Molecular Dynamics Studies on the Structure of 16S rRNA Fragment Affected by A1408G Mutation

Chem. J. Chinese Universities ›› 2010, Vol. 31 ›› Issue (9): 1815.

• Articles • Previous Articles Next Articles

Molecular Dynamics Studies on the Structure of 16S rRNA Fragment Affected by A1408G Mutation

DONG Hao, LIU Yuan-Ning^*

College of Computer Science and Technology, Jilin University, Changchun 132012, China

Received:2010-03-01 Online:2010-09-10 Published:2010-09-10
Contact: LIU Yuan-Ning. E-mail: liuyn@jlu.edu.cn
Supported by:
国家自然科学基金(批准号: 60971089)资助.

Abstract

Abstract: Using molecular dynamics simulation, the flexibility of 16S rRNA complexed with paromomycin was studied. The results indicate that the position 1408 of 16S rRNA in ribosome is very important. The substitution of adenine for guanine will change the position of two adenines(A1492 and A1493) which are involved in tRNA anticodon loop recognition, affecting the binding of aminoglycosidic antibiotics and protein translation in prokaryota. The simulation results show a good agreement with experimental data, which provi-ded some structural information for the drug design based on 16S rRNA in ribosome.

Key words: Ribosome, 16S rRNA A-site, Paromomycin, Molecular dynamics

TrendMD:

DONG Hao, LIU Yuan-Ning*. Molecular Dynamics Studies on the Structure of 16S rRNA Fragment Affected by A1408G Mutation[J]. Chem. J. Chinese Universities, 2010, 31(9): 1815.

[1]	GAO Zhiwei, LI Junwei, SHI Sai, FU Qiang, JIA Junru, AN Hailong. Analysis of Gating Characteristics of TRPM8 Channel Based on Molecular Dynamics [J]. Chem. J. Chinese Universities, 2022, 43(6): 20220080.
[2]	ZENG Xianyang, ZHAO Xi, HUANG Xuri. Mechanism of Inhibition of Glucose and Proton Cotransport Protein GlcPSe by Cytochalasin B [J]. Chem. J. Chinese Universities, 2022, 43(4): 20210822.
[3]	CHEN Hanxiang, BIAN Shaoju, HU Bin, LI Wu. Molecular Simulation of the Osmotic Pressures for LiCl-NaCl-KCl-H₂O Solution System [J]. Chem. J. Chinese Universities, 2022, 43(3): 20210727.
[4]	HU Bo, ZHU Haochen. Dielectric Constant of Confined Water in a Bilayer Graphene Oxide Nanosystem [J]. Chem. J. Chinese Universities, 2022, 43(2): 20210614.
[5]	ZHANG Mi, TIAN Yafeng, GAO Keli, HOU Hua, WANG Baoshan. Molecular Dynamics Simulation of the Physicochemical Properties of Trifluoromethanesulfonyl Fluoride Dielectrics [J]. Chem. J. Chinese Universities, 2022, 43(11): 20220424.
[6]	ZHANG Lingyu, ZHANG Jilong, QU Zexing. Dynamics Study of Intramolecular Vibrational Energy Redistribution in RDX Molecule [J]. Chem. J. Chinese Universities, 2022, 43(10): 20220393.
[7]	LI Congcong, LIU Minghao, HAN Jiarui, ZHU Jingxuan, HAN Weiwei, LI Wannan. Theoretical Study of the Catalytic Activity of VmoLac Non-specific Substrates Based on Molecular Dynamics Simulations [J]. Chem. J. Chinese Universities, 2021, 42(8): 2518.
[8]	LEI Xiaotong, JIN Yiqing, MENG Xuanyu. Prediction of the Binding Site of PIP₂ in the TREK-1 Channel Based on Molecular Modeling [J]. Chem. J. Chinese Universities, 2021, 42(8): 2550.
[9]	LIU Shasha, ZHANG Heng, YUAN Shiling, LIU Chengbu. Molecular Dynamics Simulation of Pulsed Electric Field O/W Emulsion Demulsification [J]. Chem. J. Chinese Universities, 2021, 42(7): 2170.
[10]	ZENG Yonghui, YAN Tianying. Vibrational Density of States Analysis of Proton Hydration Structure [J]. Chem. J. Chinese Universities, 2021, 42(6): 1855.
[11]	LIU Aiqing, XU Wensheng, XU Xiaolei, CHEN Jizhong, AN Lijia. Molecular Dynamics Simulation of Polymer/rod Nanocomposite [J]. Chem. J. Chinese Universities, 2021, 42(3): 875.
[12]	QI Renrui, LI Minghao, CHANG Hao, FU Xueqi, GAO Bo, HAN Weiwei, HAN Lu, LI Wannan. Theoretical Study on the Unbinding Pathway of Xanthine Oxidase Inhibitors Based on Steered Molecular Dynamics Simulation [J]. Chem. J. Chinese Universities, 2021, 42(3): 758.
[13]	HE Jinlu, LONG Run, FANG Weihai. A-site Cation Effects on Hot Carrier Relaxation in Perovskites by Nonadiabatic Molecular Dynamics Simulations ^† [J]. Chem. J. Chinese Universities, 2020, 41(3): 439.
[14]	ZHU Yuquan, ZHAO Xiaojie, ZHONG Yuan, CHEN Ziru, YAN Hong, DUAN Xue. Theoretical Study on the Construction and Characteristics of the Host-guest Intercalated Structure of Layered Double Hydroxides [J]. Chem. J. Chinese Universities, 2020, 41(11): 2287.
[15]	QU Siying, XU Qin. Different Roles of Some Key Residues in the S4 Pocket of Coagulation Factor Xa for Rivaroxaban Binding ^† [J]. Chem. J. Chinese Universities, 2019, 40(9): 1918.

Molecular Dynamics Studies on the Structure of 16S rRNA Fragment Affected by A1408G Mutation

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments