Molecular vibration-sensing component in human olfaction

XGBoost odor prediction model: finding the structure-odor relationship of odorant molecules using the extreme gradient boosting algorithm

Determining the structure-odor relationship has always been a very challenging task. The main challenge in investigating the correlation between the molecular structure and its associated odor is the ambiguous and obscure nature of verbally defined odor descriptors, particularly when the odorant molecules are from different sources. With the recent developments in machine learning (ML) technology, ML and data analytic techniques are significantly being used for quantitative structure-activity relationship (QSAR) in the chemistry domain toward knowledge discovery where the traditional Edisonian methods have not been useful. The smell perception of odorant molecules is one of the aforementioned tasks, as olfaction is one of the least understood senses as compared to other senses. In this study, the XGBoost odor prediction model was generated to classify smells of odorant molecules from their SMILES strings. We first collected the dataset of 1278 odorant molecules with seven basic odor descriptors, and then 1875 physicochemical properties of odorant molecules were calculated. To obtain relevant physicochemical features, a feature reduction algorithm called PCA was also employed. The ML model developed in this study was able to predict all seven basic smells with high precision (>99%) and high sensitivity (>99%) when tested on an independent test dataset. The results of the proposed study were also compared with three recently conducted studies. The results indicate that the XGBoost-PCA model performed better than the other models for predicting common odor descriptors. The methodology and ML model developed in this study may be helpful in understanding the structure-odor relationship.Communicated by Ramaswamy H. Sarma.

Anisotropic coupling of individual vibrational modes to a Cu(110) substrate

We present a study on the excitation of individual vibrational modes with ballistic charge carriers propagating along the Cu(110) surface. By means of the molecular nanoprobe technique, where the reversible switching of a molecule-in this case tautomerization of porphycene-is utilized to detect excitation events, we reveal anisotropic coupling of two distinct vibrational modes to the substrate. The N-H bending mode, excited below |E| ≈ 376 meV, exhibits maxima perpendicular to the rows of the Cu(110) substrate and minima along the rows. In contrast, the N-H stretching mode, excited above |E| ≈ 376 meV, displays maxima along the rows and is constant otherwise. This inversion of the anisotropy reflects the orthogonality between the N-H bending and stretching mode. Additionally, we observe an energy-dependent asymmetry in the propagation direction of charge carriers injected into the Cu(110) surface state. Hereby, the anisotropic band structure results in a correlation between the group velocity and the tunneling probability into electronic states of the substrate.

A novel synthesis method of cyclopentadecanone and cyclopentadecanolide from vegetable oil

Malania oleifera Chum is a unique renewable plant resource in China, its fruit oil has a high content of 15-tetracosenic acid, and it is a good raw material for the synthesis of cyclopentadecanone and cyclopentadecanolide. A Novel synthesis method of cyclopentadecanone and cyclopentadecanolide from vegetable oil was designed, and the synthesis yields of c cyclopentadecanone and cyclopentadecanolide were 38.5% and 63.0%, respectively. The effect of different ester groups on cyclization of α,ω-difatty acid alkyl ester in cyclopentadecanone synthesis, and effect of catalysts on cyclization ofω-hydroxycarboxylic acid triglyceride in cyclopentadecanolide synthesis were investigated. The designed synthesis strategy has the characteristics of less synthesis steps and high utilization efficiency of 15-tetracosenic acid, which has simple and economic.

Effects of musk volatile compounds on attenuated nerve injury and improving post-cerebral ischemic exercise functions

BACKGROUND

Reperfusion Injury Acute ischemic stroke is increasing in people recently and Musk, as a commonly used Traditional Chinese Medicine (TCM), has been suggested as a potential agent against acute ischemic stroke, but the efficacies and underlying mechanisms of it remain unknown.

OBJECTIVE

This study was aimed to tested the hypotheses that volatile compounds of musk could attenuate nerve injury and identify the bioactive compounds and potential mechanisms of Musk.

METHOD

Transient middle cerebral artery occlusion (MCAO) model in vivo in Sprague-Dawley rats (SD rats) was used to test this hypothesis. Collecting ingredients of Musk and their related targets were discerned from the Gas chromatography-olfactory mass spectrometry (GC-O-MS) experiment. Then the potential mechanisms and targets of the compounds were searched by network pharmacology techniques. Finally, the pathway was verified by Western Bolt (WB).

RESULTS

First, Musk treatment significantly up-regulated the relative levels of AKT1, PI3KA, and VEGFA in the hippocampus, and improved the sport functions in the post-MCAO ischemic rats in vivo. Next, twenty potential flavor active compounds were recognized by GC-O-MS. A total of 89 key targets including HIF-1, PIK3CA, TNF signaling pathway, and VEGF were identified. AKT1, HIF1A, PIK3CA, and VEGFA were viewed as the most important genes, which were validated by molecular docking simulation.

CONCLUSION

The Volatile compounds of musk can attenuate nerve injury and improving post-cerebral ischemic exercise functions by HIF1A pathways, and the combined data provide novel insight for Musk volatile compounds developed as new drug for improving reperfusion injury in acute ischemic stroke.

Sweet taste of heavy water

Hydrogen to deuterium isotopic substitution has only a minor effect on physical and chemical properties of water and, as such, is not supposed to influence its neutral taste. Here we conclusively demonstrate that humans are, nevertheless, able to distinguish D₂O from H₂O by taste. Indeed, highly purified heavy water has a distinctly sweeter taste than same-purity normal water and can add to perceived sweetness of sweeteners. In contrast, mice do not prefer D₂O over H₂O, indicating that they are not likely to perceive heavy water as sweet. HEK 293T cells transfected with the TAS1R2/TAS1R3 heterodimer and chimeric G-proteins are activated by D₂O but not by H₂O. Lactisole, which is a known sweetness inhibitor acting via the TAS1R3 monomer of the TAS1R2/TAS1R3, suppresses the sweetness of D₂O in human sensory tests, as well as the calcium release elicited by D₂O in sweet taste receptor-expressing cells. The present multifaceted experimental study, complemented by homology modelling and molecular dynamics simulations, resolves a long-standing controversy about the taste of heavy water, shows that its sweet taste is mediated by the human TAS1R2/TAS1R3 taste receptor, and opens way to future studies of the detailed mechanism of action.

