Thermodynamic binding properties of a novel umami octapeptide K1 ADEDSLA8 and its mutational variants p.A2G, p.D5E, and p.A2G + p.D5E (BMP) in complex with the umami receptor hT1R1/hT1R3

3.0 科研～小助 2025-08-26 12 7 5.04MB 12 页 1知币

侵权投诉

Thermodynamic binding properties of a novel umami octapeptide

ADEDSLA

and its mutational variants p.A2G, p.D5E, and p.A2G +p.D5E

(BMP) in complex with the umami receptor hT1R1/hT1R3

Cenk A. Andac

a,**

, Cem ¨

Ozel

b,c

, Taha M. Rababah

, Ceren Kececiler-Emir

, Kevser K¨

oklü

Duygu Aydin Tekdas

, Sevil Yücel

b,c,*

Department of Medical Pharmacology, School of Medicine, Yeditepe University, Istanbul 34755, Türkiye

Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, ˙

Istanbul 34210, Türkiye

Health Biotechnology Joint Research and Application Center of Excellence, Istanbul 34903, Türkiye

Department of Nutrition and Food Technology, Jordan University of Science and Technology, Irbid 22110, Jordan

Department of Mathematical Engineering, Yildiz Technical University, Davutpasa Campus, ˙

Istanbul 34220, Türkiye

Gebze Technical University, Technology Transfer Coordination Ofce, 41400 Gebze Türkiye

ARTICLE INFO

Keywords:

Umami peptide

Molecular docking

Molecular dynamics

T1R1/T1R3

MM-PBSA

Mutational afnity prediction (MAP)

ABSTRACT

Umami taste properties of a novel octameric peptide K

ADEDSLA

and its mutants p.A2G, p.D5E, and BMP

(KGDEESLA, beef meaty peptide) were assessed by molecular docking, and molecular dynamics (MD) (>1

sec),

MM-PBSA, and Mutational Afnity Prediction (MAP) methods. 3D-structure of the human umami taste receptor

(hT1R1/hT1R3) was homology modeled and rened MD. Docking studies yielded three primary binding sites

(PBS) for K

ADEDSLA

and BMP, one on hT1R1 and two on hT1R3. Upto 1200 nsec of MD studies revealed that

ADEDSLA

binds only to Venus Flytrap Domains (VFTD) region of hT1R1 at high afnity (ΔG

= − 11.94 kcal/

mol), while BMP does not exhibit afnity towards hT1R1/hT1R3 in the absence of glutamate. MAP analysis for p.

A2G (ΔG

= − 7.77 kcal/mol) and p.D5E (ΔG

= − 2.88 kcal/mol) strongly suggest that A

and D

DED

SLA increase the afnity and specicity of binding, posing great potential for the development of a

novel umami peptide in future studies.

1. Introduction

The sense of taste, which also plays an important role in food se-

lection, functions as a food perception system (Liu et al., 2016). Taste-

inducing molecules in the mouth bind to the taste receptors or ion-

channels distributed throughout the whole tongue and oro-pharyngeal

region, inducing intracellular signals rapidly transmitted to the brain

via the cranial nerves (Breslin & Spector, 2008; J. Zhang, Sun-

Waterhouse, et al., 2019).

Upon the discovery of special taste receptors, umami has been

scientically recognized as the fth taste to describe a meaty, broth-like,

or savory taste in 2002, alongside the other four basic tastes of sweet,

sour, salty, and bitter (Kurihara, 2015). The umami taste, isolated from

seaweed broth, was rst discovered by Kikunae Ikeda in 1908

(Lindemann, 2002;Zhang et al., 2017). Not only does the taste of umami

have a taste of its own, but it can also strengthen (salty and sweet) or

lighten (sour and bitter) other tastes (Dang et al., 2014). Monosodium

glutamate (MSG) was the rst molecule described to have an umami

taste. It was then discovered that certain purine-based ribonucleotides,

such as guanosine monophosphate (GMP) and inosine monophosphate

(IMP), have synergistic impacts with MSG and can greatly potentiate the

umami taste intensity (Zhang et al., 2017). The taste of umami has been

of particular interest to the food industry as it plays a crucial role in

accepting taste preferences and consuming many foods (Li et al., 2020).

Umami taste substances have many functions in the human body.

Umami taste substances stimulate pancreatic exocrine secretion, gastric

juice, gastric acid, and insulin release. Because of these effects, it is

known to increase digestion and reduce the dissatisfaction of foods

(Niijima et al., 1990).

Umami taste receptors are class-C G-protein-coupled receptors

* Corresponding author at: Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, ˙

Istanbul, Türkiye.

** Corresponding author at: Department of Medical Pharmacology, School of Medicine, Yeditepe University, Istanbul 34755, Türkiye.

E-mail addresses: cenk_andac@yahoo.com (C.A. Andac), cemozel@yildiz.edu.tr (C. ¨

Ozel), syucel@yildiz.edu.tr (S. Yücel).

