Table 5.
Comparative analysis of delta delta G (DDG) or ΔΔG of emerging mutations of S-glycoprotein in Omicron variant
| NMA based prediction | ΔΔG prediction | Other structure-based predictions | Minute vibrational entropy energy change between wild-type and mutant | Remarks | ||||
|---|---|---|---|---|---|---|---|---|
| Sl no | Significant mutations of Omicron variant |
ΔΔG ENCoM (kcal/mol) |
ΔΔG (kcal/mol) |
ΔΔG mCSM (kcal/mol) |
ΔΔG DUET (kcal/mol) |
ΔΔG SDM (kcal/mol) |
ΔΔSVib ENCoM (kcal mol−1 K−1) |
|
| 1 | K417N |
− 0.677, Destabilizing |
− 0.932, Destabilizing |
− 1.138, Destabilizing |
− 1.123, Destabilizing |
− 0.280, Destabilizing |
0.846 | Increase of molecule flexibility increased |
| 2 | S477N |
0.064, Destabilizing |
0.628, Stabilizing |
− 0.215, Destabilizing |
0.235, Stabilizing |
0.780, Stabilizing |
− 0.080 | Decrease of molecule flexibility |
| 3 | T478K |
0.181, Destabilizing |
1.009, Stabilizing |
− 0.695, Destabilizing |
− 0.366, Destabilizing |
− 0.070, Destabilizing |
− 0.227 | Decrease of molecule flexibility |
| 4 | D796Y |
− 0.052, Destabilizing |
0.146, Stabilizing |
0.387, Stabilizing |
0.370, Stabilizing |
− 0.010, Destabilizing |
0.065 | Increase of molecule flexibility |
| 5 | G196D |
0.897, Stabilizing |
0.193, Stabilizing |
− 2.071, Destabilizing |
− 2.248, Destabilizing |
− 2.160, Destabilizing |
− 1.121 | Decrease of molecule flexibility |
| 6 | G446S |
− 0.283, Destabilizing |
− 0.501, Destabilizing |
− 0.593, Destabilizing |
− 0.366, Destabilizing |
− 0.680, Destabilizing |
0.353 | Increase of molecule flexibility |
| 7 | E484A |
− 0.377, Destabilizing |
− 0.456, Destabilizing |
− 0.415, Destabilizing |
− 0.128, Destabilizing |
0.320, Stabilizing |
0.471 | Increase of molecule flexibility |
| 8 | T95I |
0.320, Destabilizing |
1.200, Stabilizing |
− 0.097, Destabilizing |
0.670, Stabilizing |
1.910, Stabilizing |
− 0.400 | Decrease of molecule flexibility |
| 9 | D614G |
− 0.134, Destabilizing |
0.351, Stabilizing |
− 0.514, Destabilizing |
0.171, Stabilizing |
2.510, Stabilizing |
0.168 | Decrease of molecule flexibility |
| 10 | H655Y |
0.158, Destabilizing |
1.728, Stabilizing |
1.302, Stabilizing |
1.516, Stabilizing |
0.400, Stabilizing |
− 0.197 | Decrease of molecule flexibility |
| 11 | Q493K |
0.066, Destabilizing |
0.470, Stabilizing |
0.194, Stabilizing |
0.794, Stabilizing |
0.580, Stabilizing |
− 0.082 | Decrease of molecule flexibility |
| 12 | G496S | − 0.014, Destabilizing | − 0.097, Destabilizing | − 0.763, Destabilizing | − 0.614, Destabilizing | − 1.010, Destabilizing | 0.018 | Decrease of molecule flexibility |
| 13 | N501Y |
− 0.094, Destabilizing |
− 0.203, Destabilizing |
− 0.457, Destabilizing |
− 0.471, Destabilizing |
0.280, Stabilizing |
0.117 | Decrease of molecule flexibility |
| 14 | Y505H |
− 0.305, Destabilizing |
− 0.510, Destabilizing |
− 0.119, Destabilizing |
0.143, Stabilizing |
0.380, Stabilizing |
0.381 | Decrease of molecule flexibility |
| 15 | N969K |
− 0.381, Destabilizing |
0.086, Stabilizing |
0.065, Stabilizing |
0.184, Stabilizing |
− 0.500, Destabilizing |
0.477 | Increase of molecule flexibility |
| 16 | A67V |
0.520, Stabilizing |
0.544, Stabilizing |
− 0.387, Destabilizing |
0.256, Stabilizing |
0.950, Stabilizing |
− 0.650 | Decrease of molecule flexibility |
| 17 | L981F |
0.009, Destabilizing |
0.104, Stabilizing |
− 1.241, Destabilizing |
− 1.289, Destabilizing |
− 0.69, Destabilizing |
0.012 | Increase of molecule flexibility |
| 18 | N440K |
0.045, Destabilizing |
0.064, Stabilizing |
0.243, Stabilizing |
0.876, Stabilizing |
0.780, Stabilizing |
− 0.057 | Decrease of molecule flexibility |
| 19 | N856K |
0.202, Destabilizing |
1.304, Stabilizing |
0.103, Stabilizing |
0.314, Stabilizing |
0.300, Destabilizing |
− 0.252 | Decrease of molecule flexibility |
| 20 | Q498R |
− 0.289, Destabilizing |
− 0.163, Destabilizing |
0.283, Stabilizing |
0.519, Stabilizing |
0.550, Stabilizing |
0.361 | Increase of molecule flexibility |
| 21 | S371L |
0.030, Stabilizing |
0.127, Stabilizing |
− 0.394, Destabilizing |
0.080, Stabilizing |
1.280, Stabilizing |
− 0.037 | Decrease of molecule flexibility |
| 22 | G339D |
− 0.027, Stabilizing |
0.019, Stabilizing |
− 0.69, Destabilizing |
− 0.400, Destabilizing |
0.110, Stabilizing |
0.033 | Increase of molecule flexibility |
| 23 | L212I |
− 0.028, Destabilizing |
0.090, Stabilizing |
− 0.844, Destabilizing |
− 0.334, Destabilizing |
0.490, Stabilizing |
0.035 | Increase of molecule flexibility |
| 24 | S375F |
0.578, Stabilizing |
− 0.125, Destabilizing |
− 0.948, Destabilizing |
− 0.460, Destabilizing |
1.190, Stabilizing |
− 0.723 | Decrease of molecule flexibility |
| 25 | S373P |
− 0.323, Destabilizing |
− 0.797, Destabilizing |
− 0.645, Destabilizing |
− 0.534, Destabilizing |
− 0.030, Destabilizing |
0.404 | Increase of molecule flexibility |
| 26 | N764K |
− 0.344, Destabilizing |
0.189, Stabilizing |
0.089, Stabilizing |
0.475, Stabilizing |
− 0.300, Destabilizing |
0.430 | Increase of molecule flexibility |
| 27 | T547K |
0.072, Destabilizing |
0.462, Stabilizing |
− 0.244, Destabilizing |
0.194, Stabilizing |
− 0.090, Destabilizing |
− 0.090 | Increase of molecule flexibility |
| 28 | Q954H |
0.192, Destabilizing |
0.969, Stabilizing |
− 0.676, Destabilizing |
− 0.491, Destabilizing |
0.060, Stabilizing |
− 0.240 | Decrease of molecule flexibility |