Delineating the conformational landscape of the adenosine A2A receptor during G protein coupling.

G-protein-coupled receptors (GPCRs) represent a ubiquitous membrane protein family and are important drug targets. Their diverse signaling pathways are driven by complex pharmacology arising from a conformational ensemble rarely captured by structural methods. Here, fluorine nuclear magnetic resonance spectroscopy (19F NMR) is used to delineate key functional states of the adenosine A2A receptor (A2AR) complexed with heterotrimeric G protein (Gαsß1γ2) in a phospholipid membrane milieu. Analysis of A2AR spectra as a function of ligand, G protein, and nucleotide identifies an ensemble represented by inactive states, a G-protein-bound activation intermediate, and distinct nucleotide-free states associated with either partial- or full-agonist-driven activation. The Gßγ subunit is found to be critical in facilitating ligand-dependent allosteric transmission, as shown by 19F NMR, biochemical, and computational studies. The results provide a mechanistic basis for understanding basal signaling, efficacy, precoupling, and allostery in GPCRs.

Structural Insights into the Dynamic Process of ß2-Adrenergic Receptor Signaling.

G-protein-coupled receptors (GPCRs) transduce signals from the extracellular environment to intracellular proteins. To gain structural insight into the regulation of receptor cytoplasmic conformations by extracellular ligands during signaling, we examine the structural dynamics of the cytoplasmic domain of the ß2-adrenergic receptor (ß2AR) using (19)F-fluorine NMR and double electron-electron resonance spectroscopy. These studies show that unliganded and inverse-agonist-bound ß2AR exists predominantly in two inactive conformations that exchange within hundreds of microseconds. Although agonists shift the equilibrium toward a conformation capable of engaging cytoplasmic G proteins, they do so incompletely, resulting in increased conformational heterogeneity and the coexistence of inactive, intermediate, and active states. Complete transition to the active conformation requires subsequent interaction with a G protein or an intracellular G protein mimetic. These studies demonstrate a loose allosteric coupling of the agonist-binding site and G-protein-coupling interface that may generally be responsible for the complex signaling behavior observed for many GPCRs.

The dynamic process of ß(2)-adrenergic receptor activation.

G-protein-coupled receptors (GPCRs) can modulate diverse signaling pathways, often in a ligand-specific manner. The full range of functionally relevant GPCR conformations is poorly understood. Here, we use NMR spectroscopy to characterize the conformational dynamics of the transmembrane core of the ß(2)-adrenergic receptor (ß(2)AR), a prototypical GPCR. We labeled ß(2)AR with (13)CH(3)ε-methionine and obtained HSQC spectra of unliganded receptor as well as receptor bound to an inverse agonist, an agonist, and a G-protein-mimetic nanobody. These studies provide evidence for conformational states not observed in crystal structures, as well as substantial conformational heterogeneity in agonist- and inverse-agonist-bound preparations. They also show that for ß(2)AR, unlike rhodopsin, an agonist alone does not stabilize a fully active conformation, suggesting that the conformational link between the agonist-binding pocket and the G-protein-coupling surface is not rigid. The observed heterogeneity may be important for ß(2)AR's ability to engage multiple signaling and regulatory proteins.

Balancing G protein selectivity and efficacy in the adenosine A2A receptor.

The adenosine A2A receptor (A2AR) engages several G proteins, notably Go and its cognate Gs protein. This coupling promiscuity is facilitated by a dynamic ensemble, revealed by 19F nuclear magnetic resonance imaging of A2AR and G protein. Two transmembrane helix 6 (TM6) activation states, formerly associated with partial and full agonism, accommodate the differing volumes of Gs and Go. While nucleotide depletion biases TM7 toward a fully active state in A2AR-Gs, A2AR-Go is characterized by a dynamic inactive/intermediate fraction. Molecular dynamics simulations reveal that the NPxxY motif, a highly conserved switch, establishes a unique configuration in the A2AR-Go complex, failing to stabilize the helix-8 interface with Gs, and adoption of the active state. The resulting TM7 dynamics hamper G protein coupling, suggesting kinetic gating may be responsible for reduced efficacy in the noncognate G protein complex. Thus, dual TM6 activation states enable greater diversity of coupling partners while TM7 dynamics dictate coupling efficacy.

