Theoretical studies on the interaction of guanine riboswitch with guanine and its closest analogues
文献类型：期刊论文
| 作者 | Zhang, Changqiao1; Ling, Baoping1; Zhang, Rui2; Wang, Zhiguo2; Dong, Lihua2; Liu, Yongjun1,2; Liu, Chengbu1 |
| 刊名 | MOLECULAR SIMULATION
 |
| 出版日期 | 2010 |
| 卷号 | 36期号:12页码:929-938 |
| 关键词 | Guanine Guanine Riboswitch Docking Molecular Dynamics Binding Energy |
| ISSN号 | 0892-7022 |
| 文献子类 | Article |
| 英文摘要 | 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. |
| WOS关键词 | PURINE RIBOSWITCH ; APTAMER DOMAIN ; MODIFIED PYRIMIDINES ; GENE-EXPRESSION ; LIGAND-BINDING ; MESSENGER-RNAS ; FORCE-FIELD ; DOCKING ; RECOGNITION ; SIMULATIONS |
| WOS研究方向 | Chemistry ; Physics |
| 语种 | 英语 |
| WOS记录号 | WOS:000283878300002 |
| 公开日期 | 2011-12-13 |
| 源URL | [http://ir.nwipb.ac.cn//handle/363003/1776]  |
| 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 |
| 推荐引用方式 GB/T 7714 | Zhang, Changqiao,Ling, Baoping,Zhang, Rui,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 | Zhang, Changqiao.,Ling, Baoping.,Zhang, Rui.,Wang, Zhiguo.,Dong, Lihua.,...&Liu, Chengbu.(2010).Theoretical studies on the interaction of guanine riboswitch with guanine and its closest analogues.MOLECULAR SIMULATION,36(12),929-938. |
| MLA | Zhang, Changqiao,et al."Theoretical studies on the interaction of guanine riboswitch with guanine and its closest analogues".MOLECULAR SIMULATION 36.12(2010):929-938. |
入库方式： OAI收割
来源：西北高原生物研究所
浏览0
下载0
收藏0
其他版本
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。