阳离子与 RNA 环loop 复合物的相互作用。
Interactions of cations with RNA loop-loop complexes.
机构信息
Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina, USA.
出版信息
Biophys J. 2011 Aug 3;101(3):727-35. doi: 10.1016/j.bpj.2011.06.033.
RNA loop-loop interactions are essential in many biological processes, including initiation of RNA folding into complex tertiary shapes, promotion of dimerization, and viral replication. In this article, we examine interactions of metal ions with five RNA loop-loop complexes of unique biological significance using explicit-solvent molecular-dynamics simulations. These simulations revealed the presence of solvent-accessible tunnels through the major groove of loop-loop interactions that attract and retain cations. Ion dynamics inside these loop-loop complexes were distinctly different from the dynamics of the counterion cloud surrounding RNA and depend on the number of basepairs between loops, purine sequence symmetry, and presence of unpaired nucleotides. The cationic uptake by kissing loops depends on the number of basepairs between loops. It is interesting that loop-loop complexes with similar functionality showed similarities in cation dynamics despite differences in sequence and loop size.
RNA 环loop 相互作用在许多生物过程中是必不可少的，包括 RNA 折叠成复杂的三级形状的起始、二聚化的促进和病毒复制。在本文中，我们使用显式溶剂分子动力学模拟研究了五个具有独特生物学意义的 RNA 环loop 复合物与金属离子的相互作用。这些模拟揭示了存在溶剂可及的隧道穿过 loop-loop 相互作用的大沟，吸引并保留阳离子。这些 loop-loop 复合物内的离子动力学与 RNA 周围反离子云的动力学明显不同，并且取决于环之间的碱基对数量、嘌呤序列对称性和未配对核苷酸的存在。亲环环的阳离子摄取取决于环之间的碱基对数量。有趣的是，尽管序列和环大小不同，但具有相似功能的 loop-loop 复合物在阳离子动力学方面表现出相似性。
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