Structure of the photoreceptor synaptic assembly of the extracellular matrix protein pikachurin with the orphan receptor GPR179

Precise synapse formation is essential for normal functioning of the nervous system. Retinal photoreceptors establish selective contacts with bipolar cells, aligning the neurotransmitter release apparatus with postsynaptic signaling cascades. This involves transsynaptic assembly between the dystroglycan-dystrophin complex on the photoreceptor and the orphan receptor GPR179 on the bipolar cell, which is mediated by the extracellular matrix protein pikachurin (also known as EGFLAM). This complex plays a critical role in the synaptic organization of photoreceptors and signal transmission, and mutations affecting its components cause blinding disorders in humans. Here, we investigated the structural organization and molecular mechanisms by which pikachurin orchestrates transsynaptic assembly and solved structures of the human pikachurin domains by x-ray crystallography and of the GPR179-pikachurin complex by single-particle, cryo-electron microscopy. The structures reveal molecular recognition principles of pikachurin by the Cache domains of GPR179 and show how the interaction is involved in the transsynaptic alignment of the signaling machinery. Together, these data provide a structural basis for understanding the synaptic organization of photoreceptors and ocular pathology.

Orphan receptor GPR158 serves as a metabotropic glycine receptor: mGlyR

Glycine is a major neurotransmitter involved in several fundamental neuronal processes. The identity of the metabotropic receptor mediating slow neuromodulatory effects of glycine is unknown. We identified an orphan G protein-coupled receptor, GPR158, as a metabotropic glycine receptor (mGlyR). Glycine and a related modulator, taurine, directly bind to a Cache domain of GPR158, and this event inhibits the activity of the intracellular signaling complex regulator of G protein signaling 7-G protein β5 (RGS7-Gβ5), which is associated with the receptor. Glycine signals through mGlyR to inhibit production of the second messenger adenosine 3',5'-monophosphate. We further show that glycine, but not taurine, acts through mGlyR to regulate neuronal excitability in cortical neurons. These results identify a major neuromodulatory system involved in mediating metabotropic effects of glycine, with implications for understanding cognition and affective states.

Cryo-EM structure of human GPR158 receptor coupled to the RGS7-Gβ5 signaling complex

GPR158 is an orphan G protein–coupled receptor (GPCR) highly expressed in the brain, where it controls synapse formation and function. GPR158 has also been implicated in depression, carcinogenesis, and cognition. However, the structural organization and signaling mechanisms of GPR158 are largely unknown. We used single-particle cryo–electron microscopy (cryo-EM) to determine the structures of human GPR158 alone and bound to an RGS signaling complex. The structures reveal a homodimeric organization stabilized by a pair of phospholipids and the presence of an extracellular Cache domain, an unusual ligand-binding domain in GPCRs. We further demonstrate the structural basis of GPR158 coupling to RGS7-Gβ5. Together, these results provide insights into the unusual biology of orphan receptors and the formation of GPCR-RGS complexes.

Conformational flexibility determines the Nf2/merlin tumor suppressor functions

The Neurofibromatosis type 2 gene encodes the Nf2/merlin tumor suppressor protein that is responsible for the regulation of cell proliferation. Once activated, Nf2/merlin modulates adhesive signaling pathways and thereby inhibits cell growth. Nf2/merlin controls oncogenic gene expression by modulating the Hippo pathway. By responding to several physical and biochemical stimuli, Hippo signaling determines contact inhibition of proliferation as well as organ size. The large tumor suppressor (LATS) serine/threonine-protein kinase is the key enzyme in the highly conserved kinase cascade that negatively regulates the activity and localization of the transcriptional coactivators Yes-associated protein (YAP) and its paralogue transcriptional coactivator with PDZ-binding motif (TAZ). Nf2/merlin belongs to the band 4.1, ezrin, radixin, moesin (FERM) gene family that links the actin cytoskeleton to adherens junctions, remodels adherens junctions during epithelial morphogenesis and maintains organized apical surfaces on the plasma cell membrane. Nf2/merlin and ERM proteins have a globular N-terminal cloverleaf head domain, the FERM domain, that binds to the plasma membrane, a central α-helical domain, and a tail domain that binds to its head domain. Here we present the high-resolution crystal structure of Nf2/merlin bound to LATS1 which shows that LATS1 binding to Nf2/merlin displaces the Nf2/merlin tail domain and causes an allosteric shift in the Nf2/merlin α-helix that extends from its FERM domain. This is consistent with the fact that full-length Nf2/merlin binds LATS1 ~10-fold weaker compared to LATS1 binding to the Nf2/merlin-PIP₂ complex. Our data increase our understanding of Nf2/merlin biology by providing mechanistic insights into the Hippo pathway that are relevant to several diseases in particular oncogenic features that are associated with cancers.

