Theoretical study of a putative adsorption mechanism of arginine and glutamate on goldfish 5.24 and zebrafish Z06: Statistical physics modeling, thermodynamic study, and docking simulation

• Published in: Journal of molecular structure 2025-02, Vol.1321, p.139862, Article 139862
• Main Authors: Ben Khemis, Ismahene, Aouaini, Fatma, Al-mugren, Kholoud Saad, Knani, Salah, Graba, Besma, Ben Lamine, Abdelmottaleb
• Format: Article
• Language: English
• Subjects: Amino acids; Goldfish and zebrafish olfactory receptors; Mono-layer model with one energy (MLM1E); Quantitative characterization; Statistical physics formalism; Thermodynamic functions
• ISSN: 0022-2860
• DOI: 10.1016/j.molstruc.2024.139862

•Two amino acids olfactory responses are fitted using the MLM1E model.•Physicochemical analysis of the fish olfactory systems was studied.•Quantitative characterization of 5.24 and Z06, activated by two amino acids, is investigated.•Thermodynamic study of the studied systems is realized.•Docking process is described via a molecular docking simulation. An adsorption phenomenon putatively involved in the sense of smell of arginine and glutamate amino acids in the goldfish olfactory receptor 5.24 and the zebrafish olfactory receptor Z06 was applied in this study to deeply interpret and characterize the olfaction process at a molecular level. As a result, the experimental concentration-olfactory response curves were adjusted using the mono-layer model with one energy (MLM1E). On the one hand, the physicochemical parameters involved in the chosen model were utilized to microscopically investigate the four olfactory systems. Indeed, the two amino acids were adsorbed via a non-parallel configuration, and the process of adsorption was multi-molecular. The molar adsorption energies, which ranged from 22.09 to 35.97 kJ/mol, could be utilized to define the energetic interaction types between the investigated amino acids and the two tested fish olfactory receptors. The size and adsorption energy heterogeneity of 5.24 and Z06 binding pockets were measured by estimating the pocket site size distributions or PSDs (stereographic characterization) and the adsorption energy distributions or AEDs (energetic characterization). On the other hand, these physicochemical parameters could also be applied to macroscopically investigate the four olfactory systems. Hence, three thermodynamic functions including the adsorption entropy Sa, the internal energy Eint, and the Gibbs free energy G were computed in order to investigate the disorder, the exothermicity, and the spontaneity of the studied systems, respectively. The docking modeling analysis of arginine and glutamate amino acids with goldfish 5.24 and zebrafish Z06 revealed simulated binding energies that closely matched the average adsorption energies (peaks of AEDs). These affinities corresponded to the adsorption energy bands known as olfactory bands or spectrums of vibration modes.