Authors : Nurulbahiyah Ahmad Khairudin, Kamyar Shameli, Mikio Miyake and Nur Shima Fadhilah Mazlan
Abstract: Paenibacillus polymxca β-glucosidase B (BglB) which belongs to GH family 1 is a monomeric enzyme that acts as an exo-β-glucosidase hydrolyzing cellobiose and cello oligosaccharides of higher degree polymerization by cleaving the β-1, 4 glycosidic linkage between glucosyl residues. This study is based on the binding modes of cellopentaose consisting of five glucosyl residues in the active site of BglB. A Molecular Dynamics (MD) simulation was performed at 300 K under periodic boundary condition for 5 ns using the complex structures obtained from previous reported docking study. The residues that are responsible for recognizing the glycone and aglycone subsites include Gln22, Glu167, Glu409, Glu356, Tyr298, Trp410 and Glu225, Tyr169, Asn223, Trp412, His181, Ala360, Arg243, Gln316, respectively. The findings of this study support the fact that the interaction of subsite-1 and OH is the most crucial in the enzyme-substrate complex 2 stabilization.
Nurulbahiyah Ahmad Khairudin, Kamyar Shameli, Mikio Miyake and Nur Shima Fadhilah Mazlan, 2017. Insight into Cellopentaose Binding Mode in Glycone and Aglycone Binding Site of Beta-Glucosidase B: A Molecular Dynamics Approach. Journal of Engineering and Applied Sciences, 12: 9440-9443.