GPCRdb: the G protein-coupled receptor database - an introduction.

GPCRs make up the largest family of human membrane proteins and of drug targets. Recent advances in GPCR pharmacology and crystallography have shed new light on signal transduction, allosteric modulation and biased signalling, translating into new mechanisms and principles for drug design. The GPCR database, GPCRdb, has served the community for over 20 years and has recently been extended to include a more multidisciplinary audience. This review is intended to introduce new users to the services in GPCRdb, which meets three overall purposes: firstly, to provide reference data in an integrated, annotated and structured fashion, with a focus on sequences, structures, single-point mutations and ligand interactions. Secondly, to equip the community with a suite of web tools for swift analysis of structures, sequence similarities, receptor relationships, and ligand target profiles. Thirdly, to facilitate dissemination through interactive diagrams of, for example, receptor residue topologies, phylogenetic relationships and crystal structure statistics. Herein, these services are described for the first time; visitors and guides are provided with good practices for their utilization. Finally, we describe complementary databases cross-referenced by GPCRdb and web servers with corresponding functionality.

SCUBIDOO: A Large yet Screenable and Easily Searchable Database of Computationally Created Chemical Compounds Optimized toward High Likelihood of Synthetic Tractability.

De novo drug design is widely assisted by computational approaches that enable the generation of a tremendous amount of new virtual molecules within a short time frame. While the novelty of the computationally generated compounds can easily be assessed, such approaches often neglect the synthetic feasibility of the molecules, thus creating a potential hurdle that can be a barrier to further investigation. Therefore, we have developed SCUBIDOO, a freely accessible database concept that currently holds 21 million virtual products originating from a small library of building blocks and a collection of robust organic reactions. This large data set was reduced to three representative and computationally tractable samples denoted as S, M, and L, containing 9994, 99,977, and 999,794 products, respectively. These small sets are useful as starting points for ligand identification and optimization projects. The generated products come with synthesis instructions and alerts of possible side reactions, and we show that they exhibit drug-like properties while still extending into unexplored quadrants of chemical space, thus suggesting novelty. We show multiple examples that demonstrate how SCUBIDOO can facilitate the search around initial hits. This database might be a useful idea generator for early ligand discovery projects since it allows a focus on those molecules that are likely to be synthetically feasible and can therefore be studied further. Together with its modular building block construction principle, this database is also suitable for structure-activity relationship studies or fragment-growing strategies.

The therapeutic effects of 4-phenylbutyric acid in maintaining proteostasis.

Recently, there has been an increasing amount of literature published on the effects of 4-phenylbutyric acid (4-PBA) in various biological systems. 4-PBA is currently used clinically to treat urea cycle disorders under the trade name Buphenyl. Recent studies however have explored 4-PBA in the context of a low weight molecular weight chemical chaperone. Its properties as a chemical chaperone prevent misfolded protein aggregation and alleviate endoplasmic reticulum (ER) stress. As the ER is responsible for folding proteins targeted for use in membranes or secreted out of the cell, failure of maintaining adequate ER homeostasis may lead to protein misfolding and subsequent cell and organ pathology. Accumulation of misfolded proteins within the ER activates the unfolded protein response (UPR), a molecular repair response. The activation of the UPR aims to restore ER and cellular proteostasis by regulating the rate of synthesis of newly formed proteins as well as initiating molecular programs aimed to help fold or degrade misfolded proteins. If proteostasis is not restored, the UPR may initiate pro-apoptotic pathways. It is suggested that 4-PBA may help fold proteins in the ER, attenuating the activation of the UPR, and thus potentially alleviating various pathologies. This review discusses the biomedical research exploring the potential therapeutic effects of 4-PBA in various in vitro and in vivo model systems and clinical trials, while also commenting on the possible mechanisms of action.

Bianisotropy and spatial dispersion in highly anisotropic near-infrared resonator arrays.

We measure, simulate, and analyze the optical transmission through arrays of Ag nanorod pairs and U-shaped nanostructures as a function of polarization and angle of incidence. The bianisotropic nature of the metamaterials is exhibited in data and in simulations, and we argue that the electric field rather than the magnetic field excites the low frequency "magnetic" mode. We also observe spatial dispersion in the form of frequency shifts as a function of incident angle which we attribute to coupling effects between neighboring structures. A simple model based upon coupled electromagnetic dipoles is found to provide a qualitative description for the main features observed in the spectra.

