Mechanism of domain closure of Sec7 domains and role in BFA sensitivity

Modeling the dynamic behaviors of the COPI vesicle formation regulators, the small GTPase Arf1 and its activating Sec7 guanine nucleotide exchange factor GBF1 on Golgi membranes

The components and subprocesses underlying the formation of COPI-coated vesicles at the Golgi are well understood. The coating cascade is initiated after the small GTPase Arf1 is activated by the Sec7 domain–containing guanine nucleotide exchange factor GBF1 (Golgi brefeldin A resistant guanine nucleotide exchange factor 1). This causes a conformational shift within Arf1 that facilitates stable association of Arf1 with the membrane, a process required for subsequent recruitment of the COPI coat. Although we have atomic-level knowledge of Arf1 activation by Sec7 domain–containing GEFs, our understanding of the biophysical processes regulating Arf1 and GBF1 dynamics is limited. We used fluorescence recovery after photobleaching data and kinetic Monte Carlo simulation to assess the behavior of Arf1 and GBF1 during COPI vesicle formation in live cells. Our analyses suggest that Arf1 and GBF1 associate with Golgi membranes independently, with an excess of GBF1 relative to Arf1. Furthermore, the GBF1-mediated Arf1 activation is much faster than GBF1 cycling on/off the membrane, suggesting that GBF1 is regulated by processes other than its interactions Arf1. Interestingly, modeling the behavior of the catalytically inactive GBF1/E794K mutant stabilized on the membrane is inconsistent with the formation of a stable complex between it and an endogenous Arf1 and suggests that GBF1/E794K is stabilized on the membrane independently of complex formation.

The HUS box is required for allosteric regulation of the Sec7 Arf-GEF

The Golgi complex is the central membrane and protein-sorting station in eukaryotic cells. Activation of Arf (ADP-ribosylation factor) GTPases is essential for vesicle formation via recruitment of cargo adaptors and coat proteins necessary for Golgi trafficking. Arf activation is spatially and temporally regulated by distinct guanine nucleotide exchange factors (GEFs) at different Golgi compartments. The yeast Arf-GEF Sec7 is a conserved and essential activator of Arf1 at the trans-Golgi network. Sec7 contains a highly conserved regulatory region, the homology upstream of Sec7 (HUS) box, with an unknown mechanistic role. In this study we explore how the HUS box, which is N-terminal to the catalytic domain, acts together with C-terminal regulatory domains in the allosteric activation of Sec7. We report that mutation of the HUS box disrupts positive feedback and allosteric activation of Sec7 by the GTPase Ypt31, a yeast Rab11 homolog. Taken together, our results support a model in which the inter- and intramolecular interactions of the HUS box and the C terminus are necessary for the allosteric activation of Sec7.

Structural Dynamics Control Allosteric Activation of Cytohesin Family Arf GTPase Exchange Factors

Membrane dynamic processes including vesicle biogenesis depend on Arf GTPase activation by guanine nucleotide exchange factors (GEFs) containing a catalytic Sec7 domain and a membrane targeting module such as a PH domain. The catalytic output of cytohesin family Arf GEFs is controlled by autoinhibitory interactions that impede accessibility of the exchange site in the Sec7 domain. These restraints can be relieved through activator Arf-GTP binding to an allosteric site comprising the PH domain and proximal autoinhibitory elements (Sec7-PH linker and C-terminal helix). Small angle X-ray scattering and negative-stain electron microscopy were used to investigate the structural organization and conformational dynamics of Cytohesin-3 (Grp1) in autoinhibited and active states. The results support a model in which hinge dynamics in the autoinhibited state expose the activator site for Arf-GTP binding, while subsequent C-terminal helix unlatching and repositioning unleash conformational entropy in the Sec7-PH linker to drive exposure of the exchange site.