Contents lists available at ScienceDirect

Food Chemistry

journal homepage: www.elsevier.com/locate/foodchem

https://doi.org/10.1016/j.foodchem.2025.142966

Received 29 August 2024; Received in revised form 16 January 2025; Accepted 16 January 2025

Food Chemistry 473 (2025) 142966

Available online 22 January 2025

(GPCRs). This family of taste receptors is not only available throughout

the tongue but also available all over the digestive tract and upper

respiratory tract, indicating their physiological functions in taste and

taste perception. (Davaasuren et al., 2015). The GPCR family has an

extracellular Venus Flytrap Domain (VFTD) that is recognized as a taste

recognition region for the receptor. Functional expression and mouse

gene knockout studies reported that T1R1/T1R3 is considered to be the

main receptor for the umami taste (Chaudhari et al., 2009; Li, 2009;

Zhao et al., 2003). Although a complete X-ray structure of the T1R1/

T1R3 heterodimer receptor is currently unavailable, homology-modeled

structures of the heterodimer receptor have been used in many molec-

ular docking studies (Dang et al., 2014; Li, 2009; Li et al., 2002; X. Yu

et al., 2017; Zhu et al., 2021).

In addition to glutamate, certain ribonucleotides and L-aminoacids

as well as peptides and peptidomimetics were found to evoke umami

taste. Thus, there has been increasing interest in the development of

novel umami peptides (Winkel et al., 2008). It appears in literature that

an octapeptide KGDEESLA (Lys-Gly-Asp-Glu-Glu-Ser-Leu-Ala), isolated

in 1978 from papain-treated beef gravy, was reported for the rst time to

possess an umami taste, which was then named as Beef Umami Peptide

(BMP) (Yamasaki & Maekawa, 1978). Then, an ever-increasing number

of peptides have been discovered. For instance, an enzymatic hydroly-

sate of deamidated wheat-gluten was shown to give an MSG-like umami

taste. Long linear peptides are known to have more intense umami tastes

than short-chain di-/tri-peptides (Zhang, Zhao, et al., 2019) Thus far,

more than 100 synthesized umami peptides have been reported, which

were classied based on the number of amino acid residues (Li et al.,

2020; Zhang, Sun-Waterhouse, et al., 2019) Di-/tri-peptides with umami

taste contain glutamic acid (Glu) and/or aspartic acid (Asp) as well as

hydrophilic or hydrophobic amino acids (Iwaniak et al., 2019; Zhang,

Sun-Waterhouse, et al., 2019). A number of umami and/or umami taste-

enhancing peptides/peptidomimetics have been identied in many

foods with known umami taste, including cheese, onion, soy sauce, etc.

Long peptides do not seem to benet most from hydrophilic amino acid

abundance in terms of umami avor. In addition to hydrophilic and

hydrophobic amino acids, one of the key fundamental components of

umami taste is the spatial structure of peptides. However, amino acid

sequence and conformation continue to play essential roles in taste

perception (Zhang, Sun-Waterhouse, et al., 2019). As a result, amino

acids may contribute to the avor of peptides regardless of their unique

taste. Dang et al. (2019) carried out taste studies on peptides by elec-

tronic tongue and reported that the tri-peptide DED possesses a better

umami taste than the tri-peptide DEE, while the authors were unable to

make a clear correlation between peptide aa sequences and tastes (Dang,

Hao, Zhou, et al., 2019).

Docking computations allow to predict molecular interactions be-

tween a ligand and the binding site of a protein. Although the most

recent docking tools have advanced towards predicting bound con-

formers of ligands in relatively close similarity to their x-ray co-

ordinates, computationally determined bound conformers still need to

be validated by molecular dynamics (MD) computations using advanced

forceelds (Berendsen, 1999; Sousa et al., 2006; Ziada et al., 2018).

Previously, several molecular docking studies have been carried out to

assess molecular interactions between umami peptides and the umami

receptor. Dang, Hao, Cao, et al. (2019) determined by docking studies

that T1R3 may be involved in binding umami peptides. On the contrary,

Liu et al. (2019) (Liu et al., 2019) determined by MD studies that T1R1

possesses high-afnity binding sites for small molecules and the peptide

BMP, leading to controversial discussions on in silico results by Dang

et al. (Dang, Hao, Cao, et al., 2019) and Liu et al. (Liu et al., 2019).

More recently, Yu et al. (2021) (Yu et al., 2021) implemented MD

studies for a short time (10 nsec) on interactions between 36 umami

peptides (including BMP) and the umami receptor, T1R1/T1R3. The

authors reported that T1R1 plays a crucial role in the sensation of the

umami taste. As mentioned before, Liu et al. (2019) (Liu et al., 2019)

conducted 100 nsec of MD studies with two replicas of trajectories and

reported that T1R1 possesses two adjacent binding sites for ligand

binding, which can be concurrently occupied by two ligands or sepa-

rately by a single ligand depending on the size of ligands. However, a

100-nsec MD simulation is not sufcient for such a large protein system

to reach an equilibrium state. Furthermore, even if an equilibrium state

is reached, additional production run MD simulations with three replicas

of trajectories are required to meaningfully assess the trajectories

(Knapp et al., 2018). To shed light on more meaningful and detailed

dynamic structures of T1R1/T1R3 in complex with the umami peptides,

KADEDSLA and BMP (KGDEESLA), we implemented three replicas of

200 nsec (600 nsec in total) of production MD simulations using the last

snapshot coordinates of an equilibrium MD simulation for 1000 nsec (1

sec).

