Structural Analysis For Molecular Switches Of Ras P21

Based upon the crystal structural data from PDB, the mechanism of the GTP/GDP molecular switches of ras P21 is analyzed by the method of computer simulations for macrobiomolecule.GTP's hydrolization under RasGAP's catalysis is analyzed: The environment of nucleotide-binding pocket and Structural change of ras P21 upon GTP hydrolysis are discussed; Based upon three-dimensional structural analysis of ras P21, RasGAP's structural change upon GTP hydrolysis is analyzed; The Lys949 finger is indicated that it can contribute much to the orientation and binding between RasGAP and ras P21 as well as Switchl's conformational change upon GTP hydrolysis; A model of ras P21 hydrolyzing GTP under RasGAP's catalysis is advanced and the analytic result is the basis of further mutation analysis.GTP/GDP's exchange under Sos's catalysis is analyzed: By analyzing molecular surface, molecular flexibility, accessibility of Sos and ras P21, we try to know how Sos binds ras P21 and how GTP anchors in the nucleotide-binding pocket. Basic amino acids located around the entrance for nucleotide's entering in nucleotide-binding pocket are conservative, though the tertiary structure of small G protein's GEF is diverse. The side chains of these basic amino acids extend to the entrance and form a positive electrostatic potential, which may be helpful to nucleotide's congregation, orientating nucleotide to enter the nucleotide-binding pocket properly.These analysis clarifies the relation between the function and structure of ras P21, which is valualble as reference for further research of GTP's hydrolyzation and GTP/GDP's exchange.