Mechanistic insights into the nickel-dependent allosteric response of the Helicobacter pylori NikR transcription factor.

In Helicobacter pylori, the nickel-responsive NikR transcription factor plays a key role in regulating intracellular nickel concentrations, which is an essential process for survival of this pathogen in the acidic human stomach. Nickel binding to H. pylori NikR (HpNikR) allosterically activates DNA binding to target promoters encoding genes involved in nickel homeostasis and acid adaptation, to either activate or repress their transcription. We previously showed that HpNikR adopts an equilibrium between an open conformation and DNA-binding competent cis and trans states. Nickel binding slows down conformational exchange between these states and shifts the equilibrium toward the binding-competent states. The protein then becomes stabilized in a cis conformation upon binding the ureA promoter. Here, we investigate how nickel binding creates this response and how it is transmitted to the DNA-binding domains. Through mutagenesis, DNA-binding studies, and computational methods, the allosteric response to nickel was found to be propagated from the nickel-binding sites to the DNA-binding domains via the ß-sheets of the metal-binding domain and a network of residues at the inter-domain interface. Our computational results suggest that nickel binding increases protein rigidity to slow down the conformational exchange. A thymine base in the ureA promoter sequence, known to be critical for high affinity DNA binding by HpNikR, was also found to be important for the allosteric response, while a modified version of this promoter further highlighted the importance of the DNA sequence in modulating the response. Collectively, our results provide insights into regulation of a key protein for H. pylori survival.

Dynamics and mechanistic underpinnings to pharmacology of class A GPCRs: an NMR perspective.

One-third of current pharmaceuticals target G protein-coupled receptors (GPCRs), the largest receptor superfamily in humans and mediators of diverse physiological processes. This review summarizes the recent progress in GPCR structural dynamics, focusing on class A receptors and insights derived from nuclear magnetic resonance (NMR) and other spectroscopic techniques. We describe the structural aspects of GPCR activation and the various pharmacological models that capture aspects of receptor signaling behavior. Spectroscopic studies revealed that receptors and their signaling complexes are dynamic allosteric systems that sample multiple functional states under basal conditions. The distribution of states within the conformational ensemble and the kinetics of transitions between states are regulated through the binding of ligands, allosteric modulators, and the membrane environment. This ensemble view of GPCRs provides a mechanistic framework for understanding many of the pharmacological phenomena associated with receptor signaling, such as basal activity, efficacy, and functional bias.

Activation of the A2A adenosine G-protein-coupled receptor by conformational selection.

Conformational selection and induced fit are two prevailing mechanisms to explain the molecular basis for ligand-based activation of receptors. G-protein-coupled receptors are the largest class of cell surface receptors and are important drug targets. A molecular understanding of their activation mechanism is critical for drug discovery and design. However, direct evidence that addresses how agonist binding leads to the formation of an active receptor state is scarce. Here we use (19)F nuclear magnetic resonance to quantify the conformational landscape occupied by the adenosine A2A receptor (A2AR), a prototypical class A G-protein-coupled receptor. We find an ensemble of four states in equilibrium: (1) two inactive states in millisecond exchange, consistent with a formed (state S1) and a broken (state S2) salt bridge (known as 'ionic lock') between transmembrane helices 3 and 6; and (2) two active states, S3 and S3', as identified by binding of a G-protein-derived peptide. In contrast to a recent study of the ß2-adrenergic receptor, the present approach allowed identification of a second active state for A2AR. Addition of inverse agonist (ZM241385) increases the population of the inactive states, while full agonists (UK432097 or NECA) stabilize the active state, S3', in a manner consistent with conformational selection. In contrast, partial agonist (LUF5834) and an allosteric modulator (HMA) exclusively increase the population of the S3 state. Thus, partial agonism is achieved here by conformational selection of a distinct active state which we predict will have compromised coupling to the G protein. Direct observation of the conformational equilibria of ligand-dependent G-protein-coupled receptor and deduction of the underlying mechanisms of receptor activation will have wide-reaching implications for our understanding of the function of G-protein-coupled receptor in health and disease.

