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ABSTRACT: Molecular models of amylopectin were created and investigated by computer simulation. First, single and double helices of various lengths were constructed. The 1 --> 6 branching in double and single helices of amylopectin was studied. Subunits of single helices, double helices, and branch points were used as building blocks of larger systems. The possible makeup of amylopectin unit clusters was investigated via a series of models, including single-single, double-single, and double-double helix systems. The lengths of the single helix section that linked two branch points (internal chains) was systematically varied between values of 0-10 glucose residues. It was found that certain internal chain lengths lead to parallel double helices. Thus, it was postulated that the length of internal chains may determine the degree of local crystallinity. Furthermore, it was noted that some of the low-energy arrangement of double helices could be superimposed on either the two adjacent and nonadjacent double helices of crystalline A and B starch polymorphs. In other cases, the distance between the double helices is so large that it may in fact be a model for branching between two amylopectin crystals or unit clusters. Results obtained through this work were corroborated, where possible, with information available from crystallographic, branching, and enzymatic studies.
Biopolymers 11/1999; 50(4):381-90. · 2.87 Impact Factor
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ABSTRACT: 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.
European Journal of Biochemistry 09/1995; 232(1):284-93. · 3.58 Impact Factor
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ABSTRACT: The X-ray crystal structure of lentil lectin in complex with alpha-D-glucopyranose has been determined by molecular replacement and refined to an R-value of 0.20 at 3.0 A resolution. The glucose interacts with the protein in a manner similar to that found in the mannose complexes of concanavalin A, pea lectin and isolectin I from Lathyrus ochrus. The complex is stabilized by a network of hydrogen bonds involving the carbohydrate oxygens O6, O4, O3 and O5. In addition, the alpha-D-glucopyranose residue makes van der Waals contacts with the protein, involving the phenyl ring of Phe123 beta. The overall structure of lentil lectin, at this resolution, does not differ significantly from the highly refined structures of the uncomplexed lectin. Molecular docking studies were performed with mannose and its 2-O and 3-O-m-nitro-benzyl derivatives to explain their high affinity binding. The interactions of the modelled mannose with lentil lectin agree well with those observed experimentally for the protein-carbohydrate complex. The highly flexible Me-2-O-(m-nitro-benzyl)-alpha-D-mannopyranoside and Me-3-O-(m-nitro-benzyl)-alpha-D-mannopyranoside become conformationally restricted upon binding to lentil lectin. For best orientations of the two substrates in the combining site, the loss of entropy is accompanied by the formation of a strong hydrogen bond between the nitro group and one amino acid, Gly97 beta and Asn125 beta, respectively, along with the establishment of van der Waals interactions between the benzyl group and the aromatic amino acids Tyr100 beta and Trp128 beta.
Glycoconjugate Journal 01/1995; 11(6):507-17. · 2.12 Impact Factor
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European Journal of Clinical Nutrition. 01/1992; 46:S3–S16.
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ABSTRACT: The amino acid sequences of 18 alpha-amylases have been compared by hydrophobic cluster analysis. The method was first calibrated with two alpha-amylases (Aspergillus oryzae and pig pancreas) whose three-dimensional structures are known. It was then applied to the other alpha-amylases resulting in straightforward sequence alignments which could be used for structure prediction. It was found that all alpha-amylases which were investigated display the same basic super-secondary structure with a (beta alpha)8 barrel. Most of the secondary structure elements of the protein cores could be assigned to segments of the amino acid sequences. In addition, six sub-families could be identified, based upon specific similarities occurring in the variable regions of alpha-amylases.
International Journal of Biological Macromolecules 09/1989; 11(4):217-25. · 2.45 Impact Factor
