Binding mode study of cellopentaose in β-glucosidase B via docking simulation

Abstract

Paenibacillus polymxcaβ-glucosidase B(BglB),belong to a GH family 1, is amonomeric enzyme that acts as an exo-β-glucosidase hydrolyzing cellobioseand cellooligosachharidess of higher degree of polymerization by cleaving β-1,4 glycosidic linkage exist between glucosyl residue. This study reports onbinding modes between BglB with cellopentaose which consist of five glucosylresidue. Several visual inspection and protein–ligand interaction analysis wasfocused on finding amino acid residue involve in each glucosylresidue.Computational docking calculation was performed using programGOLD generating ten solution BglB-cellopentaose complexes. From visualinspection, subsite-1 record the most interacting residue namelyGln22,Asn166, Glu167, Asn296, Glu356, Trp402, Glu409 and Trp410. Thereducingglycosyl at subsite +1 are making interacting with residue namely Trp328,Asn223 and His181. Meanwhile, the residues Arg243, Leu174, Gln316 andTyr169 making contact withreducing glycosyl at the subsite +2 and subsite +3.Lastly, onlytworesidues,His318 and Glu180 reported to make interactionwithinreducing glycosyl at subsite +4 as it is already over exposed towardsoutside of binding cleft. From overall, a total of 11 hydrogen bonds wereobserved in BglB-cellopentaose complex