Optical plasmonic resonances in split-ring resonator structures: an improved LC model.

We systematically investigate the resonant behavior of arrays of Ag nano-structures ranging from isolated simple rods, to U-shapes, to single split ring structures. We show that the lowest order plasmonic resonance associated with a rod red shifts as we create a U and SRR into the position normally associated with a simple LC mode. A second mode red shifts and grows in intensity as we extend the arms of the U-shape, and a third mode appears in the spectra as we close the arms and form a split ring structure. We performed simulations of the structures and examine the E-field and current density. The simulations show that the current path is different for these modes. We examine the behavior of the lowest order mode in detail, discuss the effects of skin depth, and present an improved LC model to describe this resonance.

Energy landscape of streptavidin-biotin complexes measured by atomic force microscopy.

The dissociation of ligand and receptor involves multiple transitions between intermediate states formed during the unbinding process. In this paper, we explored the energy landscape of the streptavidin-biotin interaction by using the atomic force microscope (AFM) to measure the unbinding dynamics of individual ligand-receptor complexes. The rupture force of the streptavidin-biotin bond increased more than 2-fold over a range of loading rates between 100 and 5000 pN/s. Moreover, the force measurements showed two regimes of loading in the streptavidin-biotin force spectrum, revealing the presence of two activation barriers in the unbinding process. Parallel experiments carried out with a streptavidin mutant (W120F) were used to investigate the molecular determinants of the activation barriers. From these experiments, we attributed the outer activation barrier in the energy landscape to the molecular interaction of the '3-4' loop of streptavidin that closes behind biotin.

Tetrachloro- and tetrabromoarsonium(V) cations: raman and 75As, 19F NMR spectroscopic characterization and X-ray crystal structures of [AsCl4][As(OTeF5)6] and [AsBr4][AsF(OTeF5)5] .

The salts [AsX4][As(OTeF5)6] and [AsBr4][AsF(OTeF5)5] (X = Cl, Br) have been prepared by oxidation of AsX3 with XOTeF5 in the presence of the OTeF5 acceptors As(OTeF5)5 and AsF(OTeF5)4. The mixed salts [AsCl4][Sb(OTeF5)6-nCl(n-2)] and [AsCl4][Sb(OTeF5)6-nCl(n)] (n > or = 2) have also been prepared. The AsBr4+ cation has been fully structurally characterized for the first time in SO2ClF solution by 75As NMR spectroscopy and in the solid state by a single-crystal X-ray diffraction study of [AsBr4][AsF(OTeFs)5]: P1, a = 9.778(4) A, b = 17.731(7) A, c = 18.870(8) A, alpha = 103.53(4)degrees, beta = 103.53(4) degrees, gamma = 105.10(4) degrees, V = 2915(2) A3, Z = 4, and R1 = 0.0368 at -183 degrees C. The crystal structure determination and solution 75As NMR study of the related [AsCl4][As(OTeF5)6] salt have also been carried out: [AsCl4][As(OTeF5)6], R3, a = 9.8741(14) A, c = 55.301(11) A, V= 4669(1) A3, Z = 6, and R1 = 0.0438 at -123 degrees C; and R3, a = 19.688(3) A, c = 55.264(11) A, V= 18552(5) A3, Z = 24, and R1 = 0.1341 at -183 degrees C. The crystal structure of the As(OTeF5)6- salt reveals weaker interactions between the anion and cation than in the previously known AsF6- salt. The AsF(OTeF5)5- anion is reported for the first time and is also weakly coordinating with respect to the AsBr4+ cation. Both cations are undistorted tetrahedra with bond lengths of 2.041(5)-2.056(3) A for AsCl4+ and 2.225(2)-2.236(2) A for AsBr4+. The Raman spectra are consistent with undistorted AsX4+ tetrahedra and have been assigned under Td point symmetry. The 35Cl/37Cl isotope shifts have been observed and assigned for AsCl4+, and the geometrical parameters and vibrational frequencies of all known and presently unknown PnX4+ (Pn = P, As, Sb, Bi; X = F, Cl, Br, I) cations have been calculated using density functional theory methods.

Preservation of noradrenergic neurons in the locus ceruleus that coexpress galanin mRNA in Alzheimer's disease.