Identification of Potential Modulators of the RGS7/Gβ5/R7BP Complex

Regulators of G protein signaling (RGS) proteins serve as critical regulatory nodes to limit the lifetime and extent of signaling via G protein-coupled receptors (GPCRs). Previously, approaches to pharmacologically inhibit RGS activity have mostly focused on the inhibition of GTPase activity by interrupting the interaction of RGS proteins with the G proteins they regulate. However, several RGS proteins are also regulated by association with binding partners. A notable example is the mammalian RGS7 protein, which has prominent roles in metabolic control, vision, reward, and actions of opioid analgesics. In vivo, RGS7 exists in complex with the binding partners type 5 G protein β subunit (Gβ5) and R7 binding protein (R7BP), which control its stability and activity, respectively. Targeting the whole RGS7/Gβ5/R7BP protein complex affords the opportunity to allosterically tune opioid receptor signaling following opioid engagement while potentially bypassing undesirable side effects. Hence, we implemented a novel strategy to pharmacologically target the interaction between RGS7/Gβ5 and R7BP. To do so, we searched for protein complex inhibitors using a time-resolved fluorescence resonance energy transfer (FRET)-based high-throughput screening (HTS) assay that measures compound-mediated alterations in the FRET signal between RGS7/Gβ5 and R7BP. We performed two HTS campaigns, each screening ~100,000 compounds from the Scripps Drug Discovery Library (SDDL). Each screen yielded more than 100 inhibitors, which will be described herein.

Molecular Deconvolution Platform to Establish Disease Mechanisms by Surveying GPCR Signaling

Despite the wealth of genetic information available, mechanisms underlying pathological effects of disease-associated mutations in components of G protein-coupled receptor (GPCR) signaling cascades remain elusive. In this study, we developed a scalable approach for the functional analysis of clinical variants in GPCR pathways along with a complete analytical framework. We applied the strategy to evaluate an extensive set of dystonia-causing mutations in G protein Gαolf. Our quantitative analysis revealed diverse mechanisms by which pathogenic variants disrupt GPCR signaling, leading to a mechanism-based classification of dystonia. In light of significant clinical heterogeneity, the mechanistic analysis of individual disease-associated variants permits tailoring personalized intervention strategies, which makes it superior to the current phenotype-based approach. We propose that the platform developed in this study can be universally applied to evaluate disease mechanisms for conditions associated with genetic variation in all components of GPCR signaling.

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A scalable platform allows multidimensional analysis of GPCR signaling

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The approach is applied to dystonia-causing mutations in G protein Gαolf

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Pathogenic variants in Gαolf disrupt GPCR signaling by diverse mechanisms

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Mechanism-based disease classification could allow targeted therapies

A High-Throughput Time-Resolved Fluorescence Energy Transfer Assay to Screen for Modulators of RGS7/Gβ5/R7BP Complex

