, In order to account for the effects of the so-called GAP arginine finger (residue Arg 789), it is necessary to position GAP with respect to NRas and extract the corresponding GAP coordinates
, leucine (Q61L), histidine (Q61H), proline (Q61P) and glutamic acid (Q61E), using PyMOL mutagenesis command [64]. Indeed, a previous X-ray structure analysis [37] concluded that the overall structural changes between the wild-type and oncogenic mutant proteins are very small. The only consistent changes appear in the Switch I (residues 30 to 38) and Switch II (residues 57 to 67) regions which have been nevertheless reported to be very mobile by several experimental studies, A.1.2 Gln 61 mutant NRas Six oncogenic mutant structures were prepared from the wild-type structure, substituting Gln 61 by arginine (Q61R), lysine (Q61K)
, A.1.3 Static modes structures
, The most representative configuration of each NRas-GTP complex was identified by a clustering algorithm [58] implemented in the AMBER package. The structures of the protein-ligand complexes together with the magnesium ion, two coordinated water molecules and water molecules present within 5Å of GTP P ? atom were subsequently energy minimized in implicit solvent, using the generalized Born model [25] until the convergence criterion was reached (root mean square gradient < 10 ?6 kcal/(mol·Å)). Following this procedure, Gln 61 mutant NRas structures for which the static modes were calculated, were extracted from the QM/MM trajectories obtained
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