Conformational thermostabilization of the beta1-adrenergic receptor in a detergent-resistant form

Exploration of structure-based drug design opportunities for mGluRs

The metabotropic glutamate receptors (mGluRs) are a subset of the Class C G-Protein Coupled Receptors (GPCRs). Recently, an emerging strategy for drug-discovery efforts targeting mGluRs has been to develop compounds acting at the so-called allosteric site in the 7-transmembrane (7TM) domain, common to all GPCRs, rather than the extracellular (EC) domain containing the orthosteric glutamate-binding site. We examine herein some of the intrinsic relative merits of targeting these two domains. Comparisons are made among amino-acid sequences in the two domains and among X-ray structures and homology models of the EC domain. We show that there is greater sequence diversity in the EC domains than in the transmembrane (TM) domains. Thus, contrary to generally accepted descriptions of there being greater evolutionary pressure to preserve the EC domain, it is the 7TM domain that is more highly conserved. Within the EC domain, the glutamate-binding site of the Venus flytrap region has hitherto received the most attention as a target site. Analysis of examples of the three-dimensional structures of the EC domains at the glutamate-binding site reveals differences as well, thereby supporting the viability of targeting the EC domain, even at the glutamate-binding site, for drug discovery. To exemplify this strategy, we present examples of active compounds identified via high-throughput docking in the EC region.

Ligand-supported purification of the urotensin-II receptor

A crucial limitation for structural and biophysical analysis of G protein-coupled receptors (GPCRs) is the inherent challenge of purifying and stabilizing these receptors in an active (agonist-bound) conformation. Peptide ligands, such as the vasoactive, cyclic hormone urotensin-II (U-II), may provide new purification tools, via high affinity, pseudo-irreversible binding suitable for ligand-based affinity purification. We show that the U-II receptor (UT) is resistant to desensitization as a result of low phosphorylation and diminished endocytosis. UT also displays an unusual proclivity to remain active with vasoconstriction sustained despite extensive washout of the ligand. To exploit these properties for ligand-supported purification, we modified the U-II ligand by attaching a biotin moiety and spacer arm to the N terminus, creating a novel affinity ligand (Bio-U-II) to interface with streptavidin media. Bio-U-II bound to UT with pharmacological properties analogous to those of the unmodified U-II ligand (high-affinity, pseudo-irreversible binding). The prebinding of Bio-U-II to UT (before exposure to detergent) facilitated specific capture of UT by stabilizing the receptor structure during solubilization with detergent. Solubilization of UT with the most compatible detergent, n-dodecyl β-d-maltoside, was dependent on the critical micelle concentration, and Gα(q/11) protein was copurified with captured Bio-U-II-UT complexes. Furthermore, captured Bio-U-II-UT complexes were resistant to dissociation at elevated temperatures, suggesting that UT is relatively thermostable, making it an ideal candidate for future structural and biophysical studies. This work demonstrates the utility of pseudo-irreversible ligands to support the purification of a GPCR during detergent extraction, resulting in the first successful purification of the UT.

The properties of thermostabilised G protein-coupled receptors (StaRs) and their use in drug discovery

G protein-coupled receptors (GPCRs) are one of the most important target classes in the central nervous system (CNS) drug discovery, however the fact they are integral membrane proteins and are unstable when purified out of the cell precludes them from a wide range of structural and biophysical techniques that are used for soluble proteins. In this study we demonstrate how protein engineering methods can be used to identify mutations which can both increase the thermostability of receptors, when purified in detergent, as well as biasing the receptor towards a specific physiologically relevant conformational state. We demonstrate this method for the adenosine A(2A) receptor and muscarinic M(1) receptor. The resultant stabilised receptors (known as StaRs) have a pharmacological profile consistent with the inverse agonist conformation. The stabilised receptors can be purified in large quantities, whilst retaining correct folding, thus generating reagents suitable for a broad range of structural and biophysical studies. In the case of the A(2A)-StaR we demonstrate that surface plasmon resonance can be used to profile the association and dissociation rates of a range of antagonists, a technique that can be used to improve the in vivo efficacy of receptor antagonists.

Mass spectrometry-based GPCR proteomics: comprehensive characterization of the human cannabinoid 1 receptor

The human cannabinoid 1 receptor (hCB1), a ubiquitous G protein-coupled receptor (GPCR), transmits cannabinergic signals that participate in diverse (patho)physiological processes. Pharmacotherapeutic hCB1 targeting is considered a tractable approach for treating such prevalent diseases as obesity, mood disorders, and drug addiction. The hydrophobic nature of the transmembrane helices of hCB1 presents a formidable difficulty to its direct structural analysis. Comprehensive experimental characterization of functional hCB1 by mass spectrometry (MS) is essential to the targeting of affinity probes that can be used to define directly hCB1 binding domains using a ligand-assisted experimental approach. Such information would greatly facilitate the rational design of hCB1-selective agonists/antagonists with therapeutic potential. We report the first high-coverage MS analysis of the primary sequence of the functional hCB1 receptor, one of the few such comprehensive MS-based analyses of any GPCR. Recombinant C-terminal hexa-histidine-tagged hCB1 (His6-hCB1) was expressed in cultured insect (Spodoptera frugiperda) cells, solubilized by a procedure devised to enhance receptor purity following metal-affinity chromatography, desalted by buffer exchange, and digested in solution with (chymo)trypsin. "Bottom-up" nanoLC-MS/MS of the (chymo)tryptic digests afforded a degree of overall hCB1 coverage (>94%) thus far reported for only two other GPCRs. This MS-compatible procedure devised for His6-hCB1 sample preparation, incorporating in-solution (chymo)trypsin digestion in the presence of a low concentration of CYMAL-5 detergent, may be applicable to the MS-based proteomic characterization of other GPCRs. This work should help enable future ligand-assisted structural characterization of hCB1 binding motifs at the amino-acid level using rationally designed and targeted covalent cannabinergic probes.

