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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
ISSN0892-7022
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
被引频次:4[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/363003/1776
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
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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.
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