Knowledge Management System of Northwest Institute of Plateau Biology, CAS
Theoretical studies on the interaction of guanine riboswitch with guanine and its closest analogues | |
Ling, Baoping1; Zhang, Rui2; Wang, Zhiguo2; Dong, Lihua2; Liu, Yongjun1,2; Zhang, Changqiao1; Liu, Chengbu1 | |
2010 | |
发表期刊 | MOLECULAR SIMULATION |
ISSN | 0892-7022 |
卷号 | 36期号:12页码:929-938 |
文章类型 | Article |
摘要 | Experimental studies (M. Mandal, B. Boese, J.E. Barrick, W. C. Winkler and R. R. Breaker, Riboswitches control fundamental biochemical pathways in bacillus subtilis and other bacteria, Cell 113 (2003), pp. 577-586) demonstrated that, besides recognising guanine with high specificity, guanine riboswitch could also bind guanine analogues, but the alteration of every functionalised position on the guanine heterocycle could cause a substantial loss of binding affinity. To investigate the nature of guanine riboswitch recognising metabolites, molecular docking and molecular dynamics simulation were carried out on diverse guanine analogues. The calculation results reveal that (1) most guanine analogues could bind to guanine riboswitch at the same binding pocket, with identical orientations and dissimilar binding energies, which is related to the positions of the functional groups; (2) the two tautomers of xanthine adopt different binding modes, and the enol-tautomer shows similar binding mode and affinity of hypoxanthine, which agrees well with the experimental results and (3) the riboswitch could form stable complexes with guanine analogues by hydrogen bonding contacts with U51 and C74. Particularly, U51 plays an important role in stabilising the complexes.; Experimental studies (M. Mandal, B. Boese, J.E. Barrick, W. C. Winkler and R. R. Breaker, Riboswitches control fundamental biochemical pathways in bacillus subtilis and other bacteria, Cell 113 (2003), pp. 577-586) demonstrated that, besides recognising guanine with high specificity, guanine riboswitch could also bind guanine analogues, but the alteration of every functionalised position on the guanine heterocycle could cause a substantial loss of binding affinity. To investigate the nature of guanine riboswitch recognising metabolites, molecular docking and molecular dynamics simulation were carried out on diverse guanine analogues. The calculation results reveal that (1) most guanine analogues could bind to guanine riboswitch at the same binding pocket, with identical orientations and dissimilar binding energies, which is related to the positions of the functional groups; (2) the two tautomers of xanthine adopt different binding modes, and the enol-tautomer shows similar binding mode and affinity of hypoxanthine, which agrees well with the experimental results and (3) the riboswitch could form stable complexes with guanine analogues by hydrogen bonding contacts with U51 and C74. Particularly, U51 plays an important role in stabilising the complexes. |
关键词 | Guanine Guanine Riboswitch Docking Molecular Dynamics Binding Energy |
WOS标题词 | Science & Technology ; Physical Sciences |
关键词[WOS] | PURINE RIBOSWITCH ; APTAMER DOMAIN ; MODIFIED PYRIMIDINES ; GENE-EXPRESSION ; LIGAND-BINDING ; MESSENGER-RNAS ; FORCE-FIELD ; DOCKING ; RECOGNITION ; SIMULATIONS |
收录类别 | SCI |
语种 | 英语 |
WOS研究方向 | Chemistry ; Physics |
WOS类目 | Chemistry, Physical ; Physics, Atomic, Molecular & Chemical |
WOS记录号 | WOS:000283878300002 |
引用统计 | |
文献类型 | 期刊论文 |
条目标识符 | http://210.75.249.4/handle/363003/1776 |
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 |
推荐引用方式 GB/T 7714 | Ling, Baoping,Zhang, Rui,Wang, Zhiguo,et al. Theoretical studies on the interaction of guanine riboswitch with guanine and its closest analogues[J]. MOLECULAR SIMULATION,2010,36(12):929-938. |
APA | Ling, Baoping.,Zhang, Rui.,Wang, Zhiguo.,Dong, Lihua.,Liu, Yongjun.,...&Liu, Chengbu.(2010).Theoretical studies on the interaction of guanine riboswitch with guanine and its closest analogues.MOLECULAR SIMULATION,36(12),929-938. |
MLA | Ling, Baoping,et al."Theoretical studies on the interaction of guanine riboswitch with guanine and its closest analogues".MOLECULAR SIMULATION 36.12(2010):929-938. |
条目包含的文件 | 下载所有文件 | |||||
文件名称/大小 | 文献类型 | 版本类型 | 开放类型 | 使用许可 | ||
Theoretical studies (1430KB) | 开放获取 | -- | 浏览 下载 |
除非特别说明,本系统中所有内容都受版权保护,并保留所有权利。
修改评论