Jm. Chen et al., ONCOGENIC AMINO-ACID SUBSTITUTIONS IN THE INHIBITORY RAP-1A PROTEIN CAUSE IT TO ADOPT A RAS-P21-LIKE CONFORMATION AS COMPUTED USING MOLECULAR-DYNAMICS, Journal of biomolecular structure & dynamics, 13(6), 1996, pp. 925-933
rap-1A is a membrane-bound G-protein in the ras superfamily that, like
the ras-p21 protein, is activated by binding GTP in place of GDP When
activated, however, this protein inhibits the action of ras-p21, whic
h is to induce mitogenesis in cells. A chimeric protein containing ras
-p21 residues 1-65 and rap-1A residues 66-184 becomes ras-p21-like in
its activity. The critical changes in sequence that result in this tra
nsformation are G26N, I27H, E30D, K31E, and E45V. All of these substit
utions occur in or around a critical effector domain of p21 that is in
volved in interacting with GTPase activating protein (GAP), raf-p74 pr
otein and inositol-3-hydroxy kinase. Using molecular dynamics, we have
computed the average low energy structures for each of the three prot
eins, ras-p21, rap-1A and mutant rap1A, called rap-M, that contains th
ese critical amino acid substitutions. We find that rap-M more closley
superimposes on ras-p21 (rms deviation 1.9 Angstrom) than on wild-typ
e rap-1A (rms deviation 3.4 Angstrom). In particular, the amino termin
al domains (residues 3-59) of both ras-p21 and rap-M are superimposabl
e while they deviate when the average structures of these two proteins
are superimposed on that of wild-type rap-1A. We have identified Pro
34 as a critical residue which may determine if the protein transforms
cells or inhibits cell transformation. In addition, we have found tha
t ras-p21 and rap-M proteins are superimposable in the region 96-110 e
xcept at Asp 105. The 96-110 domain of ras-p21 has been found to be in
volved in the binding of this protein to the nuclear transcription pro
tein, jun and its kinase, jun kinase, JNK. Both segments differ in str
ucture from that of the rap-1A segment at Asp 108, implicating this re
sidue as also being important in determining the activity of the prote
in. Overall, the oncogenic substitutions introduced into the rap-1A pr
otein cause it to adopt a conformation that is very similar to that of
ras-p21 rather than wild-type rap-1A.