Allosteric nanobodies reveal the dynamic range and diverse mechanisms of G-protein-coupled receptor activation.

G-protein-coupled receptors (GPCRs) modulate many physiological processes by transducing a variety of extracellular cues into intracellular responses. Ligand binding to an extracellular orthosteric pocket propagates conformational change to the receptor cytosolic region to promote binding and activation of downstream signalling effectors such as G proteins and ß-arrestins. It is well known that different agonists can share the same binding pocket but evoke unique receptor conformations leading to a wide range of downstream responses ('efficacy'). Furthermore, increasing biophysical evidence, primarily using the ß2-adrenergic receptor (ß2AR) as a model system, supports the existence of multiple active and inactive conformational states. However, how agonists with varying efficacy modulate these receptor states to initiate cellular responses is not well understood. Here we report stabilization of two distinct ß2AR conformations using single domain camelid antibodies (nanobodies)­a previously described positive allosteric nanobody (Nb80) and a newly identified negative allosteric nanobody (Nb60). We show that Nb60 stabilizes a previously unappreciated low-affinity receptor state which corresponds to one of two inactive receptor conformations as delineated by X-ray crystallography and NMR spectroscopy. We find that the agonist isoprenaline has a 15,000-fold higher affinity for ß2AR in the presence of Nb80 compared to the affinity of isoprenaline for ß2AR in the presence of Nb60, highlighting the full allosteric range of a GPCR. Assessing the binding of 17 ligands of varying efficacy to the ß2AR in the absence and presence of Nb60 or Nb80 reveals large ligand-specific effects that can only be explained using an allosteric model which assumes equilibrium amongst at least three receptor states. Agonists generally exert efficacy by stabilizing the active Nb80-stabilized receptor state (R80). In contrast, for a number of partial agonists, both stabilization of R80 and destabilization of the inactive, Nb60-bound state (R60) contribute to their ability to modulate receptor activation. These data demonstrate that ligands can initiate a wide range of cellular responses by differentially stabilizing multiple receptor states.

Fate of thiamethoxam from treated seeds in mesocosms and response of aquatic invertebrate communities.

Thiamethoxam is a neonicotinoid insecticide widely applied in the Canadian Prairies. It has been detected in surface waters of agro-ecosystems, including wetlands, but the potential effects on non-target invertebrate communities in these wetlands have not been well characterized. In an effort to understand better the fate of thiamethoxam in wetlands and the response of invertebrates (zooplankton and emergent insects), model systems were used to mimic wetland flooding into planted fields. Outdoor mesocosms were treated with a single application of thiamethoxam-treated canola seeds at three treatment levels based on a recommended seeding rate (i.e., 6 kg/ha; 1×, 10×, and 100× seeding rate) and monitored over ten weeks. The mean half-life of thiamethoxam in the water column was 6.2 d. There was no ecologically meaningful impact on zooplankton abundances or community structure among treatments. Statistically significant differences were observed in aquatic insect abundance between control mesocosms and the two greatest thiamethoxam treatments (10× and 100× seeding rate). The observed results indicate exposure to thiamethoxam at environmentally relevant concentrations likely does not represent a significant ecological risk to abundance and community structure of wetland zooplankton and emergent insects.

Deterministic risk assessment of firefighting water additives to aquatic organisms.