Combinatorial method for overexpression of membrane proteins in Escherichia coli

Membrane proteins constitute 20-30% of all proteins encoded by the genome of various organisms. Large amounts of purified proteins are required for activity and crystallization attempts. Thus, there is an unmet need for a heterologous membrane protein overexpression system for purification, crystallization, and activity determination. We developed a combinatorial method for overexpressing and purifying membrane proteins using Escherichia coli. This method utilizes short hydrophilic bacterial proteins, YaiN and YbeL, fused to the ends of the membrane proteins to serve as facilitating factors for expression and purification. Fourteen prokaryotic and mammalian membrane proteins were expressed using this system. Moderate to high expression was obtained for most proteins, and detergent solubilization combined with a short purification process produced stable, monodispersed membrane proteins. Five of the mammalian membrane proteins, overexpressed using our system, were reconstituted into liposomes and exhibited transport activity comparable with the native transporters.

Structure determination of the seven-helix transmembrane receptor sensory rhodopsin II by solution NMR spectroscopy

Seven-helix membrane proteins represent a challenge for structural biology. Here we report the first NMR structure determination of a detergent-solubilized seven-helix transmembrane (7TM) protein, the phototaxis receptor sensory rhodopsin II (pSRII) from Natronomonas pharaonis, as a proof of principle. The overall quality of the structure ensemble is good (backbone r.m.s. deviation of 0.48 A) and agrees well with previously determined X-ray structures. Furthermore, measurements in more native-like small phospholipid bicelles indicate that the protein structure is the same as in detergent micelles, suggesting that environment-specific effects are minimal when using mild detergents. We use our case study as a platform to discuss the feasibility of similar solution NMR studies for other 7TM proteins, including members of the family of G protein-coupled receptors.

A purified C-terminally truncated human adenosine A(2A) receptor construct is functionally stable and degradation resistant

Recent high resolution structures of modified G-protein coupled receptors (GPCRs) have provided major insight into the mechanisms of receptor-ligand binding. However understanding of the complete mechanism of GPCR function remains limited. This study characterised C-terminally truncated versions of the human adenosine A(2A) receptor (A(2A)R) with a view to producing protein suitable for structural studies. The constructs terminated at residue A316, removing the intracellular C-terminal tail, or V334, producing a C-terminal tail equivalent in length to that of rhodopsin. Higher levels of functional receptor before and after solubilisation were obtained for both C-terminally truncated constructs compared to the wild-type receptor (WT) as assessed by radioligand binding analysis using [(3)H]ZM241385. The construct which yielded the highest level of functional receptor, V334 A(2A)R, was purified in DDM to high homogeneity with a final yield of 2 mg/L. Binding analysis revealed that the purified receptor had a specific activity of 20.2+/-1.2 nmol/mg, close to the theoretical maximum. Pure V334 A(2A)R was resistant to degradation over 15 days when stored at 4 degrees C or 20 degrees C and showed remarkable functional stability when stored at 4 degrees C, retaining 84% of initial functionality after 30 days. This construct is an excellent candidate for structural studies.

Modulation of G-protein coupled receptor sample quality by modified cell-free expression protocols: a case study of the human endothelin A receptor

G-protein coupled receptors still represent one of the most challenging targets in membrane protein research. Here we present a strategic approach for the cell-free synthesis of these complex membrane proteins exemplified by the preparative scale production of the human endothelin A receptor. The versatility of the cell-free expression system was used to modulate sample quality by alteration of detergents hence presenting different solubilization environments to the synthesized protein at different stages of the production process. Sample properties after co-translational and post-translational solubilization have been analysed by evaluation of homogeneity, protein stability and receptor ligand binding competence. This is a first quality evaluation of a membrane protein obtained in two different cell-free expression modes and we demonstrate that both can be used for the production of ligand-binding competent endothelin A receptor in quantities sufficient for structural approaches. The presented strategy of cell-free expression protocol development could serve as basic guideline for the production of related receptors in similar systems.

High-throughput expression and purification of membrane proteins

High-throughput (HT) methodologies have had a tremendous impact on structural biology of soluble proteins. High-resolution structure determination relies on the ability of the macromolecule to form ordered crystals that diffract X-rays. While crystallization remains somewhat empirical, for a given protein, success is proportional to the number of conditions screened and to the number of variants trialed. HT techniques have greatly increased the number of targets that can be trialed and the rate at which these can be produced. In terms of number of structures solved, membrane proteins appear to be lagging many years behind their soluble counterparts. Likewise, HT methodologies for production and characterization of these hydrophobic macromolecules are only now emerging. Presented here is an HT platform designed exclusively for membrane proteins that has processed over 5000 targets.