Regulation of Arf activation occurs via distinct mechanisms at early and late Golgi compartments

At the Golgi complex, the biosynthetic sorting center of the cell, the Arf GTPases are responsible for coordinating vesicle formation. The Arf-GEFs activate Arf GTPases and are therefore the key molecular decision-makers for trafficking from the Golgi. In Saccharomyces cerevisiae, three conserved Arf-GEFs function at the Golgi: Sec7, Gea1, and Gea2. Our group has described the regulation of Sec7, the trans-Golgi Arf-GEF, through autoinhibition, positive feedback, dimerization, and interactions with a suite of small GTPases. However, we lack a clear understanding of the regulation of the early Golgi Arf-GEFs Gea1 and Gea2. Here we demonstrate that Gea1 and Gea2 prefer neutral over anionic membrane surfaces in vitro, consistent with their localization to the early Golgi. We illustrate a requirement for a critical mass of either Gea1 or Gea2 for cell growth under stress conditions. We show that the C-terminal domains of Gea1 and Gea2 toggle roles in the cytosol and at the membrane surface, preventing membrane binding in the absence of a recruiting interaction but promoting maximum catalytic activity once recruited. We also identify the small GTPase Ypt1 as a recruiter for Gea1 and Gea2. Our findings illuminate core regulatory mechanisms unique to the early Golgi Arf-GEFs.

Multiple interactions between an Arf/GEF complex and charged lipids determine activation kinetics on the membrane

Lipidated small GTPases and their regulators need to bind to membranes to propagate actions in the cell, but an integrated understanding of how the lipid bilayer exerts its effect has remained elusive. Here we focused on ADP ribosylation factor (Arf) GTPases, which orchestrate a variety of regulatory functions in lipid and membrane trafficking, and their activation by the guanine-nucleotide exchange factor (GEF) Brag2, which controls integrin endocytosis and cell adhesion and is impaired in cancer and developmental diseases. Biochemical and structural data are available that showed the exceptional efficiency of Arf activation by Brag2 on membranes. We determined the high-resolution crystal structure of unbound Brag2 containing the GEF (Sec7) and membrane-binding (pleckstrin homology) domains, revealing that it has a constitutively active conformation. We used this structure to analyze the interaction of uncomplexed Brag2 and of the myristoylated Arf1/Brag2 complex with a phosphatidylinositol bisphosphate (PIP₂) -containing lipid bilayer, using coarse-grained molecular dynamics. These simulations revealed that the system forms a close-packed, oriented interaction with the membrane, in which multiple PIP₂ lipids bind the canonical lipid-binding site and unique peripheral sites of the PH domain, the Arf GTPase and, unexpectedly, the Sec7 domain. We cross-validated these predictions by reconstituting the binding and kinetics of Arf and Brag2 in artificial membranes. Our coarse-grained structural model thus suggests that the high efficiency of Brag2 requires interaction with multiple lipids and a well-defined orientation on the membrane, resulting in a local PIP₂ enrichment, which has the potential to signal toward the Arf pathway.

The Sec7 N-terminal regulatory domains facilitate membrane-proximal activation of the Arf1 GTPase

The Golgi complex is the central sorting compartment of eukaryotic cells. Arf guanine nucleotide exchange factors (Arf-GEFs) regulate virtually all traffic through the Golgi by activating Arf GTPase trafficking pathways. The Golgi Arf-GEFs contain multiple autoregulatory domains, but the precise mechanisms underlying their function remain largely undefined. We report a crystal structure revealing that the N-terminal DCB and HUS regulatory domains of the Arf-GEF Sec7 form a single structural unit. We demonstrate that the established role of the N-terminal region in dimerization is not conserved; instead, a C-terminal autoinhibitory domain is responsible for dimerization of Sec7. We find that the DCB/HUS domain amplifies the ability of Sec7 to activate Arf1 on the membrane surface by facilitating membrane insertion of the Arf1 amphipathic helix. This enhancing function of the Sec7 N-terminal domains is consistent with the high rate of Arf1-dependent trafficking to the plasma membrane necessary for maximal cell growth.

