Quantitative assessment of olfactory receptors activity in immobilized nanosomes: a novel concept for bioelectronic nose

We describe how mammalian olfactory receptors (ORs) could be used as sensing elements of highly specific and sensitive bioelectronic noses. An OR and an appropriate G(alpha) protein were co-expressed in Saccharomyces cerevisiae cells from which membrane nanosomes were prepared, and immobilized on a sensor chip. By Surface Plasmon Resonance, we were able to quantitatively evaluate OR stimulation by an odorant, and G protein activation. We demonstrate that ORs in nanosomes discriminate between odorant ligands and unrelated odorants, as in whole cells. This assay also provides the possibility for quantitative assessment of the coupling efficiency of the OR with different G(alpha) subunits, without the interference of the cellular transduction pathway. Our findings will be useful to develop a new generation of electronic noses for detection and discrimination of volatile compounds, particularly amenable to micro- and nano-sensor formats.     

Study of Langmuir and Langmuir-Blodgett films of odorant-binding protein/amphiphile for odorant biosensors

To make ultrathin films for the fabrication of artificial olfactory systems, odorant biosensors, we have investigated mixed Langmuir and Langmuir-Blodgett films of odorant-binding protein/amphiphile. Under optimized experimental conditions (phosphate buffer solution, pH 7.5, OBP-1F concentration of 4 mg L(-1), target pressure 35 mN m(-1)), the mixed monolayer at the air/water interface is very stable and has been efficiently transferred onto gold supports, which were previously functionalized by self-assembled monolayers (SAMs) with 1-octadecanethiol (ODT). Atomic force microscopy and electrochemical impedance spectroscopy were used to characterize mixed Langmuir-Blodgett (LB) films before and after contact with a specific odorant molecule, isoamyl acetate. AFM phase images show a higher contrast after contact with the odorant molecule due to the new structure of the OBP-1F/ODA LB film. Non-Faradaic electrochemical spectroscopy (EIS) is used to quantify the effect of the odorant based on the electrical properties of the OBP-1F/ODA LB film, as its resistance strongly decreases from 1.18 MOmega (before contact) to 25 kOmega (after contact).     

Conformational Sensing by a Mammalian Olfactory Receptor

To identify odors, the mammalian nose deploys hundreds of olfactory receptors (ORs) from the rhodopsin-like class of the G protein-coupled receptor superfamily. Odorants having multiple rotatable bonds present a problem for the stereochemical shape-based matching process assumed to govern the sense of smell through OR–odorant recognition. We conformationally restricted the carbon chain of the odorant octanal to ask whether an OR can respond differently to different odorant conformations. By using calcium imaging to monitor signal transduction in sensory neurons expressing the mouse aldehyde OR, Olfr2, we found that the spatial position of the C7 and C8 carbon atoms of octanal, in relation to its −CHO group, determines whether an aliphatic aldehyde functions as an agonist, partial agonist or antagonist. Our experiments provide evidence that an odorant can manipulate an OR through its intrinsic conformational repertoire, in unexpected analogy to the photon-controlled aldehyde manipulation observed in rhodopsin.     

Odorant Receptor 7D4 Activation Dynamics

Deciphering how an odorant activates an odorant receptor (OR) and how changes in specific OR residues affect its responsiveness are central to understanding our sense of smell. A joint approach combining site‐directed mutagenesis and functional assays with computational modeling has been used to explore the signaling mechanics of OR7D4. In this OR, a genetic polymorphism affects our perception of androstenone. Molecular simulations totaling 0.12 ms predicted that, similarly to observations for other G‐protein‐coupled receptors with known experimental structures, an activation pathway connects the ligand and the G‐protein binding site. The 3D model activation mechanism correlates with in vitro data and notably predicts that the OR7D4 WM variant is not activated. Upon activation, an OR‐specific sequence motif is the convergence point of the mechanism. Our study suggests that robust homology modeling can serve as a powerful tool to capture OR dynamics related to smell perception.     

Identification of a Conformational Equilibrium That Determines the Efficacy and Functional Selectivity of the μ‐Opioid Receptor

G‐protein‐coupled receptor (GPCR) ligands impart differing degrees of signaling in the G‐protein and arrestin pathways, in phenomena called “biased signaling”. However, the mechanism underlying the biased signaling of GPCRs is still unclear, although crystal structures of GPCRs bound to the G protein or arrestin are available. In this study, we observed the NMR signals from methionine residues of the μ‐opioid receptor (μOR) in the balanced‐ and biased‐ligand‐bound states. We found that the intracellular cavity of μOR exists in an equilibrium between closed and multiple open conformations with coupled conformational changes on the transmembrane helices 3, 5, 6, and 7, and that the population of each open conformation determines the G‐protein‐ and arrestin‐mediated signaling levels in each ligand‐bound state. These findings provide insight into the biased signaling of GPCRs and will be helpful for development of analgesics that stimulate μOR with reduced tolerance and dependence.     

