Both ligands (FPP and H-RAS-1 carboxy tetrapeptide CVLS terminus) were docked separately with FTase following the computational procedure described in methodology section and final orientations were assembled in a ternary complex (FPP + CVLS + FTase). This complex was subjected to initial minimization (conjugate gradients, RMS = 0.01, backbone fixed) to discard high energy interactions, followed by 200 ps molecular dynamic (T = 300K, Newton equation integrated every two fs, backbone fixed). The lowest energy frame obtained by final 100 ps of MD trajectory was finally optimized using same conditions of preliminary minimization.
 |
Farnesyl Pyrophosphate
(FPP) (see the complex) |
 |
H-RAS-1 CVLS segment (see the complex) |
MTEYKLVVV GAGGVGKSAL TIQLIQNHFV DEYDPTIEDS YRKQVVIDGE TCLLDILDTA GQEEYSAMRD QYMRTGEGFL CVFAINNTKS FEDIHQYREQ IKRVKDSDDV PMVLVGNKCD LAARTVESRQ AQDLARSYGI PYIETSAKTR QGVEDAFYTL KLNPPDESGP GCMSCKCVLS |
H-RAS-1 Aminoacid sequence |