Automated docking of glucosyl disaccharides in the glucoamylase active site

To better understand the molecular basis of glucomylase selectivity, low‐energy conformers of glucosyl disaccharides obtained from relaxed‐residue conformational mapping were flexibly docked into the glucoamylase active site using AutoDock 2.2. This procedure ensures that significant conformational space is searched and can produce bound structures comparable to those obtained by protein crystallography. α‐Linked glucosyl disaccharides except α,α‐trehalose dock easily into the active site while exclusively β‐linked disaccharides do not, explaining why only the former are glucoamylase substrates. The optimized docking modes are similar at the nonreducing end of the different substrates. Individual atomic energies of intermolecular interaction allow the definite identification of key hydroxyl groups for each substrate. This approach confirmed the versatility of the second subsite of the glucoamylase active site in binding different substrates. Proteins 28:162–173, 1997. © 1997 Wiley‐Liss Inc.

[1]  A. French,et al.  Conformational analysis of the anomeric forms of sophorose, laminarabiose, and cellobiose using MM3. , 1992, Carbohydrate research.

[2]  S. Hizukuri,et al.  Actions of porcine pancreatic and Bacillus subtilis α-amylases and Aspergillus niger glucoamylase on phosphorylated (1→4)-α-D-glucan , 1983 .

[3]  B. Svensson,et al.  Refined structure for the complex of d‐gluco‐dihydroacarbose with glucoamylase from Aspergillus awamori var. X100 to 2.2 Å resolution: dual conformations for extended inhibitors bound to the active site of glucoamylase , 1995, FEBS letters.

[4]  A. French,et al.  Relaxed‐residue conformational mapping of the three linkage bonds of isomaltose and gentiobiose with MM3(92) , 1994, Biopolymers.

[5]  P. Reilly,et al.  Subsite mapping of Aspergillus niger glucoamylases I and II with malto‐ and isomaltooligosaccharides , 1989, Biotechnology and bioengineering.

[6]  P. Coutinho,et al.  Structural similarities in glucoamylase by hydrophobic cluster analysis. , 1994, Protein engineering.

[7]  P. Coutinho,et al.  Automated docking of monosaccharide substrates and analogues and methyl α‐Acarviosinide in the glucoamylase active site , 1997, Proteins.

[8]  G. Hübner,et al.  Subsite affinities of Aspergillus niger glucoamylase II determined with p-nitrophenylmaltooligosaccharides. , 1993, Biological chemistry Hoppe-Seyler.

[9]  L. Firsov,et al.  Refined structure for the complex of acarbose with glucoamylase from Aspergillus awamori var. X100 to 2.4-A resolution. , 1994, The Journal of biological chemistry.

[10]  P. Kraulis.  A program to produce both detailed and schematic plots of protein structures , 1991 .

[11]  A J Olson,et al.  Automated docking in crystallography: Analysis of the substrates of aconitase , 1993, Proteins.

[12]  P. Coutinho,et al.  Automated docking of isomaltose analogues in the glucoamylase active site , 1997 .

[13]  A. Kimura,et al.  Reaction of enzymes with starch granules: enhanced reaction of glucoamylase with gelatinized starch granules , 1996 .

[14]  B. Henrissat,et al.  Reading-frame shift in Saccharomyces glucoamylases restores catalytic base, extends sequence and improves alignment with other glucoamylases. , 1994, Protein engineering.

[15]  B. Svensson,et al.  Kinetic identification of a hydrogen bonding pair in the glucoamylase-maltose transition state complex. , 1992, Protein engineering.

[16]  P. Goodford.  A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. , 1985, Journal of medicinal chemistry.

[17]  B. Svensson,et al.  Crystallographic complexes of glucoamylase with maltooligosaccharide analogs: relationship of stereochemical distortions at the nonreducing end to the catalytic mechanism. , 1996, Biochemistry.

[18]  D. Koshland,et al.  Prediction of the structure of a receptor–protein complex using a binary docking method , 1992, Nature.

[19]  K. Kleppe,et al.  The hydrolysis of alpha-D-glucosides by amyloglucosidase from Aspergillus niger. , 1962, The Journal of biological chemistry.

[20]  R. Lemieux,et al.  How Emil Fischer was led to the lock and key concept for enzyme specificity. , 1994, Advances in carbohydrate chemistry and biochemistry.

[21]  P. Biely,et al.  Enzymically produced cyclic alpha-1,3-linked and alpha-1,6-linked oligosaccharides of D-glucose. , 1994, European journal of biochemistry.

[22]  R. Lemieux.  The Origin of the Specificity in the Recognition of Oligosaccharides by Proteins , 1990 .

[23]  S. Hizukuri,et al.  Action of glucoamylase from Aspergillus niger on phosphorylated substrate. , 1982, Biochimica et biophysica acta.

[24]  E. Mehler,et al.  Electrostatic effects in proteins: comparison of dielectric and charge models. , 1991, Protein engineering.

