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RNA base-amino acid interaction strengths derived from structures and sequences.

机译:RNA碱基与氨基酸的相互作用强度来源于结构和序列。

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摘要

We investigate RNA base-amino acid interactions by counting their contacts in structures and their implicit contacts in various functional sequences where the structures can be assumed to be preserved. These frequencies are cast into equations to extract relative interaction energetics. Previously we used this approach in considering the major groove interactions of DNA, and here we apply it to the more diverse interactions observed in RNA. Structures considered are the three different tRNA synthetase complexes, the U1A spliceosomal protein with an RNA hairpin and the BIV TAR-Tat complex. We use binding data for the base frequencies for the seryl, aspartyl and glutaminyl tRNA-synthetase and U1 RNA-protein complexes. We compare with the previously reported DNA major groove peptide contacts the results for atoms of RNA bases, usually in the major groove. There are strong similarities between the rank orders of interacting bases in the DNA and the RNA cases. The apparent strongest RNA interaction observed is between arginine and guanine which was also one of the strongest DNA interactions. The similar data for base atomic interactions, whether base paired or not, support the importance of strong atomic interactions over local structure considerations, such as groove width and alpha-helicity.
机译:我们通过计算它们在结构中的接触以及在各种功能序列中它们可能被认为被保留的隐式接触来研究RNA碱基氨基酸的相互作用。这些频率被转换成方程式以提取相对相互作用的能量学。以前,我们使用这种方法来考虑DNA的主要凹槽相互作用,在这里,我们将其应用于RNA中观察到的更多样化的相互作用。所考虑的结构是三种不同的tRNA合成酶复合物,带有RNA发夹的U1A剪接蛋白和BIV TAR-Tat复合物。我们使用结合数据为Seryl,天冬氨酰和谷氨酰胺基tRNA合成酶和U1 RNA蛋白复合物的基本频率。我们与以前报道的DNA大沟肽接触结果比较,通常是在大沟中RNA碱基的原子。 DNA和RNA案例中相互作用碱基的等级顺序之间有很强的相似性。观察到的最强的RNA相互作用是在精氨酸和鸟嘌呤之间,这也是最强的DNA相互作用之一。基本原子相互作用的相似数据,无论是否成对,都支持强原子相互作用在局部结构考虑因素(例如槽宽和α-螺旋度)方面的重要性。

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