Modeling, molecular dynamics and docking studies of a full-length Echinococcus granulosus 2DBD nuclear receptor

被引:4
|
作者
Cancela, Saira [1 ]
Esteves, Adriana [1 ]
Alvite, Gabriela [1 ]
Paulino, Margot [2 ,3 ]
机构
[1] Univ Republica, Biochem Sect, Fac Sci, Montevideo, Uruguay
[2] Univ Republica, Fac Chem, Bioinformat Ctr, Montevideo, Uruguay
[3] Univ Republica, Fac Chem, Bioinformat Ctr, Montevideo, Uruguay
来源
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS | 2023年 / 41卷 / 04期
关键词
2DBD nuclear receptor; Echinococcus granulosus; full-length 3D model; molecular dynamics; molecular docking; LIGAND-BINDING DOMAIN; HORMONE-RECEPTORS; RXR; NOMENCLATURE; INTEGRATION; SYSTEM;
D O I
10.1080/07391102.2021.2023641
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Nuclear receptors are ligand-activated transcription factors capable of regulating the expression of complex gene networks. The family includes seven subfamilies of protein with a wide phylogenetic distribution. A novel subfamily with two DNA-binding domains (2DBDs) has been first reported in Schistosoma mansoni (Platyhelminth, Trematoda). Employing an ab initio protocol and homology modeling methods, the full-length 3D structure of the Eg2DBD alpha.1 nuclear receptor from Echinococcus granulosus (Platyhelminth, Cestoda) was generated. The model analysis reveals the presence of the conserved three-layered alpha-helical sandwich structure in the ligand binding domain, and a particularly long and flexible hinge region. Molecular dynamics simulations were performed previous to dock a conformational library of fatty acids and retinoic acids. Our results indicate that oleic and linoleic acids are suitable ligands to this receptor. The ligand-protein complex is stabilized mainly by hydrogen bonds and hydrophobic interactions. The fact that 2DBD nuclear receptors have not been identified in vertebrates confers particular interest to these nuclear receptors, not only concerning their structure and function but as targets of new anthelmintic drugs. Communicated by Ramaswamy H. Sarma
引用
收藏
页码:1414 / 1423
页数:10
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