[25]  R. Lemieux.  Rhône-Poulenc Lecture. The origin of the specificity in the recognition of oligosaccharides by proteins , 1989 .

[26]  D. Goodsell,et al.  Automated docking of substrates to proteins by simulated annealing , 1990, Proteins.

[27]  B. Svensson,et al.  CHEMICAL MAPPING OF THE ACTIVE SITE OF THE GLUCOAMYLASE OF ASPERGILLUS NIGER , 1996 .

[28]  F. Quiocho.  Protein-carbohydrate interactions: basic molecular features , 1989 .

[29]  L. Firsov,et al.  Refined structure for the complex of 1-deoxynojirimycin with glucoamylase from Aspergillus awamori var. X100 to 2.4-A resolution. , 1993, Biochemistry.

[30]  E. Hehre,et al.  Configurational specificity: unappreciated key to understanding enzymic reversions and de novo glycosidic bond synthesis. I. Reversal of hydrolysis by alpha-, beta- and glucoamylases with donors of correct anomeric form. , 1969, Archives of biochemistry and biophysics.

[31]  Norman L. Allinger,et al.  Molecular mechanics. The MM3 force field for hydrocarbons. 2. Vibrational frequencies and thermodynamics , 1989 .

[32]  A. Golubev,et al.  Crystal structure of glucoamylase from Aspergillus awamori var. X100 to 2.2-A resolution. , 1994, The Journal of biological chemistry.

[33]  M. Palcic,et al.  Substrate recognition by amyloglucosidase: evaluation of conformationally biased isomaltosides. , 1993, Carbohydrate research.

[34]  A. French,et al.  Conformational analysis of the anomeric forms of kojibiose, nigerose, and maltose using MM3. , 1992, Carbohydrate research.

[35]  I. Pelczer,et al.  The Substrate Specificity of the Enzyme Amyloglucosidase (AMG). Part II. 6-Substituted Maltose Derivatives. , 1988 .

[36]  Yoshimasa Tanaka,et al.  Transition state structures for the hydrolysis of α-D-glucopyranosyl fluoride by retaining and inverting reactions of glycosylases. , 1994, The Journal of Biological Chemistry.

[37]  H. Pedersen,et al.  The substrate specificity of the enzyme amyloglucosidase (AMG). Part I. Deoxy derivatives. , 1987, Acta chemica Scandinavica. Series B: Organic chemistry and biochemistry.

[38]  L. Firsov,et al.  Refined crystal structures of glucoamylase from Aspergillus awamori var. X100. , 1994, Journal of molecular biology.

[39]  P. Coutinho,et al.  Structure-function relationships in the catalytic and starch binding domains of glucoamylase. , 1994, Protein engineering.

[40]  Norman L. Allinger,et al.  A molecular mechanics force field (MM3) for alcohols and ethers , 1990 .

[41]  A. French,et al.  Conformational analysis of trehalose disaccharides and analogues using MM3 , 1992 .

[42]  J. Duus,et al.  A nuclear magnetic resonance spectroscopic and conformational study of eight pseudo-trehaloses (D-glucopyranosyl 5a-carba-D- and -L-glucopyranosides). , 1991, Carbohydrate research.

[43]  H. Nakano,et al.  Synthesis of 2-deoxy-glucooligosaccharides through condensation of 2-deoxy-D-glucose by glucoamylase and alpha-glucosidase. , 1995, Bioscience, biotechnology and biochemistry.

[44]  J. Thiem,et al.  Synthesis of 2‐Deoxy‐maltooligosaccharides with Phosphorylase and Their Degradation with Amylases , 1995 .

[45]  P. Monsan,et al.  Production and use of glucosyltransferases fromLeuconostoc mesenteroides NRRL B-1299 for the synthesis of oligosaccharides containing α-(1→2) linkages , 1994, Applied biochemistry and biotechnology.

[46]  B. Svensson,et al.  Active site similarities of glucose dehydrogenase, glucose oxidase, and glucoamylase probed by deoxygenated substrates. , 1992, Biochemistry.

[47]  Norman L. Allinger,et al.  Molecular mechanics. The MM3 force field for hydrocarbons. 1 , 1989 .

[48]  J. Gasteiger,et al.  ITERATIVE PARTIAL EQUALIZATION OF ORBITAL ELECTRONEGATIVITY – A RAPID ACCESS TO ATOMIC CHARGES , 1980 .

[49]  A. French,et al.  Exploration of disaccharide conformations by molecular mechanics , 1993 .

[50]  P. Reilly,et al.  Kinetics, equilibria, and modeling of the formation of oligosaccharides from D‐glucose with Aspergillus niger glucoamylases I and II , 1989, Biotechnology and bioengineering.

[51]  A. French,et al.  Molecular Modeling of Two Disaccharides Containing Fructopyranose Linked to Glucopyranose , 1993 .

[52]  D S Goodsell,et al.  Automated docking of flexible ligands: Applications of autodock , 1996, Journal of molecular recognition : JMR.