Probing the Relation Between Community Evolution in Dynamic Residue Interaction Networks and Xylanase Thermostability
| Autor: | Chen Zhang, Yanrui Ding |
|---|---|
| Rok vydání: | 2021 |
| Předmět: |
Physics
Endo-1 4-beta Xylanases Hot Temperature Hydrogen bond Applied Mathematics 0206 medical engineering Stacking 02 engineering and technology Molecular Dynamics Simulation Protein Structure Secondary Prime (order theory) Evolution Molecular symbols.namesake Crystallography Molecular dynamics Helix Mutagenesis Site-Directed Genetics symbols Xylanase Amino Acids van der Waals force 020602 bioinformatics Biotechnology Thermostability |
| Zdroj: | IEEE/ACM Transactions on Computational Biology and Bioinformatics. 18:686-696 |
| ISSN: | 2374-0043 1545-5963 |
| DOI: | 10.1109/tcbb.2019.2922906 |
| Popis: | Residue-residue interactions are the basis of protein thermostability. The molecular conformations of Streptomyces lividans xylanase (xyna_strli) and Thermoascus aurantiacus xylanase (xyna_theau) at 300K, 325K and 350K were obtained by Molecular Dynamics (MD) simulations. Dynamic weighted residue interaction networks were constructed and the rigid-communities were detected using the ESPRA algorithm and the Evolving Graph+Fast-Newman algorithm. The residues in the rigid-communities are primarily located in loop2, short helixes $\alpha 2^{\prime}, \alpha 3^{\prime}, \alpha 4^{\prime}$ α 2 ' , α 3 ' , α 4 ' and helixes $\alpha 3$ α 3 and $\alpha 4$ α 4 . Thus, the rigid-community is close to the N-terminus of xylanase, which is usually stabilized to increase thermostability using site-directed mutagenesis. The evolution of the rigid-community with increasing temperature shows a stable synergistic interaction between loop2, $\alpha 2^{\prime}, \alpha 3^{\prime}$ α 2 ' , α 3 ' and $\alpha 4^{\prime}$ α 4 ' in xyna_theau. In particular, the short helixes $\alpha 2^{\prime}$ α 2 ' and $\alpha 3^{\prime}$ α 3 ' form a “thermo helix” to promote thermostability. In addition, tight global interactions between loop2, $\alpha 2^{\prime}, \alpha 3^{\prime}, \alpha 3, \alpha 4^{\prime}$ α 2 ' , α 3 ' , α 3 , α 4 ' and $\alpha 4$ α 4 of xyna_theau are identified, consisting mainly of hydrogen bonds, van der Waals forces and π-π stacking. These residue interactions are more resistant to high temperatures than those in xyna_strli. Robust residue interactions within these secondary structures are key factors influencing xyna_strli and xyna_theau thermostability. Analyzing the rigid-community can elucidate the cooperation of secondary structures, which cannot be discovered from sequence and 3D structure alone. |
| Databáze: | OpenAIRE |
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