VmmScore: An umami peptide prediction and receptor matching program based on a deep learning approach.

Peptides, with recognized physiological and medical implications, such as the ability to lower blood pressure and lipid levels, are central to our research on umami taste perception. This study introduces a computational strategy to tackle the challenge of identifying optimal umami receptors for these peptides. Our VmmScore algorithm includes two integral components: Mlp4Umami, a predictive module that evaluates the umami taste potential of peptides, and mm-Score, which enhances the receptor matching process through a machine learning-optimized molecular docking and scoring system. This system encompasses the optimization of docking structures, clustering of umami peptides, and a comparative analysis of docking energies across peptide clusters, streamlining the receptor identification process. Employing machine learning, our method offers a strategic approach to the intricate task of umami receptor determination. We undertook virtual screening of peptides derived from Lateolabrax japonicus, experimentally verifying the umami taste of three identified peptides and determining their corresponding receptors. This work not only advances our understanding of the mechanisms behind umami taste perception but also provides a rapid and cost-effective method for peptide screening. The source code is publicly accessible at https://github.com/heyigacu/mlp4umami/, encouraging further scientific exploration and collaborative efforts within the research community.

From Molecular Dynamics to Taste Sensory Perception: A Comprehensive Study on the Interaction of Umami Peptides with the T1R1/T1R3-VFT Receptor.

The research on the umami receptor-ligand interaction is crucial for understanding umami perception. This study integrated molecular simulations, sensory evaluation, and biosensor technology to analyze the interaction between umami peptides and the umami receptor T1R1/T1R3-VFT. Molecular dynamics simulations were used to investigate the dissociation process of seven umami peptides with the umami receptor T1R1/T1R3-VFT, and by calculating the potential mean force curve using the Jarzynski equation, it was found that the binding free energy of umami peptide is between -58.80 and -12.17 kcal/mol, which had a strong correlation with the umami intensity obtained by time intensity sensory evaluation. Through correlation analysis, the dissociation rate constants (0.0126-0.394 1/s) of umami peptides were found to have a great impact on umami perception. The faster the dissociation rate of umami peptides from receptors, the stronger the perceived intensity of the umami taste. This research aims to elucidate the relationship between the umami peptide-receptor interaction and umami perception, providing theoretical support for the exploration of umami perception mechanisms.

Flavor Characteristics of Umami Peptides from Wuding Chicken Revealed by Molecular Dynamics Simulation.

Wuding chicken is famous for its delicious meat, and HLEEEIK, LDDALR, and ELY were jointly extracted from different processing stages of Wuding chicken. However, whether these peptides can be used as umami supplements is unclear. The sensory evaluation tests were used to study the taste characteristics. The secondary structure of the peptides and their interaction with T1R1/T1R3 were predicted by the circular dichroism spectrum and molecular dynamics simulation. The umami threshold was 0.03125 to 0.06250 mg/mL, all of which could increase umami, saltiness, sweetness, and mask bitterness. Compared with HLEEEIK, the frequency of umami active fragments and the improvement rate of the umami score of EEE increased by 133.35% and 40.09%, respectively. Peptides were dominated by umami taste according to sensory analysis, among which EE-3 (3.18) has the highest umami intensity followed by LR-4 (2.58), HK-7 (2.13), and EY-3 (1.82). The main secondary structure of umami peptides was ß-folding, and Tyr74, Arg323, Arg272, and Gln35 were the key amino acid residues for binding of umami peptides to the receptor. This study further elucidated that the umami intensity of the peptides could be altered by changing the sequence composition of the peptides, which enhanced our understanding of the complex flavor properties of umami peptides.

Gene expression analyses of TAS1R taste receptors relevant to the treatment of cardiometabolic disease.

The sweet taste receptor (STR) is a G protein-coupled receptor (GPCR) responsible for mediating cellular responses to sweet stimuli. Early evidence suggests that elements of the STR signaling system are present beyond the tongue in metabolically active tissues, where it may act as an extraoral glucose sensor. This study aimed to delineate expression of the STR in extraoral tissues using publicly available RNA-sequencing repositories. Gene expression data was mined for all genes implicated in the structure and function of the STR, and control genes including highly expressed metabolic genes in relevant tissues, other GPCRs and effector G proteins with physiological roles in metabolism, and other GPCRs with expression exclusively outside the metabolic tissues. Since the physiological role of the STR in extraoral tissues is likely related to glucose sensing, expression was then examined in diseases related to glucose-sensing impairment such as type 2 diabetes. An aggregate co-expression network was then generated to precisely determine co-expression patterns among the STR genes in these tissues. We found that STR gene expression was negligible in human pancreatic and adipose tissues, and low in intestinal tissue. Genes encoding the STR did not show significant co-expression or connectivity with other functional genes in these tissues. In addition, STR expression was higher in mouse pancreatic and adipose tissues, and equivalent to human in intestinal tissue. Our results suggest that STR expression in mice is not representative of expression in humans, and the receptor is unlikely to be a promising extraoral target in human cardiometabolic disease.