Ben Abu, Mason and colleagues use molecular dynamics, cell-based experiments, mouse models, and human subjects to determine that, unlike ordinary water, heavy water tastes sweet to humans, but not mice. Mechanistically, this effect is mediated by the human TAS1R/TAS1R3 sweet taste receptor.

Sweet taste of heavy water

Hydrogen to deuterium isotopic substitution has only a minor effect on physical and chemical properties of water and, as such, is not supposed to influence its neutral taste. Here we conclusively demonstrate that humans are, nevertheless, able to distinguish D₂O from H₂O by taste. Indeed, highly purified heavy water has a distinctly sweeter taste than same-purity normal water and can add to perceived sweetness of sweeteners. In contrast, mice do not prefer D₂O over H₂O, indicating that they are not likely to perceive heavy water as sweet. HEK 293T cells transfected with the TAS1R2/TAS1R3 heterodimer and chimeric G-proteins are activated by D₂O but not by H₂O. Lactisole, which is a known sweetness inhibitor acting via the TAS1R3 monomer of the TAS1R2/TAS1R3, suppresses the sweetness of D₂O in human sensory tests, as well as the calcium release elicited by D₂O in sweet taste receptor-expressing cells. The present multifaceted experimental study, complemented by homology modelling and molecular dynamics simulations, resolves a long-standing controversy about the taste of heavy water, shows that its sweet taste is mediated by the human TAS1R2/TAS1R3 taste receptor, and opens way to future studies of the detailed mechanism of action.

Sensory Perception of Non-Deuterated and Deuterated Organic Compounds

The chemical background of olfactory perception has been subject of intensive research, but no available model can fully explain the sense of smell. There are also inconsistent results on the role of the isotopology of molecules. In experiments with human subjects it was found that the isotope effect is weak with acetone and D6 -acetone. In contrast, clear differences were observed in the perception of octanoic acid and D15 -octanoic acid. Furthermore, a trained sniffer dog was initially able to distinguish between these isotopologues of octanoic acid. In chromatographic measurements, the respective deuterated molecule showed weaker interaction with a non-polar liquid phase. Quantum chemical calculations give evidence that deuterated octanoic acid binds more strongly to a model receptor than non-deuterated. In contrast, the binding of the non-deuterated molecule is stronger with acetone. The isotope effect is calculated in the framework of statistical mechanics. It results from a complicated interplay between various thermostatistical contributions to the non-covalent free binding energies and it turns out to be very molecule-specific. The vibrational terms including non-classical zero-point energies play about the same role as rotational/translational contributions and are larger than bond length effects for the differential isotope perception of odor for which general rules cannot be derived.

Odors: from chemical structures to gaseous plumes

We are immersed within an odorous sea of chemical currents that we parse into individual odors with complex structures. Odors have been posited as determined by the structural relation between the molecules that compose the chemical compounds and their interactions with the receptor site. But, naturally occurring smells are parsed from gaseous odor plumes. To give a comprehensive account of the nature of odors the chemosciences must account for these large distributed entities as well. We offer a focused review of what is known about the perception of odor plumes for olfactory navigation and tracking, which we then connect to what is known about the role odorants play as properties of the plume in determining odor identity with respect to odor quality. We end by motivating our central claim that more research needs to be conducted on the role that odorants play within the odor plume in determining odor identity.

Exploring the mechanism of olfactory recognition in the initial stage by modeling the emission spectrum of electron transfer

Olfactory sense remains elusive regarding the primary reception mechanism. Some studies suggest that olfaction is a spectral sense, the olfactory event is triggered by electron transfer (ET) across the odorants at the active sites of odorant receptors (ORs). Herein we present a Donor-Bridge-Acceptor model, proposing that the ET process can be viewed as an electron hopping from the donor molecule to the odorant molecule (Bridge), then hopping off to the acceptor molecule, making the electronic state of the odorant molecule change along with vibrations (vibronic transition). The odorant specific parameter, Huang–Rhys factor can be derived from ab initio calculations, which make the simulation of ET spectra achievable. In this study, we revealed that the emission spectra (after Gaussian convolution) can be acted as odor characteristic spectra. Using the emission spectrum of ET, we were able to reasonably interpret the similar bitter-almond odors among hydrogen cyanide, benzaldehyde and nitrobenzene. In terms of isotope effects, we succeeded in explaining why subjects can easily distinguish cyclopentadecanone from its fully deuterated analogue cyclopentadecanone-d28 but not distinguishing acetophenone from acetophenone-d8.

Single-Neuron Comparison of the Olfactory Receptor Response to Deuterated and Nondeuterated Odorants

The mammalian olfactory receptors (ORs) constitute a large subfamily of the Class A G-protein coupled receptors (GPCRs). The molecular details of how these receptors convert odorant chemical information into neural signal are unknown, but are predicted by analogy to other GPCRs to involve stabilization of the activated form of the OR by the odorant. An alternative hypothesis maintains that the vibrational modes of an odorant's bonds constitute the main determinant for OR activation, and that odorants containing deuterium in place of hydrogen should activate different sets of OR family members. Experiments using heterologously expressed ORs have failed to show different responses for deuterated odorants, but experiments in the sensory neuron environment have been lacking. We tested the response to deuterated and nondeuterated versions of p-cymene, 1-octanol, 1-undecanol, and octanal in dissociated mouse olfactory receptor neurons (ORNs) by calcium imaging. In all, we tested 23 812 cells, including a subset expressing recombinant mouse olfactory receptor 2 ( Olfr2/OR-I7 ), and found that nearly all of the 1610 odorant-responding neurons were unable to distinguish the D- and H-odorants. These results support the conclusion that if mammals can perceive deuterated odorants differently, the difference arises from the receptor-independent steps of olfaction. Nevertheless, 0.81% of the responding ORNs responded differently to D- and H-odorants, and those in the octanal experiments responded selectively to H-octanal at concentrations from 3 to 100 μM. The few ORs responding differently to H and D may be hypersensitive to one of the several H/D physicochemical differences, such as the difference in H/D hydrophobicity.

