Table 1 An overview of the calculated interaction energies (kcal/mol) between key sub-structures and residues in A) B-RAFWT and B-RAFV600E and in B) B-RAFK601E and B-RAFD594V.
From: An in silico study of the molecular basis of B-RAF activation and conformational stability
A) | B-RAFWT | B-RAFV600E | ||||
|---|---|---|---|---|---|---|
Substructure | vdW | El | Total | vdW | El | Total |
A-loopa | -100.9 ± 6.9 | -200.1 ± 18.6 | -301.0 ± 16.5 | -99.1 ± 5.6 | -153.6 ± 24.4 | -252.7 ± 24.5 |
A-loop-αC-helixb | -20.2 ± 1.9 | -31.4 ± 5.9 | -51.6 ± 5.4 | -27.0 ± 3.2 | -5.8 ± 10.6 | -32.8 ± 9.9 |
A-loop-P-loopc | -12.7 ± 2.2 | -18.2 ± 5.5 | -30.9 ± 5.1 | -22.6 ± 2.0 | -11.9 ± 2.8 | -34.5 ± 3.2 |
A-loop-β6-strandd | -12.4 ± 2.7 | -31.6 ± 8.6 | -44.0 ± 8.4 | -14.2 ± 2.1 | -44.5 ± 9.3 | -58.7 ± 8.9 |
A-loop-F-loope | -18.5 ± 1.8 | -3.4 ± 4.4 | -21.9 ± 4.1 | -15.3 ± 2.7 | -20.3 ± 23.5 | -35.6 ± 23.4 |
A-loop-αG-helixf | -3.6 ± 1.3 | -33.6 ± 7.4 | -37.2 ± 7.3 | -0.7 ± 0.3 | -6.4 ± 2.5 | -7.1 ± 2.6 |
Lys601g | -14.9 ± 2.3 | -150.3 ± 15.1 | -165.2 ± 14.8 | -15.8 ± 2.3 | -137.7 ± 12.7 | -153.5 ± 12.1 |
Lys601-αC-helixh | -0.7 ± 1.5 | -73.3 ± 9.9 | -74.0 ± 9.2 | -3.2 ± 0.5 | -22.8 ± 3.1 | -26.0 ± 3.1 |
Lys483-Asp594i | -0.1 ± 0.9 | -69.0 ± 9.5 | -69.1 ± 9.0 | -0.3 ± 0.1 | -39.4 ± 4.4 | -39.7 ± 4.5 |
Lys601-Asp594j | -0.2 ± 0.6 | -58.2 ± 4.2 | -58.4 ± 4.0 | -1.5 ± 3.9 | -61.5 ± 4.5 | -63.0 ± 3.4 |
(K601-D594)-k (E501-K483) | -0.9 ± 1.7 | -70.8 ± 7.5 | -71.7 ± 6.7 | -4.0 ± 0.5 | 0.2 ± 3.5 | -3.8 ± 3.5 |
(K601-D594)-l (D576-N581) | -1.4 ± 0.4 | 2.3 ± 3.3 | 0.9 ± 3.1 | -2.1 ± 1.5 | -40.3 ± 8.7 | -42.4 ± 8.1 |
B) | B-RAF K601E | B-RAF D594V | ||||
Substructure | vdW | El | Total | vdW | El | Total |
A-loopa | -117.7 ± 5.8 | -261.5 ± 26.4 | -379.2 ± 26.6 | -105.6 ± 5.3 | -108.8 ± 12.2 | -214.4 ± 12.8 |
A-loop-αC-helixb | -34.2 ± 2.9 | -9.2 ± 12.2 | -43.4 ± 12.2 | -32.7 ± 2.7 | -27.7 ± 7.9 | -60.4 ± 7.6 |
A-loop-P-loopc | -16.2 ± 1.8 | -18.4 ± 3.8 | -34.6 ± 4.4 | -20.0 ± 1.7 | -1.9 ± 2.4 | -21.9 ± 2.9 |
A-loop-β6-strandd | -17.9 ± 2.2 | -26.9 ± 7.1 | -44.8 ± 7.2 | -18.5 ± 2.4 | -35.1 ± 7.7 | -53.6 ± 7.0 |
A-loop-F-loope | -2.6 ± 0.7 | -0.2 ± 1.6 | -2.8 ± 1.8 | -13.9 ± 2.6 | 1.1 ± 3.7 | -12.8 ± 5.0 |
A-loop-αG-helixf | -2.3 ± 1.2 | -56.5 ± 8.3 | -58.8 ± 8.4 | -0.07 ± 0.1 | 0.12 ± 1.7 | 0.05 ± 1.7 |
Lys601g | -12.1 ± 2.6 | -141.6 ± 7.2 | -153.7 ± 6.8 | -20.3 ± 2.2 | -102.9 ± 12.8 | -123.2 ± 12.7 |
Lys601-αC-helixh | -5.6 ± 1.4 | -10.8 ± 4.5 | -16.4 ± 4.1 | -5.8 ± 0.8 | -29.6 ± 3.0 | -35.4 ± 2.9 |
Lys483-Asp594i | -0.4 ± 0.6 | -52.8 ± 7.7 | -53.2 ± 7.5 | -0.02 ± 0.0 | 1.06 ± 0.3 | 1.04 ± 0.3 |
Lys601-Asp594j | -0.3 ± 0.1 | 36.4 ± 3.4 | 36.1 ± 3.3 | -0.8 ± 0.7 | -6.6 ± 1.9 | -7.4 ± 1.7 |
(K601-D594)-k (E501-K483) | -2.0 ± 1.4 | -48.9 ± 5.7 | -50.9 ± 5.5 | -4.0 ± 0.6 | -9.1 ± 2.1 | -13.1 ± 2.0 |
(K601-D594)-l (D576-N581) | -2.9 ± 0.5 | 60.9 ± 4.2 | 58.0 ± 4.0 | -2.6 ± 1.5 | -79.0 ± 6.8 | -81.6 ± 6.7 |