Structure of a C-terminal fragment of its Vps53 subunit suggests similarity of Golgi-associated retrograde protein (GARP) complex to a family of tethering complexes

The Golgi-associated retrograde protein (GARP) complex is a membrane-tethering complex that functions in traffic from endosomes to the trans-Golgi network. Here we present the structure of a C-terminal fragment of the Vps53 subunit, important for binding endosome-derived vesicles, at a resolution of 2.9 Å. We show that the C terminus consists of two α-helical bundles arranged in tandem, and we identify a highly conserved surface patch, which may play a role in vesicle recognition. Mutations of the surface result in defects in membrane traffic. The fold of the Vps53 C terminus is strongly reminiscent of proteins that belong to three other tethering complexes—Dsl1, conserved oligomeric Golgi, and the exocyst—thought to share a common evolutionary origin. Thus, the structure of the Vps53 C terminus suggests that GARP belongs to this family of complexes.     

GARP (LRRC32) is essential for the surface expression of latent TGF-β on platelets and activated FOXP3+ regulatory T cells

TGF-β family members are highly pleiotropic cytokines with diverse regulatory functions. TGF-β is normally found in the latent form associated with latency-associated peptide (LAP). This latent complex can associate with latent TGFβ-binding protein (LTBP) to produce a large latent form. Latent TGF-β is also found on the surface of activated FOXP3⁺ regulatory T cells (Tregs), but it is unclear how it is anchored to the cell membrane. We show that GARP or LRRC32, a leucine-rich repeat molecule of unknown function, is critical for tethering TGF-β to the cell surface. We demonstrate that platelets and activated Tregs co-express latent TGF-β and GARP on their membranes. The knockdown of GARP mRNA with siRNA prevented surface latent TGF-β expression on activated Tregs and recombinant latent TGF-β1 is able to bind directly with GARP. Confocal microscopy and immunoprecipitation strongly support their interactions. The role of TGF-β on Tregs appears to have dual functions, both for Treg-mediated suppression and infectious tolerance mechanism.     

Molecular architecture of the multisubunit homotypic fusion and vacuole protein sorting (HOPS) tethering complex

Membrane fusion within the eukaryotic endomembrane system depends on the initial recognition of Rab GTPase on transport vesicles by multisubunit tethering complexes and subsequent coupling to SNARE-mediated fusion. The conserved vacuolar/lysosomal homotypic fusion and vacuole protein sorting (HOPS) tethering complex combines both activities. Here we present the overall structure of the fusion-active HOPS complex. Our data reveal a flexible ≈30-nm elongated seahorse-like structure, which can adopt contracted and elongated shapes. Surprisingly, both ends of the HOPS complex contain a Rab-binding subunit: Vps41 and Vps39. The large head contains in addition to Vps41 the SNARE-interacting Vps33, whereas Vps39 is found in the bulky tip of its tail. Vps11 and Vps18 connect head and tail. Our data suggest that HOPS bridges Ypt7-positive membranes and chaperones SNAREs at fusion sites.     

Missense mutations in dystrophin that trigger muscular dystrophy decrease protein stability and lead to cross-β aggregates

A deficiency of functional dystrophin protein in muscle cells causes muscular dystrophy (MD). More than 50% of missense mutations that trigger the disease occur in the N-terminal actin binding domain (N-ABD or ABD1). We examined the effect of four disease-causing mutations—L54R, A168D, A171P, and Y231N—on the structural and biophysical properties of isolated N-ABD. Our results indicate that N-ABD is a monomeric, well-folded α-helical protein in solution, as is evident from its α-helical circular dichroism spectrum, blue shift of the native state tryptophan fluorescence, well-dispersed amide crosspeaks in 2D NMR ¹⁵N-¹H HSQC fingerprint region, and rotational correlation time calculated from NMR longitudinal (T₁) and transverse (T₂) relaxation experiments. Compared to WT, three mutants—L54R, A168D, and A171P—show a decreased α-helicity and do not show a cooperative sigmoidal melt with temperature, indicating that these mutations exist in a wide range of conformations or in a “molten globule” state. In contrast, Y231N has an α-helical content similar to WT and shows a cooperative sigmoidal temperature melt but with a decreased stability. All four mutants experience serious misfolding and aggregation. FT-IR, circular dichroism, increase in thioflavin T fluorescence, and the congo red spectral shift and birefringence show that these aggregates contain intermolecular cross-β structure similar to that found in amyloid diseases. These results indicate that disease-causing mutants affect N-ABD structure by decreasing its thermodynamic stability and increasing its misfolding, thereby decreasing the net functional dystrophin concentration.     

