Hu Wen, Qin Liu, Li Menglong, Pu Xuemei, Guo Yanzhi
College of Chemistry, Sichuan University Chengdu 610064 People's Republic of China
RSC Adv. 2018 Mar 16;8(19):10582-10592. doi: 10.1039/c8ra00598b. eCollection 2018 Mar 13.
Protein-RNA interactions are very common cellular processes, but the mechanisms of interactions are not fully understood, mainly due to the complicated RNA structures. By the elaborate investigation on RNA structures of protein-RNA complexes, it was firstly found in this paper that RNAs in these complexes could be clearly classified into three classes (high, medium and low) based on the different levels of (the percentage of base area buried in the RNA interface). In view of the three RNA classes, more detailed analyses on protein-RNA interactions were comprehensively performed from various aspects, including interface area, structure, composition and interaction force, so as to achieve a deeper understanding of the recognition specificity for the three classes of protein-RNA interactions. According to our classification strategy, the three complex classes have significant differences in terms of almost all properties. Complexes in the high class have short and extended RNA structures and behave like protein-ssDNA interactions. Their hydrogen bonds and hydrophobic interactions are strong. For complexes in low class, their RNA structures are mainly double-stranded, like protein-dsDNA interactions, and electrostatic interactions frequently occur. The complexes in medium class have the longest RNA chains and largest average interface area. Meanwhile, they do not show any preference for the interaction force. On average, in terms of composition, secondary structures and intermolecular physicochemical properties, significant feature preferences can be observed in high and low complexes, but no highly specific features are found for medium complexes. We found that our proposed is an important parameter which can be used as a new determinant to distinguish protein-RNA complexes. For high and low complexes, we can more easily understand the specificity of the recognition process from the interface features than for medium complexes. In the future, medium complexes should be our research focus to further structurally analyze from more feature aspects. Overall, this study may contribute to further understanding of the mechanism of protein-RNA interactions on a more detailed level.
蛋白质 - RNA相互作用是非常常见的细胞过程，但相互作用机制尚未完全明确，主要原因是RNA结构复杂。通过对蛋白质 - RNA复合物的RNA结构进行精细研究，本文首次发现这些复合物中的RNA可根据不同的 （RNA界面中碱基区域的埋藏百分比）水平清晰地分为三类（高、中、低）。鉴于这三类RNA，从界面面积、结构、组成和相互作用力等多个方面对蛋白质 - RNA相互作用进行了更详细的综合分析，以便更深入地理解这三类蛋白质 - RNA相互作用的识别特异性。根据我们的分类策略，这三类复合物在几乎所有性质方面都存在显著差异。高类复合物具有短而伸展的RNA结构，其行为类似于蛋白质 - 单链DNA相互作用。它们的氢键和疏水相互作用很强。对于低类复合物，其RNA结构主要是双链的，类似于蛋白质 - 双链DNA相互作用，并且经常发生静电相互作用。中类复合物具有最长的RNA链和最大的平均界面面积。同时，它们在相互作用力方面没有表现出任何偏好。平均而言，在组成、二级结构和分子间物理化学性质方面，高类和低类复合物具有显著的特征偏好，但中类复合物未发现高度特异性的特征。我们发现我们提出的 是一个重要参数，可作为区分蛋白质 - RNA复合物的新决定因素。对于高类和低类复合物，与中类复合物相比，我们可以更轻松地从界面特征理解识别过程的特异性。未来，中类复合物应成为我们的研究重点，以便从更多特征方面进行进一步的结构分析。总体而言，本研究可能有助于在更详细的层面上进一步理解蛋白质 - RNA相互作用的机制。