Biochemical methods for studying kinetic regulation of Arf1 activation by Sec7

The ADP ribosylation factor (Arf) family of small guanosine triphosphatases (GTPases) regulates vesicular transport at several locations within the cell, and is in turn regulated by guanine nucleotide exchange factors (GEFs) via a conserved catalytic domain, termed the Sec7 domain. The catalytic activity of the Sec7 domain is well characterized in the context of a few GEFs acting at the periphery of the cell. This chapter describes the techniques used to extend the biochemical analysis of activity to the much larger GEFs acting on the Arf family in the core secretory pathway, using the activity of Saccharomyces cerevisiae Sec7 on Arf1, regulating export from the trans-Golgi network, as a model. The complete methods for purification to near homogeneity of all proteins required, including several Sec7 constructs and multiple relevant small GTPases, are detailed. These are followed by methods for the quantification of the nucleotide exchange activity of Sec7 in a physiologically relevant context, including modifications required to dissect the signal integration functions of Sec7 as an effector of several other small GTPases, and methods for identifying stable Sec7-small GTPase interactions in the presence of membranes. These techniques may be extended to the analysis of similar members of the Sec7 GEF subfamily in other species and acting elsewhere in the secretory pathway.

On the use of Legionella/Rickettsia chimeras to investigate the structure and regulation of Rickettsia effector RalF

A convenient strategy to interrogate the biology of regulatory proteins is to replace individual domains by an equivalent domain from a related protein of the same species or from an ortholog of another species. It is generally assumed that the overall properties of the native protein are retained in the chimera, and that functional differences reflect only the specific determinants contained in the swapped domains. Here we used this strategy to circumvent the difficulty in obtaining crystals of Rickettsia prowazekii RalF, a bacterial protein that functions as a guanine nucleotide exchange factor for eukaryotic Arf GTPases. A RalF homolog is encoded by Legionella pneumophila, in which a C-terminal capping domain auto-inhibits the catalytic Sec7 domain and localizes the protein to the Legionella-containing vacuole. The crystal structures of domain-swapped chimeras were determined and used to construct a model of Legionella RalF with a RMSD of less than 1Å with the crystal structure, which validated the use of this approach to build a model of Rickettsia RalF. In the Rickettsia RalF model, sequence differences in the capping domain that target it to specific membranes are accommodated by a shift of the entire domain with respect to the Sec7 domain. However, local sequence changes also give rise to an artifactual salt bridge in one of the chimeras, which likely explains why this chimera is recalcitrant to activation. These findings highlight the structural plasticity whereby chimeras can be engineered, but also underline that unpredictable differences can modify their biochemical responses.

C-terminal motif within Sec7 domain regulates guanine nucleotide exchange activity via tuning protein conformation

ADP-ribosylation factors (Arfs) play key roles in controlling membrane traffic and organelle structures. The activation of Arfs from GDP to GTP binding form is triggered by the guanine exchange factors (GEFs). There are six families of Arf-GEFs with a common guanine exchange catalytic domain (Sec7 domain) and various mechanisms of guanine exchange activity regulation. A loop region (loop>J motif) just following the helix J of Sec7 domain was found conserved and important for the catalytic activity regulation of Arf-GEFs. However, the molecular detail of the role the loop>J motif plays has been yet unclear. Here, we studied the catalytic domain of Sec7p, a yeast trans-Golgi network membrane localized Arf-GEFs, and found that the loop>J motif is indispensible for its GEF catalytic activity. Crystallographic, NMR spectrum and mutagenesis studies suggested that the loop>J motif with a key conserved residue Ile1010 modulates the fine conformation of Sec7 domain and thereby regulates its guanine exchange activity.

Quantitative Analysis of Guanine Nucleotide Exchange Factors (GEFs) as Enzymes

The proteins that possess guanine nucleotide exchange factor (GEF) activity, which include about ~800 G protein coupled receptors (GPCRs),¹ 15 Arf GEFs,² 81 Rho GEFs,³ 8 Ras GEFs,⁴ and others for other families of GTPases,⁵ catalyze the exchange of GTP for GDP on all regulatory guanine nucleotide binding proteins. Despite their importance as catalysts, relatively few exchange factors (we are aware of only eight for ras superfamily members) have been rigorously characterized kinetically.^5-13 In some cases, kinetic analysis has been simplistic leading to erroneous conclusions about mechanism (as discussed in a recent review¹⁴). In this paper, we compare two approaches for determining the kinetic properties of exchange factors: (i) examining individual equilibria, and; (ii) analyzing the exchange factors as enzymes. Each approach, when thoughtfully used,^14,15 provides important mechanistic information about the exchange factors. The analysis as enzymes is described in further detail. With the focus on the production of the biologically relevant guanine nucleotide binding protein complexed with GTP (G•GTP), we believe it is conceptually simpler to connect the kinetic properties to cellular effects. Further, the experiments are often more tractable than those used to analyze the equilibrium system and, therefore, more widely accessible to scientists interested in the function of exchange factors.