Tricks of the trade used to accelerate high-resolution structure determination of membrane proteins

The rate at which X-ray structures of membrane proteins are solved is on a par with that of soluble proteins in the late 1970s. There are still many obstacles facing the membrane protein structural community. Recently, there have been several technical achievements in the field that have started to dramatically accelerate structural studies. Here, we summarize these so-called 'tricks-of-the-trade' and include case studies of several mammalian transporters.

Progress in elucidating the structural and dynamic character of G Protein-Coupled Receptor oligomers for use in drug discovery

G Protein-Coupled Receptors (GPCRs) are the most targeted group of proteins for the development of therapeutic drugs. Until the last decade, structural information about this family of membrane proteins was relatively scarce, and their mechanisms of ligand binding and signal transduction were modeled on the assumption that GPCRs existed and functioned as monomeric entities. New crystal structures of native and engineered GPCRs, together with important biochemical and biophysical data that reveal structural details of the activation mechanism(s) of this receptor family, provide a valuable framework to improve dynamic molecular models of GPCRs with the ultimate goal of elucidating their allostery and functional selectivity. Since the dynamic movements of single GPCR protomers are likely to be affected by the presence of neighboring interacting subunits, oligomeric arrangements should be taken into account to improve the predictive ability of computer-assisted structural models of GPCRs for effective use in drug design.

Stability study of the human G-protein coupled receptor, Smoothened

Smoothened is a member of the G-protein coupled receptor (GPCR) family responsible for the transduction of the Hedgehog signal to the intracellular effectors of the Hedgehog signaling pathway. Aberrant regulation of this receptor is implicated in many cancers but also in neurodegenerative disorders. Despite the pharmacological relevance of this receptor, very little is known about its functional mechanism and its physiological ligand. In order to characterize this receptor for basic and pharmacological interests, we developed the expression of human Smoothened in the yeast Saccharomyces cerevisiae and Smoothened was then purified. Using Surface Plasmon Resonance technology, we showed that human Smoothened was in a native conformational state and able to interact with its antagonist, the cyclopamine, both at the yeast plasma membrane and after purification. Thermostability assays on purified human Smoothened showed that this GPCR is relatively stable in the classical detergent dodecyl-beta-d-maltoside (DDM). The fluorinated surfactant C(8)F(17)TAC, which has been proposed to be less aggressive towards membrane proteins than classical detergents, increased Smoothened thermostability in solution. Moreover, the replacement of a glycine by an arginine in the third intracellular loop of Smoothened coupled to the use of the fluorinated surfactant C(8)F(17)TAC during the mutant purification increased Smoothened thermostability even more. These data will be very useful for future crystallization assays and structural characterization of the human receptor Smoothened.

Crystallographic characterization of N-oxide tripod amphiphiles

Tripod amphiphiles are designed to promote the solubilization and stabilization of intrinsic membrane proteins in aqueous solution; facilitation of crystallization is a long-range goal. Membrane proteins are subjects of extensive interest because of their critical biological roles, but proteins of this type can be difficult to study because of their low solubility in water. The nonionic detergents that are typically used to achieve solubility can have the unintended effect of causing protein denaturation. Tripod amphiphiles differ from conventional detergents in that the lipophilic segment contains a branchpoint, and previous work has shown that this unusual amphiphilic architecture can be advantageous relative to traditional detergent structures. Here, we report the crystal structures of several tripod amphiphiles that contain an N-oxide hydrophilic group. The data suggest that tripods can adapt themselves to a nonpolar surface by altering the hydrophobic appendage that projects toward that surface and their overall orientation relative to that surface. Although it is not possible to draw firm conclusions regarding amphiphile association in solution from crystallographic data, trends observed among the packing patterns reported here suggest design strategies to be implemented in future studies.

Structures of membrane proteins

In reviewing the structures of membrane proteins determined up to the end of 2009, we present in words and pictures the most informative examples from each family. We group the structures together according to their function and architecture to provide an overview of the major principles and variations on the most common themes. The first structures, determined 20 years ago, were those of naturally abundant proteins with limited conformational variability, and each membrane protein structure determined was a major landmark. With the advent of complete genome sequences and efficient expression systems, there has been an explosion in the rate of membrane protein structure determination, with many classes represented. New structures are published every month and more than 150 unique membrane protein structures have been determined. This review analyses the reasons for this success, discusses the challenges that still lie ahead, and presents a concise summary of the key achievements with illustrated examples selected from each class.

Transferability of thermostabilizing mutations between beta-adrenergic receptors

In previous work we described six point mutations that thermostabilised the turkey beta(1)-adrenergic receptor (tbeta(1)AR). The thermostable mutant, tbeta(1)AR-m23, had an apparent T(m) 21 degrees C higher than the native protein when solubilized in dodecylmaltoside (DDM) and, in addition, was significantly more stable in short chain detergents, which allowed its crystallization and structure determination. Identification of thermostabilizing mutations in tbeta(1)AR was performed by systematic mutagenesis followed by expressing and assaying each of the 318 mutants for their thermostability. This is time-consuming, so to facilitate studies on related receptors, we have studied the transferability of these mutations to the human adrenergic receptors, hbeta(1)AR and hbeta(2)AR, which have, respectively, 76% and 59% sequence identity to tbeta(2)AR, excluding the N- and C-termini. Thermostability assays revealed that hbeta(1)AR was much more unstable than tbeta(2)AR, whereas hbeta(2)AR was more stable than tbeta(1)AR. Addition of the 6 thermostabilizing mutations in tbeta(2)AR-m23 into both hbeta(2)AR and hbeta(2)AR increased their apparent T(m)s by 17 degrees C and 11 degrees C, respectively. In addition, the mutations affected the global conformation of the human receptors so that they were predominantly in the antagonist bound form, as was originally observed for tbeta(2)AR-m23. Thus, once thermostabilizing mutations have been identified in one G protein-coupled receptor, stabilization of close members within the subfamily is rapidly obtainable.