Galanin (GAL) innervation is hypertrophied in the basal forebrain and cortex of patients with Alzheimer's disease (AD). Increased GAL could exacerbate the cognitive and behavioral deficits of AD because GAL acts as an inhibitory modulator of cholinergic and noradren-ergic neurotransmission. The locus ceruleus (LC) may be a source of increased GAL in AD because (a) GAL is coexpressed in a subset of LC neurons, (b) GAL expression is up-regulated with neuronal injury, and (c) the LC undergoes extensive degeneration in AD. Therefore, we have used in situ hybridization histochemistry to measure GAL gene expression in the LC of AD patients and sex- and age-matched nondemented controls. Despite the extensive loss of norepinephrine neurons with AD, GAL mRNA-expressing neurons in the LC did not differ between groups. This resulted in a significant increase in the percentage of neuromelanin-pigmented cells that coexpressed GAL in AD patients compared with controls. These findings raise the possibility that the increased incidence of GAL expression among remaining LC neurons contributes to the hyperinnervation of GAL fibers in AD. Furthermore, GAL may be neuroprotective in the LC.

Absence of vasopressin expression by galanin neurons in the golden hamster: implications for species differences in extrahypothalamic vasopressin pathways.

In golden hamsters, there is a complete absence of the small diameter vasopressin (VP) neurons in the bed nucleus of the stria terminalis (BST) and medial amygdala (Me) which have been shown to exhibit steroid dependency and sexual dimorphism in many other rodent species. In rats, VP in the BST/Me is always colocalized with the neuropeptide galanin (GAL) and the sex difference in VP cell number appears to result from a sex difference in the number of GAL neurons which coexpress VP. Likewise, we reasoned that the species difference in extrahypothalamic VP pathways present in the golden hamster could result from a reduced coexpression of VP by GAL neurons in these regions. Here, we used in situ hybridization histochemistry to determine whether GAL mRNA expressing neurons are present in the BST and Me of golden hamsters despite the absence of VP expression in these regions. In addition, we have used slice binding and receptor autoradiography to identify specific GAL binding sites in the lateral septum, a probable target region of BST/Me neurons, and in situ hybridization to confirm that some of these binding sites correspond to the GALR1 GAL receptor subtype. Our findings indicate that the absence of VP expression in the BST/Me of golden hamsters results from a failure of extrahypothalamic GAL neurons to express the VP phenotype. Because GAL is expressed in the extended amygdaloid complex and GAL receptors are present in the septum of golden hamsters, GAL may play a role in modulating functions previously attributed to BST/Me pathways.

Few cholinergic neurons in the rat basal forebrain coexpress galanin messenger RNA.

The concept that galanin (GAL) is cosecreted with acetylcholine (ACh) into the ventral hippocampus is a major component of the current model delineating GAL regulation of the cholinergic memory pathways in the rat. Although GAL-immunoreactivity coexists in 50-70% of cholinergic neurons in the basal forebrain (BF) of colchicine-treated rats, the actual coexistence of these neurotransmitters in the basal state may be lower, because colchicine treatment was recently shown to both induce GAL gene expression and inhibit choline acetyltransferase (ChAT) gene expression in this brain region. We have used single and double in situ hybridization histochemistry to examine the distribution and coexistence of GAL and ChAT mRNAs in the BF of male and female rats. Compared with other forebrain regions, few GAL mRNA-expressing neurons are present within the cholinergic fields of the BF. The greatest number of GAL mRNA-expressing cells in this region are located within the nucleus of the horizontal limb of the diagonal band; but, even in this region, they represent only a small percentage (<20%) of ChAT mRNA-expressing cells. Our results indicate that few cholinergic neurons in the rat BF coexpress GAL mRNA and suggest that, in the basal state, GAL is not widely cosecreted with ACh into hippocampal memory centers.

Galanin receptors in the hippocampus and entorhinal cortex of aged Fischer 344 male rats.

