Fig 1.
Three-dimensional (3D) models of representative fungal proteins that resembled as endo-inulinase.
3D models were generated from sequences retrieved from the non-redundant protein sequence database using SWISS-MODEL web server (https://swissmodel.expasy.org/interactive). The model images were created using USCF-Chimera.
Fig 2.
Three-dimensional (3D) model of representative fungal protein, constructed based on denovo/ab-initio method of protein modeling using Bhageerath H web server (http://www.scfbio-iitd.res.in/bhageerath/bhageerath_h.jsp).
A- Reference endo-inulinase (3SC7); B- Denovo 3D model of predicted protein from Aspergillus fumigatus resembling native endo-inulinase like structure. The model images were created using USCF-Chimera.
Fig 3.
Plot of residue energies with Z-scores of representative 3D protein models, generated using PROSA web (https://prosa.services.came.sbg.ac.at/prosa.php).
The blue color shaded region in the plot corresponds to Z-scores of experimentally determined protein structures characterized by NMR analysis; grey color shaded region corresponds to Z-scores of experimentally determined protein structures characterized by X-Ray diffraction studies. The Z-scores of predicted 3D models falls within the range of experimentally determined native like protein structures.
Fig 4.
Plot showing the average 3D-ID score for each residue of A. Aspergillus ficuum reference endo-inulinase and B. Predicted endo-inulinase from Talaromyces verruculosus. The plot and scores are generated using VERIFY 3D webserver (http://servicesn.mbi.ucla.edu/Verify3d/).
Fig 5.
Ramachandran plots of representative proteins that resembled as endo-inulinase.
The plots were generated using PROCHECK module of PROTSAV webserver (http://www.scfbio-iitd.res.in/software/proteomics/protsav.jsp).
Fig 6.
Structure based sequence alignment of reference endo-inulinase from Aspergillus ficuum and the predicted protein endo-inulinase model from Talaromyces sp. for identifying unique motifs and residues required for endo-activity.
The Sequences are aligned using webserver (http://bioinformatics.org/strap/aa/).
Fig 7.
The Interaction between the active site around the conserved glutamate residue and substrate (kestopentaose) in the three-dimensional protein models of reference endo-inulinase from Aspergillus ficuum and predicted endo-inulinase from Talaromyces sp.
The docking was performed using MGL python tool and autodock 4. The interactions and hydrogen bonds formed between the substrate and the active site of enzyme was visualized using UCSF Chimera. The hydrogen bonds formed and their size were indicated in red color.
Fig 8.
RMSD plot of protein backbone of 9 predicted endo-inulinase models and a reference endo-inulinase (3SC7) after 10ns of MD simulations.
The data was generated using gromacs rms function. A. Protein back bone of enzyme-substrate complex; B. Protein backbone of enzyme without substrate. The plots were made in the work sheet.
Fig 9.
Radius of gyration (Rg) plot of protein backbone of 9 predicted endo-inulinase models and a reference endo-inulinase (3SC7) after 10ns of MD simulations.
The data was generated using gromacs gyrate function. A. Protein back bone of enzyme-substrate complex; B. Protein backbone of enzyme without substrate. The plots were made in the work sheet.
Table 1.
Experimentally characterized endo-inulinases from species identified in this study.