Recent progress in the structure determination of GPCRs, a membrane protein family with high potential as pharmaceutical targets

G protein-coupled receptors (GPCRs) constitute a highly diverse and ubiquitous family of integral membrane proteins, transmitting signals inside the cells in response to an assortment of disparate extracellular stimuli. Their strategic location on the cell surface and their involvement in crucial cellular and physiological processes turn these receptors into highly important pharmaceutical targets. Recent technological developments aimed at stabilization and crystallization of these receptors have led to significant breakthroughs in GPCR structure determination efforts. One of the successful approaches involved receptor stabilization with the help of a fusion partner combined with crystallization in lipidic cubic phase (LCP). The success of using an LCP matrix for crystallization is generally attributed to the creation of a more native, membrane-like stabilizing environment for GPCRs just prior to nucleation and to the formation of type I crystal lattices, thus generating highly ordered and strongly diffracting crystals. Here we describe protocols for reconstituting purified GPCRs in LCP, performing pre-crystallization assays, setting up crystallization trials in manual mode, detecting crystallization hits, optimizing crystallization conditions, harvesting, and collecting crystallographic data The protocols provide a sensible framework for approaching crystallization of stabilized GPCRs in LCP, however, as in any crystallization experiment, extensive screening and optimization of crystallization conditions as well as optimization of protein construct and purification steps are required. The process remains risky and these protocols do not necessarily guarantee success.

Beyond rhodopsin: G protein-coupled receptor structure and modeling incorporating the beta2-adrenergic and adenosine A(2A) crystal structures

For quite some time, the majority of GPCR models have been based on a single template structure: dark-adapted bovine rhodopsin. The recent solution of β2AR, β1AR and adenosine A(2A) receptor crystal structures has dramatically expanded the GPCR structural landscape and provided many new insights into receptor conformation and ligand binding. They will serve as templates for the next generation of GPCR models, but also allow direct validation of previous models and computational techniques. This review summarizes key findings from the new structures, comparison of existing models to these structures and highlights new models constructed from these templates.

Expression of membrane proteins at the Escherichia coli membrane for structural studies

Structural biology of membrane proteins is often limited by the first steps in obtaining sufficient yields of proteins because native sources are seldom. Heterologous systems like bacteria are then commonly employed for membrane protein over-expression. Escherichia coli is the main bacterial host used. However, overproduction of a foreign membrane protein at a non-physiological level is usually toxic for cells or leads to inclusion body formation. Those effects can be reduced by optimizing the cell growth conditions, choosing the suitable bacterial strain and expression vector, and finally co-expressing the target protein and the b-subunit of E. coli adenosine triphosphate (ATP)-synthase, which triggers the proliferation of intracytoplasmic membranes. This chapter is devoted to help the experimenter in choosing the appropriate plasmid/bacterial host combination for optimizing the amount of the target membrane protein produced in its correct folded state.

Amphipols and fluorinated surfactants: Two alternatives to detergents for studying membrane proteins in vitro

Handling integral membrane proteins in aqueous solutions traditionally relies on the use of detergents, which are surfactants capable of dispersing the components of biological membranes into mixed micelles. The dissociating character of detergents, however, most often causes solubilized membrane proteins to be unstable. This has prompted the development of alternative, less-aggressive surfactants designed to keep membrane proteins soluble, after they have been solubilized, under milder conditions. A short overview is presented of the structure, properties, and uses of two families of such surfactants: amphiphilic polymers ("amphipols") and fluorinated surfactants.

Practical considerations of membrane protein instability during purification and crystallisation

Crystallisation of integral membranes requires milligrams of purified protein in a homogeneous, monodisperse state, and crucially, the membrane protein must also be fully functional and stable. The stability of membrane proteins in solution is dependent on the type of detergents used, but unfortunately the use of the most stabilising detergent can often decrease the probability of obtaining crystals that diffract to high resolution, especially of small membrane proteins. A number of strategies have been developed to facilitate the purification of membrane proteins in a functional form, which have led to new possibilities for structure determination.

Mammalian membrane receptors expression as inclusion bodies in Escherichia coli

Integral membrane proteins, in particular receptors, regulate numerous physiological functions. The primary difficulty presented by their study in vitro is to obtain them in sufficient amounts in a functional state. Escherichia coli is a host of choice for producing recombinant proteins for structural studies. However, insertion of G-protein coupled receptors into its plasma membrane usually results in bacterial death. An alternative approach consists of targeting recombinant receptors to inclusion bodies, where they accumulate without affecting bacterial growth, and then fold them in vitro . We describe here a general approach that consists of accumulating the receptor in bacterial inclusion bodies, then purifying it under denaturing conditions. A simple assay is then described to screen for refolding conditions of the protein.