Galanin (GAL) has been proposed to be an inhibitory modulator of cholinergic memory pathways because it acts within the hippocampus to inhibit the release and antagonize the postsynaptic actions of acetylcholine. Here we have used: 1) slice binding and quantitative autoradiography to assess the density and occupancy of GAL receptors; and 2) in situ hybridization histochemistry to assess expression of the GALR1 receptor subtype in the ventral hippocampus of 3-month-old and 21-month-old Fischer 344 male rats. We detected a small but significant (p < or = 0.0003) age-related reduction in 125I-GAL binding-site density in the ventral hippocampus and entorhinal cortex under standard binding conditions. Post-hoc analysis indicated that this reduction with age persisted in the CA1 radiatum and entorhinal cortex following GTP-induced desaturation to unmask pre-existent GAL receptors occupied by endogenous ligand. It was not associated with a significant change in peak GALR1 gene expression in the hippocampus. Because a portion of GAL receptors in this region have been postulated to function as presynaptic auto-receptors on cholinergic fiber terminals, the reduction in GAL binding sites with age may be a consequence of age-related alterations in GAL receptor expression by basal forebrain cholinergic neurons which project to the ventral hippocampus.

Estrogen regulates galanin but not tyrosine hydroxylase gene expression in the rat locus ceruleus.

The neuropeptide galanin (GAL) is coexpressed by the majority of noradrenergic neurons in the rat locus ceruleus (LC) and may function as an inhibitory modulator of noradrenergic transmission. Because estrogen has been shown to induce GAL expression in other brain regions and modulate noradrenergic transmission, we used in situ hybridization histochemistry to assess the effects of chronic estrogen treatment on GAL and tyrosine hydroxylase (TH) gene expression in the LC of ovariectomized female rats. We found that GAL mRNA levels were significantly elevated in rats implanted with a Silastic capsule containing estradiol compared to sham-implanted controls. Both the average optical density (P < or = 0.05) and the labelling area (P < or = 0.007) differed significantly between the groups. In contrast, TH gene expression measured in alternate brain sections did not differ between the groups. If GAL functions as an inhibitory modulator of noradrenergic transmission as postulated, these findings suggest that chronic estrogen treatment could reduce the noradrenergic tone of the brain in the absence of significant alterations in TH expression by enhancing the level of cosecreted GAL.

Nerve growth factor induces galanin gene expression in the rat basal forebrain: implications for the treatment of cholinergic dysfunction.

Nerve growth factor (NGF) is a potential treatment for cholinergic dysfunction associated with Alzheimer's disease (AD). In rats, NGF activates gene expression of the acetylcholine synthetic enzyme choline acetyltransferase (ChAT) and prevents age- and lesion-induced degeneration of basal forebrain (BF) cholinergic neurons. Cholinergic neurons in the BF coexpress galanin (GAL), a neuropeptide that has been shown to impair performance on memory tasks possibly through the inhibition of cholinergic memory pathways. NGF up-regulates both ChAT and GAL gene expression in cultured pheochromocytoma cells; however, the effect of chronic in vivo NGF administration on GAL gene expression within the BF has not been studied. We used in situ hybridization and quantitative autoradiography to assess GAL and ChAT gene expression within the BF of adult male rats following chronic intracerebroventricular infusion of NGF or cytochrome c. We now report that, in addition to stimulating ChAT gene expression, NGF strongly up-regulated the GAL gene in the rat cholinergic BF. NGF had no effect on GAL gene expression in other noncholinergic forebrain regions. NGF induction of GAL gene expression in the BF was specific, because gene expression for another neuropeptide, neurotensin, present within noncholinergic BF neurons was unchanged. Our data provide the first evidence that in vivo NGF administration up-regulates GAL gene expression in the cholinergic BF. These results suggest that the concurrent induction of GAL in the BF could limit the ameliorating actions of NGF on cholinergic dysfunction.

GALR1 galanin receptor mRNA is co-expressed by galanin neurons but not cholinergic neurons in the rat basal forebrain.

