Physico-chemical investigations of human olfactory receptors OR10G4 and OR2B11 activated by vanillin, ethyl vanillin, coumarin and quinoline molecules using statistical physics method

Deciphering olfactory receptor binding mechanisms: a structural and dynamic perspective on olfactory receptors

Olfactory receptors, classified as G-protein coupled receptors (GPCRs), have been a subject of scientific inquiry since the early 1950s. Historically, investigations into the sensory mechanisms of olfactory receptors were often confined to behavioral characteristics in model organisms or the expression of related proteins and genes. However, with the development of cryo-electron microscopy techniques, it has gradually become possible to decipher the specific structures of olfactory receptors in insects and humans. This has provided new insights into the binding mechanisms between odor molecules and olfactory receptors. Furthermore, due to the rapid advancements in related fields such as computer simulations, the prediction and exploration of odor molecule binding to olfactory receptors have been progressively achieved through molecular dynamics simulations. Through this comprehensive review, we aim to provide a thorough analysis of research related to the binding mechanisms between odor molecules and olfactory receptors from the perspectives of structural biology and molecular dynamics simulations. Finally, we will provide an outlook on the future of research in the field of olfactory receptor sensory mechanisms.

Olfactory receptors impact pathophysiological processes of lung diseases in bronchial epithelial cells

BACKGROUND

Therapeutic options for steroid-resistant non-type 2 inflammation in obstructive lung diseases are limited. Bronchial epithelial cells are key in the pathogenesis by releasing the central proinflammatory cytokine interleukine-8 (IL-8). Olfactory receptors (ORs) are expressed in various cell types. This study examined the drug target potential of ORs by investigating their impact on associated pathophysiological processes in lung epithelial cells.

METHODS

Experiments were performed in the A549 cell line and in primary human bronchial epithelial cells. OR expression was investigated using RT-PCR, Western blot, and immunocytochemical staining. OR-mediated effects were analyzed by measuring 1) intracellular calcium concentration via calcium imaging, 2) cAMP concentration by luminescence-based assays, 3) wound healing by scratch assays, 4) proliferation by MTS-based assays, 5) cellular vitality by Annexin V/PI-based FACS staining, and 6) the secretion of IL-8 in culture supernatants by ELISA.

RESULTS

By screening 100 potential OR agonists, we identified two, Brahmanol and Cinnamaldehyde, that increased intracellular calcium concentrations. The mRNA and proteins of the corresponding receptors OR2AT4 and OR2J3 were detected. Stimulation of OR2J3 with Cinnamaldehyde reduced 1) IL-8 in the absence and presence of bacterial and viral pathogen-associated molecular patterns (PAMPs), 2) proliferation, and 3) wound healing but increased cAMP. In contrast, stimulation of OR2AT4 by Brahmanol increased wound healing but did not affect cAMP and proliferation. Both ORs did not influence cell vitality.

CONCLUSION

ORs might be promising drug target candidates for lung diseases with non-type 2 inflammation. Their stimulation might reduce inflammation or prevent tissue remodeling by promoting wound healing.

Quantitative investigations of Zebrafish olfactory receptor ORA1 responsiveness to three pheromones: Microscopic and macroscopic characterizations via an advanced statistical physics treatment

In this work, an adsorption phenomenon putatively involved in the olfactory sense of phenylacetic acid, 4-chlorophenylacetic acid, and 4-methoxyphenylacetic acid pheromones in the Zebrafish olfactory receptor ORA1 was a helpful mechanism in interpreting and characterizing the olfaction process at a molecular level. Hence, the experimental dose-olfactory response curves were fitted by applying the one-layer adsorption model with a single energy (1LM1E). On one hand, the different parameters introduced in the selected model were used to microscopically study the three olfactory systems. Indeed, the fitting results showed that phenylacetic acid displayed the greatest maximum olfactory response at saturation, due to the effect of functional groups at the R4 position. The three pheromones were docked via a non-parallel orientation and the adsorption process was a multi-molecular mechanism. The sizes of different binding pockets of ORA1 were determined through the estimation of the olfactory receptor site size distributions (stereographic characterization). The estimated adsorption energies, ranging from 17.340 to 21.332 kJ/mol, can be used to describe the energetic interactions between the studied pheromones and the Zebrafish ORA1 binding pockets. The spectrums of the adsorption energy distributions of phenylacetic acid, 4-chlorophenylacetic acid, and 4-methoxyphenylacetic acid, which were spread out from 10 to 32.5 kJ/mol, 5 to 30 kJ/mol, and 10 to 32.5 kJ/mol, respectively, was determined to estimate the corresponding olfactory bands (energetic characterization). On the other hand, three thermodynamic functions were estimated in order to macroscopically study the three olfactory systems.

