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During the activation of mitogen-activated protein kinase (MAPK) signaling, the RAS-binding domain (RBD) and cysteine-rich domain (CRD) of RAF bind to active RAS at the plasma membrane. The orientation of RAS at the membrane may be critical for formation of the RAS-RBDCRD complex and subsequent signaling. To explore how RAS membrane orientation relates to the protein dynamics within the RAS-RBDCRD complex, we perform multiscale coarse-grained and all-atom molecular dynamics (MD) simulations of KRAS4b bound to the RBD and CRD domains of RAF-1, both in solution and anchored to a model plasma membrane. Solution MD simulations describe dynamic KRAS4b-CRD conformations, suggesting that the CRD has sufficient flexibility in this environment to substantially change its binding interface with KRAS4b. In contrast, when the ternary complex is anchored to the membrane, the mobility of the CRD relative to KRAS4b is restricted, resulting in fewer distinct KRAS4b-CRD conformations. These simulations implicate membrane orientations of the ternary complex that are consistent with NMR measurements. While a crystal structure-like conformation is observed in both solution and membrane simulations, a particular intermolecular rearrangement of the ternary complex is observed only when it is anchored to the membrane. This configuration emerges when the CRD hydrophobic loops are inserted into the membrane and helices α3-5 of KRAS4b are solvent exposed. This membrane-specific configuration is stabilized by KRAS4b-CRD contacts that are not observed in the crystal structure. These results suggest modulatory interplay between the CRD and plasma membrane that correlate with RAS/RAF complex structure and dynamics, and potentially influence subsequent steps in the activation of MAPK signaling.

We have developed a pooled ORF expression technology, POET, that uses recombinational cloning and proteomic methods (two-dimensional gel electrophoresis and mass spectrometry) to identify ORFs that when expressed are likely to yield high levels of soluble, purified protein. Because the method works on pools of ORFs, the procedures needed to subclone, express, purify, and assay protein expression for hundreds of clones are greatly simplified. Small scale expression and purification of 12 positive clones identified by POET from a pool of 688 Caenorhabditis elegans ORFs expressed in Escherichia coli yielded on average 6 times as much protein as 12 negative clones. Larger scale expression and purification of six of the positive clones yielded 47-374 mg of purified protein/liter. Using POET, pools of ORFs can be constructed, and the pools of the resulting proteins can be analyzed and manipulated to rapidly acquire information about the attributes of hundreds of proteins simultaneously.

The mitochondrial H + -ATPase of the parasitic protozoan Trypanosoma brucei is shown to be developmentally regulated through the T. brucei life cycle as has been shown for components of the mitochondrial electron transport chain. We have substantiated our results by assaying not only for oligomycin-sensitive ATPase activity but also by determining the level of ATP synthetic activity. These results show that the level of ATPase present in the procyclic form of T. brucei is increased by at least threefold from that of the early bloodstream form while the ATPase activity in the late bloodstream form is only about twofold higher than the early form. ATP synthesis activity shows these same results. We have determined the level of ATP synthase protein present in the life cycle stages by Western analysis employing the antibodies that we have raised against both the water soluble F 1 and the membrane-associated F 0 moieties which we have purified from T. brucei . The Western blots of the procyclic form show strong reactivity with both the F 0 and F 1 antibodies. The other two life cycle stages, the early and the late bloodstream forms, show considerably less reactivity, paralleling the activity results. Electron micrographs of the sonicated mitochondrial fraction show inverted vesicles which are studded with knobby H + -ATPase in the procyclic form. The early bloodstream vesicles show very few of these characteristic structures, while the late bloodstream form shows a range of vesicles from nearly nude to partially studded.

This report describes the first isolation and molecular characterization of the mitochondrial F1-ATPase from Trypanosoma brucei. The isolation procedure utilized is a modified chloroform extraction procedure. In contrast to earlier reports on the F1-ATPase from other trypanosomatids, the F1-ATPase we have isolated from the procyclic form of T. brucei a complex composed of five distinct subunits. Apparent molecular weights of these subunits are 55,000 [alpha], 42,000 [beta], 32,000 [gamma], 22,000 [delta], and 17,000 [epsilon]. The F1 moiety which possesses the active site of the H(+)-ATPase has an ATPase activity in the standard Tris-HCl coupled enzyme assay with a Vmax of 22.96 mumol min-1 (mg protein)-1 and a Km value of 0.60 mM. This ATPase activity is cold labile and is not susceptible to oligomycin inhibition as is the membrane bound enzyme. Upon reconstitution with F1-ATPase depleted membranes (urea particles) the ATPase regains oligomycin sensitivity to the same extent as that found in the intact inner membrane vesicles. ATP synthesis is also restored to these particles upon reconstitution with F1. These results indicate that this F1-ATPase as isolated is intact with respect to all the critical H(+)-ATPase functions.