The neuropeptide galanin (GAL) has been proposed to be an inhibitory modulator of cholinergic transmission in the hippocampus and may impair memory by directly affecting the activity of basal forebrain (BF) cholinergic neurons. Alternatively, GAL may act indirectly and modulate the activity of other neurotransmitter systems which, in turn, influence cholinergic transmission. We have used double in situ hybridization histochemistry to evaluate the co-expression of the GAL receptor subtype, GALR1, within cholinergic neurons in the medial septum/diagonal band of adult male rats. In alternate brain sections, we assessed the co-expression of GALR1 mRNA within another forebrain cell group implicated in memory functions, the neurons of the bed nucleus of the stria terminalis (BNST) and medial amygdala (AMe) which co-express vasopressin (VP) and GAL and project to septo-hippocampus. Despite the abundance of GALR1 mRNA-expressing neurons in the cholinergic BF, we found no evidence for the co-expression of this receptor subtype within cholinergic neurons in the medial septum/diagonal band. In contrast, we detected an extensive co-expression (95%) of GALR1 mRNA within extrahypothalamic VP/GAL neurons. These results do not support the idea that GAL, acting via the GALR1 receptor, directly impairs BF cholinergic neurons but suggest, instead, that non-cholinergic neurons in the BF may play a role in mediating the inhibitory actions of GAL on cholinergic function. However, our findings provide anatomical evidence that GAL could directly modulate the activity and/or secretion pattern of extrahypothalmic VP/GAL neurons into septo-hippocampal regions.

High temperature and drought stress effects on survival of Pinus ponderosa seedlings.

We studied the effects of high temperature and drought on the survival, growth and water relations of seedlings of Pinus ponderosa (Dougl.) Lawson, one of few coniferous tree species that can successfully colonize drought-prone sites with high soil surface temperatures. Temperature profiles were measured with 0.07-mm thermocouples in a sparse ponderosa pine forest in northern Idaho. The soil surface and the adjacent 5 mm of air reached maximum temperatures exceeding 75 degrees C, well above the lethal temperature threshold for most plants. Air temperatures 50 mm above the soil surface (seedling needle height) rarely exceeded 45 degrees C. Pinus ponderosa seedlings that survived maintained basal stem temperatures as much as 15 degrees C lower than the surrounding air. The apparent threshold temperature at the seedling stem surface resulting in death was approximately 63 degrees C for less than 1 min. No correlation between seedling mortality and needle temperature was found, although some needles reached temperatures as high as 60 degrees C for periods of

Galanin gene expression declines with adulthood in the cholinergic fields of the horizontal diagonal band of male rats.

The neuropeptide galanin (GAL) influences learning and memory processes, perhaps by inhibiting cholinergic function. We recently reported that, in the rat, the nucleus of the horizontal limb of the diagonal band (HDB) exhibits the highest level of GAL mRNA coexpression by basal forebrain (BF) cholinergic neurons and, in the HDB, virtually all GAL mRNA-expressing neurons correspond to the cholinergic cell type. Since GAL gene expression is induced across puberty in many brain regions, we used in situ hybridization histochemistry and quantitative autoradiography to assess GAL gene expression across the rostro-caudal extent of the HDB in prepubertal and adult male rats and to determine whether GAL gene expression is also regulated during maturation in this BF region. Our results show that the number of GAL mRNA-expressing cells per section is significantly reduced in the HDB with adulthood. Post-hoc analysis indicated that these age-associated differences in the number of GAL mRNA-expressing cells per section could be ascribed to the rostral and central subregions of the HDB. Age-related differences in the labeling intensity of GAL mRNA-expressing neurons were also detected in the rostral and central subregions of the HDB. No age-associated differences in GAL gene expression were found in the caudal HDB subregion. These results suggest that: (1) in contrast to other brain regions, GAL gene expression in the cholinergic BF may be negatively regulated by factors concomitant with puberty; and (2) the inhibition of cholinergic function by cosecreted GAL may be enhanced prior to puberty within cholinergic neurons of the rostral and central aspects of the HDB.

Vasopressin and galanin mRNAs coexist in the nucleus of the horizontal diagonal band: a novel site of vasopressin gene expression.

Vasopressin (VP) neurons have been identified in several brain regions where VP has been hypothesized to act as a neurotransmitter or neuromodulator. In many sites, VP is colocalized with the neuropeptide galanin (GAL). Here, using single in situ hybridization histochemistry, we have identified a novel group of neurons within the nucleus of the horizontal diagonal band of Broca (HDB) that express the VP gene and have assessed the distribution of these cells in adult male and female rats (90 days old, n = 7/group). VP mRNA-expressing neurons were scattered throughout the rostrocaudal extent of the HDB, and the number of VP neurons detected unilaterally ranged from 1 to 17 cells per 20 microns section. Using double in situ hybridization histochemistry on alternate sections, we have assessed the number of cells expressing VP and/or GAL mRNA in the diagonal band and have determined the extent of their colocalization. Approximately 50% of all VP-expressing neurons in the HDB coexpressed GAL mRNA, and 33% of GAL-expressing neurons in this region coexpressed VP mRNA. No sex differences were detected in the number of neurons expressing either VP or GAL mRNA or in the incidence of coexpression of VP and GAL mRNAs in this region. VP neurons in the HDB exhibited a low level of expression, and cellular VP mRNA content did not differ between male and female rats. However, sex differences were present in the bed nucleus of the stria terminalis (BNST) of these same rats.(ABSTRACT TRUNCATED AT 250 WORDS)

