Structure and function of receptors coupled to G proteins

Adenosinergic System and Nucleoside Transporters in Attention Deficit Hyperactivity Disorder: Current Findings

Attention deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder with high heterogeneity that can affect individuals of any age. It is characterized by three main symptoms: inattention, hyperactivity, and impulsivity. These neurobehavioral alterations and neurochemical and pharmacological findings are mainly attributed to unbalanced catecholaminergic signaling, especially involving dopaminergic pathways within prefrontal and striatal areas. Dopamine receptors and transporters are not solely implicated in this imbalance, as evidence indicates that the dopaminergic signaling is modulated by adenosine activity. To this extent, alterations in adenosinergic signaling are probably involved in ADHD. Here, we review the current knowledge about adenosine's role in the modulation of chemical, behavioral and cognitive parameters of ADHD, especially regarding dopaminergic signaling. Current literature usually links adenosine receptors signaling to the dopaminergic imbalance found in ADHD, but there is evidence that equilibrative nucleoside transporters (ENTs) could also be implicated as players in dopaminergic signaling alterations seen in ADHD, since their involvement in other neurobehavioral impairments.

Gonadotropin-Releasing Hormone Receptor (GnRHR) and Hypogonadotropic Hypogonadism

Human sexual and reproductive development is regulated by the hypothalamic-pituitary-gonadal (HPG) axis, which is primarily controlled by the gonadotropin-releasing hormone (GnRH) acting on its receptor (GnRHR). Dysregulation of the axis leads to conditions such as congenital hypogonadotropic hypogonadism (CHH) and delayed puberty. The pathophysiology of GnRHR makes it a potential target for treatments in several reproductive diseases and in congenital adrenal hyperplasia. GnRHR belongs to the G protein-coupled receptor family and its GnRH ligand, when bound, activates several complex and tissue-specific signaling pathways. In the pituitary gonadotrope cells, it triggers the G protein subunit dissociation and initiates a cascade of events that lead to the production and secretion of the luteinizing hormone (LH) and follicle-stimulating hormone (FSH) accompanied with the phospholipase C, inositol phosphate production, and protein kinase C activation. Pharmacologically, GnRHR can be modulated by synthetic analogues. Such analogues include the agonists, antagonists, and the pharmacoperones. The agonists stimulate the gonadotropin release and lead to receptor desensitization with prolonged use while the antagonists directly block the GnRHR and rapidly reduce the sex hormone production. Pharmacoperones include the most recent GnRHR therapeutic approaches that directly correct the misfolded GnRHRs, which are caused by genetic mutations and hold serious promise for CHH treatment. Understanding of the GnRHR's genomic and protein structure is crucial for the most appropriate assessing of the mutation impact. Such mutations in the GNRHR are linked to normosmic hypogonadotropic hypogonadism and lead to various clinical symptoms, including delayed puberty, infertility, and impaired sexual development. These mutations vary regarding their mode of inheritance and can be found in the homozygous, compound heterozygous, or in the digenic state. GnRHR expression extends beyond the pituitary gland, and is found in reproductive tissues such as ovaries, uterus, and prostate and non-reproductive tissues such as heart, muscles, liver and melanoma cells. This comprehensive review explores GnRHR's multifaceted role in human reproduction and its clinical implications for reproductive disorders.

Dysfunctional Heteroreceptor Complexes as Novel Targets for the Treatment of Major Depressive and Anxiety Disorders

Among mental diseases, major depressive disorder (MDD) and anxiety deserve a special place due to their high prevalence and their negative impact both on society and patients suffering from these disorders. Consequently, the development of novel strategies designed to treat them quickly and efficiently, without or at least having limited side effects, is considered a highly important goal. Growing evidence indicates that emerging properties are developed on recognition, trafficking, and signaling of G-protein coupled receptors (GPCRs) upon their heteromerization with other types of GPCRs, receptor tyrosine kinases, and ionotropic receptors such as N-methyl-D-aspartate (NMDA) receptors. Therefore, to develop new treatments for MDD and anxiety, it will be important to identify the most vulnerable heteroreceptor complexes involved in MDD and anxiety. This review focuses on how GPCRs, especially serotonin, dopamine, galanin, and opioid heteroreceptor complexes, modulate synaptic and volume transmission in the limbic networks of the brain. We attempt to provide information showing how these emerging concepts can contribute to finding new ways to treat both MDD and anxiety disorders.

The Role of Neuropeptide-Stimulated cAMP-EPACs Signalling in Cancer Cells

Neuropeptides are autocrine and paracrine signalling factors and mainly bind to G protein-coupled receptors (GPCRs) to trigger intracellular secondary messenger release including adenosine 3′, 5′-cyclic monophosphate (cAMP), thus modulating cancer progress in different kind of tumours. As one of the downstream effectors of cAMP, exchange proteins directly activated by cAMP (EPACs) play dual roles in cancer proliferation and metastasis. More evidence about the relationship between neuropeptides and EPAC pathways have been proposed for their potential role in cancer development; hence, this review focuses on the role of neuropeptide/GPCR system modulation of cAMP/EPACs pathways in cancers. The correlated downstream pathways between neuropeptides and EPACs in cancer cell proliferation, migration, and metastasis is discussed to glimmer the direction of future research.

EMCBOW-GPCR: A method for identifying G-protein coupled receptors based on word embedding and wordbooks

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An computational method was developed to identify G-protein coupled receptors.

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Three word-embedding models and a bag-of-words model are used to extract original features.

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A high accuracy was achieved by using fusion information.

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A powerful tool was established.