Molecular Basis of Mammalian Odor Discrimination: A Status Report

Humans have 396 unique, intact olfactory receptors (ORs), G-protein coupled receptors (GPCRs) containing receptor-specific binding sites; other mammals have more. Activation of these transmembrane proteins by an odorant initiates a signaling cascade, evoking an action potential leading to perception of a smell. Because the number of distinguishable odorants vastly exceeds the number of ORs, research has focused on mechanisms of recognition and signaling processes for classes of odorants. In this review, selected recent examples will be presented of "deorphaned" mammalian receptors, where the OR ligands (odorants) as well as key aspects of receptor-odorant interactions were identified using odorant-mediated receptor activation data together with site-directed mutagenesis and molecular modeling. Based on cumulative evidence from OR deorphaning and olfactory receptor neuron activation studies, a receptor-ligand docking model rather than an alternative bond vibration model is suggested to best explain the molecular basis of the exquisitely sensitive odor discrimination in mammals.

How to be rational about empirical success in ongoing science: The case of the quantum nose and its critics

Empirical success is a central criterion for scientific decision-making. Yet its understanding in philosophical studies of science deserves renewed attention: Should philosophers think differently about the advancement of science when they deal with the uncertainty of outcome in ongoing research in comparison with historical episodes? This paper argues that normative appeals to empirical success in the evaluation of competing scientific explanations can result in unreliable conclusions, especially when we are looking at the changeability of direction in unsettled investigations. The challenges we encounter arise from the inherent dynamics of disciplinary and experimental objectives in research practice. In this paper we discuss how these dynamics inform the evaluation of empirical success by analyzing three of its requirements: data accommodation, instrumental reliability, and predictive power. We conclude that the assessment of empirical success in developing inquiry is set against the background of a model's interactive success and prospective value in an experimental context. Our argument is exemplified by the analysis of an apparent controversy surrounding the model of a quantum nose in research on olfaction. Notably, the public narrative of this controversy rests on a distorted perspective on measures of empirical success.

Molecular mechanism of activation of human musk receptors OR5AN1 and OR1A1 by (R)-muscone and diverse other musk-smelling compounds

Understanding olfaction at the molecular level is challenging due to the lack of crystallographic models of odorant receptors (ORs). To better understand the molecular mechanism of OR activation, we focused on chiral (R)-muscone and other musk-smelling odorants due to their great importance and widespread use in perfumery and traditional medicine, as well as environmental concerns associated with bioaccumulation of musks with estrogenic/antiestrogenic properties. We experimentally and computationally examined the activation of human receptors OR5AN1 and OR1A1, recently identified as specifically responding to musk compounds. OR5AN1 responds at nanomolar concentrations to musk ketone and robustly to macrocyclic sulfoxides and fluorine-substituted macrocyclic ketones; OR1A1 responds only to nitromusks. Structural models of OR5AN1 and OR1A1 based on quantum mechanics/molecular mechanics (QM/MM) hybrid methods were validated through direct comparisons with activation profiles from site-directed mutagenesis experiments and analysis of binding energies for 35 musk-related odorants. The experimentally found chiral selectivity of OR5AN1 to (R)- over (S)-muscone was also computationally confirmed for muscone and fluorinated (R)-muscone analogs. Structural models show that OR5AN1, highly responsive to nitromusks over macrocyclic musks, stabilizes odorants by hydrogen bonding to Tyr260 of transmembrane α-helix 6 and hydrophobic interactions with surrounding aromatic residues Phe105, Phe194, and Phe207. The binding of OR1A1 to nitromusks is stabilized by hydrogen bonding to Tyr258 along with hydrophobic interactions with surrounding aromatic residues Tyr251 and Phe206. Hydrophobic/nonpolar and hydrogen bonding interactions contribute, respectively, 77% and 13% to the odorant binding affinities, as shown by an atom-based quantitative structure-activity relationship model.

A Quantum Biomimetic Electronic Nose Sensor

We propose a technologically feasible one-dimensional double barrier resonant tunneling diode (RTD) as electronic nose, inspired by the vibration theory of biological olfaction. The working principle is phonon-assisted inelastic electron tunneling spectroscopy (IETS), modeled here using the Non-Equilibrium Green Function formalism for quantum transport. While standard IETS requires low-temperature operation to obviate the thermal broadening of spectroscopic peaks, we show that quantum confinement in the well of the RTD provides electron energy filtering in this case and could thereby allow room-temperature operation. We also find that the IETS peaks - corresponding to adsorbed foreign molecules - shift monotonically along the bias voltage coordinate with their vibrational energy, promising a selective sensor.

Vibrational Detection of Odorant Functional Groups by Drosophila melanogaster

A remarkable feature of olfaction, and perhaps the hardest one to explain by shape-based molecular recognition, is the ability to detect the presence of functional groups in odorants, irrespective of molecular context. We previously showed that Drosophila trained to avoid deuterated odorants could respond to a molecule bearing a nitrile group, which shares the vibrational stretch frequency with the CD bond. Here, we reproduce and extend this finding by showing analogous olfactory responses of Drosophila to the chemically vastly different functional groups, thiols and boranes, that nevertheless possess a common vibration at 2600 cm⁻¹. Furthermore, we show that Drosophila do not respond to a cyanohydrin structure that renders nitrile groups invisible to IR spectroscopy. We argue that the response of Drosophila to these odorants which parallels their perception in humans, supports the hypothesis that odor character is encoded in odorant molecular vibrations, not in the specific shape-based activation pattern of receptors.

