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The effect of bilirubin on Bad, Bak, and Bim pro-apoptotic factors: A molecular dynamic simulation study

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Title The effect of bilirubin on Bad, Bak, and Bim pro-apoptotic factors: A molecular dynamic simulation study
 
Creator Saffari-Chaleshtori, Javad
Shafiee, Sayed Mohammad
Heidarian, Esfandiar
 
Subject Apoptosis
Hetero-oligomerization
Homo-oligomerization
Protein conformation
Three-dimensional structure
 
Description 236-243
Bilirubin, an endogenous catabolic product of the heme catabolism, can induce apoptosis in damaged cells. This study investigated the effect of bilirubin on three pro-apoptotic factors Bad, Bak, and Bim using docking and molecular dynamics simulation. Three-dimensional structures were obtained from PubChem and RCSB servers. The simulation was accomplished at 40 nanoseconds (ns) using GROMACS 2018 simulation package before docking. Then bilirubin, as a ligand, bound to these proteins by Autodock v.4.2.6 software, and molecular dynamics simulation were performed again. The hydrophobic and hydrogen bonds at the binding site were determined using LigPlot+V.4.5.3 software. Our study revealed that bilirubin has the highest tendency to bind the Bim. This binding occurred between the 10 residues at the Bim binding site with the lowest binding energy (-8.43 kcal/mol). The docking of bilirubin to Bad, Bak, and Bim decreased Total Energy (TE), increased Radius of gyration (Rg), and root-mean-square deviation (RMSD). The coil secondary structures of Bad and Bim increased significantly after docking the bilirubin. Due to exhibiting a high tendency to interact with Bad, Bak, and Bim, bilirubin can affect their molecular dynamics and increase their activity so that, apoptosis is induced in the cell, which is considered in cancer treatment.
 
Date 2021-06-01T06:42:09Z
2021-06-01T06:42:09Z
2021-06
 
Type Article
 
Identifier 0975-0959 (Online); 0301-1208 (Print)
http://nopr.niscair.res.in/handle/123456789/57236
 
Language en_US
 
Rights CC Attribution-Noncommercial-No Derivative Works 2.5 India
 
Publisher NISCAIR-CSIR, India
 
Source IJBB Vol.58(3) [June 2021]