Enzyme structure dynamics of xylanase I from Trichoderma longibrachiatum

Abstract

BackgroundEnzyme dynamics has recently been shown to be crucial for structure-function relationship. Among various structure dynamics analysis platforms, HDX (hydrogen deuterium exchange) mass spectrometry stands out as an efficient and high-throughput way to analyze protein dynamics upon ligand binding. Despite the potential, limited research has employed the HDX mass spec platform to probe regional structure dynamics of enzymes. In particular, the technique has never been used for analyzing cell wall degrading enzymes. We hereby used xylanase as a model to explore the potential of HDX mass spectrometry for studying cell wall degrading enzymes.ResultsHDX mass spectrometry revealed significant intrinsic dynamics for the xylanase enzyme. Different regions of the enzymes are differentially stabilized in the apo enzyme. The comparison of substrate-binding enzymes revealed that xylohexaose can significantly stabilize the enzyme. Several regions including those near the reaction centres were significantly stabilized during the xylohexaose binding. As compared to xylohexaose, xylan induced relatively less protection in the enzyme, which may be due to the insolubility of the substrate. The structure relevance of the enzyme dynamics was discussed with reference to the three dimensional structure of the enzyme. HDX mass spectrometry revealed strong dynamics-function relevance and such relevance can be explored for the future enzyme improvement.ConclusionLigand-binding can lead to the significant stabilization at both regional and global level for enzymes like xylanase. HDX mass spectrometry is a powerful high-throughput platform to identify the key regions protected during the ligand binding and to explore the molecular mechanisms of the enzyme function. The HDX mass spectrometry analysis of cell wall degrading enzymes has provided a novel platform to guide the rational design of enzymes.

HDX-Analyzer: a novel package for statistical analysis of protein structure dynamics

“…Protein intrinsic dynamics has been more and more recognized as an important consideration for protein functions [ 1 ]. Several recent studies have revealed that protein dynamics plays essential roles in the catalysis and other functions [ 1 , 2 ]. Among the different techniques, HDX mass spectrometry stands out as a relatively high throughput platform to probe the backbone dynamics of the proteins [ 3 - 6 ].…”

Proceedings of the 2010 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference

“…A mixed reality surgical simulator with a VICON motion tracking system, developed for the rasping procedure in artificial cervical disc replacement surgeries is described by Tansel Halic et al , which can serve as an important training and practice tool for surgeons [ 50 ]. The potential of using hydrogen deuterium exchange (HDX) mass spectrometry for analyzing enzymes that degrade cell walls is explored by Uzuner et al [ 51 ]. They report that the HDX mass spectrometry can be a powerful tool for exploring the molecular mechanisms of enzyme functions.…”

Enhancement of the thermo-alkali-stability of xylanase II from Aspergillus usamii E001 by site-directed mutagenesis

“…The 3D structures of several thermophilic and mesophilic xylanases including Trichoderma longibrachiatum (Uzuner et al, 2010), Aspergillus niger 400264 xylanase XYNB (Xie et al, 2011), and Aspergillus kawachii (Fushinobu et al, 1998) have been studied. This provides valuable information on correlation between 3D structures and stability of xylanases.…”