1.3.2 Prediction of Secondary Structures
Results from SOPMA analysis shows that random coils dominant among secondary structure components in the protein models (Figure 1.1). The constitution of alpha helix in EGFR, K-ras oncogene protein, and TP53 were shown in Table 1.3.
The outcome from this analysis specified that EGFR, K-ras oncogene protein, and TP53 constitutes of 15, 11, and 10α helices, respectively. Besides that, Table 1.4 represents the details of the longest and shortest alpha helix of all the protein models.
1.3.3 Verification of Stability of Protein Structures
PROCHECK server was used to verify the stereo chemical quality and the geometry of protein models through Ramachandran plots (Figure 1.2). Furthermore, it was revealed that all the protein structures are in most favorable region because they had percentage value more than 80% (Table 1.5). Thus, the standard of these proteins was assessed to be immense and reliable. On top of that, PROCHECK analysis disclose that a number of residues such as TYR265 and GLU51 for EGFR while LYS180 for K-ras oncogene protein were located away from energetically favored regions of Ramachandran plot. Besides that, there are no residues found at forbade region for TP53 protein model.
Thereby, the stereo chemical interpretation of backbone phi/psi dihedral angles deduced that EGFR, K-ras oncogene protein, and TP53 have low percentage of residues among the protein models. Moreover, ProQ was utilized in order to validate “the quality” with the usage of Levitt-Gerstein (LG) score and maximum subarray (MaxSub). All the protein models were within the range for LG and MaxSub score according to the outcome exhibited for creating a good model (Table 1.5).
Table 1.2 The number disulfide bonds were quantitated by Cys_Rec prediction program.
| Protein | Cys_Rec | Score |
| EGFR | Cys_9 | –13.0 |
| Cys_13 | 39.2 | |
| Cys_17 | 100.1 | |
| Cys_25 | 98.3 | |
| Cys_26 | 104.2 | |
| Cys_30 | 104.1 | |
| Cys_34 | 90.5 | |
| Cys_42 | 48.2 | |
| Cys_45 | 56.0 | |
| Cys_54 | 58.2 | |
| Cys_58 | 49.5 | |
| Cys_85 | 55.7 | |
| Cys_89 | 54.9 | |
| Cys_101 | 50.4 | |
| Cys_105 | 44.0 | |
| Cys_120 | 63.0 | |
| Cys_123 | 73.3 | |
| Cys_127 | 75.3 | |
| Cys_131 | 61.6 | |
| Cys_156 | 33.0 | |
| Cys_264 | 45.3 | |
| Cys_293 | 43.8 | |
| Cys_300 | 56.5 | |
| Cys_304 | 46.8 | |
| Cys_309 | 66.0 | |
| Cys_317 | 65.6 | |
| Cys_320 | 60.2 | |
| Cys_329 | 49.1 | |
| Cys_333 | 42.2 | |
| Cys_349 | 42.2 | |
| Cys_352 | 32.9 | |
| Cys_356 | 62.9 | |
| Cys_365 | 70.2 | |
| Cys_373 | 54.2 | |
| Cys_376 | 54.8 | |
| Cys_385 | 35.8 | |
| Cys_389 | 41.2 | |
| Cys_411 | 78.8 | |
| Cys_414 | 85.1 | |
| Cys_418 | 84.4 | |
| Cys_422 | 26.5 | |
| Cys_430 | 3.7 | |
| KRAS | Cys_12 | –28.5 |
| Cys_51 | –74.2 | |
| Cys_80 | –72.6 | |
| Cys_118 | –56.4 | |
| Cys_185 | –15.2 | |
| TP53 | Cys_124 | –19.4 |
| Cys_135 | –1.6 | |
| Cys_141 | –17.9 | |
| Cys_176 | –9.1 | |
| Cys_182 |
|