Chemical Vapor Detection Using a Reconstituted Insect Olfactory Receptor Complex

The sensing of vapor odorants is highly demanded in the field of life and medical sciences. Although olfactory receptors (ORs) have potentials to recognize volatile organic compounds, the interaction of ORs, chemical vapors, and peptide components in olfactory mucus has yet to be analyzed to develop OR‐based sensors. A bioinspired electrophysiology technique is shown to record the response of reconstituted insect ORs to chemical vapors. To mimic the interface between ORs and olfactory mucus, OR expressing spheroids were loaded into a hydrogel microchamber array. A negative extracellular field potential shift of spheroids was successfully observed by the stimulation of their vapor cognate ligand. Importantly, the ligand repertoire of the OR of malaria vector mosquito examined by this method differed from that of in vivo studies. Our method is useful to develop protein‐based gas sensing techniques and to examine the binding of ORs and chemical vapors.     

The Mechanism of Ligand‐Induced Activation or Inhibition of μ‐ and κ‐Opioid Receptors

G‐protein‐coupled receptors (GPCRs) are important targets for treating severe diseases. However why certain molecules act as activators whereas others, with similar structures, block GPCR activation, is poorly understood since the same molecule can activate one receptor subtype while blocking another closely related receptor. To shed light on these central questions, we used all‐atom, long‐time‐scale molecular dynamics simulations on the κ‐opioid and μ‐opioid receptors (κOR and μOR). We found that water molecules penetrating into the receptor interior mediate the activating versus blocking effects of a particular ligand–receptor interaction. Both the size and the flexibility of the bound ligand regulated water influx into the receptor. The solvent‐accessible inner surface area was found to be a parameter that can help predict the function of the bound ligand.     

Genomics of selected human odorant receptors

Single nucleotide polymorphisms (SNPs) in odorant receptor genes may influence the protein sequence and consequently also the function of the receptors. An analysis of the HapMap data for human OR3A1 was performed and provided evidence that genetic differences subject to ancestry and gender can be recognized. A genomic comparison of individuals shows the diversity of odorant receptor genes and therefore potentially the variety of the sense of smell. At this time, two complete human genomes are available in public domain, which we used for this purpose.     

Genomics of selected human odorant receptors

Single nucleotide polymorphisms (SNPs) in odorant receptor genes may influence the protein sequence and consequently also the function of the receptors. An analysis of the HapMap data for human OR3A1 was performed and provided evidence that genetic differences subject to ancestry and gender can be recognized. A genomic comparison of individuals shows the diversity of odorant receptor genes and therefore potentially the variety of the sense of smell. At this time, two complete human genomes are available in public domain, which we used for this purpose. Correspondence: Anton Beyer, Institute of Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria.     

Olfactory receptors: molecular basis for recognition and discrimination of odors

The daunting task of our nose to detect and discriminate among thousands of low-molecular-weight organic compounds with diverse chemical structures and properties requires an enormous molecular recognition capacity. This is based on distinct proteins, capable of recognizing and binding odorous compounds, including odorant-binding proteins, which are supposed to shuttle odorous compounds through the nasal mucus, and most notably the odorant receptors, which are heptahelical membrane proteins coupling via G-proteins onto intracellular transduction cascades. From more than a thousand genes each olfactory neuron is supposed to express only one receptor subtype. Receptors appear to be selective but rather non-specific—i.e. a distinct odorant activates multiple receptors and individual receptors respond to multiple odorants. It is the molecular receptive range of its receptor type which determines the reaction spectrum of a sensory neuron. Populations of cells equipped with the same receptor type project their axons to common glomeruli, thereby transmitting the molecular receptive range of a receptor type into the receptive field of glomerulus. Recent insight into the molecular basis of odor recognition and the combinatorial coding principles of the olfactory system may provide some clues for the design and development of technical sensors, electronic noses. In this review more emphasis has been placed on physiological rather than analytical aspects.     