Fragment-based identification of a locus in the Sec7 domain of Arno for the design of protein-protein interaction inhibitors

By virtual screening using a fragment-based drug design (FBDD) approach, 33 fragments were selected within small pockets around interaction hot spots on the Sec7 surface of the nucleotide exchange factor Arno, and then their ability to interfere with the Arno-catalyzed nucleotide exchange on the G-protein Arf1 was evaluated. By use of SPR, NMR, and fluorescence assays, the direct binding of three of the identified fragments to Arno Sec7 domain was demonstrated and the promiscuous aggregate behavior evaluated. Then the binding mode of one fragment and of a more active analogue was solved by X-ray crystallography. This highlighted the role of stable and transient pockets at the Sec7 domain surface in the discovery and binding of interfering compounds. These results provide structural information on how small organic compounds can interfere with the Arf1-Arno Sec7 domain interaction and may guide the rational drug design of competitive inhibitors of Arno enzymatic activity.

A role for the membrane in regulating Chlamydomonas flagellar length

Flagellar assembly requires coordination between the assembly of axonemal proteins and the assembly of the flagellar membrane and membrane proteins. Fully grown steady-state Chlamydomonas flagella release flagellar vesicles from their tips and failure to resupply membrane should affect flagellar length. To study vesicle release, plasma and flagellar membrane surface proteins were vectorially pulse-labeled and flagella and vesicles were analyzed for biotinylated proteins. Based on the quantity of biotinylated proteins in purified vesicles, steady-state flagella appeared to shed a minimum of 16% of their surface membrane per hour, equivalent to a complete flagellar membrane being released every 6 hrs or less. Brefeldin-A destroyed Chlamydomonas Golgi, inhibited the secretory pathway, inhibited flagellar regeneration, and induced full-length flagella to disassemble within 6 hrs, consistent with flagellar disassembly being induced by a failure to resupply membrane. In contrast to membrane lipids, a pool of biotinylatable membrane proteins was identified that was sufficient to resupply flagella as they released vesicles for 6 hrs in the absence of protein synthesis and to support one and nearly two regenerations of flagella following amputation. These studies reveal the importance of the secretory pathway to assemble and maintain full-length flagella.

Nucleotide exchange factors: Kinetic analyses and the rationale for studying kinetics of GEFs

Exchange factors are enzymes that catalyze the exchange of GTP for GDP on guanine nucleotide binding proteins. Progress in understanding the molecular basis of action and the cellular functions of these enzymes has largely come from structural determinations (e.g., crystal structures) and studying effects on cells when expression levels of the exchange factors are perturbed or mutated exchange factors are expressed. Proportionally little effort has been expended on studying the kinetics of exchange; however, reaction rates are central to understanding enzymes. Here, we discuss the importance of kinetic analysis of exchange factors for guanine nucleotide binding proteins, with a focus on ADP-ribosylation factor (Arf) and heterotrimeric G proteins, for providing unique insights into molecular mechanisms and regulation as well as how kinetic analyses are used to complement other approaches.

Very-long-chain fatty acids are required for cell plate formation during cytokinesis in Arabidopsis thaliana

Acyl chain length is thought to be crucial for biophysical properties of the membrane, in particular during cell division, when active vesicular fusion is necessary. In higher plants, the process of cytokinesis is unique, because the separation of the two daughter cells is carried out by de novo vesicular fusion to generate a laterally expanding cell plate. In Arabidopsis thaliana, very-long-chain fatty acid (VLCFA) depletion caused by a mutation in the microsomal elongase gene PASTICCINO2 (PAS2) or by application of the selective elongase inhibitor flufenacet altered cytokinesis. Cell plate expansion was delayed and the formation of the endomembrane tubular network altered. These defects were associated with specific aggregation of the cell plate markers YFP-Rab-A2a and KNOLLE during cytokinesis. Changes in levels of VLCFA also resulted in modification of endocytosis and sensitivity to brefeldin A. Finally, the cytokinesis impairment in pas2 cells was associated with reduced levels of very long fatty acyl chains in phospholipids. Together, our findings demonstrate that VLCFA-containing lipids are essential for endomembrane dynamics during cytokinesis.

