Difference between revisions of "Team:BIT-China/Model/Docking"
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| − | + | <section class="content_container" id="mytop"> | |
| − | + | <h2 class="title-h2">MODEL-Docking </h2> | |
| − | + | <div class="cd-section" id="Purpose"> | |
| − | < | + | <h3 class="title-h3">STRUCTURE MODEL</h3> |
| − | <p class="my-content-p"> | + | <h4 class="title-h4">Purpose </h4> |
| − | + | <p class="my-content-p">In order to confirm whether this "radar" T1R2/T1R3 can "sense" the sweetness of different sweetener, we simulated the model of receptor's structure[1] [4]. It was helpful to observe how the sweeteners binding to T1R2/T1R3 receptor visually. Moreover, we expected to find some unknown sweeteners binding sites based on this model, even some ideal sweeteners are still unknown. </p> | |
| − | + | <h4 class="title-h4">Methods</h4> | |
| + | <p class="my-content-p">To make the signal input more accurate and reliable, we simulated the T1R2/T1R3 receptor's structure model through SWISS-MODEL. Meanwhile, according to Chemdraw 2D and Chemdraw 3D, we constructed some sweetners' model. And the docking process was performed by using Autodock Vina.</p> | ||
| − | + | <h4 class="title-h4">Results</h4> | |
| − | < | + | <p class="my-content-p">We used homology modeling to obtain the structure of human sweet receptor T1R2/T1R3. According to the crystal protein structure of similar receptor in mice, we only simulated ligand-binding-domain of our receptor. </p> |
| − | <p class="my-content-p"> | + | <div class="my-content-box"> |
| − | + | <img class="formula50" src="https://static.igem.org/mediawiki/2017/6/65/T--BIT-China--2017modeling_pic3.png" /> | |
| + | <span>Fig. 3 The simulated structure of human sweetness receptors' ligand-binding domain (LBD)</span> | ||
| + | </div> | ||
| + | <p class="my-content-p">Then, taking advantage of software Chemdraw 2D and Chemdraw 3D, we established some natural or artificial sweeteners' structure.</p> | ||
| + | <div class="my-content-box"> | ||
| + | <img class="formula50" src="https://static.igem.org/mediawiki/2017/5/50/T--BIT-China--2017modeling_pic4.png" /> | ||
| + | <span>Fig. 4 Three dimensional structure of some sweeteners</span> | ||
| + | </div> | ||
| + | <p class="my-content-p">Docking process was carried out under Autodock Vina (Fig. 5-7).</p> | ||
| − | + | <div class="my-img-box" style="align-items: flex-end; justify-content: space-around;"> | |
| − | + | <img style="width: 30%; height: 30%" src="https://static.igem.org/mediawiki/2017/7/7b/T--BIT-China--2017modeling_pic5.png" alt=""> | |
| − | + | <img style="width: 30%; height: 30%" src="https://static.igem.org/mediawiki/2017/5/54/T--BIT-China--2017modeling_pic6.png" alt=""> | |
| − | + | <img style="width: 25%; height: 25%" src="https://static.igem.org/mediawiki/2017/7/7c/T--BIT-China--2017modeling_pic7.png" alt=""> | |
| + | </div> | ||
<div class="my-img-box"> | <div class="my-img-box"> | ||
| − | <img | + | <span>Fig. 5． Docking result of different sweeteners </span> |
| + | <span>Fig. 6． Docking result of aspartame </span> | ||
| + | <span>Fig. 7． Docking result of stevioside </span> | ||
| + | </div> | ||
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| + | <h4 class="title-h4">Discussion</h4> | ||
| + | <p class="my-content-p">According to the results, all common, representative sweet substances can bind to human T1R2/T1R3 receptors on ligand-binding Domain (LBD). That means there are a lot of sites in receptor can provide advantage of suitable binding. Although model is only a part of the whole receptor, this domain is the most important domain for binding. It proves that this receptor can "taste" the sweetness and our project has enormous potential to be used in a wide range of sweet material testing compared to E-Tong.</p> | ||
| + | <p class="my-content-p">Our docking results estimated that ligand-binding domain (LBD) of human T1R2/T1R3 receptors could bind with almost all kinds of known sweeteners. It provided evidence that this receptor has an ability to "taste" the sweetness. Meanwhile, our results also helped us to speculate that the number of both binding-site and binding-molecule also might influence the sense of sweetness.</p> | ||