Potentiation of alpha7 nicotinic acetylcholine receptors via an allosteric transmembrane site

Positive allosteric modulators of α7 nicotinic acetylcholine receptors (nAChRs) have attracted considerable interest as potential tools for the treatment of neurological and psychiatric disorders such as Alzheimer's disease and schizophrenia. However, despite the potential therapeutic usefulness of these compounds, little is known about their mechanism of action. Here, we have examined two allosteric potentiators of α7 nAChRs (PNU-120596 and LY-2087101). From studies with a series of subunit chimeras, we have identified the transmembrane regions of α7 as being critical in facilitating potentiation of agonist-evoked responses. Furthermore, we have identified five transmembrane amino acids that, when mutated, significantly reduce potentiation of α7 nAChRs. The amino acids we have identified are located within the α-helical transmembrane domains TM1 (S222 and A225), TM2 (M253), and TM4 (F455 and C459). Mutation of either A225 or M253 individually have particularly profound effects, reducing potentiation of EC₂₀ concentrations of acetylcholine to a tenth of the level seen with wild-type α7. Reference to homology models of the α7 nAChR, based on the 4Å structure of the Torpedo nAChR, indicates that the side chains of all five amino acids point toward an intrasubunit cavity located between the four α-helical transmembrane domains. Computer docking simulations predict that the allosteric compounds such as PNU-120596 and LY-2087101 may bind within this intrasubunit cavity, much as neurosteroids and volatile anesthetics are thought to interact with GABA_A and glycine receptors. Our findings suggest that this is a conserved modulatory allosteric site within neurotransmitter-gated ion channels.     

Helical structure and stability in human apolipoprotein A-I by hydrogen exchange and mass spectrometry

Apolipoprotein A-I (apoA-I) stabilizes anti-atherogenic high density lipoprotein particles (HDL) in the circulation and governs their biogenesis, metabolism, and functional interactions. To decipher these important structure–function relationships, it will be necessary to understand the structure, stability, and plasticity of the apoA-I molecule. Biophysical studies show that lipid-free apoA-I contains a large amount of α-helical structure but the location of this structure and its properties are not established. We used hydrogen-deuterium exchange coupled with a fragmentation-separation method and mass spectrometric analysis to study human lipid-free apoA-I in its physiologically pertinent monomeric form. The acquisition of ≈100 overlapping peptide fragments that redundantly cover the 243-residue apoA-I polypeptide made it possible to define the positions and stabilities of helical segments and to draw inferences about their interactions and dynamic properties. Residues 7–44, 54–65, 70–78, 81–115, and 147–178 form α-helices, accounting for a helical content of 48 ± 3%, in agreement with circular dichroism measurements (49%). At 3 to 5 kcal/mol in free energy of stabilization, the helices are far more stable than could be achieved in isolation, indicating mutually stabilizing helix bundle interactions. However the helical structure is dynamic, unfolding and refolding in seconds, allowing facile apoA-I reorganization during HDL particle formation and remodeling.     