G Protein-Coupled Receptors (GPCRs) are one of the largest membrane protein receptor family in human, which are also important targets for many drugs. Thence, it’s of great significance to judge whether a protein is a GPCR or not. However, identifying GPCRs by experimental methods is very expensive and time-consuming. As more and more GPCR primary sequences are accumulated, it’s feasible to develop a computational model to predict GPCRs precisely and quickly. In this paper, a novel method called EMCBOW-GPCR has been proposed to improve the accuracy of identifying GPCRs based on natural language processing (NLP). For representing GPCRs, three word-embedding models and a bag-of-words model are used to extract original features. Then, the original features are thrown into a Deep-learning algorithm to extract features further and reduce the dimension. Finally, the obtained features are fed into Extreme Gradient Boosting. As shown with the results comparison, the overall prediction metrics of EMCBOW-GPCR are higher than the state of the arts. In order to be convenient for more researchers to use EMCBOW-GPCR, the method and source code have been opened in github, which are available at https://github.com/454170054/EMCBOW-GPCR, and a user-friendly web-server for EMCBOW-GPCR has been established at http://www.jci-bioinfo.cn/emcbowgpcr.

G proteins: binary switches in health and disease

Cell signaling plays critical role in health and disease. The normal functioning of body depends on the homeostasis of immunity players. One of the very important cell signaling participants is G protein-coupled receptor (GPCR). GPCRs transduce extracellular signals into target cell by binding to and activating different G proteins (G αβγ, families Gi, Gs, Gq/11, G12/13) leading to range of different functions. Abnormal GPCRs signaling leads to various abnormalities, including but not limited to, cancer, pain, cardiac problems, and asthma. Mutations, which lead to activation or inactivation of GPCR pathways, permanently alter the pathways controlled by these receptors. A large number of human cancer incidence is a consequence of genetic abnormalities in signaling pathways, which influence cell division. Some bacteria and pathogens may interfere with the GPCR signaling pathways for their survival and immune evasion. Inhibition of GPCR signaling by small inhibitors is a novel way to treat various pathological conditions. There are several types of GPCRs in human genome, which due to their central role in health and disease, are the target of many commercially available drugs. Importantly, GPCRs have huge impact on drug discovery and approximately 30% of current drug targets are GPCRs. There is a need of further studies to explore more the role of G protein and the GPCRs in human health and how certain mutations can lead to disease state. Such studies may be important to adjust the signaling pathways for health improvement.

SeQuery: an interactive graph database for visualizing the GPCR superfamily

The rate at which new protein and gene sequences are being discovered has grown explosively in the omics era, which has increasingly complicated the efficient characterization and analysis of their biological properties. In this study, we propose a web-based graphical database tool, SeQuery, for intuitively visualizing proteome/genome networks by integrating the sequential, structural and functional information of sequences. As a demonstration of our tool’s effectiveness, we constructed a graph database of G protein-coupled receptor (GPCR) sequences by integrating data from the UniProt, GPCRdb and RCSB PDB databases. Our tool attempts to achieve two goals: (i) given the sequence of a query protein, correctly and efficiently identify whether the protein is a GPCR, and, if so, define its sequential and functional roles in the GPCR superfamily; and (ii) present a panoramic view of the GPCR superfamily and its network centralities that allows users to explore the superfamily at various resolutions. Such a bottom-up-to-top-down view can provide the users with a comprehensive understanding of the GPCR superfamily through interactive navigation of the graph database. A test of SeQuery with the GPCR2841 dataset shows that it correctly identifies 99 out of 100 queried protein sequences. The developed tool is readily applicable to other biological networks, and we aim to expand SeQuery by including additional biological databases in the near future.

Discovery of BAY-298 and BAY-899: Tetrahydro-1,6-naphthyridine-Based, Potent, and Selective Antagonists of the Luteinizing Hormone Receptor Which Reduce Sex Hormone Levels in Vivo

The human luteinizing hormone receptor (hLH-R) is a member of the glycoprotein hormone family of G-protein-coupled receptors (GPCRs), activated by luteinizing hormone (hLH) and essentially involved in the regulation of sex hormone production. Thus, hLH-R represents a valid target for the treatment of sex hormone-dependent cancers and diseases (polycystic ovary syndrome, uterine fibroids, endometriosis) as well as contraception. Screening of the Bayer compound library led to the discovery of tetrahydrothienopyridine derivatives as novel, small-molecule (SMOL) hLH-R inhibitors and to the development of BAY-298, the first nanomolar hLH-R antagonist reducing sex hormone levels in vivo. Further optimization of physicochemical, pharmacokinetic, and safety parameters led to the identification of BAY-899 with an improved in vitro profile and proven efficacy in vivo. BAY-298 and BAY-899 serve as valuable tool compounds to study hLH-R signaling in vitro and to interfere with the production of sex hormones in vivo.

Phylogenetic Reclassification of Vertebrate Melatonin Receptors To Include Mel1d

The circadian and seasonal actions of melatonin are mediated by high affinity G-protein coupled receptors (melatonin receptors, MTRs), classified into phylogenetically distinct subtypes based on sequence divergence and pharmacological characteristics. Three vertebrate MTR subtypes are currently described: MT1 (MTNR1A), MT2 (MTNR1B), and Mel1c (MTNR1C / GPR50), which exhibit distinct affinities, tissue distributions and signaling properties. We present phylogenetic and comparative genomic analyses supporting a revised classification of the vertebrate MTR family. We demonstrate four ancestral vertebrate MTRs, including a novel molecule hereafter named Mel1d. We reconstructed the evolution of each vertebrate MTR, detailing genetic losses in addition to gains resulting from whole genome duplication events in teleost fishes. We show that Mel1d was lost separately in mammals and birds and has been previously mistaken for an MT1 paralogue. The genetic and functional diversity of vertebrate MTRs is more complex than appreciated, with implications for our understanding of melatonin actions in different taxa. The significance of our findings, including the existence of Mel1d, are discussed in an evolutionary and functional context accommodating a robust phylogenetic assignment of MTR gene family structure.

