Amylose chain behavior in an interacting context II. Molecular modeling of a maltopentaose fragment in the barley ?-amylase catalytic site

André, G.; Buléon, Alain; Juy, Michel; Aghajari, Nushin; Haser, R.; Tran, V.H.

doi:10.1002/(sici)1097-0282(199901)49:1<107::aid-bip10>3.0.co;2-s

Cited by 8 publications

(10 citation statements)

References 55 publications

(57 reference statements)

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“…Since molecular modeling is unable to simulate the cleavage of a covalent bond (only the quantum mechanics can theoretically answer this question and by now only quantum mechanics/molecular mechanics coupling has approached a solution to this question30), the two main steps of the catalytic event, besides the proton transfer, are deliberately chosen: the reaction steps before and after the cleavage. For the stage before the hydrolysis, a previously modeled DP5 oligosaccharide31 was chosen. Namely, the maltopentaose substrate A −1 –A–B–C–D is composed of glucose rings A −1 , A , B , C , and D linked with a α‐(1,4) bond from the nonreducing to the reducing end.…”

Section: Methodsmentioning

confidence: 99%

Putative implication of α‐amylase loop 7 in the mechanism of substrate binding and reaction products release

André¹,

Tran²

2004

Biopolymers

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Alpha-amylases are widespread endo-enzymes involved in the hydrolysis of internal alpha-(1,4) glycosidic linkages of starch polymers. Molecular modeling of amylose-amylase interactions is a step toward enzymatic mechanism understanding and rational design of new enzymes. From the crystallographic complex of barley alpha-amylase AMY2-acarbose, the static aspects of amylose-amylase docking have been characterized with a model of maltododecaose (DP12) (G. André, A. Buléon, R. Haser, and V. Tran, Biopolymers 1999, Vol. 50, pp. 751-762; G. André and V. Tran, Special Publication no. 246 1999, The Royal Society of Chemistry, H. J. Gilbert, G. J. Davies, B. Henrissat, and B. Svensson, Eds., Cambridge, pp. 165-174). These studies, consistent with the experimental subsite mapping (K. Bak-Jensen, G. André, V. Tran, and B. Svensson, Journal of Biological Chemistry, to be published), propose a propagation scheme for an amylose chain in the active cleft of AMY2. The topographical overview of alpha-amylases identified loop 7 as a conserved segment flanking the active site. Since some crystallographic experiments suspected its high flexibility, its putative motion was explored through a robotic scheme, an alternate route to dynamics simulations that consume CPU time. The present article describes the characteristics of the flexibility of loop 7: location and motion in AMY2. A back-and-forth motion with a large amplitude of more than 0.6 nm was evaluated. This movement could be triggered by two hinge residues. It results in the loop flipping over the active site to enhance the docking of the native helical substrate through specific interactions, it positions the catalytic residues, it distorts the substrate towards its transition state geometry, and finally monitors the release of the products after hydrolysis. The residues involved in the process are now rational mutation points in the hands of molecular biologists.

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Section: Methodsmentioning

confidence: 99%

Putative implication of α‐amylase loop 7 in the mechanism of substrate binding and reaction products release

André¹,

Tran²

2004

Biopolymers

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“…For all calculations, the CFF91 force field with the steepest descent minimisation was selected. This force field has been proved to be adapted to the protein/polysaccharide interaction studies [17,18]. The oligosaccharide can adopt a large range of flexible conformations from chair to skew, boat or envelope forms due to puckering.…”

Section: Molecular Modelingmentioning

confidence: 99%

Action pattern of Fusarium moniliforme endopolygalacturonase towards pectin fragments: Comprehension and prediction

André-Leroux¹,

Tessier²,

Bonnin³

2005

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

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The structures of complexes of Fusarium moniliforme endopolygalacturonase (endoPG) with non-methylated or partly methylated homogalacturonan fragments were modeled to identify the residues involved in substrate binding and to correlate the cleavage pattern with the experimental productive modes. The conformational space of the complex was extensively explored and malto- to hexo-oligogalacturonates were modeled in the active cleft. To select the most highly probable productive complex for each oligomer between DP2 and 6, four energetic criteria were defined. Noteworthingly, the results were in accordance with the experimental results showing the mode of action of this enzyme towards un-methyl-esterified oligogalacturonates. Furthermore, the amino-acid residues involved in the binding were confirmed by similar studies performed on other endoPGs. Then, the oligomers were gradually methyl-esterified at one or more positions and similar docking experiments were carried out. Markedly, the docking energies were not significantly modified by the methyl-esterification of the substrate and it is likely that the methyl-esterification of the substrate does not alter the mode of action of the enzyme. Finally, 1D sequence and 3D structure of the endopolygalacturonase of Aspergillus niger II, known to be strictly non-tolerant to methylesters, were compared with the sequence and structure of the tolerant F. moniliforme endopolygalacturonase to get to a structural comprehension of the tolerant-or not-behaviour of endoPGs with methyl-esterified pectins.

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“…As the AMY1 structure was not available, AMY1/maltododecaose was build by homology modeling using as template AMY2/maltododecaose extended from AMY2/maltodecaose (10,25,46,47) -Pro 300 (␤7 3 ␣7). The backbone was fixed at segment ends having no substrate contact to maintain structural integrity during energy minimization.…”

Section: Molecular Modeling Of Amy2 and Amy1/maltododecaosementioning

confidence: 99%

“…A maltodecaose complex was computed earlier by stepwise addition of glucosyl residues extending the acarbose molecule bound in AMY2 (10) beyond subsites Ϫ1 and ϩ2. This complex revealed that Tyr 104 AMY2 and Tyr 211 AMY2 delimit the binding groove at subsites Ϫ6 and ϩ4 (5,25,46,47). The present incorporation and removal of aromatic residues at these positions in AMY1 thus manipulate common features in protein-carbohydrate interactions, i.e.…”

mentioning

confidence: 92%

Tyrosine 105 and Threonine 212 at Outermost Substrate Binding Subsites –6 and +4 Control Substrate Specificity, Oligosaccharide Cleavage Patterns, and Multiple Binding Modes of Barley α-Amylase 1

Bak-Jensen¹,

André

Gottschalk³

et al. 2004

Journal of Biological Chemistry

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Amylose chain behavior in an interacting context II. Molecular modeling of a maltopentaose fragment in the barley ?-amylase catalytic site

Cited by 8 publications

References 55 publications

Putative implication of α‐amylase loop 7 in the mechanism of substrate binding and reaction products release

Putative implication of α‐amylase loop 7 in the mechanism of substrate binding and reaction products release

Action pattern of Fusarium moniliforme endopolygalacturonase towards pectin fragments: Comprehension and prediction

Tyrosine 105 and Threonine 212 at Outermost Substrate Binding Subsites –6 and +4 Control Substrate Specificity, Oligosaccharide Cleavage Patterns, and Multiple Binding Modes of Barley α-Amylase 1

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