Effects of oligolignol sizes and binding modes on a GH11 xylanase inhibition revealed by molecular modeling techniques

Journal article

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Publication Details

Author list: Muhammad A., Khunrae P., Sutthibutpong T.

Publisher: Springer

Publication year: 2020

Journal: Journal of Molecular Modeling (1610-2940)

Volume number: 26

Issue number: 6

ISSN: 1610-2940

eISSN: 0948-5023

URL: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85084313794&doi=10.1007%2fs00894-020-04383-8&partnerID=40&md5=0635e12bd9e2baf284f9e27e590444c3

Languages: English-Great Britain (EN-GB)

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Abstract

Lignin and phenolic compounds have been shown as the main recalcitrance for biomass decomposition, as they inhibit a number of lignocellulose-degrading enzymes. Understanding the inhibition mechanisms and energetic competitions with the native substrate is essential for the development of lignin resistive enzymes. In this study, atomistic detail of the size-dependent effects and binding modes of monomeric coniferyl alcohol, dimeric oligolignol, and tetrameric oligolignol made from coniferyl alcohols on the GH11 xylanase from Bacillus firmus strain K-1 was investigated by using molecular docking and atomistic molecular dynamics (MD) simulations. From the MD simulation results on the docked conformation of oligolignol binding within the “Cleft” and the “N-terminal,” changes were observed both for protein conformations and positional binding of ligands, as binding with “Thumb” regions was found for all oligolignin models. Moreover, the uniquely stable “N-terminal” binding of the coniferyl alcohol monomer had no effect on the highly fluctuated Thumb region, showing no sign of inhibitory effect, and was in good agreement with recent studies. However, the inhibitory effect of oligolignols was size dependent, as the estimated binding energy of the tetrameric oligolignol became stronger than that of the xylohexaose substrate, and the important binding residues were identified for future protein engineering attempts to enhance the lignin resistivity of GH11. [Figure not available: see fulltext.] © 2020, Springer-Verlag GmbH Germany, part of Springer Nature.

Keywords

Molecular Dynamics Simulations, Xylanase enzyme