2.3.5 ǀ Computational modeling of three-dimensional
(3-D) structure of cpOAS1 protein
The three-dimensional model was generated using MODELLER 10.1
(https://salilab.org/modeller/), SWISS-MODEL
(https://swissmodel.expasy.org/), PHYRE2
(http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index) and
GENO3D
(https://geno3d-prabi.ibcp.fr/cgi-bin/geno3d_automat.pl?page=/GENO3D/geno3d_home.html)
software. In MODELLER 10.1, the 3-D structure was predicted as per the
described procedure48. During this procedure, five
three-dimensional structures were generated using 4 rwp as the template.
The best possible structure was selected considering the DOPE (Discrete
Optimized Protein Energy) score. SWISS-MODEL software was used to
generate a refined 3-D model of the cpOAS1 protein. Generated cpOAS1
model was predicted sequentially with the global model quality estimate
(GMQE) and the QMEAN score49. Intensive modeling mode
was used to predict the 3-D structure using
protein homology/analogY recognition engine V 2.0
(PHYRE2)50. In this model, the template was selected
based on heuristics to maximize confidence, percentage identity and
alignment coverage. In GENO3D, out of five models, the low energy model
was selected for evaluation and further validation51.
All 3-D structures of the cpOAS1 protein generated by all the four types
of software/server were then evaluated to test the structural integrity
through various online model evaluation servers included
Errat52, PROCHECK53 and
VERIFY3D54. Ramachandran plot as evaluated by PROCHECK
was generated to check the stereochemical properties of cpOAS1 protein
structure which has been modeled55. In this plot,
structural validation was done by evaluating the number of amino acid
residues in favoured regions, allowed regions and disallowed regions.
Graphical inspections and similarity of the generated P2 model with the
template model (4rwp) were done using UCSF Chimera56(http://www.cgl.ucsf.edu/chimera/). Different protein models were
viewed in the RasMol.