Live-cell Measurement of Odorant Receptor Activation Using a Real-time cAMP Assay

The enormous sizes of the mammalian odorant receptor (OR) families present difficulties to find their cognate ligands among numerous volatile chemicals. To efficiently and accurately deorphanize ORs, we combine the use of a heterologous cell line to express mammalian ORs and a genetically modified biosensor plasmid to measure cAMP production downstream of OR activation in real time. This assay can be used to screen odorants against ORs and vice versa. Positive odorant-receptor interactions from the screens can be subsequently confirmed by testing against various odor concentrations, generating concentration-response curves. Here we used this method to perform a high-throughput screening of an odorous compound against a human OR library expressed in Hana3A cells and confirmed that the positively-responding receptor is the cognate receptor for the compound of interest. We found this high-throughput detection method to be efficient and reliable in assessing OR activation and our data provide an example of its potential use in OR functional studies.

Evidence for a shape-based recognition of odorants in vivo in the human nose from an analysis of the molecular mechanism of lily-of-the-valley odorants detection in the Lilial and Bourgeonal family using the C/Si/Ge/Sn switch strategy

We performed an analysis of possible mechanisms of ligand recognition in the human nose. The analysis is based on in vivo odor threshold determination and in vitro Ca2+ imaging assays with a C/Si/Ge/Sn switch strategy applied to the compounds Lilial and Bourgeonal, to differentiate between different molecular mechanisms of odorant detection. Our results suggest that odorant detection under threshold conditions is mainly based on the molecular shape, i.e. the van der Waals surface, and electrostatics of the odorants. Furthermore, we show that a single olfactory receptor type is responsible for odor detection of Bourgeonal at the threshold level in humans in vivo. Carrying out a QM analysis of vibrational energies contained in the odorants, there is no evidence for a vibration-based recognition.

Validity Examination of the Dissipative Quantum Model of Olfaction

Despite some inconclusive experimental evidences for the vibrational model of olfaction, the validity of the model has not been examined yet and therefore it suffers from the lack of conclusive experimental support. Here, we generalize the model and propose a numerical analysis of the dissipative odorant-mediated inelastic electron tunneling mechanism of olfaction, to be used as a potential examination in experiments. Our analysis gives several predictions on the model such as efficiency of elastic and inelastic tunneling of electrons through odorants, sensitivity thresholds in terms of temperature and pressure, isotopic effect on sensitivity, and the chiral recognition for discrimination between the similar and different scents. Our predictions should yield new knowledge to design new experimental protocols for testing the validity of the model.

Quantum effects in biology: golden rule in enzymes, olfaction, photosynthesis and magnetodetection

Despite certain quantum concepts, such as superposition states, entanglement, 'spooky action at a distance' and tunnelling through insulating walls, being somewhat counterintuitive, they are no doubt extremely useful constructs in theoretical and experimental physics. More uncertain, however, is whether or not these concepts are fundamental to biology and living processes. Of course, at the fundamental level all things are quantum, because all things are built from the quantized states and rules that govern atoms. But when does the quantum mechanical toolkit become the best tool for the job? This review looks at four areas of 'quantum effects in biology'. These are biosystems that are very diverse in detail but possess some commonality. They are all (i) effects in biology: rates of a signal (or information) that can be calculated from a form of the 'golden rule' and (ii) they are all protein-pigment (or ligand) complex systems. It is shown, beginning with the rate equation, that all these systems may contain some degree of quantumeffect, and where experimental evidence is available, it is explored to determine how the quantum analysis aids in understanding of the process.

Experimental evaluation of the generalized vibrational theory of G protein-coupled receptor activation

Recently, an alternative theory concerning the method by which olfactory proteins are activated has garnered attention. This theory proposes that the activation of olfactory G protein-coupled receptors occurs by an inelastic electron tunneling mechanism that is mediated through the presence of an agonist with an appropriate vibrational state to accept the inelastic portion of the tunneling electron's energy. In a recent series of papers, some suggestive theoretical evidence has been offered that this theory may be applied to nonolfactory G protein-coupled receptors (GPCRs), including those associated with the central nervous system (CNS). [Chee HK, June OS (2013) Genomics Inform 11(4):282-288; Chee HK, et al. (2015) FEBS Lett 589(4):548-552; Oh SJ (2012) Genomics Inform 10(2):128-132]. Herein, we test the viability of this idea, both by receptor affinity and receptor activation measured by calcium flux. This test was performed using a pair of well-characterized agonists for members of the 5-HT₂ class of serotonin receptors, 2,5-dimethoxy-4-iodoamphetamine (DOI) and N,N-dimethyllysergamide (DAM-57), and their respective deuterated isotopologues. No evidence was found that selective deuteration affected either the binding affinity or the activation by the selected ligands for the examined members of the 5-HT₂ receptor class.

The role of metals in mammalian olfaction of low molecular weight organosulfur compounds

Covering: up to the end of 2017While suggestions concerning the possible role of metals in olfaction and taste date back 50 years, only recently has it been possible to confirm these proposals with experiments involving individual olfactory receptors (ORs). A detailed discussion of recent experimental results demonstrating the key role of metals in enhancing the response of human and other vertebrate ORs to specific odorants is presented against the backdrop of our knowledge of how the sense of smell functions both at the molecular and whole animal levels. This review emphasizes the role of metals in the detection of low molecular weight thiols, sulfides, and other organosulfur compounds, including those found in strong-smelling animal excretions and plant volatiles, and those used in gas odorization. Alternative theories of olfaction are described, with evidence favoring the modified "shape" theory. The use of quantum mechanical/molecular modeling (QM/MM), site-directed mutagenesis and saturation-transfer-difference (STD) NMR is discussed, providing support for biological studies of mouse and human receptors, MOR244-3 and OR OR2T11, respectively. Copper is bound at the active site of MOR244-3 by cysteine and histidine, while cysteine, histidine and methionine are involved with OR2T11. The binding pockets of these two receptors are found in different locations in the three-dimensional seven transmembrane models. Another recently deorphaned human olfactory receptor, OR2M3, highly selective for a thiol from onions, and a broadly-tuned thiol receptor, OR1A1, are also discussed. Other topics covered include the effects of nanoparticles and heavy metal toxicants on vertebrate and fish ORs, intranasal zinc products and the loss of smell (anosmia).