Genetic diversity of chemokine XCL1 and its receptor XCR1 in murine rodents

The chemokine ligand XCL1 plays critical roles in immune responses with diverse physiological and pathological implications through interactions with a cognate G protein-coupled receptor XCR1. To shed insight into their versatile nature, we analyzed genetic variations of XCL1 and XCR1 in murine rodents, including commonly-used model organisms Mus musculus (house mouse) and Rattus norvegicus (Norway rat). Our results showed that adaptive selection has contributed to the genetic diversification of these proteins in murine lineage. Moreover, in both M. musculus and R. norvegicus, the chemokine and its receptor exhibit similar signs of selective sweeps resulting from positive selection. In light of currently available structural and interaction information for chemokines and their receptors, the similarity of XCL1/XCR1 evolutionary patterns among murine species and the parallels of their evolutionary footprints within individual species suggest that interplay could exist between the adaptively selected changes, or between the domains on which the identified changes are located, and consequently preserve the physiological interaction of XCL1 and XCR1.

Convergent reduction of V1R genes in subterranean rodents

BACKGROUND

Vomeronasal type 1 receptor genes (V1Rs) are expected to detect intraspecific pheromones. It is believed that rodents rely heavily on pheromonal communication mediated by V1Rs, but pheromonal signals are thought to be confined in subterranean rodents that live in underground burrows. Thus, subterranean rodents may show a contrasting mode of V1R evolution compared with their superterranean relatives.

RESULTS

We examined the V1R evolution in subterranean rodents by analyzing currently available genomes of 24 rodents, including 19 superterranean and 5 subterranean species from three independent lineages. We identified a lower number of putatively functional V1R genes in each subterranean rodent (a range of 22-40) compared with superterranean species (a range of 63-221). After correcting phylogenetic inertia, the positive correlation remains significant between the small V1R repertoire size and the subterranean lifestyle. To test whether V1Rs have been relaxed from functional constraints in subterranean rodents, we sequenced 22 intact V1Rs in 29 individuals of one subterranean rodent (Spalax galili) from two soil populations, which have been proposed to undergo incipient speciation. We found 12 of the 22 V1Rs to show significant genetic differentiations between the two natural populations, indicative of diversifying selection.

CONCLUSION

Our study demonstrates convergent reduction of V1Rs in subterranean rodents from three independent lineages. Meanwhile, it is noteworthy that most V1Rs in the two Spalax populations are under diversifying selection rather than relaxed selection, suggesting that functional constraints on these genes may have retained in some subterranean species.

The role of GPCRs in bone diseases and dysfunctions

The superfamily of G protein-coupled receptors (GPCRs) contains immense structural and functional diversity and mediates a myriad of biological processes upon activation by various extracellular signals. Critical roles of GPCRs have been established in bone development, remodeling, and disease. Multiple human GPCR mutations impair bone development or metabolism, resulting in osteopathologies. Here we summarize the disease phenotypes and dysfunctions caused by GPCR gene mutations in humans as well as by deletion in animals. To date, 92 receptors (5 glutamate family, 67 rhodopsin family, 5 adhesion, 4 frizzled/taste2 family, 5 secretin family, and 6 other 7TM receptors) have been associated with bone diseases and dysfunctions (36 in humans and 72 in animals). By analyzing data from these 92 GPCRs, we found that mutation or deletion of different individual GPCRs could induce similar bone diseases or dysfunctions, and the same individual GPCR mutation or deletion could induce different bone diseases or dysfunctions in different populations or animal models. Data from human diseases or dysfunctions identified 19 genes whose mutation was associated with human BMD: 9 genes each for human height and osteoporosis; 4 genes each for human osteoarthritis (OA) and fracture risk; and 2 genes each for adolescent idiopathic scoliosis (AIS), periodontitis, osteosarcoma growth, and tooth development. Reports from gene knockout animals found 40 GPCRs whose deficiency reduced bone mass, while deficiency of 22 GPCRs increased bone mass and BMD; deficiency of 8 GPCRs reduced body length, while 5 mice had reduced femur size upon GPCR deletion. Furthermore, deficiency in 6 GPCRs induced osteoporosis; 4 induced osteoarthritis; 3 delayed fracture healing; 3 reduced arthritis severity; and reduced bone strength, increased bone strength, and increased cortical thickness were each observed in 2 GPCR-deficiency models. The ever-expanding number of GPCR mutation-associated diseases warrants accelerated molecular analysis, population studies, and investigation of phenotype correlation with SNPs to elucidate GPCR function in human diseases.

Molecular Dynamics Simulations of Adenosine Receptors: Advances, Applications and Trends

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Adenosine receptors (ARs) are transmembrane proteins that belong to the G protein-coupled receptors (GPCRs) superfamily and mediate the biological functions of adenosine. To date, four AR subtypes are known, namely A1, A2A, A2B and A3 that exhibit different signaling pathways, tissue localization, and mechanisms of activation. Moreover, the widespread ARs and their implication in numerous physiological and pathophysiological conditions had made them pivotal therapeutic targets for developing clinically effective agents.

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The crystallographic success in identifying the 3D crystal structures of A2A and A1 ARs has dramatically enriched our understanding of their structural and functional properties such as ligand binding and signal transduction. This, in turn, has provided a structural basis for a larger contribution of computational methods, particularly molecular dynamics (MD) simulations, toward further investigation of their molecular properties and designing bioactive ligands with therapeutic potential. MD simulation has been proved to be an invaluable tool in investigating ARs and providing answers to some critical questions. For example, MD has been applied in studying ARs in terms of ligand-receptor interactions, molecular recognition, allosteric modulations, dimerization, and mechanisms of activation, collectively aiding in the design of subtype selective ligands.

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In this review, we focused on the advances and different applications of MD simulations utilized to study the structural and functional aspects of ARs that can foster the structure-based design of drug candidates. In addition, relevant literature was briefly discussed which establishes a starting point for future advances in the field of drug discovery to this pivotal group of drug targets.

