Activated conformations of the ras-gene-encoded p21 protein. 2. Comparison of the computed and high-resolution x-ray crystallographic structures of Gly-12 p21.

The ras-oncogene-encoded p21 protein is a G-protein that has been shown to cause the malignant transformation of normal cells and has been implicated in causing human tumors. p21 is thought to be activated by the binding of GTP in place of GDP to the protein. We have previously constructed the three-dimensional structure of the p21 protein bound to GDP from an available alpha-carbon tracing of this protein using a combination of molecular dynamics and energy minimization (Dykes, et al., J. Biomol. Struct. Dynamics, 9:1025-1044). Until the recent publication of the all-heavy-atom x-ray crystallographic molecular coordinates of p21 residues 1-166 bound to a non-hydrolyzable GTP derivative (GppNp), no all-atom structure of the p21 protein has been available in the Brookhaven National Laboratories Protein Data Bank (PDB). In this communication we compare our computed structure for the p21-GDP complex to this x-ray crystal structure. We find that the two structures agree quite closely with one another, the overall RMS deviation for the backbone being 1.47 A and 2.71 A for all of the atoms. We have identified the regions of the protein that are responsible for the most significant deviations between the two structures, i.e., residues 32-40 and 61-74. We find that the main chain in the 32-40 segment deviates significantly from residue 32 to residue 36 and the side chain phenolic rings of residue 32 differ greatly between the two structures. The 61-74 region is the least-well defined region in the whole protein crystallographically having, by far, the highest temperature factor (B-factor). The backbone and side chain conformations in the 61-74 segment differ markedly, the overall RMS deviation being 3.1 A for the backbone and 5.7 A for all atoms. Both of these regions have been found in x-ray crystallographic studies of p21-GDP and p21-GTP complexes to undergo significant changes in conformation upon the binding of GTP in place of GDP to the protein. We have further compared our computed structure of the p21 protein with the x-ray crystal structure with regard to the conformations of individual segments, in particular, structurally conserved sequences (SCR), i.e., those sequences that have structural and sequence homology to corresponding sequences in the related G-protein, bacterial elongation factor Tu(EF-Tu), and variable loop regions.(ABSTRACT TRUNCATED AT 400 WORDS)