Kinetic Model for the Activation of Mammalian Olfactory Receptor

The sense of smell is triggered by binding of odorants to a set of olfactory receptors (ORs), the activation of which generates specific patterns of neuronal signals in olfactory bulbs. Despite a long history of research and speculations, very little is known about the actual mechanism of OR activation. In particular, there is virtually no theoretical framework capable of describing the kinetics of olfactory activation at a quantitative level. Based on the fact that mammalian ORs belong to a class of G-protein coupled receptors (GPCRs) and utilizing the information available from recent studies on other types of GPCRs with known structural data, we construct a minimal kinetic model for mammalian olfactory activation, obtaining a new expression for the signal strength as a function of odorant and G-protein concentrations and defining this as odor activity (OA). The parametric dependence of OA on equilibrium dissociation and rate constants provides a new comprehensive means to describe how odorant-OR binding kinetics affects the odor signal, and offers new quantitative criteria for classifying agonistic, partially agonistic, and antagonistic (or inverse agonistic) behavior. The dependence of OA on the concentration of G-proteins also suggests a new experimental method to determine key equilibrium constants for odorant-OR and G-protein-OR association/dissociation processes.

After oxidation, zinc nanoparticles lose their ability to enhance responses to odorants

Electrical responses of olfactory sensory neurons to odorants were examined in the presence of zinc nanoparticles of various sizes and degrees of oxidation. The zinc nanoparticles were prepared by the underwater electrical discharge method and analyzed by atomic force microscopy and X-ray photoelectron spectroscopy. Small (1.2 ± 0.3 nm) zinc nanoparticles significantly enhanced electrical responses of olfactory neurons to odorants. After oxidation, however, these small zinc nanoparticles were no longer capable of enhancing olfactory responses. Larger zinc oxide nanoparticles (15 nm and 70 nm) also did not modulate responses to odorants. Neither zinc nor zinc oxide nanoparticles produced olfactory responses when added without odorants. The enhancement of odorant responses by small zinc nanoparticles was explained by the creation of olfactory receptor dimers initiated by small zinc nanoparticles. The results of this work will clarify the mechanisms for the initial events in olfaction, as well as to provide new ways to alleviate anosmia related to the loss of olfactory receptors.

The quantum mitochondrion and optimal health

A sufficiently complex set of molecules, if subject to perturbation, will self-organize and show emergent behaviour. If such a system can take on information it will become subject to natural selection. This could explain how self-replicating molecules evolved into life and how intelligence arose. A pivotal step in this evolutionary process was of course the emergence of the eukaryote and the advent of the mitochondrion, which both enhanced energy production per cell and increased the ability to process, store and utilize information. Recent research suggest that from its inception life embraced quantum effects such as 'tunnelling' and 'coherence' while competition and stressful conditions provided a constant driver for natural selection. We believe that the biphasic adaptive response to stress described by hormesis-a process that captures information to enable adaptability, is central to this whole process. Critically, hormesis could improve mitochondrial quantum efficiency, improving the ATP/ROS ratio, whereas inflammation, which is tightly associated with the aging process, might do the opposite. This all suggests that to achieve optimal health and healthy aging, one has to sufficiently stress the system to ensure peak mitochondrial function, which itself could reflect selection of optimum efficiency at the quantum level.

Differential Electrophysiological Responses to Odorant Isotopologues in Drosophilid Antennae

Olfaction presents the ultimate challenge to molecular recognition as thousands of molecules have to be recognized by far fewer olfactory receptors. We have presented evidence that Drosophila readily distinguish odorants based on their molecular vibrations using a battery of behavioral assays suggesting engagement of a molecular vibration-sensing component. Here we interrogate electrophysiologically the antennae of four Drosophilids and demonstrate conserved differential response amplitudes to aldehydes, alcohols, ketones, nitriles, and their deuterated isotopologues. Certain deuterated odorants evoked larger electroantennogram (EAG) amplitudes, while the response to the normal odorant was elevated in others. Significantly, benzonitrile isotopologues were not distinguishable as predicted. This suggests that isotopologue-specific EAG amplitudes result from differential activation of specific olfactory receptors. In support of this, odorants with as few as two deuteria evoke distinct EAG amplitudes from their normal isotopologues, and this is independent of the size of the deuterated molecule. Importantly, we find no evidence that these isotopologue-specific amplitudes depend on perireceptor mechanisms or other pertinent physical property of the deuterated odorants. Rather, our results strongly suggest that Drosophilid olfactory receptors are activated by molecular vibrations differentiating similarly sized and shaped odorants in vivo, yielding sufficient differential information to drive behavioral choices.

Odorant receptors of Drosophila are sensitive to the molecular volume of odorants

Which properties of a molecule define its odor? This is a basic yet unanswered question regarding the olfactory system. The olfactory system of Drosophila has a repertoire of approximately 60 odorant receptors. Molecules bind to odorant receptors with different affinities and activate them with different efficacies, thus providing a combinatorial code that identifies odorants. We hypothesized that the binding affinity of an odorant-receptor pair is affected by their relative sizes. The maximum affinity can be attained when the molecular volume of an odorant matches the volume of the binding pocket. The affinity drops to zero when the sizes are too different, thus obscuring the effects of other molecular properties. We developed a mathematical formulation of this hypothesis and verified it using Drosophila data. We also predicted the volume and structural flexibility of the binding site of each odorant receptor; these features significantly differ between odorant receptors. The differences in the volumes and structural flexibilities of different odorant receptor binding sites may explain the difference in the scents of similar molecules with different sizes.

