Structural and functional insights from molecular modeling, docking, and MD simulations of bacterial xylanase: implications for biofuel efficiency

Abstract

Xylan is the major hemicellulose component of the plant cell wall (second most naturally abundant carbohydrate) and is a linear polymer of β-d-xylopyranosyl units linked by β-1-4 glycosidic bonds. Microbial xylanase is an efficient xylan degrading enzyme that catalyzes the hydrolysis of internal β-1-4 glycosidic bonds and is reported to be involved in bioethanol production from lignocellulosic biomass. Due to its wide range of applications at the industrial level, it is important to understand the structural and functional aspects of xylanase. Therefore, in the present study, an in silico investigation was carried out through the docking of bacterial xylanases with multiple substrates xylobiose, xylotriose, xylotetraose, and xylopentaose to determine the molecular interaction and substrate specificity during enzymatic catalysis. The amino acid sequences of four xylanolytic bacterial species, viz., Actinosynnema pretiosum, Streptomyces sp., Spirosoma sordidisoli and Streptomyces bingchenggensis were retrieved from UniProtKB and their homologous structures were predicted using the SWISS-PROT model webserver to undertake docking studies using the xylanase enzyme of the above bacterial species and xylan as a substrate. Results of the docking studies showed that the xylanase of all the bacterial species exhibited the highest interaction with xylopentaose. Binding energy was determined using the DINC server. Further multiple sequence alignment (MEGA X), phylogenetic analysis (MEGA X), and molecular dynamics simulation (GROMACS) studies were performed. Overall, the present in silico study will reveal the importance of understanding the catalytic mechanism of substrate xylan with different bacterial xylanases, which could be helpful for the development of engineered xylanase towards the efficient production of bioethanol from lignocellulosic biomass.

Keywords

Bacterial xylanase / Lignocellulosic biomass / Molecular docking / Molecular dynamic simulation / Biofuel production

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Funding

Department of Science and Technology, Government of Odisha(ST-BT-MISC-0010-2022-2373)

RIGHTS & PERMISSIONS

Jiangnan University