G protein-coupled receptors (GPCRs) are excellent drug targets exploited by majority of the Food and Drug Administration-approved medications, but when modulated, are often accompanied by significant adverse effects. Targeting of other elements in GPCR pathways for improved safety and efficacy is thus an unmet need. The strength of GPCR signaling is tightly regulated by regulators of G protein signaling (RGS) proteins, making them attractive drug targets. We focused on a prominent RGS complex in the brain consisting of RGS7 and its binding partners Gβ5 and R7BP. These complexes play critical roles in regulating multiple GPCRs and essential physiological processes, yet no small molecule modulators are currently available to modify its function. In this study, we report a novel high-throughput approach to screen for small molecule modulators of the intramolecular transitions in the RGS7/Gβ5/R7BP complex known to be involved in its allosteric regulation. We developed a time-resolved fluorescence energy transfer-based in vitro assay that utilizes full-length recombinant proteins and shows consistency, excellent assay statistics, and high level of sensitivity. We demonstrated the potential of this approach by screening two compound libraries (LOPAC 1280 and MicroSource Spectrum). This study confirms the feasibility of the chosen strategy for identifying small molecule modulators of RGS7/Gβ5/R7BP complex for impacting signaling downstream of the GPCRs.

Structural organization of a major neuronal G protein regulator, the RGS7-Gβ5-R7BP complex

Signaling by the G-protein-coupled receptors (GPCRs) plays fundamental role in a vast number of essential physiological functions. Precise control of GPCR signaling requires action of regulators of G protein signaling (RGS) proteins that deactivate heterotrimeric G proteins. RGS proteins are elaborately regulated and comprise multiple domains and subunits, yet structural organization of these assemblies is poorly understood. Here, we report a crystal structure and dynamics analyses of the multisubunit complex of RGS7, a major regulator of neuronal signaling with key roles in controlling a number of drug target GPCRs and links to neuropsychiatric disease, metabolism, and cancer. The crystal structure in combination with molecular dynamics and mass spectrometry analyses reveals unique organizational features of the complex and long-range conformational changes imposed by its constituent subunits during allosteric modulation. Notably, several intermolecular interfaces in the complex work in synergy to provide coordinated modulation of this key GPCR regulator.

Novel GNB1 mutations disrupt assembly and function of G protein heterotrimers and cause global developmental delay in humans

Global developmental delay (GDD), often accompanied by intellectual disability, seizures and other features is a severe, clinically and genetically highly heterogeneous childhood-onset disorder. In cases where genetic causes have been identified, de novo mutations in neuronally expressed genes are a common scenario. These mutations can be best identified by exome sequencing of parent-offspring trios. De novo mutations in the guanine nucleotide-binding protein, beta 1 (GNB1) gene, encoding the Gβ1 subunit of heterotrimeric G proteins, have recently been identified as a novel genetic cause of GDD. Using exome sequencing, we identified 14 different novel variants (2 splice site, 2 frameshift and 10 missense changes) in GNB1 in 16 pediatric patients. One mutation (R96L) was recurrently found in three ethnically diverse families with an autosomal dominant mode of inheritance. Ten variants occurred de novo in the patients. Missense changes were functionally tested for their pathogenicity by assaying the impact on complex formation with Gγ and resultant mutant Gβγ with Gα. Signaling properties of G protein complexes carrying mutant Gβ1 subunits were further analyzed by their ability to couple to dopamine D1R receptors by real-time bioluminescence resonance energy transfer (BRET) assays. These studies revealed altered functionality of the missense mutations R52G, G64V, A92T, P94S, P96L, A106T and D118G but not for L30F, H91R and K337Q. In conclusion, we demonstrate a pathogenic role of de novo and autosomal dominant mutations in GNB1 as a cause of GDD and provide insights how perturbation in heterotrimeric G protein function contributes to the disease.

GNB5 mutation causes a novel neuropsychiatric disorder featuring attention deficit hyperactivity disorder, severely impaired language development and normal cognition

Background

Neuropsychiatric disorders are common forms of disability in humans. Despite recent progress in deciphering the genetics of these disorders, their phenotypic complexity continues to be a major challenge. Mendelian neuropsychiatric disorders are rare but their study has the potential to unravel novel mechanisms that are relevant to their complex counterparts.

Results

In an extended consanguineous family, we identified a novel neuropsychiatric phenotype characterized by severe speech impairment, variable expressivity of attention deficit hyperactivity disorder (ADHD), and motor delay. We identified the disease locus through linkage analysis on 15q21.2, and exome sequencing revealed a novel missense variant in GNB5. GNB5 encodes an atypical β subunit of the heterotrimeric GTP-binding proteins (Gβ5). Gβ5 is enriched in the central nervous system where it forms constitutive complexes with members of the regulator of G protein signaling family of proteins to modulate neurotransmitter signaling that affects a number of neurobehavioral outcomes. Here, we show that the S81L mutant form of Gβ5 has significantly impaired activity in terminating responses that are elicited by dopamine.

