Fig 1.
Schematic representation of the workflow of the study.
The overall process can be summarized as a series of steps that involve filtering and identifying the most damaging nsSNPs of GRIN2A, followed by a subsequent in-depth analysis of one particular nsSNP that proved to be the most deleterious.
Table 1.
Identification of deleterious nsSNPs using PHD-SNP, SNPs&GO, PANTHER, Polyphen-2, and Predict SNP2.
Fig 2.
Locations of 16 deleterious nsSNPs of GRIN2A as revealed by the Mutation3D server.
Table 2.
Surface accessibility of native and mutant proteins.
Fig 3.
Evolutionary conservation profile of amino acid residues as predicted by ConSurf.
For the identification of the most deleterious nsSNPs, ConSurf, MUpro, and HOPE outputs were analyzed and scrutinized. Finally, 9 out of the 16 mutants were considered the most impactful for the structure of the GRIN2A protein and selected for further analysis.
Table 3.
Prediction of High-Risk nsSNPs of GRIN2A Gene according to Consurf, MUPro, HOPE.
Table 4.
Refinement of the GRIN2A homology model structure using the GalaxyRefne web server.
Fig 4.
DynaMut2 prediction of inter-atomic interactions of the native DRD2 vs the mutant.
Altered interatomic interactions between the wild and the mutant residues with their neighboring atoms have been observed.
Table 5.
Predicted changes in stability as a result of mutation.
Fig 5.
RMSD analysis of wild type GRIN2A (Yellow) and I463S mutant GRIN2A protein (Red).
Fig 6.
RMSF analysis of wild type GRIN2A (Yellow) and I463S mutant GRIN2A protein (Red).
Fig 7.
Radius of gyration analysis of wild type GRIN2A (Yellow) and I463S mutant GRIN2A protein (Red).
Fig 8.
SASA analysis of wild type GRIN2A (Yellow) and I463S mutant GRIN2A protein (Red).