Tuning microbial hosts for membrane protein production

The last four years have brought exciting progress in membrane protein research. Finally those many efforts that have been put into expression of eukaryotic membrane proteins are coming to fruition and enable to solve an ever-growing number of high resolution structures. In the past, many skilful optimization steps were required to achieve sufficient expression of functional membrane proteins. Optimization was performed individually for every membrane protein, but provided insight about commonly encountered bottlenecks and, more importantly, general guidelines how to alleviate cellular limitations during microbial membrane protein expression. Lately, system-wide analyses are emerging as powerful means to decipher cellular bottlenecks during heterologous protein production and their use in microbial membrane protein expression has grown in popularity during the past months.

This review covers the most prominent solutions and pitfalls in expression of eukaryotic membrane proteins using microbial hosts (prokaryotes, yeasts), highlights skilful applications of our basic understanding to improve membrane protein production. Omics technologies provide new concepts to engineer microbial hosts for membrane protein production.

Strategies for the cloning and expression of membrane proteins

Despite the determination of thousands of high-resolution structures of soluble proteins, many features of integral membrane proteins render them difficult targets for the structural biologist. Among these, the most important challenge is in expressing sufficient quantities of active protein to support downstream purification and structure determination efforts. Over 190 unique membrane protein structures have now been solved, and noticeable trends in successful expression strategies are beginning to emerge. A number of groups have also explored high-throughput (HTP) methods for membrane protein expression, with varying degrees of success. Here we review the current state of expressing membrane proteins for functional and structural studies. We first survey successful methods that have already yielded levels of membrane protein expression sufficient for structure determination. HTP methods are also examined since these aim to explore large numbers of targets and can predict reasonable starting points for many membrane proteins. Since HTP techniques may fail, particularly for certain classes of eukaryotic targets, detailed strategies for the expression of two prominent classes of eukaryotic protein families, G-protein-coupled receptors and ion channels, are also summarized.

The impact of GPCR structures on pharmacology and structure-based drug design

After many years of effort, recent technical breakthroughs have enabled the X-ray crystal structures of three G-protein-coupled receptors (GPCRs) (beta1 and beta2 adrenergic and adenosine A(2a)) to be solved in addition to rhodopsin. GPCRs, like other membrane proteins, have lagged behind soluble drug targets such as kinases and proteases in the number of structures available and the level of understanding of these targets and their interaction with drugs. The availability of increasing numbers of structures of GPCRs is set to greatly increase our understanding of some of the key issues in GPCR biology. In particular, what constitutes the different receptor conformations that are involved in signalling and the molecular changes which occur upon receptor activation. How future GPCR structures might alter our views on areas such as agonist-directed signalling and allosteric regulation as well as dimerization is discussed. Knowledge of crystal structures in complex with small molecules will enable techniques in drug discovery and design, which have previously only been applied to soluble targets, to now be used for GPCR targets. These methods include structure-based drug design, virtual screening and fragment screening. This review considers how these methods have been used to address problems in drug discovery for kinase and protease targets and therefore how such methods are likely to impact GPCR drug discovery in the future.

G-protein-coupled receptor structures were not built in a day

Among the most exciting recent developments in structural biology is the structure determination of G-protein-coupled receptors (GPCRs), which comprise the largest class of membrane proteins in mammalian cells and have enormous importance for disease and drug development. The GPCR structures are perhaps the most visible examples of a nascent revolution in membrane protein structure determination. Like other major milestones in science, however, such as the sequencing of the human genome, these achievements were built on a hidden foundation of technological developments. Here, we describe some of the methods that are fueling the membrane protein structure revolution and have enabled the determination of the current GPCR structures, along with new techniques that may lead to future structures.

Revolutionizing membrane protein overexpression in bacteria

The bacterium Escherichia coli is the most widely used expression host for overexpression trials of membrane proteins. Usually, different strains, culture conditions and expression regimes are screened for to identify the optimal overexpression strategy. However, yields are often not satisfactory, especially for eukaryotic membrane proteins. This has initiated a revolution of membrane protein overexpression in bacteria. Recent studies have shown that it is feasible to (i) engineer or select for E. coli strains with strongly improved membrane protein overexpression characteristics, (ii) use bacteria other than E. coli for the expression of membrane proteins, (iii) engineer or select for membrane protein variants that retain functionality but express better than the wild‐type protein, and (iv) express membrane proteins using E. coli‐based cell‐free systems.

Dual activities of odorants on olfactory and nuclear hormone receptors

We have screened an odorant compound library and discovered molecules acting as chemical signals that specifically activate both G-protein-coupled olfactory receptors (ORs) on the cell surface of olfactory sensory neurons and the human nuclear estrogen receptor alpha (ER) involved in transcriptional regulation of cellular differentiation and proliferation in a wide variety of tissues. Hence, these apparent dual active odorants induce distinct signal transduction pathways at different subcellular localizations, which affect both neuronal signaling, resulting in odor perception, and the ER-dependent transcriptional control of specific genes. We demonstrate these effects using fluorescence-based in vitro and cellular assays. Among these odorants, we have identified synthetic sandalwood compounds, an important class of molecules used in the fragrance industry. For one estrogenic odorant we have also identified the cognate OR. This prompted us to compare basic molecular recognition principles of odorants on the two structurally and apparent functionally non-related receptors using computational modeling in combination with functional assays. Faced with the increasing evidence that ORs may perform chemosensory functions in a number of tissues outside of the nasal olfactory epithelium, the unraveling of these molecular ligand-receptor interaction principles is of critical importance. In addition the evidence that certain olfactory sensory neurons naturally co-express ORs and ERs may provide a direct functional link between the olfactory and hormonal systems in humans. Our results are therefore useful for defining the structural and functional characteristics of ER-specific odorants and the role of odorant molecules in cellular processes other than olfaction.

