Liposomes in the study of GDP/GTP cycle of Arf and related small G proteins

In vitro reconstitution of small GTPase regulation

Small GTPases play essential roles in the organization of eukaryotic cells. In recent years, it has become clear that their intracellular functions result from intricate biochemical networks of the GTPase and their regulators that dynamically bind to a membrane surface. Due to the inherent complexities of their interactions, however, revealing the underlying mechanisms of action is often difficult to achieve from in vivo studies. This review summarizes in vitro reconstitution approaches developed to obtain a better mechanistic understanding of how small GTPase activities are regulated in space and time.

Direct binding of cytosolic NDP kinases to membrane lipids is regulated by nucleotides

In spite of their complete lack of any structural features that characterize membrane proteins, cytosolic nucleoside-diphosphate kinases (NDPKs) have been found repeatedly to associate with membranes. In some instances the recruitment of cytosolic NDPKs to membranes was attributed to interactions with peripheral or integral membrane proteins, but in many cases the mechanism underlying the association of NDPKs with membranes remained unknown. We show here that cytosolic NDPKs bind directly to membrane lipids in a dynamic process that is controlled by its substrates, nucleoside tri- and diphosphates, and can be fully reconstituted with chemically defined, protein-free phospholipids and recombinant NDPK, or with purified NDPK. Our results uncover a novel mechanism for the reversible targeting of soluble NDPKs to membranes, where they may act as a reservoir of high energy phosphate, supporting the operation of membrane-based processes that utilize nucleotides other than ATP, such as intracellular traffic and phospholipid biosynthesis.

Discrete determinants in ArfGAP2/3 conferring Golgi localization and regulation by the COPI coat

From yeast to mammals, two types of GTPase-activating proteins, ArfGAP1 and ArfGAP2/3, control guanosine triphosphate (GTP) hydrolysis on the small G protein ADP-ribosylation factor (Arf) 1 at the Golgi apparatus. Although functionally interchangeable, they display little similarity outside the catalytic GTPase-activating protein (GAP) domain, suggesting differential regulation. ArfGAP1 is controlled by membrane curvature through its amphipathic lipid packing sensor motifs, whereas Golgi targeting of ArfGAP2 depends on coatomer, the building block of the COPI coat. Using a reporter fusion approach and in vitro assays, we identified several functional elements in ArfGAP2/3. We show that the Golgi localization of ArfGAP3 depends on both a central basic stretch and a carboxy-amphipathic motif. The basic stretch interacts directly with coatomer, which we found essential for the catalytic activity of ArfGAP3 on Arf1-GTP, whereas the carboxy-amphipathic motif interacts directly with lipid membranes but has minor role in the regulation of ArfGAP3 activity. Our findings indicate that the two types of ArfGAP proteins that reside at the Golgi use a different combination of protein-protein and protein-lipid interactions to promote GTP hydrolysis in Arf1-GTP.

GEF and glucosylation assays on liposome-bound Rac

Rac binds tightly to lipid membranes through a lipid modification. The influence of the lipid membrane environment on the multiple interactions of Rac has not been well documented. In this chapter, we detail a method to prepare geranyl-geranylated Rac bound to liposomes of defined composition. With this method, one can dissect some lipid-protein interactions that facilitate the interaction of Rac with other proteins such as guanine nucleotide exchange factors and bacterial toxins.

From decanoate micelles to decanoic acid/dodecylbenzenesulfonate vesicles

Different aspects of mixtures of decanoic acid and sodium decanoate were investigated in aqueous solution up to a total concentration of 300 mM. Depending on the ratio of ionized to nonionized decanoic acid, micelles or vesicles form above the critical concentrations of micelle (cmc) or the critical concentration for vesicle formation (cvc). The micelles and the vesicles are always present together with nonmicellized or nonvesiculized decanoate. The latter was determined for different total concentrations. On the basis of titration curves, by application of the Gibbs phase rule, and on the basis of differential scanning calorimetry measurements and an electron microscopy analysis, the pH region within which vesicles exist was identified (pH 6.8-7.8). At pH 7.0, the concentration of nonvesiculized decanoate is approximately 20 mM. Decanoic acid/decanoate vesicles can be sized down by the extrusion technique to form stable and mainly unilamellar vesicles with a mean diameter of less than 100 nm. By coaddition of an equimolar amount of sodium dodecylbenzenesulfonate (SDBS) to decanoic acid, vesicles also formed below pH 6.8. These mixed vesicles were investigated as potential templates for the peroxidase-catalyzed polymerization of aniline at pH 4.3. Furthermore, decanaote micelles (at pH 11.0) were applied as reaction modifiers for the simultaneous competitive alkaline hydrolysis of p-nitrophenylacetate and fluorescein diacetate. While the rate of hydrolysis of fluorescein diacetate is slowed considerably in the presence of the micelles in comparison with the micelle-free system, the rate of hydrolysis of p-nitrophenylacetate remains almost unaffected.

Purification and functional properties of yeast Sec12 GEF

In order to reconstitute the generation of COPII vesicles from synthetic liposomes, the minimum requirements are the coat components, Sar1p GTPase, Sec23/24p, Sec13/31p, and a nonhydrolyzable GTP analog such as GMP-PNP. However, in the presence of GTP, nucleotide hydrolysis by Sar1p renders the coat insufficiently stable to sustain vesicle budding. Sar1p GTPase activity was activated by the Sec23/24p GTPase-activating protein (GAP), and further accelerated 10-fold by Sec13/31p. In order to study GTP-dependent budding, we introduced the Sar1p guanine nucleotide exchange factor (GEF), Sec12p. We evaluated Sar1p activation by Sec12p and the dynamics of coat assembly and disassembly in the presence of both Sec12p and Sec23/24p. The cytoplasmic domain of Sec12p activated Sar1p with a turnover 10-fold higher than the GAP activity of Sec23p in the presence of Sec13/31p. As a result, the entire COPII coat remains stable in the presence of GTP. Here, we describe methods to purify Sec12p, real-time fluorescence assays to evaluate COPII coat formation, and the relevant kinetic analyses.