure of the complex of a pancreatic alpha-amylase with a carbohydrate inhibitor refined to 2.2-A resolution.

An X-ray structure analysis of a crystal of pig pancreatic alpha-amylase (EC 3.2.1.1) that was soaked with acarbose (a pseudotetrasaccharide alpha-amylase inhibitor) showed electron density corresponding to five fully occupied subsites in the active site. The crystal structure was refined to an R-factor of 15.3%, with a root mean square deviation in bond distances of 0.015 A. The model includes all 496 residues of the enzyme, one calcium ion, one chloride ion, 393 water molecules, and five bound sugar rings. The pseudodisaccharide acarviosine that is the essential structural unit responsible for the activity of all inhibitors of the acarbose type was located at the catalytic center. The carboxylic oxygens of the catalytically competent residues Glu233 and Asp300 form hydrogen bonds with the "glycosidic" NH group of the acarviosine group. The third residue of the catalytic triad Asp197 is located on the opposite side of the inhibitor binding cleft with one of its carbonyl oxygens at a 3.3-A distance from the anomeric carbon C-1 of the inhibitor center. Binding of inhibitor induces structural changes at the active site of the enzyme. A loop region between residues 304 and 309 moves in toward the bound saccharide, the resulting maximal mainchain movement being 5 A for His305. The side chain of residue Asp300 rotates upon inhibitor binding and makes strong van der Waals contacts with the imidazole ring of His299. Four histidine residues (His101, His201, His299, and His305) are found to be hydrogen-bonded with the inhibitor. Many protein-inhibitor hydrogen bond interactions are observed in the complex structure, as is clear hydrophobic stacking of aromatic residues with the inhibitor surface. The chloride activator ion and structural calcium ion are hydrogen-bonded via their ligands and water molecules to the catalytic residues.

The enzymic synthesis, by transglucosylation of a homologous series of glycosidically substituted malto-oligosaccharides, and their use as amylase substrates

(1 → 4)-α- d-Glucan 4-glucosyltransferase (EC2.4.1.19) of klebsiella pneumoniae transforms maltose (G2) into d-glucose (G1) and a mixture of malto-oligosaccharides (G 2—G 9), and maltotriose (G3) into G l—G ll in addition to cyclo-hexa-, -hepta-, and -octa-amyloses (cG 6—8). It produces a similar mixture, but with higher amounts of G 2—G 11, by transfer from cyclohexaamylose to G 1. By using p-nitrophenyl α- and β- d-glucosides, 4 methylumbelliferyl α- d-glucoside, and strophanthyl α- d-glucoside as acceptors and cyclohexaamylose as donor, a homologous series of substituted malto-oligosaccharides having chain lengths of up to 12 d-glucose residues was produced. High-pressure liquid chromatography on Bio-Gel P 2 permitted separation of these products of transferase activity on analytical and preparative scales. By the same technique, the nitration product of phenyl hepta- O-acetyl-α-maltoside, after deacetylation, was separated into about equal amounts of the o- and p-isomers. The synthetic p-nitrophenyl α-maltoside ( pNPG 2) was used to identify the first member of the series of biochemical transfer-products. p-Nitrophenyl maltotrioside ( pNPG 3) and maltotetraoside ( pNPG 4) were shown to be the higher homologues. They are very good substrates for human and pig-pancreatic alpha amylase. This substrate behavior may be measured conveniently in the case ofpNPG3 by the rapid liberation of nitrophenolate; the enzyme used pNPG 4 only on addition of α- d-glucosidase. Human-parotis amylase of equal starch-splitting activity as the pancreatic enzyme acts upon pNPG 3 and pNPG 4 but about 100 times more slowly.