How Far Does a Receptor Influence Vibrational Properties of an Odorant?

The biophysical mechanism of the sense of smell, or olfaction, is still highly debated. The mainstream explanation argues for a shape-based recognition of odorant molecules by olfactory receptors, while recent investigations suggest the primary olfactory event to be triggered by a vibrationally-assisted electron transfer reaction. We consider this controversy by studying the influence of a receptor on the vibrational properties of an odorant in atomistic details as the coupling between electronic degrees of freedom of the receptor and the vibrations of the odorant is the key parameter of the vibrationally-assisted electron transfer. Through molecular dynamics simulations we elucidate the binding specificity of a receptor towards acetophenone odorant. The vibrational properties of acetophenone inside the receptor are then studied by the polarizable embedding density functional theory approach, allowing to quantify protein-odorant interactions. Finally, we judge whether the effects of the protein provide any indications towards the existing theories of olfaction.

Differential Odour Coding of Isotopomers in the Honeybee Brain

The shape recognition model of olfaction maintains that odorant reception probes physicochemical properties such as size, shape, electric charge, and hydrophobicity of the ligand. Recently, insects were shown to distinguish common from deuterated isotopomers of the same odorant, suggesting the involvement of other molecular properties to odorant reception. Via two-photon functional microscopy we investigated how common and deuterated isoforms of natural odorants are coded within the honeybee brain. Our results provide evidence that (i) different isotopomers generate different neuronal activation maps, (ii) isotopomer sensitivity is a general mechanism common to multiple odorant receptors, and (iii) isotopomer specificity is highly consistent across individuals. This indicates that honeybee’s olfactory system discriminates between isotopomers of the same odorant, suggesting that other features, such as molecular vibrations, may contribute to odour signal transduction.

Probing the local environment of a single OPE3 molecule using inelastic tunneling electron spectroscopy

We study single-molecule oligo(phenylene ethynylene)dithiol junctions by means of inelastic electron tunneling spectroscopy (IETS). The molecule is contacted with gold nano-electrodes formed with the mechanically controllable break junction technique. We record the IETS spectrum of the molecule from direct current measurements, both as a function of time and electrode separation. We find that for fixed electrode separation the molecule switches between various configurations, which are characterized by different IETS spectra. Similar variations in the IETS signal are observed during atomic rearrangements upon stretching of the molecular junction. Using quantum chemistry calculations, we identity some of the vibrational modes which constitute a chemical fingerprint of the molecule. In addition, changes can be attributed to rearrangements of the local molecular environment, in particular at the molecule-electrode interface. This study shows the importance of taking into account the interaction with the electrodes when describing inelastic contributions to transport through single-molecule junctions.

Unravelling the Olfactory Sense: From the Gene to Odor Perception

Although neglected by science for a long time, the olfactory sense is now the focus of a panoply of studies that bring new insights and raises interesting questions regarding its functioning. The importance in the clarification of this process is of interest for science, but also motivated by the food and perfume industries boosted by a consumer society with increasingly demands for higher quality standards. In this review, a general overview of the state of art of science regarding the olfactory sense is presented with the main focus on the peripheral olfactory system. Special emphasis will be given to the deorphanization of the olfactory receptors (ORs), a critical issue because the specificity and functional properties of about 90% of human ORs remain unknown mainly due to the difficulties associated with the functional expression of ORs in high yields.

What is so special about smell? Olfaction as a model system in neurobiology

Neurobiology studies mechanisms of cell signalling. A key question is how cells recognise specific signals. In this context, olfaction has become an important experimental system over the past 25 years. The olfactory system responds to an array of structurally diverse stimuli. The discovery of the olfactory receptors (ORs), recognising these stimuli, established the olfactory pathway as part of a greater group of signalling mechanisms mediated by G-protein-coupled receptors (GPCRs). GPCRs are the largest protein family in the mammalian genome and involved in numerous fundamental physiological processes. The OR family exhibits two characteristics that make them an excellent model system to understand GPCRs: its size and the structural diversity of its members. Research on the OR binding site investigates what amino acid sequences determine the receptor-binding capacity. This promises a better understanding of how the basic genetic makeup of GPCRs relates to their diversification in ligand-binding capacities.

Dissipation enhanced vibrational sensing in an olfactory molecular switch

Motivated by a proposed olfactory mechanism based on a vibrationally activated molecular switch, we study electron transport within a donor-acceptor pair that is coupled to a vibrational mode and embedded in a surrounding environment. We derive a polaron master equation with which we study the dynamics of both the electronic and vibrational degrees of freedom beyond previously employed semiclassical (Marcus-Jortner) rate analyses. We show (i) that in the absence of explicit dissipation of the vibrational mode, the semiclassical approach is generally unable to capture the dynamics predicted by our master equation due to both its assumption of one-way (exponential) electron transfer from donor to acceptor and its neglect of the spectral details of the environment; (ii) that by additionally allowing strong dissipation to act on the odorant vibrational mode, we can recover exponential electron transfer, though typically at a rate that differs from that given by the Marcus-Jortner expression; (iii) that the ability of the molecular switch to discriminate between the presence and absence of the odorant, and its sensitivity to the odorant vibrational frequency, is enhanced significantly in this strong dissipation regime, when compared to the case without mode dissipation; and (iv) that details of the environment absent from previous Marcus-Jortner analyses can also dramatically alter the sensitivity of the molecular switch, in particular, allowing its frequency resolution to be improved. Our results thus demonstrate the constructive role dissipation can play in facilitating sensitive and selective operation in molecular switch devices, as well as the inadequacy of semiclassical rate equations in analysing such behaviour over a wide range of parameters.

