文章基本信息

标题：Structure of a low-population binding intermediate in protein-RNA recognition
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作者：Aditi N. Borkar ; Michael F. Bardaro ; Carlo Camilloni 等
期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2016
卷号：113
期号：26
页码：7171-7176
DOI：10.1073/pnas.1521349113
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：The interaction of the HIV-1 protein transactivator of transcription (Tat) and its cognate transactivation response element (TAR) RNA transactivates viral transcription and represents a paradigm for the widespread occurrence of conformational rearrangements in protein-RNA recognition. Although the structures of free and bound forms of TAR are well characterized, the conformations of the intermediates in the binding process are still unknown. By determining the free energy landscape of the complex using NMR residual dipolar couplings in replica-averaged metadynamics simulations, we observe two low-population intermediates. We then rationally design two mutants, one in the protein and another in the RNA, that weaken specific nonnative interactions that stabilize one of the intermediates. By using surface plasmon resonance, we show that these mutations lower the release rate of Tat, as predicted. These results identify the structure of an intermediate for RNA-protein binding and illustrate a general strategy to achieve this goal with high resolution.
关键词：RNA structure ; NMR spectroscopy ; metadynamics ; exact RDC restraints ; tensor-free method