Exploring the effects of lipid oxidation and free fatty acids on the development of volatile compounds in grouper during cold storage based on multivariate analysis

To investigate the relationship between lipid oxidation and the development of volatile compounds (VOCs) in grouper lipid during cold storage, lipids were extracted from grouper as a single-factor study to avoid the complex interactions between microorganisms and proteins. Lipid oxidation during storage and the content of 12 long-chain fatty acids (FAs) in grouper lipids were evaluated. The HS-SPME-GC-MS technique was used to analyze the VOCs in grouper lipids, and a total of 13 key VOCs, primarily comprising alcohols and aldehydes, were screened. Pearson correlation analysis showed a strong acorrelation between these 13 key VOCs, which influenced the overall flavor of grouper lipids, and lipid oxidation, mainly involving secondary oxidation of lipids and the oxidation of long-chain polyunsaturated fatty acids, such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). Possible solutions for grouper lipid deterioration were proposed, providing a reference for maintaining the overall quality of grouper and regulating flavor formation.

Molecular mechanisms of caramel-like odorant-olfactory receptor interactions based on a computational chemistry approach

Molecular mechanisms of caramel-like odorant-olfactory receptor interactions were investigated based on molecular docking and molecular dynamics simulations. The transmembrane regions TM-3, TM-5 and TM-6 of receptors were main contributors of amino acid residues in the docking. Molecular docking results showed that hydrogen bonding and pi-pi stacking were the key forces for the stabilization of caramel-like odorants. The binding energies were positively correlated with the molecular weight of caramel-like odorants. Residues Asn155 (84%, OR2W1), Asn206 (86%, OR8D1), Ser155 (77%, OR8D1), Asp179 (87%, OR5M3), Val182 (84%, OR2J2) and Tyr260 (94%, OR2J2) with high frequencies played an important role in the complexes formation. Odorants 4-hydroxy-5-methylfuran-3(2H)-one (16#) and methylglyoxal (128#) were screened by molecular field-based similarity analysis, which tended to bind to the receptors OR1G1 and OR52H1 respectively, resulting a caramel-like aroma perception. The obtained results are useful for better understanding the perception of caramel-like odorants and their high-throughput screening.

Quantitative characterizations of mOR-EG activated by vanilla odorants using advanced statistical physics modeling

An advanced monolayer adsorption model of an ideal gas was successfully employed to investigate the adsorption of vanillin, vanillin methyl ether, vanillin ethyl ether, and vanillin acetate odorants on mouse eugenol olfactory receptor mOR-EG. In order to understand the adsorption process putatively introduced in olfactory perception, model parameters were analyzed. Hence, fitting results showed that the studied vanilla odorants were linked in mOR-EG binding pockets with a non-parallel orientation, and their adsorption was a multi-molecular process (n > 1). The adsorption energy values that ranged from 14.021 to 19.193 kJ/mol suggested that the four vanilla odorants were physisorbed on mOR-EG (ΔE^a < 40 kJ/mol) and the adsorption mechanism may be considered as an exothermic mechanism (ΔE^a > 0). The estimated parameters may also be utilized for the quantitative characterization of the interactions of the studied odorants with mOR-EG to determine the corresponding olfactory bands ranging from 8 to 24.5 kJ/mol.

Combined cross-linked enzyme aggregates of cyclodextrin glucanotransferase and maltogenic amylase from Bacillus lehensis G1 for maltooligosaccharides synthesis

