Indirect characterizations of mOR-EG: Modeling analysis of five concentration-olfactory response curves via an advanced monolayer adsorption model

Theoretical modeling of 2,4-dichlorophenoxyacetic acid on acid-treated peanut skin: microscopic analysis via statistical physics treatment

In this study, the experimental adsorption isotherms of 2,4-dichlorophenoxyacetic acid (2,4-DA) on peanut skin treated with sulfuric acid were analyzed under different temperatures and characterized by Fourier transform infrared spectroscopy. The adsorption mechanism was interpreted based on statistical physics theory using the homogeneous double-layer model with one energy (HDLM1E). The modeling results indicated that the removal of 2,4-DA molecules occurred through a multi-interactive adsorption mechanism at temperatures of 25, 35, and 45 °C (0.76 < n < 0.99). In comparison, at 55 °C, a monomolecular adsorption mechanism was observed (n = 1.00). At 25 °C, the adsorbent demonstrated excellent performance in the 2,4-DA removal, with a maximum capacity of 244.33 mg/g. The increase in temperature reduced the adsorbent's performance in removing 2,4-DA molecules because it increased thermal collisions, which harmed the system. From an energetic point of view, the adsorbent showed less effectiveness in removing the herbicide at high temperatures, indicating an exothermic adsorption process. The surface adsorption energies ranged from 4.72 to 6.06 kJ/mol, indicating the predominance of a physisorption mechanism. Therefore, the adsorption process at low temperatures is essential for industrial applications to ensure efficient wastewater treatment. This result is possible using an adsorbent from peanut skin subjected to acid treatment. Finally, the creation of an adsorbent from acid-treated peanut (Arachis hypogaea) skin presents an excellent alternative, yielding exceptional results in removing the 2,4-DA herbicide.

Computational approaches for decoding structure-saltiness enhancement and aroma perception mechanisms of odorants: From machine learning to molecular simulation

The unclear relationship between structure and saltiness enhancement limits the development and application of savory odorants. The structure characteristic-saltiness enhancement perception (SEP) mechanisms of savory odorants were investigated by machine learning, molecular docking, and site-directed mutagenesis simulations. The XGBoost model (R2 = 0.96) showed better prediction on the maximum saltiness-enhancement ability of odorants based on their structures. The important features of the odorants contributing to SEP were analyzed by Shapley additive explanations (SHAP). Results showed that phenyl and aldehyde groups had significant positive contributions to SEP, with SHAP values of + 2.94 and + 0.74, respectively. Molecular docking and site-directed mutagenesis simulations elucidated the interaction region, forces, and key sites between savory odorants and olfactory receptors. Results showed TM3, TM5 and TM6 were the main interaction regions of the savory odorants prioritize binding with OR1A1 and OR1D2, resulting in the characteristic aromas. Hydrogen bonding and hydrophobic interactions were the key driving forces. Phe203, Asn109, and Asn155 of OR1A1 were partially important residues involved in the interactions with savory odorants. These findings presented a quick screening approach for savory odorants and revealed their SEP mechanism, providing theoretical guidance to facilitate the application of odor-induced salt reduction in food industry.

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.

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.