| + | <p class="my-content-p">However, our model still needs optimization. We plan to enhance the docking model and the more professional direct would be supplied by it.</p> | ||
| + | |||
| + | <p class="my-content-p">At the same time, we also find the situation of different sweeteners combination is different, for example the binding number, binding concentration and so on, which demonstrates people for the perception of sweet substances not only depends on the sweetness of the sweetener, but also on the concentration and the number of binding. In the future, it can provide the guidance for us to develop sweetness standards.</p> | ||
| + | |||
| + | <p class="my-content-p">But our model needs to be improved, in the future, we will use molecular dynamics modeling (molecular docking) and other methods to modify the sweet receptor model utilizing software Gauss View through the Gaussian force field and other mechanical system. The appropriate deformation of the small molecular material is also going to be simulated for making docking results be closer to the real situation.</p> | ||
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Revision as of 14:01, 27 October 2017
MODEL-Docking
STRUCTURE MODEL
Purpose
In order to confirm whether this "radar" T1R2/T1R3 can "sense" the sweetness of different sweetener, we simulated the model of receptor's structure[1] [4]. It was helpful to observe how the sweeteners binding to T1R2/T1R3 receptor visually. Moreover, we expected to find some unknown sweeteners binding sites based on this model, even some ideal sweeteners are still unknown.
Methods
To make the signal input more accurate and reliable, we simulated the T1R2/T1R3 receptor's structure model through SWISS-MODEL. Meanwhile, according to Chemdraw 2D and Chemdraw 3D, we constructed some sweetners' model. And the docking process was performed by using Autodock Vina.
Results
We used homology modeling to obtain the structure of human sweet receptor T1R2/T1R3. According to the crystal protein structure of similar receptor in mice, we only simulated ligand-binding-domain of our receptor.
Fig. 3 The simulated structure of human sweetness receptors' ligand-binding domain (LBD)
Then, taking advantage of software Chemdraw 2D and Chemdraw 3D, we established some natural or artificial sweeteners' structure.
Fig. 4 Three dimensional structure of some sweeteners
Docking process was carried out under Autodock Vina (Fig. 5-7).
Discussion
According to the results, all common, representative sweet substances can bind to human T1R2/T1R3 receptors on ligand-binding Domain (LBD). That means there are a lot of sites in receptor can provide advantage of suitable binding. Although model is only a part of the whole receptor, this domain is the most important domain for binding. It proves that this receptor can "taste" the sweetness and our project has enormous potential to be used in a wide range of sweet material testing compared to E-Tong.
Our docking results estimated that ligand-binding domain (LBD) of human T1R2/T1R3 receptors could bind with almost all kinds of known sweeteners. It provided evidence that this receptor has an ability to "taste" the sweetness. Meanwhile, our results also helped us to speculate that the number of both binding-site and binding-molecule also might influence the sense of sweetness.
However, our model still needs optimization. We plan to enhance the docking model and the more professional direct would be supplied by it.
At the same time, we also find the situation of different sweeteners combination is different, for example the binding number, binding concentration and so on, which demonstrates people for the perception of sweet substances not only depends on the sweetness of the sweetener, but also on the concentration and the number of binding. In the future, it can provide the guidance for us to develop sweetness standards.
But our model needs to be improved, in the future, we will use molecular dynamics modeling (molecular docking) and other methods to modify the sweet receptor model utilizing software Gauss View through the Gaussian force field and other mechanical system. The appropriate deformation of the small molecular material is also going to be simulated for making docking results be closer to the real situation.
