Chawla Mohit, Chermak Edrisse, Zhang Qingyun, Bujnicki Janusz M, Oliva Romina, Cavallo Luigi
King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia.
Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia.
Nucleic Acids Res. 2017 Nov 2;45(19):11019-11032. doi: 10.1093/nar/gkx757.
The specific folding pattern and function of RNA molecules lies in various weak interactions, in addition to the strong base-base pairing and stacking. One of these relatively weak interactions, characterized by the stacking of the O4' atom of a ribose on top of the heterocycle ring of a nucleobase, has been known to occur but has largely been ignored in the description of RNA structures. We identified 2015 ribose-base stacking interactions in a high-resolution set of non-redundant RNA crystal structures. They are widespread in structured RNA molecules and are located in structural motifs other than regular stems. Over 50% of them involve an adenine, as we found ribose-adenine contacts to be recurring elements in A-minor motifs. Fewer than 50% of the interactions involve a ribose and a base of neighboring residues, while approximately 30% of them involve a ribose and a nucleobase at least four residues apart. Some of them establish inter-domain or inter-molecular contacts and often implicate functionally relevant nucleotides. In vacuo ribose-nucleobase stacking interaction energies were calculated by quantum mechanics methods. Finally, we found that lone pair-π stacking interactions also occur between ribose and aromatic amino acids in RNA-protein complexes.
除了强碱基对和堆积作用外，RNA分子的特定折叠模式和功能还取决于各种弱相互作用。其中一种相对较弱的相互作用，其特征是核糖的O4'原子堆积在核碱基的杂环环之上，这种相互作用虽已为人所知，但在RNA结构描述中大多被忽视。我们在一组高分辨率的非冗余RNA晶体结构中鉴定出2015个核糖-碱基堆积相互作用。它们广泛存在于结构化RNA分子中，且位于常规茎以外的结构基序中。其中超过50%涉及腺嘌呤，因为我们发现核糖-腺嘌呤接触是A- minor基序中的重复元素。不到50%的相互作用涉及核糖与相邻残基的碱基，而约30%的相互作用涉及核糖与至少相隔四个残基的核碱基。其中一些建立了结构域间或分子间的接触，并且常常涉及功能相关的核苷酸。通过量子力学方法计算了真空中核糖-核碱基堆积相互作用能。最后，我们发现在RNA-蛋白质复合物中，核糖与芳香族氨基酸之间也存在孤对-π堆积相互作用。
