A Comparative Study to Decipher the Structural and Dynamics Determinants Underlying the Activity and Thermal Stability of GH-11 Xylanases.

Jelena Vucinic,Sophie Barbe,Cédric Montanier,Gleb Novikov,Thomas Schiex,Claire Dumon

doi:10.3390/ijms22115961

Abstract

With the growing need for renewable sources of energy, the interest for enzymes capable of biomass degradation has been increasing. In this paper, we consider two different xylanases from the GH-11 family: the particularly active GH-11 xylanase from Neocallimastix patriciarum, NpXyn11A, and the hyper-thermostable mutant of the environmentally isolated GH-11 xylanase, EvXyn11TS. Our aim is to identify the molecular determinants underlying the enhanced capacities of these two enzymes to ultimately graft the abilities of one on the other. Molecular dynamics simulations of the respective free-enzymes and enzyme–xylohexaose complexes were carried out at temperatures of 300, 340, and 500 K. An in-depth analysis of these MD simulations showed how differences in dynamics influence the activity and stability of these two enzymes and allowed us to study and understand in greater depth the molecular and structural basis of these two systems. In light of the results presented in this paper, the thumb region and the larger substrate binding cleft of NpXyn11A seem to play a major role on the activity of this enzyme. Its lower thermal stability may instead be caused by the higher flexibility of certain regions located further from the active site. Regions such as the N-ter, the loops located in the fingers region, the palm loop, and the helix loop seem to be less stable than in the hyper-thermostable EvXyn11TS. By identifying molecular regions that are critical for the stability of these enzymes, this study allowed us to identify promising targets for engineering GH-11 xylanases. Eventually, we identify NpXyn11A as the ideal host for grafting the thermostabilizing traits of EvXyn11TS.

Highlights

With the increasing need for renewable and sustainable sources of fuels and chemicals that could help reduce pollution and global warming caused by industrial activities, the importance of biomass-degradation-capable enzymes in biorefinery processes has been rapidly increasing
Specific activity on wheat arabinoxylan (WAX) and melting temperature (Tm ) of NpXyn11A and EvXyn11TS were measured in the same conditions
NpXyn11A shows higher SASA than EvXyn11TS, which is consistent with the higher number of enzyme–solvent hydrogen bonds detected in NpXyn11A Ȧll of these analyses indicate that the mesostable NpXyn11A enzyme is less tightly packed than the hyper-thermostable EvXyn11TS enzyme, and possesses a lower number of static intrahydrogen bonds and less-stable salt bridges

Summary

Introduction

With the increasing need for renewable and sustainable sources of fuels and chemicals that could help reduce pollution and global warming caused by industrial activities, the importance of biomass-degradation-capable enzymes in biorefinery processes has been rapidly increasing. Xylanases are widely used in industrial processes including pulp and paper, food, and animal feed [2]. Given their ability to contribute to the degradation of hemicellulose and arabinoxylans—the second most abundant renewable biomaterial available after cellulose inside lignocellulosic polymers—their importance in biorefinery processes is rapidly increasing [3]. The development of such effective and competitive bioprocesses requires enzymes that remain highly active under industrial conditions, notably at high temperature. Understanding the molecular basis underlying the thermostability and activity of xylanases is of paramount interest for optimizing their properties and meeting industrial constraints

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Conclusion