Conclusions

We demonstrate that these deficits originate from the impaired expression of the mutant Gβ5 protein, resulting in the decreased ability to stabilize regulator of G protein signaling complexes. Our data suggest that this novel neuropsychiatric phenotype is the human equivalent of Gnb5 deficiency in mice, which manifest motor deficits and hyperactivity, and highlight a critical role of Gβ5 in normal behavior as well as language and motor development in humans.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-016-1061-6) contains supplementary material, which is available to authorized users.

Trace metals in water, sediment and bivalves of a tropical estuary, west coast of India

Trace metal pollution was studied in water, sediment and three selected bivalves in Mandovi and Chapora estuaries of Goa. The trace metal in water and sediment of Mandovi was higher than in Chapora. The concentration in the tissues was in the range of 1205.2-2506.7 ppm for Paphia malabarica, 1906.2-2802.6 ppm for Perna viridis and 778.7-1607.5 ppm for Saccostrea cucullata in Mandovi estuary. Tha values for Chapora were 199.4-625.8 ppm for P. malabarica, 812.6-1220.2 for P. viridis and 392.5-418.6 ppm for S. cucullata. The anthropogenic input of metal in Mandovi estuary appears to be mainly responsible for the high accumulation of trace metals. These bivalves have potential to serve as indicator for metal contamination in seafood of Goa.

Lipid-directed vinculin dimerization

Vinculin localizes to cellular adhesions where it regulates motility, migration, development, wound healing, and response to force. Importantly, vinculin loss results in cancer phenotypes, cardiovascular disease, and embryonic lethality. At the plasma cell membrane, the most abundant phosphoinositide, phosphatidylinositol 4,5-bisphosphate (PIP2), binds the vinculin tail domain, Vt, and triggers homotypic and heterotypic interactions that amplify binding of vinculin to the actin network. Binding of PIP2 to Vt is necessary for maintaining optimal focal adhesions, for organizing stress fibers, for cell migration and spreading, and for the control of vinculin dynamics and turnover of focal adhesions. While the recently determined Vt/PIP2 crystal structure revealed the conformational changes occurring upon lipid binding and oligomerization, characterization of PIP2-induced vinculin oligomerization has been challenging in the adhesion biology field. Here, via a series of novel biochemical assays not performed in previous studies that relied on chemical cross-linking, we characterize the PIP2-induced vinculin oligomerization. Our results show that Vt/PIP2 forms a tight dimer with Vt or with the muscle-specific vinculin isoform, metavinculin, at sites of adhesion at the cell membrane. Insight into how PIP2 regulates clustering and into mechanisms that regulate cell adhesion allows the development for a more definite sensor for PIP2, and our developed techniques can be applied generally and thus open the door for the characterization of many other protein/PIP2 complexes under physiological conditions.

Lipid binding promotes oligomerization and focal adhesion activity of vinculin

PIP₂ binds vinculin and directs its oligomerization, which promotes proper focal adhesion structure and function.

Adherens junctions (AJs) and focal adhesion (FA) complexes are necessary for cell migration and morphogenesis, and for the development, growth, and survival of all metazoans. Vinculin is an essential regulator of both AJs and FAs, where it provides links to the actin cytoskeleton. Phosphatidylinositol 4,5-bisphosphate (PIP₂) affects the functions of many targets, including vinculin. Here we report the crystal structure of vinculin in complex with PIP₂, which revealed that PIP₂ binding alters vinculin structure to direct higher-order oligomerization and suggests that PIP₂ and F-actin binding to vinculin are mutually permissive. Forced expression of PIP₂-binding–deficient mutants of vinculin in vinculin-null mouse embryonic fibroblasts revealed that PIP₂ binding is necessary for maintaining optimal FAs, for organization of actin stress fibers, and for cell migration and spreading. Finally, photobleaching experiments indicated that PIP₂ binding is required for the control of vinculin dynamics and turnover in FAs. Thus, through oligomerization, PIP₂ directs a transient vinculin sequestration at FAs that is necessary for proper FA function.

