Introduction
In this article, we will be exploring X-Ray crystallography techniques. And through it, we will determine the 3-dimensional structure of the PPAR delta protein, which is bound to the Merck compound L-165,041.
Aim
To determine the three-dimensional structure of the PPAR delta protein rounded to the L-165, 041 (Merck Compound) using the X-ray crystallography techniques.
Theory
1. PPAR stands for Peroxisome Proliferator-Activated Receptor Delta.
2. This is a kind of protein that depends on ligands. It regulates the transcription of genes, which is related to lipid metabolism and cholesterol metabolism.
3. Merck was the man behind developing compound L-165.
4. This compound acts as the selective PPAR delta agonist.
5. The interacting nature between this ligand and protein is presently unknown.
PPAR
Requirements
1. PPAR delta protein
3. A beam of X-ray photons
4. Various Computer Programs
Procedure
Step 1: To gain more understanding of the biology of the PPAR delta, you first need to take PPAR delta protein and Merck compound L-165, 041.
Step 2: Now, co-crystallize them.
Step 3: After this, use X-ray crystallography to visualize the structure.
Step 4: To perform X-ray crystallography. First, you need to diffract the proteins (microscopic in nature) with a beam of X-ray photons. The charged coupled device collects these X-ray photons.
Step 5: The X-ray protons must be powerful enough to be produced only at synchrotron facilities. For instance, Advanced Light Source is located at the Lawrence Berkeley National Laboratory.
Step 6: To calculate a 2.5 Angstrom resolution electron density and refine, scale, and integrate the diffraction data of the crystal lattice, use several computer programs.
Step 7: Record your observations.
Merck Compound L-165,041
Observations
1. Using the information, we constructed a model of the protein-ligand structure.
2. In the center of the PPAR delta, the ligand-binding site was found.
3. The reason behind holding the ligand in this site was the hydrogen bond and Van der forces between them and the surrounding amino acids of the protein.
Result
1. The structure that we obtained in our experiment, may help us in designing new compounds. And this may have improved interaction with the PPAR delta.
2. The greater understanding of the biology of PPAR delta may affect the use of future drugs in society, which is facing the growing issue of cholesterol metabolism.
Precautions
1. Make sure that the photon beams are extremely powerful.
2. Record your observation carefully.
Conclusion
In this experiment, we determined the three-dimensional structure of PPAR delta protein which is rounded to the Merck compound L-165, 041.
Viva Questions With Answers
Q.1 What was the aim of your experiment?
ANS. We aimed to determine the three-dimensional structure of the PPAR delta protein rounded to the L-165, 041 (Merck Compound) using X-ray crystallography techniques.
Q.2 What is the full form of PPAR structure
ANS. Peroxisome Proliferator-Activated Receptor Delta.
Q.3 What kind of three-dimensional structure did you obtain in the experiment?
ANS. In the center of the three-dimensional structure, we found a ligand-binding site.
Q.4 What forces were responsible for holding the ligand in its position?
ANS. Van der Waal forces and hydrogen bonding
Saquib Siddiqui is a Mechanical Engineer and a content creator. He has special interest in science experiments and teaches the same to school and college students. He is also a technical lead at RUDE LABS PVT. LTD.
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