Emotional sentience and the nature of phenomenal experience

When phenomenal experience is examined through the lens of physics, several conundrums come to light including: Specificity of mind-body interactions, feelings of free will in a deterministic universe, and the relativity of subjective perception. The new biology of "emotion" can shed direct light upon these issues, via a broadened categorical definition that includes both affective feelings and their coupled (yet often subconscious) hedonic motivations. In this new view, evaluative (good/bad) feelings that trigger approach/avoid behaviors emerged with life itself, a crude stimulus-response information loop between organism and its environment, a semiotic signaling system embodying the first crude form of "mind". Emotion serves the ancient function of sensory-motor self-regulation and affords organisms - at every level of complexity - an active, adaptive, role in evolution. A careful examination of the biophysics involved in emotional "self-regulatory" signaling, however, acknowledges constituents that are incompatible with classical physics. This requires a further investigation, proposed herein, of the fundamental nature of "the self" as the subjective observer central to the measurement process in quantum mechanics, and ultimately as an active, unified, self-awareness with a centrally creative role in "self-organizing" processes and physical forces of the classical world. In this deeper investigation, a new phenomenological dualism is proposed: The flow of complex human experience is instantiated by both a classically embodied mind and a deeper form of quantum consciousness that is inherent in the universe itself, implying much deeper - more Whiteheadian - interpretations of the "self-regulatory" and "self-relevant" nature of emotional stimulus. A broad stroke, speculative, intuitive sketch of this new territory is then set forth, loosely mapped to several theoretical models of consciousness, potentially relevant mathematical devices and pertinent philosophical themes, in an attempt to acknowledge the myriad questions - and limitations - implicit in the quest to understand "sentience" in any ontologically pansentient universe.

Mode-selective vibrational modulation of charge transport in organic electronic devices

The soft character of organic materials leads to strong coupling between molecular, nuclear and electronic dynamics. This coupling opens the way to influence charge transport in organic electronic devices by exciting molecular vibrational motions. However, despite encouraging theoretical predictions, experimental realization of such approach has remained elusive. Here we demonstrate experimentally that photoconductivity in a model organic optoelectronic device can be modulated by the selective excitation of molecular vibrations. Using an ultrafast infrared laser source to create a coherent superposition of vibrational motions in a pentacene/C₆₀ photoresistor, we observe that excitation of certain modes in the 1,500–1,700 cm⁻¹ region leads to photocurrent enhancement. Excited vibrations affect predominantly trapped carriers. The effect depends on the nature of the vibration and its mode-specific character can be well described by the vibrational modulation of intermolecular electronic couplings. This presents a new tool for studying electron–phonon coupling and charge dynamics in (bio)molecular materials.

The electronic properties of organic molecules are sensitive to structural dynamics, but device control through this phenomenon has not been attained. Bakulin et al. show that the photoconductivity can be modulated by selective excitation of molecular vibrations in an organic optoelectronic device.

Implausibility of the vibrational theory of olfaction

The vibrational theory of olfaction assumes that electron transfer occurs across odorants at the active sites of odorant receptors (ORs), serving as a sensitive measure of odorant vibrational frequencies, ultimately leading to olfactory perception. A previous study reported that human subjects differentiated hydrogen/deuterium isotopomers (isomers with isotopic atoms) of the musk compound cyclopentadecanone as evidence supporting the theory. Here, we find no evidence for such differentiation at the molecular level. In fact, we find that the human musk-recognizing receptor, OR5AN1, identified using a heterologous OR expression system and robustly responding to cyclopentadecanone and muscone, fails to distinguish isotopomers of these compounds in vitro. Furthermore, the mouse (methylthio)methanethiol-recognizing receptor, MOR244-3, as well as other selected human and mouse ORs, responded similarly to normal, deuterated, and (13)C isotopomers of their respective ligands, paralleling our results with the musk receptor OR5AN1. These findings suggest that the proposed vibration theory does not apply to the human musk receptor OR5AN1, mouse thiol receptor MOR244-3, or other ORs examined. Also, contrary to the vibration theory predictions, muscone-d30 lacks the 1,380- to 1,550-cm(-1) IR bands claimed to be essential for musk odor. Furthermore, our theoretical analysis shows that the proposed electron transfer mechanism of the vibrational frequencies of odorants could be easily suppressed by quantum effects of nonodorant molecular vibrational modes. These and other concerns about electron transfer at ORs, together with our extensive experimental data, argue against the plausibility of the vibration theory.

Neuroreceptor activation by vibration-assisted tunneling

G protein-coupled receptors (GPCRs) constitute a large family of receptor proteins that sense molecular signals on the exterior of a cell and activate signal transduction pathways within the cell. Modeling how an agonist activates such a receptor is fundamental for an understanding of a wide variety of physiological processes and it is of tremendous value for pharmacology and drug design. Inelastic electron tunneling spectroscopy (IETS) has been proposed as a model for the mechanism by which olfactory GPCRs are activated by a bound agonist. We apply this hyothesis to GPCRs within the mammalian nervous system using quantum chemical modeling. We found that non-endogenous agonists of the serotonin receptor share a particular IET spectral aspect both amongst each other and with the serotonin molecule: a peak whose intensity scales with the known agonist potencies. We propose an experiential validation of this model by utilizing lysergic acid dimethylamide (DAM-57), an ergot derivative, and its deuterated isotopologues; we also provide theoretical predictions for comparison to experiment. If validated our theory may provide new avenues for guided drug design and elevate methods of in silico potency/activity prediction.