Past firefighting water additives were found to contain perfluorinated compounds that could persist in the environment resulting in potential adverse effects to biota. Since this revelation, manufacturers have introduced alternative firefighting water additives that are fluorine free, but few studies have investigated the fate and effects in the environment of these new additives. Firefighting water additives could enter aquatic ecosystems through run-off, leaching or direct application. Therefore, there is a need to investigate the potential effect that firefighting water additives could have on aquatic biota. This study investigated the toxicity of six firefighting water additives: Eco-Gel™, Thermo-Gel™, FireAde™, Fire-Brake™, Novacool Foam™, and F-500™ to aquatic biota. The toxicities of firefighting water additives to Lemna minor (duckweed), Daphnia magna (water flea), Hexagenia spp. larvae (mayfly), Lampsilis fasciola (wavy-rayed lampmussel) and Oncorhynchus mykiss (rainbow trout) were investigated through acute and chronic static and semi-static tests to estimate LC50 values for survival and EC50 values for immobility and/or reproduction endpoints. A large variation in toxicities among the firefighting water additives and among the test species was observed. Based on a worst-case exposure scenario of direct application, several firefighting water additives were found to pose a hazard to aquatic organisms. An exposure rate representative of a direct overhead application by a water bomber during a forest fire was used in the hazard assessment. For example, the hazard quotients determined for the D. magna acute toxicity tests ranged from 0.20 for Eco-Gel to 317 for F-500 in the forest pool (15 cm) scenario. This study presents the first deterministic risk assessment of firefighting water additives in aquatic ecosystems.

A review of the effectiveness of vegetated buffers to mitigate pesticide and nutrient transport into surface waters from agricultural areas.

A relatively large number of studies have investigated the effectiveness of vegetated buffer strips at reducing the movement of pesticides and nutrients from agriculture fields. This review outlines the observed influence of different factors (e.g., buffer width, slope, runoff intensity, soil composition, plant community) that can influence the efficacy of vegetated buffers in pesticide and nutrient retention. The reported effectiveness of vegetated buffers reducing the movement of pesticides and nutrients ranged from 10 to 100% and 12-100%, respectively. Buffer width is the factor that is most frequently considered by various jurisdictions when making recommendations on vegetated buffer strip implementation. However, the literature clearly illustrates that there is a great deal of variation in pesticide or nutrient reduction for a given buffer width. This indicates that other factors play an important role in buffer efficacy (e.g., ratio of source area to buffer area, soil composition and structure, runoff intensity, plant community structure) in addition to the width of the vegetative buffer area. These factors need to be considered when making recommendations on vegetated buffer strip construction in agroecosystems. This review has also identified a number of other gaps in the understanding of the effectiveness of vegetated buffers at reducing the movement of pesticides and nutrients from the areas of application.

Substrate-Based Allosteric Regulation of a Homodimeric Enzyme.

Many enzymes operate through half-of-the sites reactivity wherein a single protomer is catalytically engaged at one time. In the case of the homodimeric enzyme, fluoroacetate dehalogenase, substrate binding triggers closing of a regulatory cap domain in the empty protomer, preventing substrate access to the remaining active site. However, the empty protomer serves a critical role by acquiring more disorder upon substrate binding, thereby entropically favoring the forward reaction. Empty protomer dynamics are also allosterically coupled to the bound protomer, driving conformational exchange at the active site and progress along the reaction coordinate. Here, we show that at high concentrations, a second substrate binds along the substrate-access channel of the occupied protomer, thereby dampening interprotomer dynamics and inhibiting catalysis. While a mutation (K152I) abrogates second site binding and removes inhibitory effects, it also precipitously lowers the maximum catalytic rate, implying a role for the allosteric pocket at low substrate concentrations, where only a single substrate engages the enzyme at one time. We show that this outer pocket first desolvates the substrate, whereupon it is deposited in the active site. Substrate binding to the active site then triggers the empty outer pocket to serve as an interprotomer allosteric conduit, enabling enhanced dynamics and sampling of activation states needed for catalysis. These allosteric networks and the ensuing changes resulting from second substrate binding are delineated using rigidity-based allosteric transmission theory and validated by nuclear magnetic resonance and functional studies. The results illustrate the role of dynamics along allosteric networks in facilitating function.

Activation processes in ligand-activated G protein-coupled receptors: A case study of the adenosine A2A receptor.