Visualizing the GPCR Network: Classification and Evolution

In this study, we delineate an unsupervised clustering algorithm, minimum span clustering (MSC), and apply it to detect G-protein coupled receptor (GPCR) sequences and to study the GPCR network using a base dataset of 2770 GPCR and 652 non-GPCR sequences. High detection accuracy can be achieved with a proper dataset. The clustering results of GPCRs derived from MSC show a strong correlation between their sequences and functions. By comparing our level 1 MSC results with the GPCRdb classification, the consistency is 87.9% for the fourth level of GPCRdb, 89.2% for the third level, 98.4% for the second level, and 100% for the top level (the lowest resolution level of GPCRdb). The MSC results of GPCRs can be well explained by estimating the selective pressure of GPCRs, as exemplified by investigating the largest two subfamilies, peptide receptors (PRs) and olfactory receptors (ORs), in class A GPCRs. PRs are decomposed into three groups due to a positive selective pressure, whilst ORs remain as a single group due to a negative selective pressure. Finally, we construct and compare phylogenetic trees using distance-based and character-based methods, a combination of which could convey more comprehensive information about the evolution of GPCRs.

G protein-coupled receptors: the evolution of structural insight

G protein-coupled receptors (GPCR) comprise a diverse superfamily of over 800 proteins that have gained relevance as biological targets for pharmaceutical drug design. Although these receptors have been investigated for decades, three-dimensional structures of GPCR have only recently become available. In this review, we focus on the technological advancements that have facilitated efforts to gain insights into GPCR structure. Progress in these efforts began with the initial crystal structure determination of rhodopsin (PDB: 1F88) in 2000 and has continued to the most recently published structure of the A_1AR (PDB: 5UEN) in 2017. Numerous experimental developments over the past two decades have opened the door for widespread GPCR structural characterization. These efforts have resulted in the determination of three-dimensional structures for over 40 individual GPCR family members. Herein we present a comprehensive list and comparative analysis of over 180 individual GPCR structures. This includes a summary of different GPCR functional states crystallized with agonists, dual agonists, partial agonists, inverse agonists, antagonists, and allosteric modulators.

"Manganese-induced neurotoxicity: a review of its behavioral consequences and neuroprotective strategies"

Manganese (Mn) is an essential heavy metal. However, Mn’s nutritional aspects are paralleled by its role as a neurotoxicant upon excessive exposure. In this review, we covered recent advances in identifying mechanisms of Mn uptake and its molecular actions in the brain as well as promising neuroprotective strategies. The authors focused on reporting findings regarding Mn transport mechanisms, Mn effects on cholinergic system, behavioral alterations induced by Mn exposure and studies of neuroprotective strategies against Mn intoxication. We report that exposure to Mn may arise from environmental sources, occupational settings, food, total parenteral nutrition (TPN), methcathinone drug abuse or even genetic factors, such as mutation in the transporter SLC30A10. Accumulation of Mn occurs mainly in the basal ganglia and leads to a syndrome called manganism, whose symptoms of cognitive dysfunction and motor impairment resemble Parkinson’s disease (PD). Various neurotransmitter systems may be impaired due to Mn, especially dopaminergic, but also cholinergic and GABAergic. Several proteins have been identified to transport Mn, including divalent metal tranporter-1 (DMT-1), SLC30A10, transferrin and ferroportin and allow its accumulation in the central nervous system. Parallel to identification of Mn neurotoxic properties, neuroprotective strategies have been reported, and these include endogenous antioxidants (for instance, vitamin E), plant extracts (complex mixtures containing polyphenols and non-characterized components), iron chelating agents, precursors of glutathione (GSH), and synthetic compounds that can experimentally afford protection against Mn-induced neurotoxicity.

Epidermal growth factor, latrophilin, and seven transmembrane domain-containing protein 1 marker, a novel angiogenesis marker

Epidermal growth factor, latrophilin, and seven transmembrane domain-containing protein 1 on chromosome 1 (ELTD1), an orphan adhesion G-protein coupled receptor, was reported as a regulator of angiogenesis, also involved in cancer progression and development. More recently, ELTD1 was identified as a potential new tumor marker for high-grade glioma. ELTD1, belongs to the G-protein coupled receptor superfamily that comprises the biggest receptor family in the human genome. Following the discovery of ELTD1 almost a decade ago, only a few research groups have attempted to find its role in normal and tumor cells, important information about this receptor remaining still unknown. The ELTD1 ligand has not currently been identified and intracellular signaling studies have not yet been performed in normal or tumor cells. Although the current published data on ELTD1 function and structure are rather limited, this receptor seems to be very important, not only as biomarker, but also as molecular target in glioblastoma. This review summarizes and discusses the current knowledge on ELTD1 structure, function, and its role in both physiological and tumoral angiogenesis.

The Antitumor Activity of Plant-Derived Non-Psychoactive Cannabinoids

As a therapeutic agent, most people are familiar with the palliative effects of the primary psychoactive constituent of Cannabis sativa (CS), Δ(9)-tetrahydrocannabinol (THC), a molecule active at both the cannabinoid 1 (CB1) and cannabinoid 2 (CB2) receptor subtypes. Through the activation primarily of CB1 receptors in the central nervous system, THC can reduce nausea, emesis and pain in cancer patients undergoing chemotherapy. During the last decade, however, several studies have now shown that CB1 and CB2 receptor agonists can act as direct antitumor agents in a variety of aggressive cancers. In addition to THC, there are many other cannabinoids found in CS, and a majority produces little to no psychoactivity due to the inability to activate cannabinoid receptors. For example, the second most abundant cannabinoid in CS is the non-psychoactive cannabidiol (CBD). Using animal models, CBD has been shown to inhibit the progression of many types of cancer including glioblastoma (GBM), breast, lung, prostate and colon cancer. This review will center on mechanisms by which CBD, and other plant-derived cannabinoids inefficient at activating cannabinoid receptors, inhibit tumor cell viability, invasion, metastasis, angiogenesis, and the stem-like potential of cancer cells. We will also discuss the ability of non-psychoactive cannabinoids to induce autophagy and apoptotic-mediated cancer cell death, and enhance the activity of first-line agents commonly used in cancer treatment.