A computational study of a recreated G protein-GEF reaction intermediate competent for nucleotide exchange: fate of the Mg ion

Small G-proteins of the superfamily Ras function as molecular switches, interacting with different cellular partners according to their activation state. G-protein activation involves the dissociation of bound GDP and its replacement by GTP, in an exchange reaction that is accelerated and regulated in the cell by guanine-nucleotide exchange factors (GEFs). Large conformational changes accompany the exchange reaction, and our understanding of the mechanism is correspondingly incomplete. However, much knowledge has been derived from structural studies of blocked or inactive mutant GEFs, which presumably closely represent intermediates in the exchange reaction and yet which are by design incompetent for carrying out the nucleotide exchange reaction. In this study we have used comparative modelling to recreate an exchange-competent form of a late, pre-GDP-ejection intermediate species in Arf1, a well-characterized small G-protein. We extensively characterized three distinct models of this intermediate using molecular dynamics simulations, allowing us to address ambiguities related to the mutant structural studies. We observed in particular the unfavorable nature of Mg associated forms of the complex and the establishment of closer Arf1-GEF contacts in its absence. The results of this study shed light on GEF-mediated activation of this small G protein and on predicting the fate of the Mg ion at a critical point in the exchange reaction. The structural models themselves furnish additional targets for interfacial inhibitor design, a promising direction for exploring potentially druggable targets with high biological specificity.

Golgicide A reveals essential roles for GBF1 in Golgi assembly and function

ADP-ribosylation factor 1 (Arf1) plays a critical role in regulating secretory traffic and membrane transport within the Golgi of eukaryotic cells. Arf1 is activated by guanine nucleotide exchange factors (ArfGEFs) which confer spatial and temporal specificity to vesicular transport. We describe here the discovery and characterization of Golgicide A (GCA), a potent, highly specific, and reversible inhibitor of the cis-Golgi ArfGEF, GBF1. Inhibition of GBF1 function resulted in rapid dissociation of COPI vesicle coat from Golgi membranes and subsequent disassembly of the Golgi and trans-Golgi network (TGN). Secretion of soluble and membrane-associated proteins was arrested at the ER-Golgi intermediate compartment, whereas endocytosis and recycling of transferrin was unaffected by GBF1 inhibition. Internalized shiga toxin was arrested within the endocytic compartment and was unable to reach the dispersed TGN. Collectively, these results highlight the central role for GBF1 in coordinating bidirectional transport and maintaining structural integrity of the Golgi.

Cytohesin-1: structure, function, and ARF activation

Mammalian cytohesins are a family of very similar guanine nucleotide-exchange proteins (GEPs) that activate ADP-ribosylation factors (ARFs). Cytohesins are multifunctional molecules comprising a Sec7 domain that is responsible for the GEP activity, a PH domain that binds specific phosphatidylinositol phosphates, and a coiled-coil domain responsible for homodimerization and interaction with other proteins. Cytohesin proteins are ubiquitous and have been implicated in several functions including cell spreading and adhesion, chemotaxis, protein trafficking, and cytoskeletal rearrangements, only some of which appear to depend on their ability to activate ARFs. Unlike the GEP activity of BIG1 and BIG2, the acceleration by cytohesins of guanine nucleotide exchange to generate active ARF-GTP is not inhibited by the fungal metabolite brefeldin, A (BFA). This chapter is concerned for the most part with cytohesin-1 and the assay of its GEP activity.