Functionalization of β-caryophyllene generates novel polypharmacology in the endocannabinoid system

The widespread dietary plant sesquiterpene hydrocarbon β-caryophyllene (1) is a CB2 cannabinoid receptor-specific agonist showing anti-inflammatory and analgesic effects in vivo. Structural insights into the pharmacophore of this hydrocarbon, which lacks functional groups other than double bonds, are missing. A structure-activity study provided evidence for the existence of a well-defined sesquiterpene hydrocarbon binding site in CB2 receptors, highlighting its exquisite sensitivity to modifications of the strained endocyclic double bond of 1. While most changes on this element were detrimental for activity, ring-opening cross metathesis of 1 with ethyl acrylate followed by amide functionalization generated a series of new monocyclic amides (11a, 11b, 11c) that not only retained the CB2 receptor functional agonism of 1 but also reversibly inhibited fatty acid amide hydrolase (FAAH), the major endocannabinoid degrading enzyme, without affecting monoacylglycerol lipase (MAGL) and α,β hydrolases 6 and 12. Intriguingly, further modification of this monocyclic scaffold generated the FAAH- and endocannabinoid substrate-specific cyclooxygenase-2 (COX-2) dual inhibitors 11e and 11f, which are probes with a novel pharmacological profile. Our study shows that by removing the conformational constraints induced by the medium-sized ring and by introducing functional groups in the sesquiterpene hydrocarbon 1, a new scaffold with pronounced polypharmacological features within the endocannabinoid system could be generated. The structural and functional repertoire of cannabimimetics and their yet poorly understood intrinsic promiscuity may be exploited to generate novel probes and ultimately more effective drugs.

Post-Translational Modifications of TRP Channels. Cells. 2014;3:258-287. [PMID: 24717323 DOI: 10.3390/cells3020258]

Transient receptor potential (TRP) channels constitute an ancient family of cation channels that have been found in many eukaryotic organisms from yeast to human. TRP channels exert a multitude of physiological functions ranging from Ca²⁺ homeostasis in the kidney to pain reception and vision. These channels are activated by a wide range of stimuli and undergo covalent post-translational modifications that affect and modulate their subcellular targeting, their biophysical properties, or channel gating. These modifications include N-linked glycosylation, protein phosphorylation, and covalent attachment of chemicals that reversibly bind to specific cysteine residues. The latter modification represents an unusual activation mechanism of ligand-gated ion channels that is in contrast to the lock-and-key paradigm of receptor activation by its agonists. In this review, we summarize the post-translational modifications identified on TRP channels and, when available, explain their physiological role.

Honeybees (Apis mellifera) learn to discriminate the smell of organic compounds from their respective deuterated isotopomers

The understanding of physiological and molecular processes underlying the sense of smell has made considerable progress during the past three decades, revealing the cascade of molecular steps that lead to the activation of olfactory receptor (OR) neurons. However, the mode of primary interaction of odorant molecules with the OR proteins within the sensory cells is still enigmatic. Two different concepts try to explain these interactions: the 'odotope hypothesis' suggests that OR proteins recognize structural aspects of the odorant molecule, whereas the 'vibration hypothesis' proposes that intra-molecular vibrations are the basis for the recognition of the odorant by the receptor protein. The vibration hypothesis predicts that OR proteins should be able to discriminate compounds containing deuterium from their common counterparts which contain hydrogen instead of deuterium. This study tests this prediction in honeybees (Apis mellifera) using the proboscis extension reflex learning in a differential conditioning paradigm. Rewarding one odour (e.g. a deuterated compound) with sucrose and not rewarding the respective analogue (e.g. hydrogen-based odorant) shows that honeybees readily learn to discriminate hydrogen-based odorants from their deuterated counterparts and supports the idea that intra-molecular vibrations may contribute to odour discrimination.

Quality-space theory in olfaction

Quality-space theory (QST) explains the nature of the mental qualities distinctive of perceptual states by appeal to their role in perceiving. QST is typically described in terms of the mental qualities that pertain to color. Here we apply QST to the olfactory modalities. Olfaction is in various respects more complex than vision, and so provides a useful test case for QST. To determine whether QST can deal with the challenges olfaction presents, we show how a quality space (QS) could be constructed relying on olfactory perceptible properties and the olfactory mental qualities then defined by appeal to that QS of olfactory perceptible properties. We also consider how to delimit the olfactory QS from other modalities. We further apply QST to the role that experience plays in refining our olfactory discriminative abilities and the occurrence of olfactory mental qualities in non-conscious olfactory states. QST is shown to be fully applicable to and useful for understanding the complex domain of olfaction.

Physicochemical vs. Vibrational Descriptors for Prediction of Odor Receptor Responses

Responses of olfactory receptors (ORs) can be predicted by applying machine learning methods on a multivariate encoding of an odorant's chemical structure. Physicochemical descriptors that encode features of the molecular graph are a popular choice for such an encoding. Here, we explore the EVA descriptor set, which encodes features derived from the vibrational spectrum of a molecule. We assessed the performance of Support Vector Regression (SVR) and Random Forest Regression (RFR) to predict the gradual response of Drosophila ORs. We compared a 27-dimensional variant of the EVA descriptor against a set of 1467 descriptors provided by the eDragon software package, and against a 32-dimensional subset thereof that has been proposed as the basis for an odor metric consisting of 32 descriptors (HADDAD). The best prediction performance was reproducibly achieved using SVR on the highest-dimensional feature set. The low-dimensional EVA and HADDAD feature sets predicted odor-OR interactions with similar accuracy. Adding charge and polarizability information to the EVA descriptor did not improve the results but rather decreased predictive power. Post-hoc in vivo measurements confirmed these results. Our findings indicate that EVA provides a meaningful low-dimensional representation of odor space, although EVA hardly outperformed "classical" descriptor sets.

Opsin, a structural model for olfactory receptors?

Receptor-ligand interaction: Olfactory receptors (ORs) are G-protein-coupled receptors (GPCRs), which detect signaling molecules such as hormones and odorants. The structure of opsin, the GPCR employed in vision, with a detergent molecule bound deep in its orthosteric ligand-binding pocket provides a template for OR homology modeling, thus enabling investigation of the structural basis of the mechanism of odorant-receptor recognition.