Here we review concepts related to an ensemble description of G-protein-coupled receptors (GPCRs). The ensemble is characterized by both inactive and active states, whose equilibrium populations and exchange rates depend sensitively on ligand, environment, and allosteric factors. This review focuses on the adenosine A2 receptor (A2A R), a prototypical class A GPCR. 19 F Nuclear Magnetic Resonance (NMR) studies show that apo A2A R is characterized by a broad ensemble of conformers, spanning inactive to active states, and resembling states defined earlier for rhodopsin. In keeping with ideas associated with a conformational selection mechanism, addition of agonist serves to allosterically restrict the overall degrees of freedom at the G protein binding interface and bias both states and functional dynamics to facilitate G protein binding and subsequent activation. While the ligand does not necessarily "induce" activation, it does bias sampling of states, increase the cooperativity of the activation process and thus, the lifetimes of functional activation intermediates, while restricting conformational dynamics to that needed for activation.

The role of vegetated buffers in agriculture and their regulation across Canada and the United States.

A vegetated buffer, barrier, or filter strip is a parcel of land that is designated to separate land used for agriculture from valued aquatic or terrestrial habitats. It exists partly with the intent to diffuse runoff and to impeded sediment, nutrients, pesticides, and other constituents from reaching off-site surface waters. Mandatory buffer implementation is regulated at various levels of government in North America - from the federal to the state and provincial levels, and by some municipalities and counties. To better understand the degree and breadth of oversight, we undertook a comprehensive search and review of vegetative buffer regulations across North America. We determined the width of buffer required, under what habitat or field conditions, for which pesticides, and application type, amongst other attributes. For ground application, margins ranged from 1 m to upwards of greater than 4000 m depending on protection goals, with some being compound specific and others being generally applied to all registered pesticides/compounds. These buffers tended to be used most often to protect surface water, groundwater (e.g. drinking water wells), and nearby sensitive crops, but the required distances are generally not consistent between jurisdictions, regardless of the stated protection goals. We recommend that a thorough science-based review take place, with input from relevant stakeholders, to harmonize vegetated buffer size for effective surface water protection where ecological, climatic, and agricultural conditions are sufficiently similar in North America.

The facultatively parasitic ciliated protozoan, Tetrahymena glochidiophila (Lynn, 2018), causes a reduction in viability of freshwater mussel glochidia.

This study investigated the effect of a previously uncharacterized species of ciliated protozoan, Tetrahymena glochidiophila, on the viability of glochidia from three species of freshwater mussel (Lampsilis siliquoidea, Lampsilis fasciola, and Lampsilis cardium). Over the course of 72 h, the viability of glochidia exposed to T. glochidiophila declined by >60% while the decline in the viability of uninfected glochidia was <10%. The density of T. glochidiophila increased >1000-fold during the experiment in treatments with infected glochidia. Lampsilis cardium glochidia were also either exposed to gill rinsate or gill contents from infected gravid female L. siliquoidea for the purpose of elucidating the location of the greatest density of ciliates within infected mussels. Glochidia exposed to gill contents declined significantly (p < 0.05) more than glochidia exposed to gill rinsate. Finally, a clone of ciliates was isolated from infected glochidia and cultured on bacterized medium. The clonal culture was then used to expose uninfected glochidia for the purpose of further confirming a parasitic relationship between glochidia and T. glochidiophila. The viability of glochidia exposed to T. glochidiophila from the clonal culture declined significantly relative to uninfected glochidia but not to the extent of glochidia exposed to ciliates from the gills of infected L. siliquoidea.

Tetrahymena glochidiophila n. sp., a new species of Tetrahymena (Ciliophora) that causes mortality to glochidia larvae of freshwater mussels (Bivalvia).

A ciliate protozoan was discovered whose presence coincided with a rapid decrease in the viability (i.e. ability to close valves) of glochidia of the freshwater mussel Lampsilis siliquoidea. Microscopic examination showed it to be a histophagous tetrahymenine ciliate. Small subunit (SSU) rRNA and cytochrome c oxidase subunit 1 (cox1) barcode sequences from cultured cells showed that it belongs to the same new species isolated from water samples as a free-living ciliate. Phylogenetic analyses place this new ciliate in the same clade with the macrostome species Tetrahymena paravorax, and we propose the name T. glochidiophila n. sp. for this new species. The phylogeny provides further support for the hypothesis that histophagy was a life history trait of the ancestor of Tetrahymena.