Ligand-bound structures of 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase fromMoraxella catarrhalisreveal a water channel connecting to the active site for the second step of catalysis

KdsC, the third enzyme of the 3-deoxy-D-manno-octulosonic acid (KDO) biosynthetic pathway, catalyzes a substrate-specific reaction to hydrolyze 3-deoxy-D-manno-octulosonate 8-phosphate to generate a molecule of KDO and phosphate. KdsC is a phosphatase that belongs to the C0 subfamily of the HAD superfamily. To understand the molecular basis for the substrate specificity of this tetrameric enzyme, the crystal structures of KdsC fromMoraxella catarrhalis(Mc-KdsC) with several combinations of ligands, namely metal ion, citrate and products, were determined. Various transition states of the enzyme have been captured in these crystal forms. The ligand-free and ligand-bound crystal forms reveal that the binding of ligands does not cause any specific conformational changes in the active site. However, the electron-density maps clearly showed that the conformation of KDO as a substrate is different from the conformation adopted by KDO when it binds as a cleaved product. Furthermore, structural evidence for the existence of an intersubunit tunnel has been reported for the first time in the C0 subfamily of enzymes. A role for this tunnel in transferring water molecules from the interior of the tetrameric structure to the active-site cleft has been proposed. At the active site, water molecules are required for the formation of a water bridge that participates as a proton shuttle during the second step of the two-step phosphoryl-transfer reaction. In addition, as the KDO biosynthesis pathway is a potential antibacterial target, pharmacophore-based virtual screening was employed to identify inhibitor molecules for theMc-KdsC enzyme.

Purification and biophysical characterization of an 11S globulin from Wrightia tinctoria exhibiting hemagglutinating activity

Wrightia tinctoria globulin (WTG), one of the major seed storage proteins, was isolated for the first time from seeds of the medicinal plant. WTG was extracted and purified to homogeneity in two steps using anion-exchange and size-exclusion chromatographies. On an SDS-PAGE gel under non-reducing conditions, a major band of ~56 kDa was observed; under reducing conditions, however, two major polypeptides, one with molecular weight ~32-34 kDa and the other with molecular weight ~22-26 kDa were observed. Intact mass determination by MALDI-TOF supported this observation. The N-terminal amino acid sequence of WTG matched in NCBI database with an expressed sequence tag obtained from the c-DNA of developing embryo m-RNA of Wrightia tinctoria. The EST sequence was further substantiated by partial de novo internal sequencing using MALDI-TOF/TOF. The high sequence homology with seed storage protein 11S globulin confirmed that WTG is a type of 11S globulin. Circular dichroism analysis showed that the secondary structure of WTG consists predominantly of β-sheets (44.2%) and moderate content of α-helices (10.3%). WTG showed hemagglutinating property indicating that the protein may possess lectin-like activity. WTG was crystallized at 20 Å°C by the vapour diffusion method using PEG 400 as precipitant. The crystals belonged to the orthorhombic space group P212121 with cell dimensions of a=109.9Å, b=113.2Å and c=202.2Å with six molecules per asymmetric unit. Diffraction data were collected to a resolution of 2.2Å under cryocondition. Preliminary structure solution of WTG indicated the possibility of a hexameric assembly in its asymmetric unit.

Biochemical studies and ligand-bound structures of biphenyl dehydrogenase from Pandoraea pnomenusa strain B-356 reveal a basis for broad specificity of the enzyme