Activation of A2b adenosine receptor regulates ovarian cancer cell growth: involvement of Bax/Bcl-2 and caspase-3

A2b adenosine receptor (A2bAR) acts as a potent regulator of cell growth in various cell lines. The present study was designed to understand the controlling mechanism of A2bAR agonist (NECA)-induced apoptosis in ovarian cancer cells. Real-time PCR and western blotting assays were used to evaluate the gene and protein expression profiles of A2bAR, respectively. MTT assay was used to study the cell proliferation effect of A2bAR agonist (NECA). Detection of apoptosis was conducted using annexin V-FITC/PI staining, caspase-3 activation assay, and the expression of Bax and Bcl-2 proteins analysis. The mitochondrial membrane potential (ΔΨM) was analyzed by employing JC-1 prob. The mRNA and protein expression levels of A2bAR in ovarian cancer cells were detected. NECA significantly reduced cell viability in a dose-dependent manner in OVCAR-3 and Caov-4 cell lines. The growth inhibition effect of NECA was related to the induction of cell apoptosis, which was manifested by annexin V-FITC staining, activation of caspase-3, and loss of mitochondrial membrane potentials (ΔΨm). In addition, downregulation of the regulatory protein Bcl-2 and upregulation of Bax protein by NECA were also observed. These findings demonstrated that NECA induces apoptosis via the mitochondrial signaling pathway. Thus, A2bAR agonists may be a potential agent for induction of apoptosis in ovarian cancer cells.

In silico characterization of binding mode of CCR8 inhibitor: homology modeling, docking and membrane based MD simulation study

Human CC-chemokine receptor 8 (CCR8) is a crucial drug target in asthma that belongs to G-protein-coupled receptor superfamily, which is characterized by seven transmembrane helices. To date, there is no X-ray crystal structure available for CCR8; this hampers active research on the target. Molecular basis of interaction mechanism of antagonist with CCR8 remains unclear. In order to provide binding site information and stable binding mode, we performed modeling, docking and molecular dynamics (MD) simulation of CCR8. Docking study of biaryl-ether-piperidine derivative (13C) was performed inside predefined CCR8 binding site to get the representative conformation of 13C. Further, MD simulations of receptor and complex (13C-CCR8) inside dipalmitoylphosphatidylcholine lipid bilayers were performed to explore the effect of lipids. Results analyses showed that the Gln91, Tyr94, Cys106, Val109, Tyr113, Cys183, Tyr184, Ser185, Lys195, Thr198, Asn199, Met202, Phe254, and Glu286 were conserved in both docking and MD simulations. This indicated possible role of these residues in CCR8 antagonism. However, experimental mutational studies on these identified residues could be effective to confirm their importance in CCR8 antagonism. Furthermore, calculated Coulombic interactions represented the crucial roles of Glu286, Lys195, and Tyr113 in CCR8 antagonism. Important residues identified in this study overlap with the previous non-peptide agonist (LMD-009) binding site. Though, the non-peptide agonist and currently studied inhibitor (13C) share common substructure, but they differ in their effects on CCR8. So, to get more insight into their agonist and antagonist effects, further side-by-side experimental studies on both agonist (LMD-009) and antagonist (13C) are suggested.

Molecular aspects, genomic arrangement and immune responsive mRNA expression profiles of two CXC chemokine receptor homologs (CXCR1 and CXCR2) from rock bream, Oplegnathus fasciatus

The CXCR1 and CXCR2 are the prototypical receptors and are the only known receptors for mammalian ELR+ (Glu-Leu-Arg) CXC chemokines, including CXCL8 (interleukin 8). These receptors transduce the ELR+ chemokine signals and operate the downstream signaling pathways in inflammation and innate immunity. In this study, we report the identification and characterization of CXCR1 and CXCR2 genes from rock bream fish (OfCXCR1 and OfCXCR2) at the molecular level. The cDNA and genomic DNA sequences of the OfCXCR1 and OfCXCR2 were identified from a transcriptome library and a custom-constructed BAC library, respectively. Both OfCXCR genes consisted of two exons, separated by an intron. The 5'-flanking regions of OfCXCR genes possessed multiple putative transcription factor binding sites related to immune response. The coding sequences of OfCXCR1 and OfCXCR2 encoded putative peptides of 355 and 360 amino acids (aa), respectively. The deduced aa sequences of OfCXCR1 and OfCXCR2 comprised of a G-protein coupled receptors (GPCR) family 1 profile with a GPCR signature and a DRY motif. In addition, seven conserved transmembrane regions were predicted in both OfCXCRs. While our multiple alignment study revealed the functionally significant conserved elements of the OfCXCR1 and OfCXCR2, phylogeny analyses further confirmed their position in teleost sub clade, in which they manifested an evolutionary relatedness with other fish counterparts. Based on comparative analyses, teleost CXC chemokine receptors appear to be distinct from their non-fish orthologs in terms of evolution (both CXCR1 and CXCR2) and genomic organization (CXCR2). Quantitative real-time PCR (qPCR) detected the transcripts of OfCXCR1 and OfCXCR2 in eleven examined tissues, with higher levels in head kidney, kidney and spleen highlighting their crucial importance in immunity. In vitro stimulation of peripheral blood leukocytes (PBLs) with concanavalin A (Con A) resulted in modulation of OfCXCR2 transcription, but not that of OfCXCR1. In addition, the magnitude of the OfCXCR1 and OfCXCR2 transcripts in head kidney and spleen was differentially increased after the in vivo administration of immune stimulants, LPS and poly I:C and in the infection models injected with rock bream irido virus, Edwardsiella tarda and Streptococcus iniae. These lines of evidence suggest that these receptors may play an important role(s) in immune responsive signaling during pathogenesis of rock bream.

