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Título:
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Substrate distortion in the Michaelis complex of Bacillus 1,3–1,4-β-glucanase: insight from first principles molecular dynamics simulations
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Autor/a:
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Planas, Antoni (Planas Sauter); Biarnés Fontal, Xevi; Nieto, Joan; Rovira i Virgili, Carme
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Otros autores:
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Universitat Ramon Llull. IQS |
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Abstract:
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The structure and dynamics of the enzyme-substrate complex of Bacillus 1,3–1,4-β-glucanase, one of the most active glycoside hydrolases, is investigated by means of Car-Parrinello molecular dynamics simulations (CPMD) combined with force field molecular dynamics (QM/MM CPMD). It is found that the substrate sugar ring located at the –1 subsite adopts a distorted 1S3 skew-boat conformation upon binding to the enzyme. With respect to the undistorted 4C1 chair conformation, the 1S3 skew-boat conformation is characterized by: (a) an increase of charge at the anomeric carbon (C1), (b) an increase of the distance between C1 and the leaving group, and (c) a decrease of the intraring O5-C1 distance. Therefore, our results clearly show that the distorted conformation resembles both structurally and electronically the transition state of the reaction in which the substrate acquires oxocarbenium ion character, and the glycosidic bond is partially broken. Together with analysis of the substrate conformational dynamics, it is concluded that the main determinants of substrate distortion have a structural origin. To fit into the binding pocket, it is necessary that the aglycon leaving group is oriented toward the β region, and the skew-boat conformation naturally fulfills this premise. Only when the aglycon is removed from the calculation the substrate recovers the all-chair conformation, in agreement with the recent determination of the enzyme product structure. The QM/MM protocol developed here is able to predict the conformational distortion of substrate binding in glycoside hydrolases because it accounts for polarization and charge reorganization at the –1 sugar ring. It thus provides a powerful tool to model E·S complexes for which experimental information is not yet available. |
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Fecha de creación:
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01-2006 |
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Materias (CDU):
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577 - Bioquímica. Biologia molecular. Biofísica |
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Materia(s):
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Bacil antràcic
Glicòsids
Dinàmica molecular
Enzymes
Glycoside hydrolases
Molecular dynamics simulations
Aglycon |
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Derechos:
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© The American Society for Biochemistry and Molecular Biology
L'accés als continguts d'aquest document queda condicionat a l'acceptació de les condicions d'ús establertes per la següent llicència Creative Commons:http://creativecommons.org/licenses/by/4.0/ |
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Páginas:
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10 p. |
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Tipo de documento:
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Artículo
Artículo - Versión publicada |
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DOI:
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https://doi.org/10.1074/jbc.m507643200
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Editor:
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The American Society for Biochemistry and Molecular Biology
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Publish at:
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Journal of Biological Chemistry. Vol.281, n.3 (2006), p.1432–1441
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Compartir:
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