Towards an Understanding of Oxidative Damage in an a-L-Arabinofuranosidase of Trichoderma reesei: a Molecular Dynamics Approach

Castano Uruena, Jesus; Zhou, Mowei; Schilling, Jonathan S.

doi:10.1007/s12010-021-03594-w

Towards an Understanding of Oxidative Damage in an a-L-Arabinofuranosidase of Trichoderma reesei: a Molecular Dynamics Approach

Journal Article · Mon Jun 14 00:00:00 EDT 2021 · Applied Biochemistry and Biotechnology

DOI:https://doi.org/10.1007/s12010-021-03594-w· OSTI ID:1807694

Castano Uruena, Jesus ^[1]; ^[2]; Schilling, Jonathan S. ^[3]

Univ. of Minnesota, Minneapolis, MN (United States). Bioproducts and Biosystems Engineering; Marine and Costal Research Institute/INVEMAR, Santa Marta (Colombia)
Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
Univ. of Minnesota, Minneapolis, MN (United States). Bioproducts and Biosystems Engineering

Trichoderma reesei is a ‘workhorse’ fungus that produces glycosyl hydrolases (e.g., cellulases) at high titers for use in industrial bioprocessing. In this study, we focused on two side-chain hemicellulases, a-L-arabinofuranosidases and a-D-galactosidases, which are important for the treatment of lignocellulosic biomass, but susceptible to oxidative damage that can occur during industrial processing. The molecular details that render these enzymes inactive have not yet been identified. To approach this issue, we used proteomics to identify amino acid residues that were oxidized after a relevant oxidative treatment (Fenton reaction). These oxidative modifications were included in the 3D-protein structures, and using molecular dynamics simulations, we then studied the behaviors of non-modified and oxidized enzymes. These simulations showed significant alterations of the conformational stability of proteins when oxidized, as evidenced by changes in root mean square deviation (RMSD) and principal component analyses (PCA) trajectories. Likewise, enzyme-ligand interactions such as hydrogen bonds were greatly reduced in quantity and quality in the oxidized proteins. Finally, free energy landscape plots showed that there was a more rugged energy surface in the oxidized proteins, implying a less favorable reaction pathway. These results reveal the basis for loss of function in these carbohydrate active enzymes (CAZYs) in T. reesei.

View Accepted Manuscript (DOE)

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-76RL01830; SC0019427

OSTI ID:: 1807694

Report Number(s):: PNNL-SA--158426

Journal Information:: Applied Biochemistry and Biotechnology, Journal Name: Applied Biochemistry and Biotechnology Journal Issue: 10 Vol. 193; ISSN 0273-2289

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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Towards an Understanding of Oxidative Damage in an a-L-Arabinofuranosidase of Trichoderma reesei: a Molecular Dynamics Approach

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