Heterodimerization of mouse orexin type 2 receptor variants and the effects on signal transduction

Orexin-A and Orexin-B play important roles in many physiological processes in which Orexins orchestrate diverse downstream effects via two G-protein coupled receptors: Orexin1R and Orexin2R. Two alternative C-terminus splice variants of the mouse Orexin receptors mOX2alphaR and mOX2betaR have recently been identified. This study explored the possibility of heterodimerization between mOX2alphaR and mOX2betaR, and investigated novel signal transduction characteristics after stimulation. The dimerization of mOX2alphaR and mOX2betaR was confirmed by BRET and co-immunoprecipitation assays. Meanwhile, in HEK293 cells, co-expression of mOX2alphaR and mOX2betaR resulted in a strengthened increase in activation of ERK1/2, with maximal activation at 5 min and 100 nM. Furthermore, heterodimerization also elicits stronger intracellular Ca2+ elevation after Orexin(s) stimulation, followed by a slower decline in intracellular Ca2+ to a steady endpoint Protein Kinase C Inhibitor significantly inhibited these downstream effects. In addition, the cAMP response element reporter activities were significantly reduced, whereas the serum response element luciferase and the T-lymphocyte activation of nuclear factor-responsive element reporter activity were significantly up-regulated after Orexin(s) stimulation. Besides, Orexin-A/-B induced a significantly higher rate of HEK293 cell proliferation in cells co-expressing mOX2alphaR/mOX2betaR compared to the control group. Taken together, we provide conclusive evidence that mOX2alphaR can form a functional heterodimer with mOX2betaR and this leads to increased PKC and decreased protein kinase A activity by ERK signal pathway leading to a significant increase in cell proliferation. The nature of this signaling pathway has significant implications for the role of Orexin in the regulation of physiological processes including the homeostasis of feeding.

Adenosine receptors: expression, function and regulation

Adenosine receptors (ARs) comprise a group of G protein-coupled receptors (GPCR) which mediate the physiological actions of adenosine. To date, four AR subtypes have been cloned and identified in different tissues. These receptors have distinct localization, signal transduction pathways and different means of regulation upon exposure to agonists. This review will describe the biochemical characteristics and signaling cascade associated with each receptor and provide insight into how these receptors are regulated in response to agonists. A key property of some of these receptors is their ability to serve as sensors of cellular oxidative stress, which is transmitted by transcription factors, such as nuclear factor (NF)-κB, to regulate the expression of ARs. Recent observations of oligomerization of these receptors into homo- and heterodimers will be discussed. In addition, the importance of these receptors in the regulation of normal and pathological processes such as sleep, the development of cancers and in protection against hearing loss will be examined.

Using ensemble SVM to identify human GPCRs N-linked glycosylation sites based on the general form of Chou's PseAAC

As the most frequent drug target, G-protein coupled receptors (GPCRs) are a large family of seven transmembrane receptors that sense molecules outside the cell and activate inside signal transduction pathways. Glycosylation is one of the most complex post-translational modifications (PTMs) of proteins in eukaryotic cells. It plays important roles in a variety of cellular functions, including protein folding, protein trafficking and localization, cell-cell interactions and epitope recognition. Therefore, investigating the exact position of glycosylation site in GPCR sequence can provide useful clues for drug design and other biotechnology applications. Experimental identification of glycosylation sites is expensive and laborious. Hence, there is a significant interest in the development of computational methods for reliable prediction of glycosylation sites from amino acid sequences. In this article, we presented an effective method to recognize the sites of human GPCRs by combining amino acid hydrophobicity with ensemble support vector machine. The prediction accuracy, sensitivity, specificity, Matthews correlation coefficient and area under the curve values were 94.4, 89.7, 98.9%, 0.895 and 0.989, respectively. The establishment of such a fast and accurate prediction method will speed up the pace of identifying proper GPCRs functional sites to facilitate drug discovery.

Dramatic expansion and developmental expression diversification of the methuselah gene family during recent Drosophila evolution

Functional studies of the methuselah/methuselah-like (mth/mthl) gene family have focused on the founding member mth, but little is known regarding the developmental functions of this receptor or any of its paralogs. We undertook a comprehensive analysis of developmental expression and sequence divergence in the mth/mthl gene family. Using in situ hybridization techniques, we detect expression of six genes (mthl1, 5, 9, 11, 13, and 14) in the embryo during gastrulation and development of the gut, heart, and lymph glands. Four receptors (mthl3, 4, 6, and 8) are expressed in the larval central nervous system, imaginal discs, or both, and two receptors (mthl10 and mth) are expressed in both embryos and larvae. Phylogenetic analysis of all mth/mthl genes in five Drosophila species, mosquito and flour beetle structured the mth/mthl family into several subclades. mthl1, 5, and 14 are present in most species, each forming a separate clade. A newly identified Drosophila mthl gene (CG31720; herein mthl15) formed another ancient clade. The remaining Drosophila receptors, including mth, are members of a large "superclade" that diversified relatively recently during dipteran evolution, in many cases within the melanogaster subgroup. Comparing the expression patterns of the mth/mthl "superclade" paralogs to the embryonic expression of the singleton ortholog in Tribolium suggests both subfunctionalization and acquisition of novel functionalities. Taken together, our findings shed novel light on mth as a young member of an adaptively evolving developmental gene family.

The significance of G protein-coupled receptor crystallography for drug discovery

Crucial as molecular sensors for many vital physiological processes, seven-transmembrane domain G protein-coupled receptors (GPCRs) comprise the largest family of proteins targeted by drug discovery. Together with structures of the prototypical GPCR rhodopsin, solved structures of other liganded GPCRs promise to provide insights into the structural basis of the superfamily's biochemical functions and assist in the development of new therapeutic modalities and drugs. One of the greatest technical and theoretical challenges to elucidating and exploiting structure-function relationships in these systems is the emerging concept of GPCR conformational flexibility and its cause-effect relationship for receptor-receptor and receptor-effector interactions. Such conformational changes can be subtle and triggered by relatively small binding energy effects, leading to full or partial efficacy in the activation or inactivation of the receptor system at large. Pharmacological dogma generally dictates that these changes manifest themselves through kinetic modulation of the receptor's G protein partners. Atomic resolution information derived from increasingly available receptor structures provides an entrée to the understanding of these events and practically applying it to drug design. Supported by structure-activity relationship information arising from empirical screening, a unified structural model of GPCR activation/inactivation promises to both accelerate drug discovery in this field and improve our fundamental understanding of structure-based drug design in general. This review discusses fundamental problems that persist in drug design and GPCR structural determination.