Evidence of citation bias in the pesticide ecotoxicology literature.

As scientists, we are tasked with letting evidence guide our conclusions. In the world of pesticides this takes on added importance as the data can influence ecological and human health outcomes and regulations, and even the manner in which we grow food. Yet, there seems to be a reticence to engage with the totality of the pesticide ecotoxicology literature, especially papers that report few or no effects or low risk to non-target organisms. We suspected that these studies would have fewer citations than studies that report significant effects or risk for the same compound, and this would be unrelated to the strength of the study, e.g., high quality studies with few or no effects would be cited less frequently than weaker studies that reported effects. To investigate this, we examined a subset of literature around the herbicide atrazine. We found that papers reporting an effect had significantly more citations per year than those that did not (p < 0.05). There was no significant relationship between the strength of the study and number of citations, but a general trend for weaker studies to have greater number of citations. The impact factor of journals was not positively correlated with the strength of the study methods, but studies that reported effects were published in journals with a greater mean impact factor than those that reported no effects (p < 0.05). This analysis reveals evidence of citation bias within the pesticide ecotoxicology literature, as well as bias by journals to publish studies that report effects, regardless of study quality.

Bioaccumulation of sediment-associated substituted phenylamine antioxidants in Tubifex tubifex and Lampsilis siliquoidea.

Substituted phenylamine antioxidants (SPAs) are additives in a variety of commercial polymers (e.g., lubricants, plastics, etc.). Based on their physicochemical properties, if SPAs were to enter an aquatic system, they would likely partition into sediment and have the capacity to bioaccumulate in biota. This study investigated the potential of four sediment-associated SPAs, diphenylamine (DPA), N-phenyl-1-naphthalene (PNA), N-(1,3-dimethylbutyl)-N'-phenyl-1,4-phenylenediamine (DPPDA), and 4,4'-methylene-bis[N-sec-butylaniline] (MBA) to accumulate in the tissues of freshwater mussels (Lampsilis siliquoidea) and oligochaete worms (Tubifex tubifex). Mussels and worms were exposed to sediment spiked with individual SPAs for 28 d. The concentration of SPAs was measured in the gill, gonad, and remaining viscera of the mussels and entire body of the worms. The majority of biota-sediment accumulation factors (28-d BSAFs) for the different tissues of mussels were < 1. The highest concentrations of SPAs were consistently observed in the gill tissue of mussels relative to the gonad and viscera. The 28-d BSAFs for DPPDA and MBA for worms were < 1, and for DPA and PNA, they ranged from 0.38-2.13 and 1.54-33.24, respectively. The higher 28-d BSAFs observed for worms compared to mussels were likely because worms are endobenthic and feed on sediment-associated organic matter. PNA and DPPDA have similar octanol-water partition coefficients (Kow) but greater 28-d BSAFs were observed for PNA compared to DPPDA for both species. This observation provides evidence that biota may be able to metabolize and/or excrete SPAs with similar physicochemical properties at considerably different rates. The 28-d BSAFs observed for sediment-associated SPAs are lower than those typically required for a chemical to be classified as bioaccumulative.

In Situ Reconstitution of the Adenosine A2A Receptor in Spontaneously Formed Synthetic Liposomes.

Cell transmembrane receptors play a key role in the detection of environmental stimuli and control of intracellular communication. G protein-coupled receptors constitute the largest transmembrane protein family involved in cell signaling. However, current methods for their functional reconstitution in biomimetic membranes remain both challenging and limited in scope. Herein, we describe the spontaneous reconstitution of adenosine A2A receptor (A2AR) during the de novo formation of synthetic liposomes via native chemical ligation. The approach takes advantage of a nonenzymatic and chemoselective method to rapidly generate A2AR embedded phospholiposomes from receptor solubilized in n-dodecyl-ß-d-maltoside analogs. In situ lipid synthesis for protein reconstitution technology proceeds in the absence of dialysis and/or detergent absorbents, and A2AR assimilation into synthetic liposomes can be visualized by microscopy and probed by radio-ligand binding.