Maltooligosaccharides (MOS) are functional oligosaccharides that can be synthesized through enzymatic cascade reaction between cyclodextrin glucanotransferase (CGTase) and maltogenic amylase (Mag1) from Bacillus lehensis G1. To address the problems of low operational stability and non-reusability of free enzymes, both enzymes were co-immobilized as combined cross-linked enzyme aggregates (Combi-CLEAs-CM) with incorporation of bovine serum albumin (BSA) and Tween 80 (Combi-CLEAs-CM-add). Combi-CLEAs-CM and Combi-CLEAs-CM-add showed activity recoveries of 54.12 % and 69.44 %, respectively after optimization. Combi-CLEAs-CM-add showed higher thermal stability at higher temperatures (40 °C) with longer half-life (46.20 min) as compared to those of free enzymes (36.67 min) and Combi-CLEAs-CM (41.51 min). Both combi-CLEAs also exhibited higher pH stability over pH 5 to pH 9, and displayed excellent reusability with >50 % of initial activity retained after four cycles. The reduction in K_m value of about 22.80 % and 1.76-fold increase in starch hydrolysis in comparison to Combi-CLEAs-CM attested the improvement of enzyme-substrate interaction by Tween 80 and pores formation by BSA in Combi-CLEAs-CM-add. The improved product specificity of Combi-CLEAs-CM-add also produced the highest yield of MOS (492 mg/g) after 3 h. Therefore, Combi-CLEAs-CM-add with ease of preparation, excellent reusability and high operational stability is believed to be highly efficacious biocatalyst for MOS production.

Advanced investigation of a putative adsorption process of nine non key food odorants (non-KFOs) on the broadly tuned human olfactory receptor OR2W1: Statistical physics modeling and molecular docking study

In the present paper, statistical physics formalism was used to understand the olfactory perception via the investigation of dose-olfactory response curves of a putative adsorption process of nine non key food odorants (non-KFOs) on the broadly tuned human olfactory receptor OR2W1, in order to quantitative characterize the interactions between the nine studied non-KFOs, i. e., furfuryl sulfide, furfuryl disulfide, benzyl methyl disulfide, furfuryl methyl disulfide, benzyl methyl sulfide, 1-phenylethanethiol, benzyl mercaptan, furfuryl methyl sulfide and 3-phenylpropanol molecules and OR2W1 binding sites at a molecular level. Two advanced adsorption models have been proposed: the advanced monolayer monoenergy model (monolayer model with identical and independent olfactory receptor binding sites) (Model 1) and the advanced monolayer model with two independent types of olfactory receptor binding sites (Model 2). It was concluded that the monolayer monoenergy model was selected as the most adequate model to fit the experimental dose-olfactory response curves tabulated in literature. Actually, the numerical values of the three fitted physico-chemical parameters (RM1, n and C1) were obtained by a non-linear regression. Indeed, modeling results suggested that the number of docked non-KFOs per OR2W1 binding site n values (1.24 < n < 1.94) was always superior to 1, which indicated the non-parallel orientation of the studied odorants on the olfactory receptor and the multi-molecular adsorption mechanism. The estimated molar adsorption energy ΔEa values (ranged from 6.07 to 12.16 kJ/mol) for the nine olfactory systems confirmed the physical the exothermic characters of the adsorption process since ΔEa values were lower than 40 kJ/mol and positive. Furthermore, these estimated parameters were applied to characterize stereographically and energetically the interaction between the nine non-KFOs and OR2W1 through the determination of the human receptor binding site size distributions (RSDs) and the adsorption energy distributions (AEDs), which were spread out from 0.25 to 6.50 nm and from 0 to 22.50 kJ/mol, respectively. The docking computation between these nine non-KFOs and OR2W1 proved that the estimated binding affinities were belonged to the adsorption energies spectrum in general and the specific adsorption energy band or the molecular vibration modes limited spectrum (between 2.50 kJ/mol and 17 kJ/mol) (approximate olfactory band).

New insights on the adsorption of floral odorants on Apis cerana cerana olfactory receptor AcerOr1: Theoretical modeling and thermodynamic study

