Difference between revisions of "Part:BBa K2368003:Experience"

Revision as of 15:53, 25 October 2017

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Please enter how you used this part and how it worked out.

Applications of BBa_K2368003

In our experiment, this part is used to accept the signal inputted in our whole pathway.

Part 1: Dry experiments of T1R2

1、Structure models

Purpose

In order to confirm whether this “radar” T1R2/T1R3 can “sense” the sweetness of different sweetener, we simulate the receptor structure model. It helps us to understand how the sweeteners binding to T1R2/T1R3 receptor visually. Otherwise we hope to find some unknown sweeteners binding sites based on this model, even some ideal but unknown sweeteners.

Method

Initially, to make the signal input more accurate and reliable, we simulate the T1R2/T1R3 receptor structure model using SWISS-MODEL. Additionally, we prepare some sweeteners’ PDB file based on Chemdraw 2D and Chemdraw 3D. And the docking process is performed by using Autodock Vina.

Result

We used homology modeling method to get the structure of human sweet receptorT1R2/T1R3. The quality of the simulate structure within normal range and it only contain the ligand-binding-domain based on the crystal protein structure of Mice.

Fig. 2 The simulate structure of human sweetness receptors ligand-binding domain (LBD)

Then we use software Chemdraw 2D and Chemdraw 3D to build PDB files of some classic sweeteners.

Fig. 3 The 3D structure of some sweeteners

The docking process is carried out under Autodock Vina (Fig. 4-6).

Fig. 4 The docking result of different sweeteners

Fig. 5 The docking result of aspartame

Fig. 6 The docking result of stevioside

2、T1R2/T1R3 receptor activation part

The part is about the sweeteners binding to the receptor and the GPCR produce the initial signal through changing structure. For T1R2/T1R3, we divide the process of inducing signal into four conditions of T1R2/T1R3 as show in Fig. 7. And the reaction between different conditions of protein is used ODEs to describe it. The all ODEs are shown follow.

Fig. 6 The docking result of stevioside

User Reviews

UNIQ3c8187bbf2294397-partinfo-00000000-QINU UNIQ3c8187bbf2294397-partinfo-00000001-QINU

@@ Line 21: / Line 21: @@
 <p>Then we use software Chemdraw 2D and Chemdraw 3D to build PDB files of some classic sweeteners.</p>
-[[File:T-BIT-China-2017parts-33.png|center|250px|默认文字]]
+[[File:T-BIT-China-2017parts-33.png|center|500px|默认文字]]
 <p style="text-align: center">Fig. 3 The 3D structure of some sweeteners</i></p><p></p>
 <p>The docking process is carried out under Autodock Vina (Fig. 4-6).</p>
 [[File:T-BIT-China-2017parts-4.png|center|250px|默认文字]]
 <p style="text-align: center">Fig. 4 The docking result of different sweeteners </i></p>
-[[File:T-BIT-China-2017part-5.png|center|250px|默认文字]]
+[[File:T-BIT-China-2017parts-5.png|center|250px|默认文字]]
 <p style="text-align: center">Fig. 5 The docking result of aspartame </i></p>
 [[File:T-BIT-China-2017part-6.png|center|250px|默认文字]]
 <p style="text-align: center">Fig. 6 The docking result of stevioside </i></p>
-<p></p>
+<p>2、T1R2/T1R3 receptor activation part  </p>
-<p></p>
+<p>The part is about the sweeteners binding to the receptor and the GPCR produce the initial signal through changing structure. For T1R2/T1R3, we divide the process of inducing signal into four conditions of T1R2/T1R3 as show in Fig. 7. And the reaction between different conditions of protein is used ODEs to describe it. The all ODEs are shown follow.  </p>
+[[File:T-BIT-China-2017parts-7.png|center|250px|默认文字]]
+<p style="text-align: center">Fig. 6 The docking result of stevioside </i></p>
 <p></p>
 ===User Reviews===