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 angstrom and 2.71 angstrom 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 angstrom for the backbone and 5.7 angstrom 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. Besides finding close agreement in backbone and side chain conformations in these segments, except for the two regions noted above, we find that there is a good correlation between the RMS deviation of a given segment and the average B-factor for that segment. This result suggests that, besides the differences in conformation in residues 32-40 and 61-74 caused by the presence of different ligands bound to the protein, differences in structures between computed and x-ray structures may be caused by thermal fluctuations of segments in the x-ray structure. Overall, our method for computing the structure of the p21 protein from its alpha-carbons appears to be reliable and of general use. A basic observation that emerges from this comparative study is that the SCRs of the protein appear to determine the low energy conformations. of variable loop regions. including the side chain conformations in these regions. This observation is consistent with the hypothesis that folding proteins contain nucleation sequences that guide the folding process by adopting their native-like structures and compel adjacent sequences to adopt compatible conformations.