Apis cerana cerana counted on its sensitive olfactory system to make survival activities in the surrounding environment and the olfactory receptors can be considered as a primary requirement of odorant detection, recognition and coding. Indeed, the exploitation of the olfactory system of insects in particular the Asian honeybee "Apis cerana cerana" can be the best experimental model to investigate the essentials of the chemosensitivity and may help to better understand the olfactory perception in insects. Hence, an advanced statistical physics modeling via the monolayer model with single energy (n ≠ 1) of the three dose-olfactory responses curves indicated that undecanoic acid, 1-octyl alcohol and 1-nonanol were docked with a mixed parallel and non-parallel orientation on AcerOr1. Furthermore, in the present work, the Apis cerana cerana olfactory receptor AcerOr1 showed high sensitivity and discrimination power to detect undecanoic acid, 1-octyl alcohol and 1-nonanol with concentrations at half saturations values of 10^-7 mol/L and the molar adsorption energy values obtained from data fitting results, which were ranged from 17.91 to 24.00 kJ/mol, confirmed the exothermic and the physisorption nature of the adsorption of the studied floral odorants on AcerOr1. The studied experimental dose-response curves of undecanoic acid, 1-octyl alcohol and 1-nonanol provided access to quantitative (i.e., stereographic and energetic) characterizations of AcerOr1 via the determination of the olfactory receptor site size distributions (RSDs) and the adsorption energy distributions (AEDs). The stereographic characterization showed RSDs spread out from 0.20 to 8 nm presenting average values corresponding to the maximum of the peaks at 1.50 nm, at 1.10 nm and at 1.04 nm for undecanoic acid, 1-octyl alcohol and 1-nonanol, respectively. The energetic characterization presented AEDs ranged from 0 to 40 kJ/mol showing an approximate adsorption energy bands defined between 7.50 and 27.50 kJ/mol, between 15 and 33 kJ/mol and between 13.50 and 34.50 kJ/mol for undecanoic acid, 1-octyl alcohol and 1-nonanol, respectively. The utilization of the analytical expression of the olfactory threshold allowed giving important and helpful informations about the occupation rate of AcerOr1 binding sites that fired a minimal olfactory response at a honeybee olfactory receptor. Hence, the olfactory response can be detected only when 1.97 %, 1.13 % and 2.00 % of AcerOr1 binding sites were occupied by undecanoic acid, 1-octyl alcohol and 1-nonanol, respectively. Lastly, by means of the selected model, the thermodynamic potentials, such as the adsorption entropy, the Gibbs free enthalpy and the internal energy could be calculated and interpreted.

Comparative Analysis of Olfactory Receptor Repertoires Sheds Light on the Diet Adaptation of the Bamboo-Eating Giant Panda Based on the Chromosome-Level Genome

The giant panda (Ailuropoda melanoleuca) is the epitome of a flagship species for wildlife conservation and also an ideal model of adaptive evolution. As an obligate bamboo feeder, the giant panda relies on the olfaction for food recognition. The number of olfactory receptor (OR) genes and the rate of pseudogenes are the main factors affecting the olfactory ability of animals. In this study, we used the chromosome-level genome of the giant panda to identify OR genes and compared the genome sequences of OR genes with five other Ursidae species (spectacled bear (Tremarctos ornatus), American black bear (Ursus americanus), brown bear (Ursus arctos), polar bear (Ursus maritimus) and Asian black bear (Ursus thibetanus)). The giant panda had 639 OR genes, including 408 functional genes, 94 partial OR genes and 137 pseudogenes. Among them, 222 OR genes were detected and distributed on 18 chromosomes, and chromosome 8 had the most OR genes. A total of 448, 617, 582, 521 and 792 OR genes were identified in the spectacled bear, American black bear, brown bear, polar bear and Asian black bear, respectively. Clustering analysis based on the OR protein sequences of the six species showed that the OR genes distributed in 69 families and 438 subfamilies based on sequence similarity, and the six mammals shared 72 OR gene subfamilies, while the giant panda had 31 unique OR gene subfamilies (containing 35 genes). Among the 35 genes, there are 10 genes clustered into 8 clusters with 10 known human OR genes (OR8J3, OR51I1, OR10AC1, OR1S2, OR1S1, OR51S1, OR4M1, OR4M2, OR51T1 and OR5W2). However, the kind of odor molecules can be recognized by the 10 known human OR genes separately, which needs further research. The phylogenetic tree showed that 345 (about 84.56%) functional OR genes were clustered as Class-II, while only 63 (about 15.44%) functional OR genes were clustered as Class-I, which required further and more in-depth research. The potential odor specificity of some giant panda OR genes was identified through the similarity to human protein sequences. Sequences similar to OR2B1, OR10G3, OR11H6 and OR11H7P were giant panda-specific lacking, which may be related to the transformation and specialization from carnivore to herbivore of the giant panda. Since our reference to flavoring agents comes from human research, the possible flavoring agents from giant panda-specific OR genes need further investigation. Moreover, the conserved motifs of OR genes were highly conserved in Ursidae species. This systematic study of OR genes in the giant panda will provide a solid foundation for further research on the olfactory function and variation of the giant panda.

