Table 2.
Structural characterized features used in the graph constructions for the PI-resistance mutants to IDV and LPV
| Vpocketa (Å3) | AllosCommb | ΔΔG score / ΔSc (kcal/mol) | RMSd (Å) | |
|---|---|---|---|---|
| Indinavir (IDV) — molecular weight = ~614 g/mol | ||||
| IDV_0 (major/minor) | 1929.67 (1863.57) | 0.989 (0.745) | −1.37 / −1.18 | 1.14 |
| IDV_1 (major/minor) | 1884.57 | 0.770 (0.825) | 4.32 / −0.45 | 1.09 |
| IDV_2 (major/minor) | 1769.62 | 0.518 (0.468) | 2.14 / 0.72 | 1.04 |
| Lopinavir (LPV) — molecular weight = ~629 g/mol | ||||
| LPV_0 (wt) | 1659.68 (2201.32) | 0.696 (0.257) | 0.13 / 0.34 | 0.88 |
| LPV_1 (major/minor) | 1872.66 | 0.590 (0.547) | 4.53 / 0.58 | 1.0 |
| LPV_2 (major/minor) | 1867.24 | 0.665 (0.452) | 1.51 / −0.15 | 0.98 |
| LPV_3 (major/minor) | 1781.42 | 0.8 (0.646) | 4.28 / 1.47 | 1.06 |
| LPV_4 (major/minor) | 2029.70 | 0.769 (0.646) | 1.51 / 0.48 | 1.08 |
| LPV_5 (minor) | 2051.45 | 0.167 (0.944) | 1.28 / 0.62 | 1.08 |
| LPV_6 (minor) | 2034.89 | 0.385 (0.944) | 2.27 / 0.78 | 1.08 |
aPocket volume of the native protease [PDB: 1ODW], which contains no mutations in the presence of corresponding PIs, is shown in parentheses for comparison purpose. In the cases of wild type proteases LPV_0, there is a single mutation found (i.e. L63P) in the structures when compared to the native protease sequence. The complexes that contain the quadruple mutants and show increased pocket volume are in bold
bFor comparison purposes of allosteric effect, communication estimated values of the native protease were shown in parentheses
cΔΔG and ΔS scores represent free energy and vibrational energy respectively, demonstrating thermo-stability of the protease when mutated from the native protease