Galanin-binding sites in the female rat brain are regulated across puberty yet similar to the male pattern in adulthood.

The neuropeptide galanin (GAL) has been implicated in a variety of neuroendocrine functions and has been shown to be regulated by gonadal hormones in several brain regions. We have used slice binding and quantitative autoradiography techniques to determine whether the activation of GAL pathways across puberty in female rats is associated with changes in the density of GAL binding in telencephalic and diencephalic regions as we previously observed in male rats. We have also asked whether sex differences in GAL immunoreactivity and GAL gene expression detected in some brain regions would be paralleled by sex differences in 125I-GAL-binding density in adult male and female rat brains. To control for intrinsic differences in the level of endogenous GAL synthesis and release, brain slices from prepubertal female and adult male and female rats were treated with guanosine 5'-triphosphate (GTP) to induce dissociation of endogenous GAL from its binding sites prior to incubation with radiolabeled ligand. 125I-GAL binding was significantly reduced in seven brain regions of adult compared with prepubertal female rats. These regions included the islands of Calleja (p < or = 0.03), the medial amygdaloid nucleus, posterodorsal division (p < or = 0.05), median eminence (p < or = 0.02), medial habenular nucleus (p < or = 0.05), rhomboid thalamic nucleus (p < or = 0.05), and paraventricular (p < or = 0.05) and intermediodorsal (p < or = 0.02) thalamic nuclei. Only one region, the lateral preoptic area, exhibited significantly enhanced 125I-GAL binding in adult female (p < or = 0.04) compared with prepubertal animals.(ABSTRACT TRUNCATED AT 250 WORDS)

Sex difference in coexpression by galanin neurons accounts for sexual dimorphism of vasopressin in the bed nucleus of the stria terminalis.

Vasopressin (VP) neurons in the bed nucleus of the stria terminalis (BNST) are steroid sensitive and sexually dimorphic. The number of VP messenger RNA (mRNA)-expressing neurons is larger in male than in female rats. This initial observation suggested that sexual dimorphism resulted from enhanced proliferation and/or survival of VP neurons after gonadal hormone exposure during the critical perinatal period. However, galanin (GAL) and VP mRNAs were recently reported to be coexpressed in the BNST of adult male rats, and GAL gene expression, unlike VP gene expression, is not sexually dimorphic. These findings are consistent with the hypothesis that the sex difference in VP cell number in the BNST results from a sex difference in the number of GAL neurons dedicated to express the VP gene. To test this hypothesis, double in situ hybridization histochemistry was performed for GAL and VP mRNAs in the BNST of adult male and female rats. For quantification, the posterior BNST was divided into its two anatomical regions: medial (BSTM) and lateral (BSTL) divisions. Extending previous results for the whole BNST, the number of GAL-expressing cells in either the BSTM or the BSTL was not sexually dimorphic. A significant sex difference was found in the number of GAL cells coexpressing VP in the BSTM (mean +/- SE, male, 124 +/- 8; female, 56 +/- 6; P < or = 0.0001), but not in the BSTL (male, 80 +/- 9; female, 83 +/- 15). Accordingly, the number of cells expressing GAL mRNA only was significantly lower (P < or = 0.002) in the BSTM of male (43 +/- 5) than in female (85 +/- 9) rats. Evidence is provided that the reduced incidence of coexpression of VP by GAL neurons in the BSTM of female rats may account for the reported sex difference in VP cell number in the entire BNST. The results suggest that gonadal hormones in the perinatal period may not influence the proliferation and/or survival of VP neurons in the BNST per se but influence, instead, the capacity of GAL neurons to synthesize VP.