Rapid and reversible methods for perturbing the function of specific proteins are desirable tools for probing complex biological systems. We have developed a general technique to regulate the stability of specific proteins in mammalian cells using cell-permeable, synthetic molecules. We engineered mutants of the human FKBP12 protein that are rapidly and constitutively degraded when expressed in mammalian cells, and this instability is conferred to other proteins fused to these destabilizing domains. Addition of a synthetic ligand that binds to the destabilizing domains shields them from degradation, allowing fused proteins to perform their cellular functions. Genetic fusion of the destabilizing domain to a gene of interest ensures specificity, and the attendant small-molecule control confers speed, reversibility, and dose-dependence to this method. This general strategy for regulating protein stability should enable conditional perturbation of specific proteins with unprecedented control in a variety of experimental settings.

Many signaling, cytoskeletal, and transport proteins have to be localized to the plasma membrane (PM) in order to carry out their function. We surveyed PM-targeting mechanisms by imaging the subcellular localization of 125 fluorescent protein-conjugated Ras, Rab, Arf, and Rho proteins. Out of 48 proteins that were PM-localized, 37 contained clusters of positively charged amino acids. To test whether these polybasic clusters bind negatively charged phosphatidylinositol 4,5-bisphosphate [PI(4,5)P 2 ] lipids, we developed a chemical phosphatase activation method to deplete PM PI(4,5)P 2 . Unexpectedly, proteins with polybasic clusters dissociated from the PM only when both PI(4,5)P 2 and phosphatidylinositol 3,4,5-trisphosphate [PI(3,4,5)P 3 ] were depleted, arguing that both lipid second messengers jointly regulate PM targeting.Small guanosine triphosphatases (GTPases) from the Ras, Rho, Arf, and Rab subfamilies often exert their role at the PM where they control diverse signaling, cytoskeletal, and transport processes (1-3). KRas, CDC42, and other family members require a cluster of positively charged amino acids for PM localization and activity (2, 4). In vitro studies indicate that the physiological PM binding partner of such polybasic clusters could be phosphatidylserine, which has one negative charge, or the less abundant lipid second messenger PI(4,5)P 2 , which has four negative charges (5-7). We took a genomic survey approach and investigated PM-targeting mechanisms by confocal imaging of 125 cyan fluorescent protein (CFP)-tagged constitutively active small GTPases (8). Expression in NIH3T3 and HeLa cells showed that 48 small GTPases were fully or partially localized to the PM (Fig. 1A and fig. S1).Thirty-seven of these PM-localized small GTPases had C-terminal polybasic clusters consisting of four or more Lys or Arg residues at positions 5 to 20 from the C terminus ( Fig. 1B and fig. S1). Polybasic clusters were found in three forms: They were present together with N-terminal myristoylation consensus sequences (as in Arl4) (9) or with C-terminal prenylation consensus sequences (as in KRas) (5, 6, 10), or they lacked lipid modifications (as in Rit) (11). We called these three combinations polybasic-myristoyl, polybasic-prenyl, and polybasic-nonlipid PM-targeting motifs, respectively. A number of remaining PMtargeted small GTPases had a combined prenylation and palmitoylation consensus sequence that mediated PM targeting without requiring polybasic amino acids (as does that of HRas) (Fig. 1D).To test whether polybasic clusters are anchored to the PM by binding to PI(4,5)P 2 (14), we hydrolyzed PM PI(4,5)P 2 by rapid targeting of Inp54p, a 5′ specific PI(4,5)P 2 phosphatase (15), to the PM. This method is based on a PM-localized FK506-binding protein (FKBP12)-rapamycin-binding (FRB) construct and a cytosolic Inp54p enzyme conjugated with FKBP12 (CF-Inp) that can be translocated to the PM by chemical heterodimerization by using a rapamycin analog, iRap (16).In experiments where we monitored PI(4,5)P...

Dimerization and oligomerization are general biological control mechanisms contributing to the activation of cell membrane receptors, transcription factors, vesicle fusion proteins, and other classes of intra- and extracellular proteins. Cell permeable, synthetic ligands were devised that can be used to control the intracellular oligomerization of specific proteins. To demonstrate their utility, these ligands were used to induce intracellular oligomerization of cell surface receptors that lacked their transmembrane and extracellular regions but contained intracellular signaling domains. Addition of these ligands to cells in culture resulted in signal transmission and specific target gene activation. Monomeric forms of the ligands blocked the pathway. This method of ligand-regulated activation and termination of signaling pathways has the potential to be applied wherever precise control of a signal transduction pathway is desired.

Rapamycin is an important immunosuppressant, a possible anticancer therapeutic, and a widely used research tool. Essential to its various functions is its ability to bind simultaneously to two different proteins, FKBP and mTOR. Despite its widespread use, a thorough analysis of the interactions between FKBP, rapamycin, and the rapamycin-binding domain of mTOR, FRB, is lacking. To probe the affinities involved in the formation of the FKBP.rapamycin.FRB complex, we used fluorescence polarization, surface plasmon resonance, and NMR spectroscopy. Analysis of the data shows that rapamycin binds to FRB with moderate affinity (K(d) = 26 +/- 0.8 microM). The FKBP12.rapamycin complex, however, binds to FRB 2000-fold more tightly (K(d) = 12 +/- 0.8 nM) than rapamycin alone. No interaction between FKBP and FRB was detected in the absence of rapamycin. These studies suggest that rapamycin's ability to bind to FRB, and by extension to mTOR, in the absence of FKBP is of little consequence under physiological conditions. Furthermore, protein-protein interactions at the FKBP12-FRB interface play a role in the stability of the ternary complex.