Estrogen inhibits D2S receptor-regulated Gi3 and Gs protein interactions to stimulate prolactin production and cell proliferation in lactotropic cells

The neurotransmitter dopamine (DA) is known to inhibit prolactin (PRL) secretion and the proliferation of lactotropes in the pituitary gland. Dopamine-2 (D2) receptor short (D2S) isoform is expressed in a reduced level while the D2 receptor long (D2L) isoform is expressed in an elevated level during estradiol (E(2))-induced PRL production and cell proliferation in lactotropes. To evaluate the role of these D2 receptor isoforms in E(2)-regulated lactotropic cell function, we compared E(2) effects on the level of PRL, cell proliferation, and G proteins in enriched lactotropes and lactotrope-derived PR1 cells containing only D2S isoform (D2S cells), D2L isoform (D2L cells), or no D2 receptor (V cells). Additionally, we determined the effects of G protein blockade on the E(2)-induced PRL production and cell proliferation in these cells. We here show that E(2) actions on G proteins, PRL production, and cell proliferation were maximally achieved in D2S cells, oppositely or marginally achieved in D2L cells, and absent in V cells. We also show that the DA and pertussis toxin modulations of E(2) actions on PRL, G proteins, and cell proliferation were maximally achieved in D2S cells compared with in D2L or V cells. Furthermore, we provide evidence for the existence of an inhibitory action of Gi3 on Gs that is under the control of the D2S receptor and is inhibited by E(2). These results suggest that the suppression of D2S-regulated Gi3 inhibition of Gs protein may be one of the mechanisms controlling E(2)-activated PRL synthesis and cell proliferation in lactotropes.

Intracellular Loop 2 Peptides of the Human 5HT1a Receptor are Differential Activators of Gi

Peptide mimics of intracellular loop 2 (ic2) of the human 5HT1a receptor have been studied with respect to their ability to inhibit agonist binding via interference with receptor-G-protein coupling. These peptides give shallow concentration-effect relationships. Additionally, these peptides have been studied with respect to their ability to trigger the signal transduction system of this Gi-coupled receptor. Two signaling parameters have been quantified: concentration of intracellular cAMP and changes in incorporation into the G protein of a stable analog of GTP. In both cases, peptide mimics near midloop of ic2 actually show agonist activity with efficacy falling off toward both loop termini near TM 3 and TM 4. Previous results have suggested that the loop region near the TM3/ic2 interface is primarily responsible for receptor-G-protein coupling, while the current result emphasizes the mid-ic2 loop region's ability to activate the G protein following initial coupling. A limited number of peptides from the receptor's TM5/ic3 loop vicinity were also studied regarding agonist inhibition and G-protein activation. These peptides provide additional evidence that the human 5HT1a receptor, TM5/ic3 loop region, is involved in both coupling and activation actions. Overall, these results provide further information about potential pharmacological intervention and drug development with respect to the human 5HT1a receptor/G-protein system. Finally, the structural evidence generated here provides testable models pending crystallization and X-ray analysis of the receptor.

Using core hydrophobicity to identify phosphorylation sites of human G protein-coupled receptors

As the most frequent drug target, G protein-coupled receptors (GPCRs) are a large family of seven trans-membrane receptors that sense molecules outside the cell and activate inside signal transduction pathways. The activity and lifetime of activated receptors are regulated by receptor phosphorylation. Therefore, investigating the exact positions of phosphorylation sites in GPCRs sequence could provide useful clues for drug design and other biotechnology applications. Experimental identification of phosphorylation sites is expensive and laborious. Hence, there is significant interest in the development of computational methods for reliable prediction of phosphorylation sites from amino acid sequences. In this article, we presented a simple and effective method to recognize phosphorylation sites of human GPCRs by combining amino acid hydrophobicity and support vector machine. The prediction accuracy, sensitivity, specificity, Matthews correlation coefficient and area under the curve values for phosphoserine, phosphothreonine, and phosphotyrosine were 0.964, 0.790, 0.999, 0.866, 0.941; 0.954, 0.800, 0.985, 0.828, 0.958; and 0.976, 0.820, 0.993, 0.861, 0.959, respectively. The establishment of such a fast and accurate prediction method will speed up the pace of identifying proper GPCRs sites to facilitate drug discovery.

Grouper (Epinephelus coioides) CXCR4 is expressed in response to pathogens infection and early stage of development

Chemokine (C-X-C motif) receptor 4 (CXCR4) from orange-spotted grouper (Epinephelus coioides) was identified and characterized in this study. gCXCR4 shared common features in protein sequence and predicted structure of CXCR4 family. This suggested that gCXCR4 is a member of G protein-coupled receptors with seven transmembrane domains. The expression patterns revealed that gCXCR4 may play a key role in early development of grouper. Furthermore, overexpression of gCXCR4-GFP for 48 h had significant effects on the GF-1 cell viability. gCXCR4 protein was mainly expressed in the marginal zone of head kidney and on the surface of intestinal villi. gCXCR4 expression can be detected in all the examined tissues and significantly up-regulated in eye and brain, which are the main targets for nervous necrosis virus (NNV) infection and replication. gCXCR4 gene expression can be induced in the spleen and eye by lipopolysaccharide and NNV, respectively. Our data suggested that gCXCR4 may not only play a role in the early immune response to microbial infection but also restrain to the immune system and central nervous system.