The role of apolipoprotein AI domains in lipid binding

Apolipoprotein AI (apoAI) is the principal protein constituent of high density lipoproteins and it plays a key role in human cholesterol homeostasis; however, the structure of apoAI is not clearly understood. To test the hypothesis that apoAI is organized into domains, three deletion mutants of human apoAI expressed in Escherichia coli were studied in solution and in reconstituted high density lipoprotein particles. Each mutant lacked one of three specific regions that together encompass almost the entire 243 aa sequence of native apoAI (apoAI Δ44-126, apoAI Δ139-170, and apoAI Δ190-243). Circular dichroism spectroscopy showed that the α-helical content of lipid-free apoAI Δ44-126 was 27% while the other mutants and native apoAI averaged 55 ± 2%, suggesting that the missing N-terminal portion contains most of the α-helical structure of lipid-free apoAI. ApoAI Δ44-126 exhibited the largest increase in α-helix upon lipid binding (125% increase versus an average of 25% for the others), confirming the importance of the C-terminal half of apoAI in lipid binding. Denaturation studies showed that the N-terminal half of apoAI is primarily responsible for α-helix stability in the lipid-free state, whereas the C terminus is required for α-helix stability when lipid-bound. We conclude that the N-terminal half (aa 44–126) of apoAI is responsible for most of the α-helical structure and the marginal stability of lipid-free apoAI while the C terminus (aa 139–243) is less organized. The increase in α-helical content observed when native apoAI binds lipid results from the formation of α-helix primarily in the C-terminal half of the molecule.     

Structural basis of Vps33A recruitment to the human HOPS complex by Vps16

The multisubunit homotypic fusion and vacuole protein sorting (HOPS) membrane-tethering complex is required for late endosome-lysosome and autophagosome-lysosome fusion in mammals. We have determined the crystal structure of the human HOPS subunit Vps33A, confirming its identity as a Sec1/Munc18 family member. We show that HOPS subunit Vps16 recruits Vps33A to the human HOPS complex and that residues 642–736 are necessary and sufficient for this interaction, and we present the crystal structure of Vps33A in complex with Vps16(642–736). Mutations at the binding interface disrupt the Vps33A–Vps16 interaction both in vitro and in cells, preventing recruitment of Vps33A to the HOPS complex. The Vps33A–Vps16 complex provides a structural framework for studying the association between Sec1/Munc18 proteins and tethering complexes.Eukaryotic cells tightly regulate the movement of macromolecules between their membrane-bound compartments. Multiple proteins and protein complexes interact to identify vesicles or organelles destined to fuse, bring them into close proximity, and then fuse their membranes, thereby allowing their contents to mix (1). Multisubunit tethering complexes modulate key steps in these fusion events by recognizing specific Rab-family small GTPases on the membrane surfaces, physically docking the membranes and then recruiting the machinery that effects the membrane fusion (2, 3).In metazoans, the multisubunit tethering complex homologous to the yeast homotypic fusion and vacuole protein sorting (HOPS) complex (4–7) is required for the maturation of endosomes (8); the delivery of cargo to lysosomes (9) and lysosome-related organelles, such as pigment granules in Drosophila melanogaster (10); and the fusion of autophagosomes with late endosomes/lysosomes (11). The mammalian HOPS complex comprises six subunits (Vps11, Vps16, Vps18, Vps33A, Vps39, and Vps41) (4–6). Homologs of HOPS components can be identified in almost all eukaryotic genomes (12) and are thought to be essential; for example, removal of the Vps33A homolog carnation (car) in Drosophila is lethal during larval development (13).HOPS components have been identified in animal models of human disease. A missense point mutation in the murine Vps33a gene gives rise to the buff mouse phenotype, characterized by pigmentation, platelet activity, and motor deficiencies (14). This phenotype closely resembles the clinical presentation of Hermansky–Pudlak syndrome (HPS) (15), and a mutation in the human VPS33A gene has been observed in a patient with HPS who lacked mutations at other known HPS loci (14). In metazoans, there is a second homolog of yeast Vps33 called Vps33B, but disruption of the VPS33B gene in humans gives rise to a clinical phenotype distinct from HPS (16).Human Vps33A is predicted to be a member of the Sec1/Munc18 (SM) family of proteins (7, 17) that, together with SNAREs, comprise the core machinery essential for membrane fusion in eukaryotes (18). Three SNAREs with glutamine residues at the center of their SNARE domain (Q_a-, Q_b-, and Q_c-SNAREs) and one with a central arginine residue (R-SNARE) associate to form a four-helical bundle, the trans-SNARE complex. Formation of this trans-SNARE complex by SNAREs on adjacent membranes drives the fusion of these membranes (18). SM proteins are essential regulators of this process, promoting membrane fusion by correctly formed (cognate) SNARE complexes (18). Although a comprehensive understanding of how SM proteins achieve this still remains elusive, it is clear that SM proteins bind directly both to individual SNAREs and to SNARE complexes (18, 19). Most SM proteins bind strongly and specifically to an N-terminal segment of their cognate Q_a-SNARE, the N-peptide, and this interaction is thought to recruit the SM protein to the site of SNARE-mediated fusion (20, 21).When considered as a whole, the HOPS complex has the functional characteristics of an SM protein: It binds SNAREs and SNARE complexes (5, 22–24), and yeast HOPS has been shown to promote SNARE-mediated membrane fusion (25, 26). Recent biochemical analysis of Vps33, the yeast Vps33A homolog, shows it to be capable of binding isolated SNARE domains and SNARE complexes but not the N-terminal domain or full cytosolic portion of the Q_a-SNARE Vam3 (23, 24). Data from the yeast HOPS complex are consistent with a model whereby Vps33 provides the SM functionality of HOPS, accelerating SNARE-mediated fusion, whereas the rest of the HOPS complex recruits Vps33 (and thus SM function) to the site of SNARE-mediated fusion (24).Although a recent EM study has defined the overall topology of the yeast HOPS complex (27), atomic resolution insights into the assembly of the HOPS complex have thus far been unavailable. Here, we present the 2.4-Å resolution structure of human Vps33A, confirming its structural identity as an SM protein. We have mapped the HOPS epitope that binds Vps33A to a helical fragment comprising residues 642–736 of Vps16, solved the structure of this complex to 2.6-Å resolution, and identified mutations at the binding interface that disrupt the Vps33A–Vps16 complex both in vitro and in cultured cells.     

