Theoretical studies on the interaction of modified pyrimidines and purines with purine riboswitch

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	Theoretical studies on the interaction of modified pyrimidines and purines with purine riboswitch
	Ling, Baoping 1; Wang, Zhiguo 1,2; Zhang, Rui 1,2; Meng, Xianghua 1,3; Liu, Yongjun 1,2; Zhang, Changqiao 1; Liu, Chengbu 1
	2009-08-01
发表期刊	JOURNAL OF MOLECULAR GRAPHICS & MODELLING
ISSN	1093-3263
卷号	28 期号:1 页码:37-45
文章类型	Article
摘要	Recent experimental study [S.D. Gilbert, S.J. Mediatore, R.T. Batey, Modified pyrimidine specifically bind the purine riboswitch, J. Am. Chem. Soc. 128 (2006) 14214-14215] demonstrated that the purine riboswitch could specifically bind some ligands other than purines such as amino-pyrimidines, and the authors proposed that the five-membered ring of purine was not required for recognition. To get insight into the interaction details, we used molecular docking method to investigate the interactions of a mutant form of guanine riboswitch with a series of amino-purines, amino-pyrimidines and imidazole derivatives, and employed molecular simulation method to study the dynamic behavior of the selected complexes. The calculation results reveal that (1) all the amino-purines and amino-pyrimidines bind in a same cavity composed of four nucleobases including U22, U47, U51 and U74, which is consistent with the experimental results, while the two imidazole derivatives adopt other binding modes; (2) the purines are engulfed within three-way junction motifs, but most pyrimidines only form two-way junctions with the riboswitch; (3) the number and position of amino substituents could seriously affect the binding of pyrimidines. As riboswitches are potentially excellent candidates for antibiotic therapeutics, these findings may be useful for understanding the range of compounds that riboswitch can specifically recognize. (C) 2009 Elsevier Inc. All rights reserved.; Recent experimental study [S.D. Gilbert, S.J. Mediatore, R.T. Batey, Modified pyrimidine specifically bind the purine riboswitch, J. Am. Chem. Soc. 128 (2006) 14214-14215] demonstrated that the purine riboswitch could specifically bind some ligands other than purines such as amino-pyrimidines, and the authors proposed that the five-membered ring of purine was not required for recognition. To get insight into the interaction details, we used molecular docking method to investigate the interactions of a mutant form of guanine riboswitch with a series of amino-purines, amino-pyrimidines and imidazole derivatives, and employed molecular simulation method to study the dynamic behavior of the selected complexes. The calculation results reveal that (1) all the amino-purines and amino-pyrimidines bind in a same cavity composed of four nucleobases including U22, U47, U51 and U74, which is consistent with the experimental results, while the two imidazole derivatives adopt other binding modes; (2) the purines are engulfed within three-way junction motifs, but most pyrimidines only form two-way junctions with the riboswitch; (3) the number and position of amino substituents could seriously affect the binding of pyrimidines. As riboswitches are potentially excellent candidates for antibiotic therapeutics, these findings may be useful for understanding the range of compounds that riboswitch can specifically recognize. (C) 2009 Elsevier Inc. All rights reserved.
关键词	Pyrimidine Purine Purine Riboswitch Docking Molecular Dynamics
WOS标题词	Science & Technology ; Life Sciences & Biomedicine ; Technology ; Physical Sciences
关键词[WOS]	MOLECULAR-DYNAMICS SIMULATION ; GENE-EXPRESSION ; STRUCTURAL BASIS ; MALACHITE GREEN ; LIGAND-BINDING ; MESSENGER-RNAS ; APTAMER DOMAIN ; FREE-ENERGIES ; FORCE-FIELD ; RECOGNITION
收录类别	SCI
语种	英语
WOS研究方向	Biochemistry & Molecular Biology ; Computer Science ; Crystallography ; Mathematical & Computational Biology
WOS类目	Biochemical Research Methods ; Biochemistry & Molecular Biology ; Computer Science, Interdisciplinary Applications ; Crystallography ; Mathematical & Computational Biology
WOS记录号	WOS:000271356700006
引用统计	被引频次：12[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://210.75.249.4/handle/363003/1842
专题	中国科学院西北高原生物研究所
作者单位	1.Shandong Univ, Sch Chem & Chem Engn, Jinan 250100, Shandong, Peoples R China 2.Chinese Acad Sci, NW Inst Plateau Biol, Xining 810001, Qinghai, Peoples R China 3.Qufu Nornal Univ, Dept Chem, Qufu 273165, Shandong, Peoples R China
推荐引用方式 GB/T 7714	Ling, Baoping,Wang, Zhiguo,Zhang, Rui,et al. Theoretical studies on the interaction of modified pyrimidines and purines with purine riboswitch[J]. JOURNAL OF MOLECULAR GRAPHICS & MODELLING,2009,28(1):37-45.
APA	Ling, Baoping.,Wang, Zhiguo.,Zhang, Rui.,Meng, Xianghua.,Liu, Yongjun.,...&Liu, Chengbu.(2009).Theoretical studies on the interaction of modified pyrimidines and purines with purine riboswitch.JOURNAL OF MOLECULAR GRAPHICS & MODELLING,28(1),37-45.
MLA	Ling, Baoping,et al."Theoretical studies on the interaction of modified pyrimidines and purines with purine riboswitch".JOURNAL OF MOLECULAR GRAPHICS & MODELLING 28.1(2009):37-45.