Observation of "ionic lock" formation in molecular dynamics simulations of wild-type beta 1 and beta 2 adrenergic receptors

G protein coupled receptors (GPCRs) are a large family of integral membrane proteins involved in signal transduction pathways, making them appealing drug targets for a wide spectrum of diseases. The recently crystallized structures of two engineered adrenergic receptors have opened new avenues for the understanding of the molecular mechanisms of action of GPCRs. Taking the two crystal structures as a starting point, we carried out submicrosecond molecular dynamics simulations of wild-type beta(1) and beta(2) adrenergic receptors in a lipid bilayer under physiological conditions. These simulations give access to structural and dynamic properties of the receptors in pseudo in vivo conditions. For both systems the overall fold properties of the transmembrane region as well as the binding pocket remain close to the crystal structure of the engineered systems, thus suggesting that the ligand binding mode is not affected by the introduced modifications. Both simulations indicate the presence of one or two internal water molecules absent in both crystal structures and essential for the stabilization of the binding pocket at the interface between transmembrane helices III, IV, and V. The different interactions arising from the substitution of Tyr308 in beta(2)AR into Phe325 in beta(1)AR induce different conformations of the homologous Asn(6.55) inside the binding pockets of the two receptors, suggesting a possible origin of receptor specificity in agonist binding. The equilibrated structures of both receptors recover all of the previously suggested features of inactive GPCRs including formation of a salt bridge between the cytoplasmatic moieties of helices III and VI ("ionic lock") that is absent in the crystal structures.

Engineering a G protein-coupled receptor for structural studies: stabilization of the BLT1 receptor ground state

Structural characterization of membrane proteins is hampered by their instability in detergent solutions. We modified here a G protein-coupled receptor, the BLT1 receptor of leukotriene B(4), to stabilize it in vitro. For this, we introduced a metal-binding site connecting the third and sixth transmembrane domains of the receptor. This modification was intended to restrain the activation-associated relative movement of these helices that results in a less stable packing in the isolated receptor. The modified receptor binds its agonist with low-affinity and can no longer trigger G protein activation, indicating that it is stabilized in its ground state conformation. Of importance, the modified BLT1 receptor displays an increased temperature-, detergent-, and time-dependent stability compared with the wild-type receptor. These data indicate that stabilizing the ground state of this GPCR by limiting the activation-associated movements of the transmembrane helices is a way to increase its stability in detergent solutions; this could represent a forward step on the way of its crystallization.

Characterization of a CorA Mg2+ transport channel from Methanococcus jannaschii using a Thermofluor-based stability assay

The Thermofluor assay has been a valuable asset in structural genomics, providing a high-throughput method for assessing the crystallizability of proteins. The technique has been well characterized for soluble proteins but has been less extensively described for membrane proteins. Here we show the successful application of a Thermofluor-based stability assay to an ion channel, CorA from Methanococcus jannaschii. Optimization of the concentration of free detergent within the assay was important, as excessive concentrations mask the fluorescence change associated with thermal unfolding of the protein. CorA was shown to be stabilized by low pH, but relatively insensitive to salt concentration. Divalent metal cations were also capable of stabilizing the protein, in the order Co2+>Ni2+>Mn2+>Mg2+>Ca2+. Finally, removal of the oligohistidine tag was also shown to improve the thermal stability of CorA. Conclusions are drawn from this detailed study about the general applicability of this technique to other membrane proteins.

Development and crystallization of a minimal thermostabilised G protein-coupled receptor

Structure determination of G protein-coupled receptors is still in its infancy and many factors affect whether crystals are obtained and whether the diffraction is of sufficient quality for structure determination. We recently solved the structure of a thermostabilised turkey beta 1-adrenergic receptor by crystallization in the presence of the detergent octylthioglucoside. Three factors were essential for this success. Firstly, truncations were required at the N-terminus to give optimal expression. Secondly, 6 thermostabilising point mutations were incorporated to make the receptor sufficiently stable in short-chain detergents to allow crystallization. Thirdly, truncations at the C-terminus and within cytoplasmic loop 3, in combination with the removal of the palmitoylation site, were required to obtain well-diffracting crystals in octylthioglucoside. Here, we describe the strategy employed and the utility of thermostability assays in assessing how point mutations, truncations, detergents and ligands combine to develop a construct that forms diffraction-grade crystals.

The structure and function of G-protein-coupled receptors

G-protein-coupled receptors (GPCRs) mediate most of our physiological responses to hormones, neurotransmitters and environmental stimulants, and so have great potential as therapeutic targets for a broad spectrum of diseases. They are also fascinating molecules from the perspective of membrane-protein structure and biology. Great progress has been made over the past three decades in understanding diverse GPCRs, from pharmacology to functional characterization in vivo. Recent high-resolution structural studies have provided insights into the molecular mechanisms of GPCR activation and constitutive activity.