Biphenyl dehydrogenase, a member of short-chain dehydrogenase/reductase enzymes, catalyzes the second step of the biphenyl/polychlorinated biphenyls catabolic pathway in bacteria. To understand the molecular basis for the broad substrate specificity of Pandoraea pnomenusa strain B-356 biphenyl dehydrogenase (BphB(B-356)), the crystal structures of the apo-enzyme, the binary complex with NAD(+), and the ternary complexes with NAD(+)-2,3-dihydroxybiphenyl and NAD(+)-4,4'-dihydroxybiphenyl were determined at 2.2-, 2.5-, 2.4-, and 2.1-Å resolutions, respectively. A crystal structure representing an intermediate state of the enzyme was also obtained in which the substrate binding loop was ordered as compared with the apo and binary forms but it was displaced significantly with respect to the ternary structures. These five structures reveal that the substrate binding loop is highly mobile and that its conformation changes during ligand binding, starting from a disorganized loop in the apo state to a well organized loop structure in the ligand-bound form. Conformational changes are induced during ligand binding; forming a well defined cavity to accommodate a wide variety of substrates. This explains the biochemical data that shows BphB(B-356) converts the dihydrodiol metabolites of 3,3'-dichlorobiphenyl, 2,4,4'-trichlorobiphenyl, and 2,6-dichlorobiphenyl to their respective dihydroxy metabolites. For the first time, a combination of structural, biochemical, and molecular docking studies of BphB(B-356) elucidate the unique ability of the enzyme to transform the cis-dihydrodiols of double meta-, para-, and ortho-substituted chlorobiphenyls.

Expression, purification, crystallization and preliminary crystallographic studies of cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase from Pandoraea pnomenusa B-356

cis-Biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB) is involved in the aerobic biodegradation of biphenyl and polychlorinated biphenyls. BphB from Pandoraea pnomenusa strain B-356 was overexpressed in Escherichia coli, purified to homogeneity and crystallized. Crystals were obtained by the sitting-drop vapour-diffusion method using polyethylene glycol 3350 and 0.2 M sodium malonate. A BphB crystal diffracted to 2.8 Å resolution and belonged to space group P4(3)2(1)2, with unit-cell parameters a = b = 75.2, c = 180.4 Å. Preliminary crystallographic analysis indicated the presence of two molecules in the asymmetric unit, giving a Matthews coefficient of 2.2 Å(3) Da(-1) and a solvent content of 44%.

Crystallization and preliminary X-ray diffraction analysis of the complex of Kunitz-type tamarind trypsin inhibitor and porcine pancreatic trypsin

The complex of Tamarindus indica Kunitz-type trypsin inhibitor and porcine trypsin has been crystallized by the sitting-drop vapour-diffusion method using ammonium acetate as precipitant and sodium acetate as buffer. The homogeneity of complex formation was checked by size-exclusion chromatography and further confirmed by reducing SDS-PAGE. The crystals diffracted to 2.0 angstrom resolution and belonged to the tetragonal space group P4(1), with unit-cell parameters a = b = 57.1, c = 120.1 angstrom. Preliminary X-ray diffraction analysis indicated the presence of one unit of inhibitor-trypsin complex per asymmetric unit, with a solvent content of 45%.

Purification, crystallization and preliminary crystallographic studies of a Kunitz-type proteinase inhibitor from tamarind (Tamarindus indica) seeds

A Kunitz-type proteinase inhibitor has been purified from tamarind (Tamarindus indica) seeds. SDS-PAGE analysis of a purified sample showed a homogeneous band corresponding to a molecular weight of 21 kDa. The protein was identified as a Kunitz-type proteinase inhibitor based on N-terminal amino-acid sequence analysis. It was crystallized by the vapour-diffusion method using PEG 6000. The crystals belonged to the orthorhombic space group C222(1), with unit-cell parameters a = 37.2, b = 77.1, c = 129.1 A. Diffraction data were collected to a resolution of 2.7 A. Preliminary crystallographic analysis indicated the presence of one proteinase inhibitor molecule in the asymmetric unit, with a solvent content of 44%.

Isolation, purification, crystallization and preliminary crystallographic studies of chitinase from tamarind (Tamarindus indica) seeds

A protein with chitinase activity has been isolated and purified from tamarind (Tamarindus indica) seeds. N-terminal amino-acid sequence analysis of this protein confirmed it to be an approximately 34 kDa endochitinase which belongs to the acidic class III chitinase family. The protein was crystallized by the vapour-diffusion method using PEG 4000. The crystals belonged to the tetragonal space group P4(1), with two molecules per asymmetric unit. Diffraction data were collected to a resolution of 2.6 A.