Understanding the conformational change and inhibition of hyperthermophilic GH10 xylanase in ionic liquid

Abstract

Xylan is an abundant hemicellulosic feedstock of pentose sugars present in the Lignocellulose biomass, offering massive potential for the generation of biofuel and numerous value-added by-products. The extraction of xylan is a major challenge due to the typical organization of cellulose, hemicellulose and lignin. Ionic Liquid (IL) is a promising solvent for the deconstruction of the complex lignocellulosic structure. However, the residual IL present in the pretreated xylan significantly affects xylanase activity during the hydrolysis. Thus, a molecular understanding focusing on the IL-xylanase interaction needs to be explored for developing IL tolerant xylanases for efficient xylan hydrolysis. In this study, atomistic molecular dynamics (MD) simulations were performed to investigate the IL tolerance of hyperthermophilic GH10B xylanase from Thermotoga maritima (TmXYN10B) in both aqueous and water/1-Ethyl-3-methylimidazolium acetate (EmimAc) binary solvent systems. The enzyme was stable in all solvents at high temperature (363 K). However, the opening and closing motions of the xylanase were lost in high EmimAc concentration. Besides, the formation of a considerable number of hydrogen bonds between acetate anion and amino acids at the enzyme surface might change its native motion in high EmimAc system. The IL induced conformational change was charecterized by constructing Protein Structure Network (PSN) on each snapshot from the MD simulation trajectory. Here we captured the enzyme conformational change by identifying disjoint cliques and communities at the active site in high EmimAc concentration. Furthermore, Emim cations populated the active site with higher binding occupancy and suggested to inhibit the enzymatic hydrolysis. Finally, this study provides a theoretical understanding of the reduced activity of the TmXYN10B xylanase in IL, which can pave the path for engineering xylanases for biofuel production.