Rapamycin is an immunosuppressive drug that binds simultaneously to the 12-kDa FK506-and rapamycin-binding protein (FKBP12, or FKBP) and the FKBP-rapamycin binding (FRB) domain of the mammalian target of rapamycin (mTOR) kinase. The resulting ternary complex has been used to conditionally perturb protein function, and one such method involves perturbation of a protein of interest through its mislocalization. We synthesized two rapamycin derivatives that possess large substituents at the C-16 position within the FRB-binding interface, and these derivatives were screened against a library of FRB mutants using a three-hybrid assay in Saccharomyces cerevisiae. Several FRB mutants responded to one of the rapamycin derivatives, and twenty of these mutants were further characterized in mammalian cells. The mutants most responsive to the ligand were fused to yellow fluorescent protein, and fluorescence levels in the presence and absence of the ligand were measured to determine stability of the fusion proteins. Wild-type and mutant FRB domains were expressed at low levels in the absence of the rapamycin derivative, and expression levels rose up to 10-fold upon treatment with ligand. The synthetic rapamycin derivatives were further analyzed using quantitative mass spectrometry, and one of the compounds was found to contain contaminating rapamycin. Furthermore, uncontaminated analogs retained the ability to inhibit mTOR, although with diminished potency relative to rapamycin. The ligand-dependent stability displayed by wild-type FRB and FRB mutants as well as the inhibitory potential and purity of the rapamycin derivatives should be considered as potentially confounding experimental variables when using these systems.A common approach for studying complex biological processes is to perturb a protein of interest and observe subsequent changes to the biological system. The classical approach of disrupting a gene and studying the resultant phenotype is problematic for examining essential genes. As a result, several conditional techniques have been developed including the tetracycline/doxycycline and Cre recombinase/lox P systems, where control is exerted at the transcriptional level (1, 2). At the post-transcriptional level, RNA interference (RNAi) 2 is becoming rapidly used as a method of gene silencing (3), but RNAi lacks tunability and does not affect existing protein levels. An ideal perturbation method would directly affect the protein with a cell-permeable probe that rapidly and reversibly targets a specific protein of interest.Small molecules have been very useful as conditional perturbants; however, the lack of specificity of many of these reagents can make it difficult to unambiguously interpret results. One approach to ensure specificity is to chemically modify a small molecule with a large substituent, and this technique has been widely used to interrogate specific protein tyrosine kinases that possess a complementary cavity-forming mutation (4, 5). An alternative system has recently been developed using a cellperm...