期刊
JOURNAL OF MOLECULAR BIOLOGY
卷 304, 期 1, 页码 55-68出版社
ACADEMIC PRESS LTD
DOI: 10.1006/jmbi.2000.4173
关键词
molecular dynamics; entropy/enthalpy compensation; transcription
资金
- NIDA NIH HHS [DA00060] Funding Source: Medline
- NIGMS NIH HHS [GM39929] Funding Source: Medline
The hydroxyl radical footprint of the TATA-binding protein (TBP) bound to the high-affinity sequence TATAAAAG of the adenovirus 2 major late promoter has been quantitatively compared to a 2 ns molecular dynamics simulation of the complex in aqueous solution at room temperature using the CHARMM23 potential. The nucleotide-by-nucleotide analysis of the TBP-TATA hydroxyl radical footprint correlates with the solvent-accessible surface calculated from the dynamics simulation. The results suggest that local reactivity towards OH radicals results from the interplay between the local DNA geometry imposed by TBP binding, and the dynamics of the side-chains contacting the sugar hydrogen atoms. Analysis of the dynamics suggests that, over time, TBP forms stable interactions with the sugar-phosphate backbone through multiple contacts to different partners. This mechanism results in an enthalpic advantage to complex formation at a low entropic cost. (C) 2000 Academic Press.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据