Amino acids sequence-based analysis of arginine deiminase from different prokaryotic organisms: An in silico approach

被引：3
作者：
Abdollahi S. [1 ,4 ]
Morowvat M.H. [1 ,2 ,3 ]
Savardashtaki A. [1 ]
Irajie C. [1 ,2 ]
Najafipour S. [4 ]
Zarei M. [3 ]
Ghasemi Y. [1 ,2 ,3 ]
机构：
[1] Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, P.O. Box 71348-14366, Shiraz
[2] Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, P.O. Box 71468-64685, Shiraz
[3] Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, P.O. Box 71468-64685, Shiraz
[4] Department of Microbiology, School of Medicine, Fasa University of Medical Sciences, P.O. Box 74616-86688, Fasa
来源：
Morowvat, Mohammad H. (mhmorowvat@sums.ac.ir); Morowvat, Mohammad H. (mhmorowvat@sums.ac.ir); Morowvat, Mohammad H. (mhmorowvat@sums.ac.ir) | 1600年 / Bentham Science Publishers卷 / 14期
关键词：
Arginine deiminase; In silico; Multiple sequence alignment; Phylogenetic analysis; Physico-chemical properties; Therapeutic proteins;
D O I：
10.2174/1872208314666200324114441
中图分类号：
学科分类号：
摘要：
Background: Arginine deiminase is a bacterial enzyme, which degrades L-arginine. Some human cancers such as hepatocellular carcinoma (HCC) and melanoma are auxotrophic for arginine. Therefore, PEGylated arginine deiminase (ADI-PEG20) is a good anticancer candidate with antitumor effects. It causes local depletion of L-arginine and growth inhibition in arginine-auxotrophic tumor cells. The FDA and EMA have granted orphan status to this drug. Some recently published patents have dealt with this enzyme or its PEGylated form. Objective: Due to increasing attention to it, we aimed to evaluate and compare 30 arginine deimi-nase proteins from different bacterial species through in silico analysis. Methods: The exploited analyses included the investigation of physicochemical properties, multiple sequence alignment (MSA), motif, superfamily, phylogenetic and 3D comparative analyses of arginine deiminase proteins thorough various bioinformatics tools. Results: The most abundant amino acid in the arginine deiminase proteins is leucine (10.13%) while the least amino acid ratio is cysteine (0.98%). Multiple sequence alignment showed 47 con-served patterns between 30 arginine deiminase amino acid sequences. The results of sequence homology among 30 different groups of arginine deiminase enzymes revealed that all the studied sequences located in amidinotransferase superfamily. Based on the phylogenetic analysis, two major clusters were identified. Considering the results of various in silico studies; we selected the five best candidates for further investigations. The 3D structures of the best five arginine deiminase proteins were generated by the I-TASSER server and PyMOL. The RAMPAGE analysis revealed that 81.4%-91.4%, of the selected sequences, were located in the favored region of arginine deiminase proteins. Conclusion: The results of this study shed light on the basic physicochemical properties of thirty major arginine deiminase sequences. The obtained data could be employed for further in vivo and clinical studies and also for developing the related therapeutic enzymes. © 2020 Bentham Science Publishers.
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页码：235 / 246
页数：11
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