Investigation of an Olfactoryly Active Ring-Like Conformer of a Chain-Type Odorant, (3S)-3,7-dimethyloctanal,by computer calculation and graphics

The odor of (3S)-3,7-dimethyloctanal, a chain-type odorant, has some resemblance to that of ethyl (1 R, 6S)-2,2,6-trimethylcyclohexane-1-carboxylate, a ring-type odorant. We investigated the ring-like conformers of (3S)-3,7-dimethyloctanal. Two approaches, (i) systematic conformational analysis and (ii) construction of the initial structure by referring to the structure of the ring-type odorant, were considered in the search for ring-like conformers of the chain-type odorant. As a result, it was found that two stable ring-like conformers of (3S)-3,7-dimethyloctanal, obtained from the two approaches, resembled conformers of ethyl (1R, 6S)-2,2,6-trimethylcyclohexane-1-carboxylate in their three-dimensional structural features. The shapes of the two ring-like ones were not exactly the same but were quite similar. Therefore, the two ring-like conformers were considered to approximate the olfactoryly active conformer that binds and stimulates the same odor receptor as that for ethyl (1R,6S)-2,2,6-trimethylcyclohexane-1-carboxylate. In addition, ring-like conformers of another chain-type odorant, 2-methylpent-2-enal, were investigated to check the validity of the calculation method used.     

Controlled synthesis of a structurally characterized family of sterically constrained heterocyclic alkoxy-modified titanium alkoxides

The reaction of [Ti(mu-ONep)(ONep)3]2 (ONep = OCH2C(CH3)3) with a series of heterocyclic methanol derivatives [tetrahydrofurfuryl alcohol (H-OTHF), thiophene methanol (H-OTPM), or 2-pyridylcarbinol (H-OPy)-collectively termed H-OR*], led to the isolation of a novel family of OR*-substituted titanium alkoxide precursors. Independent of the initial stoichiometry for the H-OTHF reaction, a monosubstituted, dinuclear species was isolated as [(ONep)3Ti(muc-OTHF)]2 (1). For 1, each Ti was octahedrally (Oh) bound by three terminal ONep ligands, one bidentate bridging OTHF ligand (muc-OTHF), and an oxygen from the other muc-OTHF ligand. For the OTPM derivatives, the product was identified as [(ONep)3Ti(mu-OTPM)]2 (2). For this ligand, the soft S atom does not bind to the Ti but the O atom does act as a bridge between the two trigonal bipyramidal bound Ti metal centers. The OPy system yielded (OPy)2Ti(OR)2 independent of the OR and the stoichiometry used [OR = ONep (3), OCHMe2 (4), OCMe3 (5)]. For 3-5, the two OPy ligands chelate to the Oh-bound Ti metal center with two terminal OR ligands. Compounds 1-5 were fully characterized using a variety of analytical techniques. An initial investigation of the proposed chemical stability of the '(OPy)2Ti' moiety of 3-5 to alcoholysis exchange pathways involving (i) alkyl alcohols, (ii) aryl alcohols, (iii) substituted phenols, (iv) H-OR* derivatives, and (v) silanols proved successful through the isolation of a novel family of structurally characterized (OPy)2Ti(OR')2 (7-24) compounds.     

Synthesis, coordination to Au(I) and photophysical properties of a novel polyfluorinated benzothiazolephosphine ligand

The reaction between Ph2PH and C6F5CNS leads to the formation of the polyfluorinated benzothiazolephosphine ligand Ph2P(CNS)(C6F4) 1. The mechanism of the reaction involves the addition of the phosphine to the isothiocyanate and subsequent intramolecular nucleophilic aromatic substitution. This new ligand reacts with gold(I) substrates producing complexes [AuCl{Ph2P(CNS)(C6F4)}] 2 and [Au(C6F5){Ph2P(CNS)(C6F4)}] 3. Both the ligand 1 and complexes 2 and 3 display phosphorescence with emissions arising from n(P) -->pi*(heterocyclic ring) excited state for 1 and pi-->pi*(heterocyclic ring) excited state for 2 and 3. DFT and TD-DFT calculations agree with these results.     

