The function of the R domain of CFTR has not yet been fully established. The cis-trans proline isomerase cyclophilin A stimulates channel activity, and stimulation depends on the presence of highly conserved prolines at positions 740, 750 and 759. When the prolines at these positions, which normally exist in the cis conformation, are locked into the trans conformation by mutation to alanine (the P3A mutant), the open probability (Po) of P3A is high and is not further increased by cyclophilin A. We speculated that one mechanism by which this could occur was by promoting CFTR dimerization, which has been shown to increase Po, and that the P3A-CFTR might favor dimerization more strongly than the native sequence. To test the hypothesis that R-R interaction occurs and is stronger in the P3A-R mutants, we investigated R-R interactions. GST-R and StrepII-R proteins expressed in E.coli could interact with R domain protein translated in vitro as well as with full length CFTR. In similar assays, the P3A mutant of R domain also interacts with R domain and P3A-R. The P3A-R-P3A-R interaction is stronger than the R-R interaction, which corroborates our data from the channel study and supports our hypothesis. Studies of deletion constructs of the isolated R domain and of full length CFTR localize the region of interaction to the N-terminal portion of R. (after a.a. 708). Particularly, the last 22 a.a residues (838-859) of R are essential for this binding. R-R interaction possibly plays a role in channel gating.