Typical Umami Ligand-Induced Binding Interaction and Conformational Change of T1R1-VFT.

Umami taste receptor type 1 member 1/3 (T1R1/T1R3) heterodimer has multiple ligand-binding sites, most of which are located in T1R1-Venus flytrap domain (T1R1-VFT). However, the critical binding process of T1R1-VFT/umami ligands remains largely unknown. Herein, T1R1-VFT was prepared with a sufficient amount and functional activity, and its binding characteristics with typical umami molecules (monosodium l-glutamate, disodium succinate, beefy meaty peptide, and inosine-5'-monophosphate) were explored via multispectroscopic techniques and molecular dynamics simulation. The results showed that, driven mainly by hydrogen bond, van der Waals forces, and electrostatic interactions, T1R1-VFT bound to umami compound at 1:1 (stoichiometric interaction) and formed T1R1-VFT/ligand complex (static fluorescence quenching) with a weak binding affinity (Ka values: 252 ± 19 to 1169 ± 112 M-1). The binding process was spontaneous and exothermic (ΔG, -17.72 to -14.26 kJ mol-1; ΔH, -23.86 to -12.11 kJ mol-1) and induced conformational changes of T1R1-VFT, which was mainly reflected in slight unfolding of α-helix (Δα-helix < 0) and polypeptide chain backbone structure. Meanwhile, the binding of the four ligands stabilized the active conformation of the T1R1-VFT pocket. This work provides insight into the binding interaction between T1R1-VFT/umami ligands and improves understanding of how umami receptor recognizes specific ligand molecules.

Preparation, Sensory Characterization, and Umami-Enhancing Mechanism of Novel Peptide Glycoconjugates.

Previous studies supposed that Amadori rearrangement products (ARPs) of peptides might have better umami-enhancing abilities. To confirm this, five ARPs (EP-ARP, AH-ARP, EE-ARP, ß-AH-ARP, RFPHADF-ARP) were synthesized using a food-grade preparation method, and their chemical structures were clearly demonstrated by mass spectrometry and 1D/2D NMR. Sensory experiments showed that ARPs had better umami-enhancing abilities than the corresponding peptides in this research, though their enhancing performance varied. ARPs showed a synergistic effect with multiple umami substances (MSG and GMP), while their corresponding peptides did not. RFPHADF-ARP had good umami-enhancing capacity, despite that RFPHADF was a bitter peptide without any umami/umami-enhancing property. RFPHADF-ARP could bind to the T1R3, which is beneficial to the stability of the active conformation of the umami receptor. The introduction of glucose via the Maillard reaction increased the binding force of RFPHADF with the umami receptor by influencing the electron density distribution and offering more binding groups (hydroxide group).

Research progress in the screening and evaluation of umami peptides.

Umami is an important element affecting food taste, and the development of umami peptides is a topic of interest in food-flavoring research. The existing technology used for traditional screening of umami peptides is time-consuming and labor-intensive, making it difficult to meet the requirements of high-throughput screening, which limits the rapid development of umami peptides. The difficulty in performing a standard measurement of umami intensity is another problem that restricts the development of umami peptides. The existing methods are not sensitive and specific, making it difficult to achieve a standard evaluation of umami taste. This review summarizes the umami receptors and umami peptides, focusing on the problems restricting the development of umami peptides, high-throughput screening, and establishment of evaluation standards. The rapid screening of umami peptides was realized based on molecular docking technology and a machine learning method, and the standard evaluation of umami could be realized with a bionic taste sensor. The progress of rapid screening and evaluation methods significantly promotes the study of umami peptides and increases its application in the seasoning industry.

Identification and comparison of umami-peptides in commercially available dry-cured Spanish mackerels (Scomberomorus niphonius).

Dry-cured Spanish mackerel (DSM; Scomberomorus niphonius) is a popularity worldwide dry-cured marine fish product due to its salty and umami flavor. Umami peptides from eight commercial DSMs were identified and compared, and their molecular mechanisms were evaluated via molecular simulation. The results showed that the sequence of peptides varied in different DSMs, wherein only ten sequences were repeated across multiple samples and the remaining 19 were detected in only one sample. The sensory characteristics of eight repeated peptides were evaluated, and four were found to exhibit umami taste and umami-enhancing effects, including Arg-Asp, Asp-Gly-Val, Asp-Arg, and Asp-Lys. They all had a strong affinity for umami receptors, and several amino acid residues of the receptors were mobilized as binding sites to form hydrogen bonds and hydrophobic bonds in ligand-receptor interactions. These results indicated that DSM was rich in umami and umami-enhancing peptides, but their sequence were different in different DSMs.

Understanding the molecular mechanism of umami recognition by T1R1-T1R3 using molecular dynamics simulations.