A helix-to-coil transition at the ε-cut site in the transmembrane dimer of the amyloid precursor protein is required for proteolysis

Processing of amyloid precursor protein (APP) by γ-secretase is the last step in the formation of the Aβ peptides associated Alzheimer's disease. Solid-state NMR spectroscopy is used to establish the structural features of the transmembrane (TM) and juxtamembrane (JM) domains of APP that facilitate proteolysis. Using peptides corresponding to the APP TM and JM regions (residues 618–660), we show that the TM domain forms an α-helical homodimer mediated by consecutive GxxxG motifs. We find that the APP TM helix is disrupted at the intracellular membrane boundary near the ε-cleavage site. This helix-to-coil transition is required for γ-secretase processing; mutations that extend the TM α-helix inhibit ε cleavage, leading to a low production of Aβ peptides and an accumulation of the α- and β-C-terminal fragments. Our data support a progressive cleavage mechanism for APP proteolysis that depends on the helix-to-coil transition at the TM-JM boundary and unraveling of the TM α-helix.     

Mechanistic link between β barrel assembly and the initiation of autotransporter secretion

Autotransporters are bacterial virulence factors that contain an N-terminal extracellular (“passenger”) domain and a C-terminal β barrel (“β”) domain that anchors the protein to the outer membrane. The β domain is required for passenger domain secretion, but its exact role in autotransporter biogenesis is unclear. Here we describe insights into the function of the β domain that emerged from an analysis of mutations in the Escherichia coli O157:H7 autotransporter EspP. We found that the G1066A and G1081D mutations slightly distort the structure of the β domain and delay the initiation of passenger domain translocation. Site-specific photocrosslinking experiments revealed that the mutations slow the insertion of the β domain into the outer membrane, but do not delay the binding of the β domain to the factor that mediates the insertion reaction (the Bam complex). Our results demonstrate that the β domain does not simply target the passenger domain to the outer membrane, but promotes translocation when it reaches a specific stage of assembly. Furthermore, our results provide evidence that the Bam complex catalyzes the membrane integration of β barrel proteins in a multistep process that can be perturbed by minor structural defects in client proteins.Autotransporters are a very large superfamily of virulence factors produced by Proteobacteria and Chlamydia that consist of an N-terminal extracellular domain (passenger domain) and a C-terminal β barrel domain (β domain) that anchors the protein to the outer membrane (OM) (1). Passenger domains range in size from ∼20 kDa to over 400 kDa and have been shown to mediate a variety of different virulence functions (2). Following their translocation across the OM, many passenger domains are released from the cell surface by a proteolytic cleavage. Experimental and in silico studies have suggested that virtually all passenger domains form a β-helical structure, despite the fact that their primary amino acid sequence is poorly conserved (3–6). β domains are generally ∼30 kDa in size, and although they also display considerable sequence diversity, they can all be identified as members of the pfam03797 (smart00869) family of protein domains. Several divergent β domains have been crystallized and have been shown to form nearly superimposable 12-stranded β barrels that are traversed by an α-helical segment (7–10). The α-helical segment generally extends into the extracellular space and links the passenger domain to the β domain. In a few cases, however, the passenger domain is released in an intrabarrel cleavage reaction that leaves a small α-helical segment inside the barrel (11). Available evidence suggests that the incorporation of the α-helical segment into the β domain pore occurs in the periplasm (where the β domain appears to undergo considerable folding) and is required for the integration of the β domain into the OM (12).Although there is general agreement that the passenger domain is translocated across the OM in a C- to N-terminal direction (13, 14), the mechanism of translocation has been hotly debated. Early experiments in which the β domain was deleted showed that it plays an essential role in translocation and led to the proposal that it forms a channel through which the covalently linked passenger domain is secreted (15). Recently, however, several findings have challenged the “autotransporter” hypothesis. Crystallographic analysis has shown that the pore formed by the