Probing the Relation Between Community Evolution in Dynamic Residue Interaction Networks and Xylanase Thermostability

Area of Science:

• Protein Biochemistry
• Computational Biology
• Enzyme Engineering

Background:

• Protein thermostability is crucial for industrial applications and is primarily governed by residue-residue interactions.
• Xylanases from different organisms exhibit varying degrees of heat resistance, necessitating detailed structural and dynamic analyses.

Purpose of the Study:

• To investigate the molecular dynamics and residue interactions contributing to the thermostability of Streptomyces lividans xylanase (xyna_strli) and Thermoascus aurantiacus xylanase (xyna_theau).
• To identify specific structural regions and interaction networks responsible for enhanced thermal resistance in xyna_theau.

Main Methods:

• Molecular Dynamics (MD) simulations were performed on xyna_strli and xyna_theau at temperatures of 300K, 325K, and 350K.
• Dynamic weighted residue interaction networks were constructed.
• Rigid-communities within the proteins were detected using the ESPRA and Evolving Graph+Fast-Newman algorithms.

Main Results:

• Rigid-communities, crucial for thermostability, were identified in loop2, short helices (α2", α3", α4"), and helices (α3, α4) near the N-terminus.
• Thermoascus aurantiacus xylanase (xyna_theau) exhibited stable synergistic interactions within its rigid-community, forming a 'thermo helix' (α2" and α3") that enhances thermostability.
• Xyna_theau displayed tighter global interactions (hydrogen bonds, van der Waals forces, π-π stacking) within its rigid-community, which were more resistant to high temperatures compared to xyna_strli.

Conclusions:

• Robust residue interactions within specific secondary structures, particularly in the identified rigid-communities, are key determinants of xylanase thermostability.
• The 'thermo helix' and tight global interactions in xyna_theau significantly contribute to its superior heat resistance.
• Analyzing rigid-communities provides insights into the cooperation of secondary structures for thermostability, which are not evident from sequence or 3D structure alone.