Molecular Dynamics Simulation on the Complex of the Tobramycin and 16S rRNA A Site

Chem. J. Chinese Universities

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Molecular Dynamics Simulation on the Complex of the Tobramycin and 16S rRNA A Site

FENG Yu¹, ZHANG Xu-Dong¹, CHENG Wei-Xian¹,CAO Huai¹, LIU Ci-Quan^1,2*

1. Modern Biological Research Center, Yunnan University, Kunming 650091, China;
2. Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China

Received:2007-02-27 Revised:1900-01-01 Online:2007-11-10 Published:2007-11-10
Contact: LIU Ci-Quan

Abstract

Abstract: A 3.6 ns molecular dynamics simulation was carried out on the complex system of tobramycin and 16S rRNA in order to understand the speciality recognition mechanism between tobramycin and 16S rRNA at the molecular level. The results demonstrate that two looped out bases(A1492 and A1493) of the A site is the flexible part, while ringⅠand ringⅡ of tobramycin are the most conservative elements. Moreover, ringⅠand ringⅡ of tobramycin may be function conservative unit which may participate in the specificity recognition for tobramycin binding to the 16S rRNA A site. In addition, a structural water molecule was detected during the whole MD simulation trajectory, which bridged the contacts between ringⅡ(N3)and ringⅠ(N6') of tobramycin and enhanced the rigid of tobramycin structure. There is one hydration site with the higher water density in the vicinity of ringⅠand ringⅡ of tobramycin. This result is consistent with the crystal structure detected that the most water-medial hydrogen bonds were listed in the same situation. Our study illustrates that recognition mechanism between tobramycin and 16S rRNA A site was due to a few hydrogen bond and water molecule interactions, which play a great role in designing high affinity and speciality inhibitors of 16S rRNA A site based on tobramycin.

Key words: Molecular dynamics, Tobramycin, 16S rRNA A site, Hydration density

CLC Number:

O641

TrendMD:

FENG Yu¹, ZHANG Xu-Dong¹, CHENG Wei-Xian¹,CAO Huai¹, LIU Ci-Quan^1,2*. Molecular Dynamics Simulation on the Complex of the Tobramycin and 16S rRNA A Site[J]. Chem. J. Chinese Universities, doi: .

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Molecular Dynamics Simulation on the Complex of the Tobramycin and 16S rRNA A Site

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