β domain is ∼10 Å in diameter and therefore only wide enough to accommodate a completely unfolded polypeptide in a hairpin conformation or a single polypeptide in an α-helical conformation. Molecular dynamics simulations have confirmed that the β domain is extremely stable and unlikely to expand spontaneously (16, 17). Nevertheless, both native and modified passenger domains that have acquired tertiary structure in the periplasm are secreted efficiently by the autotransporter pathway (18, 19). Furthermore, the observation that the peptide inside the β domain is in an α-helical conformation at an early stage of translocation is incompatible with passenger domain translocation through the β domain pore (20). Finally, crosslinking experiments (13) have shown that during its transit across the OM, the passenger domain interacts with BamA, a component of a complex that binds to β barrel proteins and facilitates their integration into the OM by an unknown mechanism (21–24). Interestingly, members of the BamA superfamily produced by bacteria and chloroplasts have been shown to mediate protein translocation reactions (25). In addition to BamA, which consists of a β barrel domain and five periplasmic POTRA (polypeptide transport associated) domains, the Bam complex contains four lipoproteins called BamB, BamC, BamD, and BamE.An analysis of the interactions between cellular factors and the β domain of a model autotransporter produced by Escherichia coli O157:H7 called EspP has recently led to a new model in which the translocation of the passenger domain and the assembly of the β domain are interconnected (26). EspP is a member of the SPATE (serine protease autotransporters of Enterobacteraceae) family of autotransporters whose passenger domains are released in an intrabarrel cleavage reaction (11). Site-specific photocrosslinking experiments showed that the EspP β domain interacts with the periplasmic chaperone Skp and components of the Bam complex in a temporally and spatially regulated fashion in vivo. Skp is a homotrimer that resembles a jellyfish with long, flexible α-helical tentacles that form a large central cavity (27, 28). The results revealed that although the entire β domain initially interacts with Skp, discrete regions of the polypeptide subsequently interact with BamA, BamB, and BamD. The data suggest the existence of an assembly intermediate in which the EspP β domain is effectively surrounded by components of the Bam complex. Interestingly, the results also suggested that the passenger domain is not only normally secreted and cleaved before the completion of β domain assembly, but that the completion of β domain assembly is strictly dependent on the completion of passenger domain translocation. To account for these results and other recent observations on autotransporter biogenesis, it was proposed that the passenger domain is secreted through a channel comprised of an incompletely closed β domain, BamA, and possibly other factors that have not yet been identified (26).Although these results provide insight into the later stages of autotransporter assembly, they do not address the mechanism by which the translocation of the passenger domain across the OM is initiated. One possibility is that once the β domain captures the appropriate α-helical peptide in the periplasm, it simply serves as a targeting signal that guides the passenger domain to the OM. In that case, it is likely that the initiation of passenger domain translocation would be closely coupled to the binding of the β domain to the Bam complex. Alternatively, the initiation of translocation might depend on the completion of an additional step in β domain assembly that occurs after the β domain docks onto the Bam complex. Here we describe an analysis of several EspP β domain mutants that strongly supports the latter hypothesis. We found that the mutation of two highly conserved residues, G1066 and G1081, perturbs the stability of the β domain and delays the initiation of passenger domain translocation. In vivo site-specific photocrosslinking and other experiments showed that the mutations delay both the exposure of the passenger domain on the cell surface after the β domain binds to the Bam complex and the integration of the β domain into the lipid bilayer. By uncoupling the initiation of translocation from the interaction of the β domain with the Bam complex, our results imply that the β domain must undergo a transition after it reaches the OM before translocation can begin. Moreover, our results suggest that the Bam complex facilitates the integration of β barrel proteins into the OM in a reaction that can be divided into discrete stages.     