Allosteric tuning of the intra-cavity binding properties of a calix[6]arene through external binding to a ZnII center coordinated to amino side chains

Molecular recognition by calix[6]arene-based receptors bearing three primary alkylamino side chain arms (1) is described. Complexation of Zn(II) ion provides the dinuclear mu-hydroxo complex 2G(OH), XRD characterization of which, together with solution studies, provided evidence of its hosting of neutral polar organic guests G. Treatment of this complex with a carboxylic acid or a sulfonamide (XH) results in the formation of mononuclear species 3G(X), one of which (X = Cl) has been characterized by XRD. A dicationic complex 3G(RNH2) is obtained upon treatment of 2G(OH) with a mixture of an alkylamine and a strong acid. Each of these Zn(II) complexes features a tetrahedral metal ion bound to the three amino arms of ligand 1 and to an exogenous ligand (either HO-, X-, or RNH2) sitting outside of the cavity. As a result, the metal ion structures the calixarene core, constraining it in a cone conformation suitable for guest hosting. The receptor properties of these compounds have been explored in detail and are compared with those of the trisammonium receptor 1G(3H+), based on the same calixarene core, as well as those of the trisimidazole-based dicationic Zn funnel complexes. This study reveals very different host properties, in spite of the common hydrophobic, pi-basic, and hydrogen-bonding acceptor properties of the calixarene cores. A harder external ligand produces a less polarized receptor that is consequently particularly sensitive to the hydrogen-bonding ability of its guest. The less electron-rich the apical ligand, and a fortiori the trisammonium host, the more sensitive the receptor to the dipole moment of the guest. All this stands in contrast with the funnel Zn complexes, in which the coordination link plays a dominant role. It is also shown that the asymmetry of an exo-coordinated enantiopure amino ligand is sensed by the guest. This supramolecular system nicely illustrates how the receptor properties of a hydrophobic cavity can be allosterically tuned by the environment.     

Receptor‐Bound Conformation of Cilengitide Better Represented by Its Solution‐State Structure than the Solid‐State Structure

The X‐ray crystal and NMR spectroscopic structures of the peptide drug candidate Cilengitide (cyclo(RGDf(NMe)Val)) in various solvents are obtained and compared in addition to the integrin receptor bound conformation. The NMR‐based solution structures exhibit conformations closely resembling the X‐ray structure of Cilengitide bound to the head group of integrin αvβ3. In contrast, the structure of pure Cilengitide recrystallized from methanol reveals a different conformation controlled by the lattice forces of the crystal packing. Molecular modeling studies of the various ligand structures docked to the αvβ3 integrin revealed that utilization of the solid‐state conformation of Cilengitide leads—unlike the solution‐based structures—to a mismatch of the ligand–receptor interactions compared with the experimentally determined structure of the protein–ligand complex. Such discrepancies between solution and crystal conformations of ligands can be misleading during the structure‐based lead optimization process and should thus be taken carefully into account in ligand orientated drug design.     

Group 4 complexes of a new [OSSO]-type dianionic ligand. Coordination chemistry and preliminary polymerization catalysis studies

A straightforward synthesis of a new type of tetradentate dianionic [OSSO]-type ligand is described. This ligand features an ethylenedithiol core bridged via methylene groups to substituted phenols, thus representing an S analogue of the [ONNO]-type Salan ligands. The [OSSO]H2 ligand precursor reacted with titanium(IV) isopropoxide and with zirconium(IV) tert-butoxide to give the corresponding [OSSO]-M(OR)2 complexes, which formed as single C2-symmetric isomers but were fluxional according to variable-temperature NMR. An X-ray structure of [OSSO]-Zr(O-t-Bu)2 supported the fac-fac wrapping mode of the ligand. The dibenzyl complex [OSSO]-Zr(bn)2 that was obtained by a reaction between the ligand precursor and tetrabenzylzirconium was found to be an active 1-hexene polymerization catalyst upon activation with B(C6F5)3, leading to a stereoirregular polymer despite its C2 symmetry.     

Investigation of the binding of a carbohydrate-mimetic peptide to its complementary anticarbohydrate antibody by STD-NMR spectroscopy and molecular-dynamics simulations