Taste receptor T1R1-T1R3 can be activated by binding to several natural ligands, e.g., l-glutamate and 5'-ribonucleotides etc., thereby stimulating the umami taste. The molecular mechanism of umami recognition at atomic details, however, remains elusive. Here, using homology modeling, molecular docking and molecular dynamics (MD) simulations, we investigate the effects of five natural umami ligands on the structural dynamics of T1R1-T1R3. Our work identifies the key residues that are directly involved in recognizing the binding ligands. In addition, two adjacent binding sites in T1R1 are determined for substrate binding, and depending on the molecular size and chemical properties of the incoming ligand, one or both binding sites can be occupied. More interestingly, the ligand binding can modulate the pocket size, which is likely correlated with the closing and opening motions of T1R1. We then classify these five ligands into two groups according to their different binding effects on T1R1, which likely associate with the distinct umami signals stimulated by various ligands. This work warrants new experimental assays to further validate the theoretical model and provides guidance to design more effective umami ligands.

Muscle regulatory factors regulate T1R3 taste receptor expression.

T1R3 is a T1R class of G protein-coupled receptors, composing subunit of the umami taste receptor when complexed with T1R1. T1R3 was originally discovered in gustatory tissue but is now known to be expressed in a wide variety of tissues and cell types such the intestine, pancreatic ß-cells, skeletal muscle, and heart. In addition to taste recognition, the T1R1/T1R3 complex functions as an amino acid sensor and has been proposed to be a control mechanism for the secretion of hormones, such as cholecystokinin, insulin, and duodenal HCO3(-) and activates the mammalian rapamycin complex 1 (MTORC1) to inhibit autophagy. T1R3 knockout mice have increased rate of autophagy in the heart, skeletal muscle and liver. Thus, T1R3 has multiple physiological functions and is widely expressed in vivo. However, the exact mechanisms regulating T1R3 expression are largely unknown. Here, we used comparative genomics and functional analyses to characterize the genomic region upstream of the annotated transcriptional start of human T1R3. This revealed that the T1R3 promoter in human and mouse resides in an evolutionary conserved region (ECR). We also identified a repressive element located upstream of the human T1R3 promoter that has relatively high degree of conservation with rhesus macaque. Additionally, the muscle regulatory factors MyoD and Myogenin regulate T1R3 expression and T1R3 expression increases with skeletal muscle differentiation of murine myoblast C2C12 cells. Taken together, our study raises the possibility that MyoD and Myogenin might control skeletal muscle metabolism and homeostasis through the regulation of T1R3 promoter activity.

Rubemamine and Rubescenamine, Two Naturally Occurring N-Cinnamoyl Phenethylamines with Umami-Taste-Modulating Properties.

Sensory screening of a series of naturally occurring N-cinnamoyl derivatives of substituted phenethylamines revealed that rubemamine (9, from Chenopodium album) and rubescenamine (10, from Zanthoxylum rubsecens) elicit strong intrinsic umami taste in water at 50 and 10 ppm, respectively. Sensory tests in glutamate- and nucleotide-containing bases showed that the compounds influence the whole flavor profile of savory formulations. Both rubemamine (9) and rubescenamine (10) at 10-100 ppm dose-dependently positively modulated the umami taste of MSG (0.17-0.22%) up to threefold. Among the investigated amides, only rubemamine (9) and rubescenamine (10) are able to directly activate the TAS1R1-TAS1R3 umami taste receptor. Moreover, both compounds also synergistically modulated the activation of TAS1R1-TAS1R3 by MSG. Most remarkably, rubemamine (9) was able to further positively modulate the IMP-enhanced TAS1R1-TAS1R3 response to MSG ∼ 1.8-fold. Finally, armatamide (11), zanthosinamide (13), and dioxamine (14), which lack intrinsic umami taste in vivo and direct receptor response in vitro, also positively modulated receptor activation by MSG about twofold and the IMP-enhanced MSG-induced TAS1R1-TAS1R3 responses approximately by 50%. In sensory experiments, dioxamine (14) at 25 ppm in combination with 0.17% MSG exhibited a sensory equivalent to 0.37% MSG.

An efficient Escherichia coli expression system for the production of a functional N-terminal domain of the T1R3 taste receptor.

Sweet taste is mediated by a dimeric receptor composed of two distinct subunits, T1R2 and T1R3, whereas the T1R1/T1R3 receptor is involved in umami taste perception. The T1R1, T1R2, and T1R3 subunits are members of the small family of class C G protein-coupled receptors (GPCRs). The members of this family are characterized by a large N-terminal domain (NTD), which is structurally similar to bacterial periplasmic-binding proteins and contains the primary ligand-binding site. In a recent study, we described a strategy to produce a functional dimeric human T1R3-NTD. Although the protein was expressed as inclusion bodies (IBs) using the Escherichia coli system, the conditions for the refolding of functional hT1R3-NTD were determined using a fractional factorial screen coupled to a binding assay. Here, we report that this refolding strategy can be used to produce T1R1- and T1R2-NTDs in large quantities. We also discuss that our findings could be more generally applicable to other class C GPCR-NTDs, including the γ-aminobutyric acid type B receptor (GABABR), the extracellular calcium-sensing receptor (CaSR) and the large family of pheromone (V2R) orphan receptors.