Fourier transform infrared spectroscopy reveals a rigid α-helical assembly for the tetrameric Streptomyces lividans K+ channel

The structure of the tetrameric K⁺ channel from Streptomyces lividans in a lipid bilayer environment was studied by polarized attenuated total reflection Fourier transform infrared spectroscopy. The channel displays approximately 43% α-helical and 25% β-sheet content. In addition, H/D exchange experiments show that only 43% of the backbone amide protons are exchangeable with solvent. On average, the α-helices are tilted 33° normal to the membrane surface. The results are discussed in relationship to the lactose permease of Escherichia coli, a membrane transport protein.     

Absence of the β subunit (cchb1) of the skeletal muscle dihydropyridine receptor alters expression of the α1 subunit and eliminates excitation-contraction coupling

The multisubunit (α_1S, α₂/δ, β₁, and γ) skeletal muscle dihydropyridine receptor transduces transverse tubule membrane depolarization into release of Ca²⁺ from the sarcoplasmic reticulum, and also acts as an L-type Ca²⁺ channel. The α_1S subunit contains the voltage sensor and channel pore, the kinetics of which are modified by the other subunits. To determine the role of the β₁ subunit in channel activity and excitation-contraction coupling we have used gene targeting to inactivate the β₁ gene. β₁-null mice die at birth from asphyxia. Electrical stimulation of β₁-null muscle fails to induce twitches, however, contractures are induced by caffeine. In isolated β₁-null myotubes, action potentials are normal, but fail to elicit a Ca²⁺ transient. L-type Ca²⁺ current is decreased 10- to 20-fold in the β₁-null cells compared with littermate controls. Immunohistochemistry of cultured myotubes shows that not only is the β₁ subunit absent, but the amount of α_1S in the membrane also is undetectable. In contrast, the β₁ subunit is localized appropriately in dysgenic, mdg/mdg, (α_1S-null) cells. Therefore, the β₁ subunit may not only play an important role in the transport/insertion of the α_1S subunit into the membrane, but may be vital for the targeting of the muscle dihydropyridine receptor complex to the transverse tubule/sarcoplasmic reticulum junction.     