Advanced investigation of the olfactory perception of semiochemical TMT on OR5K1 and Olfr175 by statistical physics approach

The adsorption of the trimethylthiazoline (TMT) on the human olfactory receptor OR5K1 and the mouse olfactory receptor Olfr175 was the object of the present paper. The main contribution of this work was to characterize stereographically and energetically OR5K1 and Olfr175 activated by trimethylthiazoline molecules docked on the human and the mouse olfactory binding pockets using the grand canonical ensemble in statistical physics. The experimental data and the advanced statistical physics models revealed that the adsorption of the trimethylthiazoline on the human olfactory receptor OR5K1 can be interpreted using the monolayer model with single energy, while the monolayer model with two energies described the interaction between the trimethylthiazoline molecules and the mouse olfactory receptor Olfr175. In fact, the investigated odorant was shown to be docked by a multi-docking process and non parallel orientation on OR5K1 and Olfr175 since the values of the number of TMT molecules per binding site n were superior to 1. The proposed models were applied to calculate the human and the mouse olfactory receptor binding site size distributions relative to TMT, which were spread out from 0.30 to 20 nm with a maximum at about 1.75 nm for OR5K1 and from 1 to 25 nm with a peak at about 4.25 nm for Olfr175. Furthermore, it was found from the calculated molar adsorption energies, which were lower than 11 kJ/mol, that physical adsorption process was occurred in the two olfactory systems. The adsorption energy distributions relative to TMT can be also calculated in order to understand of olfaction process in general through the determination of olfactory bands (i. e., adsorption energy distribution bands), which were situated between 0 and 10.50 kJ/mol and between 3 and 12.50 kJ/mol for OR5K1 and Olfr175, respectively. Referring to the investigation of thermodynamic functions governing the adsorption process such as the adsorption entropy, the Gibbs free enthalpy and the internal energy, it may be noted that the disorder peak of the two olfactory systems was reached when the equilibrium concentration was equal to the concentration at half saturation. In addition, the Gibbs free enthalpy and the internal energy were calculated and their negative values indicated that the adsorption process involved in the olfactory mechanism was exothermic and spontaneous nature.

Theoretical study of the olfactory perception of floral odorant on OR10J5 and Olfr16 using the grand canonical ensemble in statistical physics approach

In this work, two experimental dose-response curves of lyral molecules on the OR10J5 and the Olfr16 were employed in order to examine the evolution of physico-chemical parameters involved in the selected statistical physics model(s) to investigate the human and the mouse smelling of a floral scent. Indeed, one layer adsorption model on one type of sites with one energy (1LAM1T1E) and one layer adsorption model on two types of sites with two energies (1LAM2T2E), considered as appropriate models for the adsorption of lyral molecules on the OR10J5 and Olfr16, respectively, have been applied to fit the experimental data. Stereographic and energetic physico-chemical parameters, namely: the maximum response(s) at saturation, the number of docked molecules per olfactory receptor binding site and the concentration(s) at half saturation, were investigated to retrieve helpful information to describe the adsorption process putatively introduced in the olfaction perception. Thus, the advanced modeling results indicated that the studied molecules were docked with a non-parallel orientation (n > 1). Furthermore, for the two olfactory systems, the molar adsorption energies estimated from curves modeling were inferior to 11 kJ/mol, which showed the physisorption process of the adsorption of lyral molecules on OR10J5 and Olfr16. The 1LAM2T2E and the 1LAM1T1E were applied to estimate the OR10J5 and the Olfr175 RSDs, respectively. Hence, lyral RSDs were spread out from 0.7 to 20 nm with maximums at about 4 nm for OR10J5 and at about 3.65 nm for Olfr16. In addition, by using the two advanced models, the olfactory responses of lyral on OR10J5 and Olfr16 can be used for the energetic characterization of the lyral-OR10J5/Olfr16 binding sites interactions and allowed access to the adsorption energy distributions (AEDs). Then, two approximate olfactory bands can be determined for lyral molecules docked on OR10J5 and Olfr16, which are defined between 3 and 15.5 kJ/mol and between 3.5 and 13.5 kJ/mol, respectively. Lastly, thanks to the proposed models the adsorption entropy of the studied systems can be calculated to describe the disorder and the order on OR10J5 and Olfr16 surfaces (disorder peak of the two olfactory systems was attained when the equilibrium concentration was equal to the concentration at half saturation). Furthermore, the Gibbs free enthalpy and the internal energy were estimated and their negative values indicated that the adsorption phenomenon involved in the olfactory perception was spontaneous and exothermic nature.