In vitro inhibition studies of coumarin derivatives on Bos taurus enolase and elucidating their interaction by molecular docking, molecular dynamics simulations and MMGB(PB)SA binding energy calculation

Sarıyer, Emrah; Kocer, Sinem; Danış, Özkan; Turgut-Balık, Dilek

doi:10.1016/j.bioorg.2021.104796

Cited by 4 publications

(2 citation statements)

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“…19 In contrast to molecular docking, MD simulation, reflecting the dynamic binding between umami peptides and T1R1/T1R3, can be used to elucidate complex dynamic processes in protein systems, such as binding energy 20 and stability, 21 and it can also clarify the binding between ligands and receptors by using root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (R g ), interaction energy, and other parameters. 22 This study aimed to reveal the flavor characteristics of HK-7, EY-3, and LR-6 peptides by triangle, electronic tongue, and dose-feedback tests and predict the secondary structure information on the three umami peptides by using a circular dichroism spectrum (CD). MD simulations have been used to study the interactions between umami peptides and umami receptor.…”

Section: ■ Introductionmentioning

confidence: 99%

“…Molecular dynamics simulation (MD), based on Newtonian mechanics, an effective technique to reflect the macroscopic properties of substances through microscopic systems, can better understand the structural changes between receptor proteins and ligands at the molecular level, which is widely used to explore the interaction mechanism and conformational relationship between food proteins and other food compounds . In contrast to molecular docking, MD simulation, reflecting the dynamic binding between umami peptides and T1R1/T1R3, can be used to elucidate complex dynamic processes in protein systems, such as binding energy and stability, and it can also clarify the binding between ligands and receptors by using root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration ( R g ), interaction energy, and other parameters …”

Section: Introductionmentioning

confidence: 99%

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

Jia,

Yang,

Liao

et al. 2024

J. Agric. Food Chem.

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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 βfolding, 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.

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Section: ■ Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%