Impaired autophagic function in rat islets with aging

Type 2 diabetes is characterized by a deficit in β-cell function and mass, and its incidence increases with age. Autophagy is a highly regulated intracellular process for degrading cytoplasmic components, particularly protein aggregates and damaged organelles. Impaired or deficient autophagy is believed to cause or contribute to aging and age-related disease. Autophagy may be necessary to maintain structure, mass, and function of pancreatic β-cells. In this study, we investigated the effects of age on β-cell function and autophagy in pancreatic islets of 4-month-old (young), 14-month-old (adult), and 24-month-old (old) male Wistar rats. We found that islet β-cell function decreased gradually with age. Protein expression of the autophagy markers LC3/Atg8 and Atg7 exhibited a marked decline in aged islets. The expression of Lamp-2, a good indicator of autophagic degradation rate, was significantly reduced in the islets of old rats, suggesting that autophagic degradation is decreased in the islets of aged rats. However, protein expression of beclin-1/Atg6, which plays an important role in the induction and formation of the pre-autophagosome structure by associating with a multimeric complex of autophagy regulatory proteins (Atg14, Vps34/class 3 PI3 kinase, and Vps15), was most prominent in the islets of adult rats, and was higher in 24-month-old islets than in 4-month-old islets. The levels of p62/SQSTM1 and polyubiquitin aggregates, representing the functions of autophagy and proteasomal degradation, were increased in aging islets. 8-Hydroxydeoxyguanosine, a marker of mitochondrial and nuclear DNA oxidative damage, exhibited strong immunostaining in old islets. Analysis by electron microscopy demonstrated swelling and disintegration of cristae in the mitochondria of aged islets. These results suggest that β-cell and autophagic function in islets decline simultaneously with increasing age in Wistar rats, and that impaired autophagy in the islets of older rats may cause accumulation of misfolded and aggregated proteins and reduce the removal of abnormal mitochondria in β-cells, leading to reduced β-cell function. Dysfunctional autophagy in islets during the aging process may be an important mechanism leading to the development of type 2 diabetes.     

Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering

Previous rotamer libraries showed little significant clustering for asparagine χ₂ or glutamine χ₃ values, but none of those studies corrected amide orientations or omitted disordered side chains. The current survey used 240 proteins at ≤1.7 Å resolution with <50% homology and <30 clashes per thousand atoms (atomic overlap ≥0.4 Å). All H atoms were added and optimized, and amide orientation was flipped by 180° if required by H bonding or atomic clashes. A side chain was included only if its amide orientation was clearly determined and if no atom had a B factor ≥40, alternate conformation, or severe clash; that selection process yielded 1,490 Asn and 863 Gln side chains. Clear clustering was observed for Asn χ₂ and Gln χ₃ (except when Gln χ₂ is trans). For Gln, five major and four minor rotamers cover 87% of examples. For Asn, there are seven backbone-independent rotamers covering 94% of examples plus rotamers specified for strictly α-helical, β, and left-handed (+) Asn. Although the strongest influence on χ angles is avoidance of atomic clashes (especially with the NH₂ hydrogens), some Asn or Gln rotamers are influenced by favorable van der Waals contacts and others by specific local H-bond patterns.     

beta-arrestin 2 oligomerization controls the Mdm2-dependent inhibition of p53

β-arrestins (β-arrs), two ubiquitous proteins involved in serpentine heptahelical receptor regulation and signaling, form constitutive homo- and heterooligomers stabilized by inositol 1,2,3,4,5,6-hexakisphosphate (IP6). Monomeric β-arrs are believed to interact with receptors after agonist activation, and therefore, β-arr oligomers have been proposed to represent a resting biologically inactive state. In contrast to this, we report here that the interaction with and subsequent titration out of the nucleus of the protooncogene Mdm2 specifically require β-arr2 oligomers together with the previously characterized nucleocytoplasmic shuttling of β-arr2. Mutation of the IP6-binding sites impair oligomerization, reduce interaction with Mdm2, and inhibit p53-dependent antiproliferative effects of β-arr2, whereas the competence for receptor regulation and signaling is maintained. These observations suggest that the intracellular concentration of β-arr2 oligomers might control cell survival and proliferation.     

Expression of GARP selectively identifies activated human FOXP3+ regulatory T cells

