The ras-like GTP binding proteins cdc42, rac, and rho regulate diverse cellular processes including cell growth and actin remodeling associated with changes in cell morphology, growth, adhesion, and motility (1-4). In fibroblasts, cdc42 regulates actin polymerization and focal complexes necessary for filopodia formation, rac mediates actin polymerization and focal complex assembly within lamellipodia and membrane ruffles, and rho induces actin stress fiber and focal adhesion (FA) complex formation (5). A hierarchical relationship exists among cdc42, rac, and rho, whereby cdc42 regulates rac activity and rac regulates rho activity, suggesting that these proteins may orchestrate the spatial and temporal changes in the actin cytoskeleton necessary for cell movement (5, 6). cdc42 and rac also regulate activation of the c-Jun N-terminal kinase/stressactivated kinase via a mitogen-activated protein (MAP) kinase pathway (7-9), and rac and rho are essential for ras transformation (10, 11). cdc42, rho, and rac all appear to stimulate c-fos transcription (12), as well as cell cycle progression through GI and subsequent DNA synthesis (9). The activation state of ras-like GTP binding proteins is positively regulated by guanine nucleotide exchange factors (GEFs) that promote the exchange of GDP for GTP, and negatively by GTPase activating proteins (2). A number of putative GEFs for rho-like GTPases have been identified by sequence comparison (2), and several of these demonstrate GEF activity in vitro. The dbl and ost oncogene products have cdc42 and rho GEF activity (13-15); the lbc oncogene product has rho GEF activity (16); the invasion-inducing Tiaml gene product has cdc42, rho, and rac GEF activity (17); and the yeast CDC24 gene product has cdc42 GEF activity (18). LAR is a broadly expressed transmembrane protein tyrosine phosphatase (PTPase) comprised of a cell adhesion-like extracellular region and two intracellular PTPase domains (19)(20)(21)(22). A role for LAR in regulating cell-matrix interactions was proposed, as LAR colocalizes with a coiled-coil protein, termed LAR interacting protein 1 (LIP.1) at the ends of FAs (23), and LAR expression was observed at regions of association between cells and basement membrane in various tissues (19). To identify putative substrates and other proteins involved in LAR-mediated signal transduction, we screened for proteins that bind the LAR PTPase domains using the interaction-trap assay and coimmunoprecipitation studies. A protein thus isolated is a novel multidomain GEF we have named Trio because it contains three enzyme domains: two GEF domains, one of which has racl GEF activity and the other has rhoA GEF activity, and a serine/threonine kinase (PSK) domain. In addition, Trio contains four N-terminal spectrinlike domains, two pleckstrin-like domains, and an Ig-like domain. Because proteins with cdc42, rac, or rho GEF activity are generally involved in regulating cytoskeletal organization (1), it is likely that Trio in conjunction with LAR plays a key role in coordinating the ...

Aromatic residues are frequently found in helical and beta-barrel integral membrane proteins enriched at the membrane-water interface. Although the importance of these residues in membrane protein folding has been rationalized by thermodynamic partition measurements using peptide model systems, their contribution to the stability of bona fide membrane proteins has never been demonstrated. Here, we have investigated the contribution of interfacial aromatic residues to the thermodynamic stability of the beta-barrel outer membrane protein OmpA from Escherichia coli in lipid bilayers by performing extensive mutagenesis and equilibrium folding experiments. Isolated interfacial tryptophanes contribute -2.0 kcal/mol, isolated interfacial tyrosines contribute -2.6 kcal/mol, and isolated interfacial phenylalanines contribute -1.0 kcal/mol to the stability of this protein. These values agree well with the prediction from the Wimley-White interfacial hydrophobicity scale, except for tyrosine residues, which contribute more than has been expected from the peptide models. Double mutant cycle analysis reveals that interactions between aromatic side chains become significant when their centroids are separated by less than 6 A but are nearly insignificant above 7 A. Aromatic-aromatic side chain interactions are on the order of -1.0 to -1.4 kcal/mol and do not appear to depend on the type of aromatic residue. These results suggest that the clustering of aromatic side chains at membrane interfaces provides an additional heretofore not yet recognized driving force for the folding and stability of integral membrane proteins.

The retinoblastoma (Rb) antioncogene encodes a nuclear phosphoprotein, p105-Rb, that forms protein complexes with the adenovirus E1A and SV40 large T oncoproteins. A novel, aberrant Rb protein detected in J82 bladder carcinoma cells was not able to form a complex with E1A and was less stable than p105-Rb. By means of a rapid method for the detection of mutations in Rb mRNA, this defective Rb protein was observed to result from a single point mutation within a splice acceptor sequence in J82 genomic DNA. This mutation eliminates a single exon and 35 amino acids from its encoded protein product.

The mixed lineage leukemia (MLL) gene plays a critical role in epigenetic regulation of gene expression and is a frequent target of chromosomal translocations leading to leukemia. MLL plant homeodomain 3 (PHD3) is lost in all MLL translocation products, and reinsertion of PHD3 into MLL fusion proteins abrogates their transforming activity. PHD3 has been shown to interact with the RNA-recognition motif (RRM) domain of human nuclear Cyclophilin33 (CYP33). Here, we show that CYP33 mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. This downregulation correlates with the reduction of trimethylated lysine 4 of histone H3 (H3K4me3) and histone H3 acetylation. We have structurally characterized both the PHD3 and CYP33 RRM domains and analyzed their binding to one another. The PHD3 domain binds H3K4me3 (preferentially) and the CYP33 RRM domain at distinct sites. Our binding data show that binding of H3K4me3 to PHD3 and binding of the CYP33 RRM domain to PHD3 are mutually inhibitory, implying that PHD3 is a molecular switch for the transition between activation and repression of target genes. To explore the possible mechanism of CYP33/PHD3-mediated repression, we have analyzed the CYP33 proline isomerase activity on various H3 and H4 peptides and shown selectivity for two sites in H3. Our results provide a possible mechanism for the MLL PHD3 domain to act as a switch between activation and repression.