Volume 6, Issue 3 (Fall 2019)
jhbmi 2019, 6(3): 255-263 |
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Saeinia A H, Taghizadeh M, Alavi S M. Investigating Dynamic Properties of Residues of Warfarin-Azapropazone Binding Site in Human Serum Albumin. jhbmi 2019; 6 (3) :255-263
URL: http://jhbmi.ir/article-1-388-en.html
URL: http://jhbmi.ir/article-1-388-en.html
Ph.D. in Bioinformatics, Biotechnology Dept., Faculty of Advance Science and Technology, Tehran Medical Science, Islamic Azad University, Tehran, Iran
Abstract: (4953 Views)
Introduction: Human Serum Albumin (HSA) is one of the most important proteins in blood that can bind a wide range of components and different drugs such as Warfarin and is also circulated in the body by HSA. Therefore, studying HSA is very significant in pharmacology. In this research, dynamic behavior of residues of Warfain binding site of HSA has been investigated.
Methods: Firstly, PDB format of HSA was downloaded from RCSB (PDB ID:2BX8) which was in complex with Azapropazone. After that, molecular dynamics simulation was during 30ns by GROMACS package. CHIMERA software was used to discover residues of binding site.
Results: After RMSD analysis was done on residues of binding site, it was seen that Arginines 186 and 218 have a wide fluctuations in their RMSD plot. Also, two Lysines 185 & 190 have nearly wide fluctuations of RMSD, this fluctuations were less than Arginine's, however. Other residues such as Glycine 189 have few fluctuations. Fluctuations in RMSD have direct relationship with accessible surface area (ASA) of the residues.
Conclusions: The results show that the Warfarin binding site in HSA can have various conformational situations because of the dynamics of its residues. This problem can be important to drug design. Overall, according to the results in this study, residues have been divided into 3 categories. Among them, Tryptophan 214 according to different articles is one of the most important residues site and based on our result, it stays on category of small mobility.
Methods: Firstly, PDB format of HSA was downloaded from RCSB (PDB ID:2BX8) which was in complex with Azapropazone. After that, molecular dynamics simulation was during 30ns by GROMACS package. CHIMERA software was used to discover residues of binding site.
Results: After RMSD analysis was done on residues of binding site, it was seen that Arginines 186 and 218 have a wide fluctuations in their RMSD plot. Also, two Lysines 185 & 190 have nearly wide fluctuations of RMSD, this fluctuations were less than Arginine's, however. Other residues such as Glycine 189 have few fluctuations. Fluctuations in RMSD have direct relationship with accessible surface area (ASA) of the residues.
Conclusions: The results show that the Warfarin binding site in HSA can have various conformational situations because of the dynamics of its residues. This problem can be important to drug design. Overall, according to the results in this study, residues have been divided into 3 categories. Among them, Tryptophan 214 according to different articles is one of the most important residues site and based on our result, it stays on category of small mobility.
Keywords: Human Serum Albumin, Molecular Dynamics simulation, Sudlow site I, Azapropazone, RMSD
eprint link: http://eprints.kmu.ac.ir/id/eprint/32281
eprint link: http://eprints.kmu.ac.ir/id/eprint/32281
Type of Study: Original Article |
Subject:
Bioinformatics
Received: 2019/04/14 | Accepted: 2019/06/17
Received: 2019/04/14 | Accepted: 2019/06/17
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