Thermodynamic binding characteristics of a novel octameric peptide

with an aa sequence of K

ADEDSLA

(abbreviated KADEDSLA) were

investigated in this study. The peptide was optimally designed by

mutating the beef umami peptide (BMP, with an aa sequence of

GDEESLA

) at two distinct AA points where amino acids with com-

parable physical properties could be substituted. In this sense, G

(gly-

cin) of BMP was replaced with A (alanine), both being hydrophobic

amino acid residues, and E

(glutamate) of BMP was swapped out for D

(aspartate), both representing negatively charged amino acids, to

generate KA

DED

SLA.

Lastly, the p.A2G, p.D5E, and p.A2G +p.D5E (BMP) peptide afn-

ities towards possible binding sites of the umami receptor T1R1/T1R3

were studied in silico by MM-PBSA (Molecular Mechanics-Poisson

Boltzmann) (Andac et al., 2021) and MAP (Mutational Afnity Predic-

tion) methods using three independent MD production trajectories (200

nsec each) of KADEDSLA in complex with T1R1/T1R3 using the last

snapshot coordinates of an equilibrium MD simulation for 1

sec.

2. Materials and methods

2.1. Methods

2.1.1. Homology modeling and molecular docking

Structure coordinates for the extracellular Venus ytrap domains

(VFTD) of the hT1R1/hT1R3 complex were homology modeled by

Modeller v9.1 (licensed Linux version) (Martí-Renom et al., 2000) using

the X-ray coordinates of the T1R3 domain of the medaka sh taste re-

ceptor (PDB ID: 5X2O, chain B) (Nuemket et al., 2017), whose sequence

(aa residues 62–490) exhibits sequence identities of 35.60 % and 36.82

% with the extracellular domains of hT1R1 (Uniprot ID: Q7RTX1) and

hT1R3 (Uniprot ID: Q7RTX0), respectively; see supplementary Fig. S1.

Indeed, the hT1R1/hT1R3 receptor exists as a heterogenic dimer, whose

dimeric coordinates were determined by superposing the modeled

structure of hT1R1 and hT1R3 with the X-ray coordinates of the T1R2a

domain (chain A) and T1R3 domain (chain B) of the medaka sh taste

receptor (PDB ID: 5X2O) (Nuemket et al., 2017).

Homology-modeled coordinates of T1R1/T1R3 were further rened

by implicit solvent MD simulation. The addition of the cytine disulde

bond and parameterization of the initial structures were implemented

by the LEaP module of Amber v18 (Case, Belfon, Ben-Shalom, Brozell,

Cerutti, Cheatham, et al., 2020) using the AMBER.ff19SB force eld

(Tian et al., 2020) in a Generalized Born (GB) implicit water environ-

ment (Nguyen et al., 2013). Cystine (CYX) disulfuric bonds were

generated for T1R1 (between CYX residues 47:87, 333:339, 345:348,

387:392) and T1R3 (between CYX residues 42:83, 350:353, 390:395).

The homology-modeled coordinates of hT1R1/hT1R3 were initially

minimized over 10,000 steps by the pmemd module of AMBER v18

(Case, Belfon, Ben-Shalom, Brozell, Cerutti, Cheatham, et al., 2020),

followed by a temperature equilibration phase at 300 K over 20 psec (at

2 fsec time steps over 10 K iterations) using an innite cutoff for elec-

trostatic interactions (cut =999) and a Langevin thermostat with a

collision frequency γ =1.0 psec

−1

. Temperature-equilibrated co-

ordinates were then used for 45 nsec (at 3 fsec time steps over 15 M

C.A. Andac et al.

Food Chemistry 473 (2025) 142966

文档加载中……请稍候！
如果长时间未打开，您也可以点击刷新试试。

下载文档到电脑，查找使用更方便

1 知币 7人已下载

立即下载

Thermodynamic binding properties of a novel umami octapeptide K1 ADEDSLA8 and its mutational variants p.A2G, p.D5E, and p.A2G + p.D5E (BMP) in complex with the umami receptor hT1R1/hT1R3.pdf

共12页,预览4页

还剩页未读，继续阅读

Thermodynamic binding properties of a novel umami octapeptide K1 ADEDSLA8 and its mutational variants p.A2G, p.D5E, and p.A2G + p.D5E (BMP) in complex with the umami receptor hT1R1/hT1R3

相关推荐

开通VIP享超值会员特权

作者详情

相关内容

推荐作者

热门标签

举报选择: