Abstract
Development of chimeric enzymes by protein engineering can more efficiently contribute toward biomass conversion for bioenergy generation. Therefore, prior to experimental validation, a computational approach by modeling and molecular dynamic simulation can assess the structural and functional behavior of chimeric enzymes. In this study, a bifunctional chimera, CtXyn11A-BoGH43A comprising an efficient endoxylanase (CtXyn11A) from Clostridium thermocellum and xylosidase (BoGH43A) from Bacteroides ovatus was computationally designed and its binding and stability analysis with xylooligosaccharides were performed. The modeled chimera showed β-jellyroll fold for CtXyn11A and 5-bladed β-propeller fold for BoGH43A module. Stereo-chemical properties analyzed by Ramachandran plot showed 98.8% residues in allowed region, validating the modeled chimera. The catalytic residues identified by multiple sequence alignment were Glu94 and Glu184 for CtXyn11A and Asp229 and Glu384 for BoGH43A modules. CtXyn11A followed retaining-type, whereas BoGH43A enforced inverting-type of reaction mechanism during xylan hydrolysis as revealed by superposition and GH11 and GH43 familial analyses. Molecular docking studies showed binding energy, (ΔG) − 4.54 and − 4.18 kcal/mol for CtXyn11A and BoGH43A modules of chimera, respectively, with xylobiose, while − 3.94 and − 3.82 kcal/mol for CtXyn11A and BoGH43A modules of chimera, respectively, with xylotriose. MD simulation of CtXyn11A-BoGH43A complexed with xylobiose and xylotriose till 100 ns displayed stability by RMSD, compactness by Rg and conformational stability by SASA analyses. The lowered values of RMSF in active-site residues, Glu94, Glu184, Asp229, Asp335 and Glu384 confirmed the efficient binding of chimera with xylobiose and xylotriose. These results were in agreement with the earlier experimental studies on CtXyn11A releasing xylooligosaccharides from xylan and BoGH43A releasing d-xylose from xylooligosaccharides and xylobiose. The chimera showed stronger affinity in terms of total short-range interaction energy; − 190 and − 121 kJ/mol for with xylobiose and xylotriose, respectively. The bifunctional chimera, CtXyn11A-BoGH43A showed stability and integrity with xylobiose and xylotriose. The designed chimera can be constructed and applied for efficient biomass conversion.
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The authors declare that all data and materials as well as software application or custom code used in this study support their published claims and comply with the field standards.
Abbreviations
- GH:
-
Glycoside hydrolase
- MD:
-
Molecular dynamics
- RMSD:
-
Root-mean-square deviation
- Rg :
-
Radius of gyration
- SASA:
-
Solvent accessible surface area
- RMSF:
-
Root-mean-square-fluctuation
- MPD:
-
(4S)-2-methyl-2, 4-Pentanediol
- EDG:
-
1, 4-Di-oxy-1, 4-imino-l-Arabinitol
- XBB:
-
Xylobiose
- XTI:
-
Xylotriose
- XTT:
-
Xylotetraose
- XPT:
-
Xylopentaose
- Chimera:
-
CtXyn11A-BoGH43A
- CAZy:
-
Carbohydrate active enzyme database
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Acknowledgements
The authors thankfully acknowledge the financial support through a DBT-PAN-IIT Centre for Bioenergy: Phase II, Grant (No. BT/PR41982/PBD/26/822/2021), from Department of Biotechnology, Ministry of Science and Technology, New Delhi, India.
Funding
This study was funded by DBT-PAN-IIT Centre for Bioenergy: Phase II, Grant (No. BT/PR41982/PBD/26/822/2021).
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AG came up with the concept and devised the goals. SJ did the computational modeling, molecular docking and MD simulation of xylooligosaccharides with chimaera. PVG contributed in significance of the work, active site analysis, construction of the phylogeny and manuscript formatting. BC helped in simulation studies. The paper was written by SJ, PVG and AG.
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Accession numbers: CtXyn11A: GenBank Accession—WP_014522591.1. BtGH43A: Uniprot ID: A7LXT8.1.
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Ji, S., Gavande, P.V., Choudhury, B. et al. Computational design and structure dynamics analysis of bifunctional chimera of endoxylanase from Clostridium thermocellum and xylosidase from Bacteroides ovatus. 3 Biotech 13, 59 (2023). https://doi.org/10.1007/s13205-023-03482-6
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DOI: https://doi.org/10.1007/s13205-023-03482-6