Saturation transfer difference (STD)‐NMR spectroscopy was used to probe experimentally the bioactive solution conformation of the carbohydrate mimic MDWNMHAA 1 of the O‐polysaccharide of Shigella flexneri Y when bound to its complementary antibody, mAb SYA/J6. Molecular dynamics simulations using the ZymeCAD? Molecular Dynamics platform were also undertaken to give a more accurate picture of the conformational flexibility and the possibilities for bound ligand conformations. The ligand topology, or the dynamic epitope, was mapped with the CORCEMA‐ST (COmplete Relaxation and Conformational Exchange Matrix Analysis of Saturation Transfer) program that calculates a total matrix analysis of relaxation and exchange effects to generate predicted STD‐NMR intensities from simulation. The comparison of these predicted STD enhancements with experimental data was used to select a representative binding mode. A protocol that employed theoretical STD effects calculated at snapshots during the entire course of a molecular dynamics (MD) trajectory of the peptide bound to the Fv portion of the antibody, and not the averaged atomic positions of receptor–ligand complexes, was also examined. In addition, the R factor was calculated on the basis of STD (fit) to avoid T1 bias, and an effective R factor, R_eff, was defined such that if the calculated STD (fit) for proton k was within error of the experimental STD (fit) for proton k, then that calculated STD (fit) for proton k was not included in the calculation of the R factor. This protocol was effective in deriving the antibody‐bound solution conformation of the peptide which also differed from the bound conformation determined by X‐ray crystallography; however, several discrepancies between experimental and calculated STD (fit) values were observed. The bound conformation was therefore further refined with a simulated annealing refinement protocol known as STD‐NMR intensity‐restrained CORCEMA optimization (SICO) to give a more accurate representation of the bound peptide epitope. Further optimization was required in this case, but a satisfactory correlation between experimental and calculated STD values was obtained. Attempts were also made to obtain STD enhancements with a synthetic pentasaccharide hapten, corresponding to the O‐polysaccharide, while bound to the antibody. However, unfavorable kinetics of binding in this system prevented sufficient STD build‐up, which, in turn, hindered a rigorous analysis via full STD build‐up curves.     

Synthesis of a new conformation-constrained L-tyrosine analogue as a potential scaffold for SH2 domain ligands

The enantioselective synthesis of a new tricyclic tyrosine analogue is reported. This conformation-constrained SH2 domain ligand scaffold 2 was designed on the basis of the natural ligand, whose structure contains the elements of a tyrosine moiety having chi(1) and chi(2) angles constrained to values observed for a phosphotyrosyl (pTyr) residue bound to the p56(lck) SH2 domain. It represents a unique, highly constrained amino acid, which may be of value in signal transduction studies. Three key steps, an asymmetric tandem Michael addition, an intramolecular Friedel-Crafts reaction, and an intramolecular Mannich reaction, were successfully applied in the presented synthetic route.     

Improvement of Ligand Affinity and Thermodynamic Properties by NMR‐Based Evaluation of Local Dynamics and Surface Complementarity in the Receptor‐Bound State

The thermodynamic properties of a ligand in the bound state affect its binding specificity. Strict binding specificity can be achieved by introducing multiple spatially defined interactions, such as hydrogen bonds and van der Waals interactions, into the ligand–receptor interface. These introduced interactions are characterized by restricted local dynamics and improved surface complementarity in the bound state. In this study, we experimentally evaluated the local dynamics and the surface complementarity of weak‐affinity ligands in the receptor‐bound state by forbidden coherence transfer analysis in free‐bound exchange systems (Ex‐FCT), using the interaction between a ligand, a myocyte‐enhancer factor 2A (MEF2A) docking peptide, and a receptor, p38α, as a model system. The Ex‐FCT analyses successfully provided information for the rational design of a ligand with higher affinity and preferable thermodynamic properties for p38α.     

Accurate theoretical prediction of vibrational frequencies in an inhomogeneous dynamic environment: a case study of a glutamate molecule in water solution and in a protein-bound form

We propose a hierarchical approach to model vibrational frequencies of a ligand in a strongly fluctuating inhomogeneous environment such as a liquid solution or when bound to a macromolecule, e.g., a protein. Vibrational frequencies typically measured experimentally are ensemble averaged quantities which result (in part) from the influence of the strongly fluctuating solvent. Solvent fluctuations can be sampled effectively by a classical molecular simulation, which in our model serves as the first, low level of the hierarchy. At the second high level of the hierarchy a small subset of system coordinates is used to construct a patch of the potential surface (ab initio) relevant to the vibration in question. This subset of coordinates is under the influence of an instantaneous external force exerted by the environment. The force is calculated at the lower level of the hierarchy. The proposed methodology is applied to model vibrational frequencies of a glutamate in water and when bound to the Glutamate receptor protein and its mutant. Our results are in close agreement with the experimental values and frequency shifts measured by the Jayaraman group by the Fourier transform infrared spectroscopy [Q. Cheng et al., Biochem. 41, 1602 (2002)]. Our methodology proved useful in successfully reproducing vibrational frequencies of a ligand in such a soft, flexible, and strongly inhomogeneous protein as the Glutamate receptor.