Molecular dynamics simulation of the solution structures of Ha-ras-p21 GDP and GTP complexes: flexibility, possible...

Unconstrained molecular dynamics simulations of the GDP and GTP complexes of Ha-ras p21 protein are performed in aqueous environment for 500 ps, using the GROMOS force field. The solvated structures are mutually compared as well as to the X-ray structures [Tong, L. A., de Vos, A. M., Milburn, M. V., & Kim, S. H. (1991) J. Mol. Biol. 217, 503-516; Pai, E. F., Krengel, U., Petsko, G. A., Goody, R. S., Kabsh, W., & Wittinghofer, A. (1990) EMBO J. 9, 2351-2359]. The simulations show areas of flexibility, with deviations from the original structures. The parts that show differences between the two solvated forms are those from residues 12 to 17, 25 to 38, 41 to 51, 57 to 73, 99 to 112, and 120 to 152, coincident with areas of flexibility. Some of these areas also show differences between the X-ray structures and are part of loops on the surface of the protein. Many of the residues in the ends of these loops undergo dihedral transitions during the solvation process. Of all the dihedral transitions observed, 62% occur around the ends of these loops. This suggests that the ends of the areas from 12 to 17, 25 to 38, and 57 to 73 are the hinge points of the conformational transition between the GTP and the GDP forms. The study of the nucleotide interactions in the solution forms shows that residues 29, 30, and 35 establish contacts with the gamma-phosphate and the sugar ring of the GTP and thus these contacts could be proposed as the possible levers of the conformational transition that accompanies GTP hydrolysis.