G protein-coupled receptors involved in GnRH regulation: molecular insights from human disease

In the past two decades, an increasing body of evidence has demonstrated that several G protein-coupled receptor (GPCR)-ligand pairs are critical for normal human reproductive development and function. Patients harboring genetic insults in either the receptors or their cognate ligands have presented with reproductive disorders characterized by varying degrees of GnRH deficiency. These disorders include idiopathic hypogonadotropic hypogonadism (IHH) and Kallmann Syndrome (KS). Conversely, mutations in some of these ligand-receptor pairs have been associated with accelerated reproductive maturation, manifested as central precocious puberty (CPP). To date, a series of elegant studies have characterized four GPCRs that play important roles in the neuroendocrine control of human reproductive development and function: GnRHR, KISS1R, PROKR2 and NK3R. Furthermore, these studies provide insights into the mechanisms by which mutations in these receptors give rise to reproductive disease phenotypes. This report will review mutations identified in GPCRs involved in the neuroendocrine control of the human reproductive axis with the aims of elucidating structure-function relationships of these GPCRs and identifying correlations between these structure-function relationships and the genotypic-phenotypic characterization of the patients.

GPCR-2L: predicting G protein-coupled receptors and their types by hybridizing two different modes of pseudo amino acid compositions

G protein-coupled receptors (GPCRs) are among the most frequent targets of therapeutic drugs. With the avalanche of newly generated protein sequences in the post genomic age, to expedite the process of drug discovery, it is highly desirable to develop an automated method to rapidly identify GPCRs and their types. A new predictor was developed by hybridizing two different modes of pseudo-amino acid composition (PseAAC): the functional domain PseAAC and the low-frequency Fourier spectrum PseAAC. The new predictor is called GPCR-2L, where "2L" means that it is a two-layer predictor: the 1st layer prediction engine is to identify a query protein as GPCR or not; if it is, the prediction will be automatically continued to further identify it as belonging to one of the following six types: (1) rhodopsin-like (Class A), (2) secretin-like (Class B), (3) metabotropic glutamate/pheromone (Class C), (4) fungal pheromone (Class D), (5) cAMP receptor (Class E), or (6) frizzled/smoothened family (Class F). The overall success rate of GPCR-2L in identifying proteins as GPCRs or non-GPCRs is over 97.2%, while identifying GPCRs among their six types is over 97.8%. Such high success rates were derived by the rigorous jackknife cross-validation on a stringent benchmark dataset, in which none of the included proteins had ≥40% pairwise sequence identity to any other protein in a same subset. As a user-friendly web-server, GPCR-2L is freely accessible to the public at http://icpr.jci.edu.cn/, by which one can obtain the 2-level results in about 20 s for a query protein sequence of 500 amino acids. The longer the sequence is, the more time it may usually need. The high success rates reported here indicate that it is a quite effective approach to identify GPCRs and their types with the functional domain information and the low-frequency Fourier spectrum analysis. It is anticipated that GPCR-2L may become a useful tool for both basic research and drug development in the areas related to GPCRs.

Classification of G-protein coupled receptors based on support vector machine with maximum relevance minimum redundancy and genetic algorithm

Background

Because a priori knowledge about function of G protein-coupled receptors (GPCRs) can provide useful information to pharmaceutical research, the determination of their function is a quite meaningful topic in protein science. However, with the rapid increase of GPCRs sequences entering into databanks, the gap between the number of known sequence and the number of known function is widening rapidly, and it is both time-consuming and expensive to determine their function based only on experimental techniques. Therefore, it is vitally significant to develop a computational method for quick and accurate classification of GPCRs.

Results

In this study, a novel three-layer predictor based on support vector machine (SVM) and feature selection is developed for predicting and classifying GPCRs directly from amino acid sequence data. The maximum relevance minimum redundancy (mRMR) is applied to pre-evaluate features with discriminative information while genetic algorithm (GA) is utilized to find the optimized feature subsets. SVM is used for the construction of classification models. The overall accuracy with three-layer predictor at levels of superfamily, family and subfamily are obtained by cross-validation test on two non-redundant dataset. The results are about 0.5% to 16% higher than those of GPCR-CA and GPCRPred.

Conclusion

The results with high success rates indicate that the proposed predictor is a useful automated tool in predicting GPCRs. GPCR-SVMFS, a corresponding executable program for GPCRs prediction and classification, can be acquired freely on request from the authors.

Signaling through G protein coupled receptors

Heterotrimeric G proteins (Galpha, Gbeta/Ggamma subunits) constitute one of the most important components of cell signaling cascade. G Protein Coupled Receptors (GPCRs) perceive many extracellular signals and transduce them to heterotrimeric G proteins, which further transduce these signals intracellular to appropriate downstream effectors and thereby play an important role in various signaling pathways. GPCRs exist as a superfamily of integral membrane protein receptors that contain seven transmembrane alpha-helical regions, which bind to a wide range of ligands. Upon activation by a ligand, the GPCR undergoes a conformational change and then activate the G proteins by promoting the exchange of GDP/GTP associated with the Galpha subunit. This leads to the dissociation of Gbeta/Ggamma dimer from Galpha. Both these moieties then become free to act upon their downstream effectors and thereby initiate unique intracellular signaling responses. After the signal propagation, the GTP of Galpha-GTP is hydrolyzed to GDP and Galpha becomes inactive (Galpha-GDP), which leads to its re-association with the Gbeta/Ggamma dimer to form the inactive heterotrimeric complex. The GPCR can also transduce the signal through G protein independent pathway. GPCRs also regulate cell cycle progression. Till to date thousands of GPCRs are known from animal kingdom with little homology among them, but only single GPCR has been identified in plant system. The Arabidopsis GPCR was reported to be cell cycle regulated and also involved in ABA and in stress signaling. Here I have described a general mechanism of signal transduction through GPCR/G proteins, structure of GPCRs, family of GPCRs and plant GPCR and its role.

cAMP-dependent signal pathways in unicellular eukaryotes

The review summarizes current data about mechanisms of signal transduction with participation of cAMP (cyclic adenosine monophosphate) and elements of the complex cAMP-protein kinase A (PKA) signal pathway in unicellular eukaryotes. Conceptions of evolutionary origin of eukaryotic signal transduction systems are developed.