Chemokine receptors and other G protein-coupled receptors

PURPOSE OF REVIEW

Class A G protein-coupled receptors (GPCRs), including the chemokine receptors, CCR5 and CXCR4, share a seven transmembrane-spanning alpha-helix architecture that accommodates signal propagation from across biological membranes. CXCR4 and CCR5 are utilized as co-receptors during HIV viral entry and, therefore, crystal structures of GPCRs aid in the understanding of their function in viral entry.

RECENT FINDINGS

Recent progress in structure determination of class A GPCRs, which include vertebrate and invertebrate rhodopsin as well as adrenergic and adenosine receptors, provides molecular templates for how this diverse group of transmembrane receptors functions. Each of these GPCRs differs in how specific ligands bind to the transmembrane core, underscoring that additional structures of GPCRs from other subfamilies are needed to facilitate rational drug design. More recent studies also indicate a need to consider the more complex character of GPCRs, such as their oligomerization and dynamics.

SUMMARY

Recently, the atomic structures of invertebrate rhodopsin, beta1-adrenergic and beta2-adrenergic receptors and the A(2A)-adenosine receptor have been solved via X-ray crystallography. The impact that these structures have on the biochemistry of viral entry and signal transduction is discussed. Because the chemokine receptors have proven refractory to structural studies thus far, further structural study of the chemokine receptors will be essential to understanding ligand binding, activation and function as co-receptors during viral entry.

Thermostabilization of the neurotensin receptor NTS1

Structural studies on G protein-coupled receptors (GPCRs) have been hampered for many years by their instability in detergent solution and by the number of potential conformations that receptors can adopt. Recently, the structures of the β₁ and β₂ adrenergic receptors and the adenosine A_2a receptor were determined with antagonist bound, a receptor conformation that is thought to be more stable than the agonist-bound state. In contrast to these receptors, the neurotensin receptor NTS1 is much less stable in detergent solution. We have therefore used a systematic mutational approach coupled to activity assays to identify receptor mutants suitable for crystallisation, both alone and in complex with the peptide agonist, neurotensin. The best receptor mutant, NTS1-7m, contained 4 point mutations. It showed increased stability compared to the wild type receptor, in the absence of ligand, after solubilisation with a variety of detergents. In addition, NTS1-7m bound to neurotensin was more stable than unliganded NTS1-7m. Of the four thermostabilising mutations, only one residue (A86L) is predicted to be in the lipid environment. In contrast, I260A appears to be buried within the transmembrane helix bundle, F342A may form a distant part of the putative ligand binding site, whereas F358A is likely to be in a region important for receptor activation. NTS1-7m binds neurotensin with a similar affinity to the wild-type receptor. However, agonist dissociation was slower, and NTS1-7m activated G proteins poorly. The affinity of NTS1-7m for the antagonist SR48692 was also lower than that of the wild-type receptor. Thus we have successfully stabilised NTS1 in an agonist-binding conformation that does not efficiently couple to G proteins.

Selection and characterization of DARPins specific for the neurotensin receptor 1

We describe here the selection and characterization of designed ankyrin repeat proteins (DARPins) that bind specifically to the rat neurotensin receptor 1 (NTR1), a G-protein coupled receptor (GPCR). The selection procedure using ribosome display and the initial clone analysis required <10 microg of detergent-solubilized, purified NTR1. Complex formation with solubilized GPCR was demonstrated by ELISA and size-exclusion chromatography; additionally, the GPCR could be detected in native membranes of mammalian cells using fluorescence microscopy. The main binding epitope in the GPCR lies within the 33 amino acids following the seventh transmembrane segment, which comprise the putative helix 8, and additional binding interactions are possibly contributed by the cytoplasmic loop 3, thus constituting a discontinuous epitope. Since the selected binders recognize the GPCR both in detergent-solubilized and in membrane-embedded forms, they will be potentially useful both in co-crystallization trials and for signal transduction experiments.

Discovery of new GPCR biology: one receptor structure at a time

G-protein-coupled receptors (GPCRs) are the largest family of proteins in the human genome. Within the last year, we have witnessed a relative explosion in the amount of structural information available for the GPCR family with two new structures of opsin in the presence and absence of transducin peptide, four new structures of beta-adrenergic receptors, and a recent structure of the human adenosine A2A receptor. The new biological insight being gained, such as the highly divergent extracellular loops and areas of structural convergence within the transmembrane helices, allows us to chart a course for further investigation into this important class of membrane proteins.

Heterologous expression and purification of the serotonin type 4 receptor from transgenic mouse retina

Recent breakthroughs in the solution of X-ray structures for G protein-coupled receptors (GPCRs) with diffusible ligands have employed extensively mutated or recombined receptor fusion proteins heterologously expressed in conventional in vitro cell-based systems. While these advances now show that crystallization of non-rhodopsin members of this superfamily can be accomplished, the use of radically modified proteins may limit the relevance of the derived structures for precision-guided drug design. To better enable the study of native GPCR structures, we report here efforts to engineer an in vivo expression system that harnesses the photoreceptor system of the retina to express heterologous GPCRs with native human sequences in a biochemically homogeneous and pharmacologically functional conformation. As an example, we show that the human 5HT4 receptor, when placed under the influence of the mouse opsin promoter and an opsin rod outer segment (ROS) targeting sequence, localized to ROS of transgenic mouse retina. The resulting receptor protein was uniformly glycosylated and pharmacologically intact as demonstrated by immunoblotting and radioligand binding assays. Upon solubilization, the retinal 5HT4 receptor retained the binding properties of its initial state in retinal membranes. With the engineered T7 monoclonal epitope sequence, the solubilized receptor was easily purified by one-step immunoaffinity chromatography and the purified receptor in detergent solution preserved its ligand binding properties. This expression method may prove generally useful for generating functional, high-quality GPCR protein.