The molecules that define human regulatory T cells (Tregs) phenotypically and functionally remain to be fully characterized. We recently showed that activated human Tregs express mRNA for a transmembrane protein called glycoprotein A repetitions predominant (GARP, or LRRC32). Here, using a GARP-specific mAb, we demonstrate that expression of GARP on activated Tregs correlates with their suppressive capacity. However, GARP was not induced on T cells activated in the presence of TGFβ, which expressed high levels of FOXP3 and lacked suppressive function. Ectopic expression of FOXP3 in conventional T cells was also insufficient for induction of GARP expression in most donors. Functionally, silencing GARP in Tregs only moderately attenuated their suppressive activity. CD25+ T cells sorted for high GARP expression displayed more potent suppressive activity compared with CD25+GARP− cells. Remarkably, CD25+GARP− T cells expanded in culture contained 3–5 fold higher IL-17-secreting cells compared with either CD25+GARP+ or CD25−GARP− cells, suggesting that high GARP expression can potentially discriminate Tregs from those that have switched to Th17 lineage. We also determined whether GARP expression correlates with FOXP3-expressing T cells in human immunodeficiency virus (HIV) −infected subjects. A subset of HIV+ individuals with high percentages of FOXP3+ T cells did not show proportionate increase in GARP+ T cells. This finding suggests that higher FOXP3 levels observed in these HIV+ individuals is possibly due to immune activation rather than to an increase in Tregs. Our findings highlight the significance of GARP both in dissecting duality of Treg/Th17 cell differentiation and as a marker to identify bona fide Tregs during diseases with chronic immune activation.     

Na,K-ATPase transport from endoplasmic reticulum to Golgi requires the Golgi spectrin–ankyrin G119 skeleton in Madin Darby canine kidney cells

Spectrin (βIΣ) and ankyrin (Ank_G119) associate with Golgi membranes and the dynactin complex, but their role in vesicle trafficking remains uncertain. We find that the actin-binding domain and membrane-association domain 1 (MAD1) of βI spectrin together form a constitutive Golgi targeting signal in transfected MDCK cells. Expression of this signal in transfected cells disrupts the endogenous Golgi spectrin skeleton and blocks transport of α- and β-Na,K-ATPase and vesicular stomatitis virus-G protein from the endoplasmic reticulum (ER) but does not disrupt the formation of Golgi stacks, the distribution of β-COP, or the transport and surface display of E-cadherin. The Golgi spectrin skeleton is thus required for the transport of a subset of membrane proteins from the ER to the Golgi. We postulate that together with polyfunctional adapter proteins such as Ank_G119, Golgi spectrin forms a docking complex that acts prior to the cis-Golgi, presumably with vesicular–tubular clusters (VTCs or ERGIC), to sequester specific membrane proteins into vesicles transiting between the ER and Golgi, and subsequently (probably involving other isoforms of spectrin and ankyrin) to mediate cargo transport within the Golgi and to other membrane compartments. We hypothesize that this vesicular spectrin–ankyrin adapter-protein trafficking (or tethering) system (SAATS) mediates the capture and transport of many membrane proteins and acts in conjunction with vesicle-targeting molecules to effect the efficient transport of cargo proteins.     

A mouse model for the renal salt-wasting syndrome pseudohypoaldosteronism

Aldosterone-dependent epithelial sodium transport in the distal nephron is mediated by the absorption of sodium through the highly selective, amiloride-sensitive epithelial sodium channel (ENaC) made of three homologous subunits (α, β, and γ). In human, autosomal recessive mutations of α, β, or γENaC subunits cause pseudohypoaldosteronism type 1 (PHA-1), a renal salt-wasting syndrome characterized by severe hypovolemia, high plasma aldosterone, hyponatremia, life-threatening hyperkaliemia, and metabolic acidosis. In the mouse, inactivation of αENaC results in failure to clear fetal lung liquid at birth and in early neonatal death, preventing the observation of a PHA-1 renal phenotype. Transgenic expression of αENaC driven by a cytomegalovirus promoter in αENaC(−/−) knockout mice [αENaC(−/−)Tg] rescued the perinatal lethal pulmonary phenotype and partially restored Na⁺ transport in renal, colonic, and pulmonary epithelia. At days 5–9, however, αENaC(−/−)Tg mice showed clinical features of severe PHA-1 with metabolic acidosis, urinary salt-wasting, growth retardation, and 50% mortality. Adult αENaC(−/−)Tg survivors exhibited a compensated PHA-1 with normal acid/base and electrolyte values but 6-fold elevation of plasma aldosterone compared with wild-type littermate controls. We conclude that partial restoration of ENaC-mediated Na⁺ absorption in this transgenic mouse results in a mouse model for PHA-1.