Molecular dynamics simulations of transducin: interdomain and front to back communication in activation and nucleotide exchange

The dynamic events that underlie the nucleotide exchange process for the Galpha subunit of transducin (Galpha(t)) were studied with nanosecond time-scale molecular dynamics simulations. The modeled systems include the active and inactive forms of the wild-type Galpha(t) and three of its mutants (GDP-bound form only): F332A, A322S, and Q326A that are known to exhibit various degrees of enhancement of their basal and receptor-catalyzed rates of nucleotide exchange (150-fold, 70-fold and WT-like, respectively). The results of these computational experiments reveal a number of nucleotide-dependent structural and dynamic changes (involving the alpha(B)-alpha(C) loop, the inter-domain orientation of the helical and GTPase domains and the alpha(5) helix) that were not observed in the various crystal structures of Galpha(t). Notably, the results show the existence of a front to back communication device (involving the beta(2)-beta(3) hairpin, the alpha(1) helix and the alpha(5) helix), strategically located near all elements susceptible to be involved in receptor-mediated activation/nucleotide exchange. The wild-type simulations suggest that the dynamic interplay between the elements of this device would be critical for the activation of the Galpha(t) subunit. This inference is confirmed by the results of the computational experiments on the mutants that show that even in their GDP-bound forms, the A322S and F332A mutants acquire an "active-like" structure and dynamics phenotype. The same is not true for the Q326A mutant whose structural and dynamic properties remain similar to those of the GDP-bound WT. Taken together the results suggest a nucleotide exchange mechanism, analogous to that found in the Arf family GTPases, in which a partially activated state, achievable from a receptor-mediated action of the front to back communication device either by displacement of the C-terminal alpha(5) helix, of the N-terminal alpha(N) helix, or of the Gbetagamma subunit, could precede the dissociation of GDP from the native Galpha subunit.

Integrating three views of Arf1 activation dynamics

The proteins Arno and Gea2 of the Sec7 family can promote GDP-GTP exchange on Arf1, a small GTP-binding protein, which coordinates coated vesicle formation for protein transport within the cell. Crystal structures of the essential Sec7 domain (Sec7d) of Gea2 in the free and Arf1-bound forms suggest that conformational dynamics of the Sec7d as well as those of the G-protein play a role in nucleotide exchange. Starting from a set of complementary crystal structures, we compared the collective movements of unbound Gea2 and Arno Sec7 domains, Arf1-GDP, and the Arf1-Gea2(Sec7d) nucleotide-free complex using normal modes analyses. In all unbound Sec7d analyses, significant low-energy movements were found to lead to closure of the hydrophobic groove towards the form seen in the Arf1-Gea2(Sec7d) complex, suggesting that groove closure is a general feature of the Sec7 family. Low-energy movements in Arf1-GDP implicate critical switch 1 and 2 residues which are coupled to modifications in the myristoylated N-terminal-helix binding site at the other end of the "interswitch" beta hairpin. It is suggested that Sec7d groove closure upon docking of the two molecules may permit extraction of switch 1 from Arf1-GDP and prepare the complex for movement of the interswitch, which is central to the membrane-linked exchange activity. Large-scale collective movements in the Arf1-Sec7d complex appear to participate in the insertion of the Sec7d Glu finger into the GDP binding site to promote actual nucleotide release.

Crystal structure of ARF1*Sec7 complexed with Brefeldin A and its implications for the guanine nucleotide exchange mechanism

ARF GTPases are activated by guanine nucleotide exchange factors (GEFs) of the Sec7 family that promote the exchange of GDP for GTP. Brefeldin A (BFA) is a fungal metabolite that binds to the ARF1*GDP*Sec7 complex and blocks GEF activity at an early stage of the reaction, prior to guanine nucleotide release. The crystal structure of the ARF1*GDP*Sec7*BFA complex shows that BFA binds at the protein-protein interface to inhibit conformational changes in ARF1 required for Sec7 to dislodge the GDP molecule. Based on a comparative analysis of the inhibited complex, nucleotide-free ARF1*Sec7 and ARF1*GDP, we suggest that, in addition to forcing nucleotide release, the ARF1-Sec7 binding energy is used to open a cavity on ARF1 to facilitate the rearrangement of hydrophobic core residues between the GDP and GTP conformations. Thus, the Sec7 domain may act as a dual catalyst, facilitating both nucleotide release and conformational switching on ARF proteins.