Studies on the stability of the human cone visual pigments

The retina of vertebrates contains two kinds of photoreceptor cells, rods and cones, which contain their specific visual pigments that are responsible for scotopic and photopic vision, respectively. In cone photoreceptor cells, there are three types of color pigments: blue, green and red, each with a distinctive absorption maximum. The goal of this investigation was to identify optimal conditions under which these pigments could be obtained and isolated in a stable form, thereby facilitating structural studies using high-resolution approaches. For this purpose, all three human cone opsins were initially expressed in mammalian cells, reconstituted with 11-cis retinal, detergent solubilized, purified and their stability compared with rod rhodopsin. As all three pigments showed dramatically reduced stability relative to rhodopsin, site-directed mutagenesis was used in an attempt to engineer stability into the green cone pigment. The mutations introduced some structural motifs and sites of posttranslational modification present in rhodopsin, as well as amino acid substitutions that have been found to stabilize the rod opsin apo-protein. We also modified the hydrophobic environment of the green cone pigment by varying the detergent and detergent/lipid composition used during solubilization and purification, and compared them with the retinal reconstituted pigment in membranes. Our results show that these changes do not significantly improve the inherent instability of the human cone pigments, and in some cases, lead to a decrease in stability and protein aggregation. We conclude that further efforts are required to stabilize the human cone pigments in a form suitable for high-resolution structural studies.

Purification of recombinant G-protein-coupled receptors

Structural and functional analysis of most G-protein-coupled receptors (GPCRs) requires their expression and purification in functional form. The produced amount of recombinant membrane-inserted receptors depends on the optimal combination of a particular GPCR and production host; optimization of expression is still a matter of trial-and-error. Prior to purification, receptors must be extracted from the membranes by use of detergent(s). The choice of an appropriate detergent for solubilization and purification is crucial to maintain receptors in their functional state. The initial enrichment can be carried out by affinity chromatography using a general affinity tag (e.g., poly-histidine tag). If the first purification step does not yield pure receptor protein, purification to homogeneity can often be achieved by use of a subsequent receptor-specific ligand column. If suitable immobilized ligands are not available, size exclusion chromatography or other techniques need to be applied. Many GPCRs become unstable upon detergent extraction from lipid membranes, and measures for stabilization are discussed. As an example, the purification of a functional neurotensin receptor to homogeneity in milligram quantities is given below.

Structural insights into G-protein-coupled receptor activation

G-protein-coupled receptors (GPCRs) are the largest family of eukaryotic plasma membrane receptors, and are responsible for the majority of cellular responses to external signals. GPCRs share a common architecture comprising seven transmembrane (TM) helices. Binding of an activating ligand enables the receptor to catalyze the exchange of GTP for GDP in a heterotrimeric G protein. GPCRs are in a conformational equilibrium between inactive and activating states. Crystallographic and spectroscopic studies of the visual pigment rhodopsin and two beta-adrenergic receptors have defined some of the conformational changes associated with activation.

The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist

The adenosine class of heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) mediates the important role of extracellular adenosine in many physiological processes and is antagonized by caffeine. We have determined the crystal structure of the human A2A adenosine receptor, in complex with a high-affinity subtype-selective antagonist, ZM241385, to 2.6 angstrom resolution. Four disulfide bridges in the extracellular domain, combined with a subtle repacking of the transmembrane helices relative to the adrenergic and rhodopsin receptor structures, define a pocket distinct from that of other structurally determined GPCRs. The arrangement allows for the binding of the antagonist in an extended conformation, perpendicular to the membrane plane. The binding site highlights an integral role for the extracellular loops, together with the helical core, in ligand recognition by this class of GPCRs and suggests a role for ZM241385 in restricting the movement of a tryptophan residue important in the activation mechanism of the class A receptors.

Directed evolution of a G protein-coupled receptor for expression, stability, and binding selectivity

We outline a powerful method for the directed evolution of integral membrane proteins in the inner membrane of Escherichia coli. For a mammalian G protein-coupled receptor, we arrived at a sequence with an order-of-magnitude increase in functional expression that still retains the biochemical properties of wild type. This mutant also shows enhanced heterologous expression in eukaryotes (12-fold in Pichia pastoris and 3-fold in HEK293T cells) and greater stability when solubilized and purified, indicating that the biophysical properties of the protein had been under the pressure of selection. These improvements arise from multiple small contributions, which would be difficult to assemble by rational design. In a second screen, we rapidly pinpointed a single amino acid substitution in wild type that abolishes antagonist binding while retaining agonist-binding affinity. These approaches may alleviate existing bottlenecks in structural studies of these targets by providing sufficient quantities of stable variants in defined conformational states.