Theoretical studies on the interaction of modified pyrimidines and purines with purine riboswitch
文献类型：期刊论文
| 作者 | Ling, Baoping1; Wang, Zhiguo1,2; Zhang, Rui1,2; Meng, Xianghua1,3; Liu, Yongjun1,2; Zhang, Changqiao1; Liu, Chengbu1 |
| 刊名 | journal of molecular graphics & modelling
 |
| 出版日期 | 2009-08-01 |
| 卷号 | 28期号:1页码:37-45 |
| 关键词 | Pyrimidine Purine Purine riboswitch Docking Molecular dynamics |
| ISSN号 | 1093-3263 |
| 中文摘要 | 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. |
| 英文摘要 | 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. |
| WOS标题词 | science & technology ; life sciences & biomedicine ; technology ; physical sciences |
| 类目[WOS] | biochemical research methods ; biochemistry & molecular biology ; computer science, interdisciplinary applications ; crystallography ; mathematical & computational biology |
| 研究领域[WOS] | biochemistry & molecular biology ; computer science ; crystallography ; mathematical & computational biology |
| 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记录号 | WOS:000271356700006 |
| 公开日期 | 2011-12-13 |
| 源URL | [http://ir.nwipb.ac.cn//handle/363003/1842]  |
| 专题 | 西北高原生物研究所_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. |
入库方式： OAI收割
来源：西北高原生物研究所
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