Phylogenetic analysis of Sec7-domain-containing Arf nucleotide exchangers

The eukaryotic family of ADP-ribosylation factor (Arf) GTPases plays a key role in the regulation of protein trafficking, and guanine-nucleotide exchange is crucial for Arf function. Exchange is stimulated by members of another family of proteins characterized by a 200-amino acid Sec7 domain, which alone is sufficient to catalyze exchange on Arf. Here, we analyzed the phylogeny of Sec7-domain-containing proteins in seven model organisms, representing fungi, plants, and animals. The phylogenetic tree has seven main groups, of which two include members from all seven model systems. Three groups are specific for animals, whereas two are specific for fungi. Based on this grouping, we propose a phylogenetically consistent set of names for members of the Sec7-domain family. Each group, except for one, contains proteins with known Arf exchange activity, implying that all members of this family have this activity. Contrary to the current convention, the sensitivity of Arf exchange activity to the inhibitor brefeldin A probably cannot be predicted by group membership. Multiple alignment reveals group-specific domains outside the Sec7 domain and a set of highly conserved amino acids within it. Determination of the importance of these conserved elements in Arf exchange activity and other cellular functions is now possible.

Conformational states of the small G protein Arf-1 in complex with the guanine nucleotide exchange factor ARNO-Sec7

Arf1 is a small G protein involved in vesicular trafficking, and although it is only distantly related to Ras, it adopts a similar three-dimensional structure. In the present work, we study Arf1 bound to GDP and GTP and its interactions with one of its guanosine nucleotide exchange factors, ARNO-Sec7. The (31)P NMR spectra of Arf1.GDP.Mg(2+) and Arf1.GTP.Mg(2+) share the general features typical for all small G proteins studied so far. Especially, the beta-phosphate resonances of the bound nucleotide are shifted strongly downfield compared with the resonance positions of the free magnesium complexes of GDP and GTP. However, no evidence for an equilibrium between two conformational states of Arf1.GDP.Mg(2+) or Arf1.GTP.Mg(2+) could be observed as it was described earlier for Ras and Ran. Glu(156) of ARNO-Sec7 has been suggested to play as "glutamic acid finger" an important role in the nucleotide exchange mechanism. In the millimolar concentration range used in the NMR experiments, wild type ARNO-Sec7 and ARNO-Sec7(E156D) do weakly interact with Arf1.GDP.Mg(2+) but do not form a strong complex with magnesium-free Arf1.GDP. Only wild type ARNO-Sec7 competes weakly with GDP on Arf1.GDP.Mg(2+) and leads to a release of GDP when added to the solution. The catalytically inactive mutants ARNO-Sec7(E156A) and ARNO-Sec7(E156K) induce a release of magnesium from Arf1.GDP.Mg(2+) but do not promote GDP release. In addition, ARNO-Sec7 does not interact or only very weakly interacts with the GTP-bound form of Arf1, opposite to the observation made earlier for Ran, where the nucleotide exchange factor RCC1 forms a complex with Ran.GTP.Mg(2+) and is able to displace the bound GTP.

Structural snapshots of the mechanism and inhibition of a guanine nucleotide exchange factor

Small GTP-binding (G) proteins are activated by GDP/GTP nucleotide exchange stimulated by guanine nucleotide exchange factors (GEFs). Nucleotide dissociation from small G protein-GEF complexes involves transient GDP-bound intermediates whose structures have never been described. In the case of Arf proteins, small G proteins that regulate membrane traffic in eukaryotic cells, such intermediates can be trapped either by the natural inhibitor brefeldin A or by charge reversal at the catalytic glutamate of the Sec7 domain of their GEFs. Here we report the crystal structures of these intermediates that show that membrane recruitment of Arf and nucleotide dissociation are separate reactions stimulated by Sec7. The reactions proceed through sequential rotations of the Arf.GDP core towards the Sec7 catalytic site, and are blocked by interfacial binding of brefeldin A and unproductive stabilization of GDP by charge reversal. The structural characteristics of the reaction and its modes of inhibition reveal unexplored ways in which to inhibit the activation of small G proteins.