Department of Pharmacy, University of Patras, 26504, Patras, Greece.
Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy.
Biomol NMR Assign. 2021 Apr;15(1):165-171. doi: 10.1007/s12104-020-10000-9. Epub 2021 Jan 9.
SARS-CoV-2 RNA, nsP3c (non-structural Protein3c) spans the sequence of the so-called SARS Unique Domains (SUDs), first observed in SARS-CoV. Although the function of this viral protein is not fully elucidated, it is believed that it is crucial for the formation of the replication/transcription viral complex (RTC) and of the interaction of various viral "components" with the host cell; thus, it is essential for the entire viral life cycle. The first two SUDs, the so-called SUD-N (the N-terminal domain) and SUD-M (domain following SUD-N) domains, exhibit topological and conformational features that resemble the nsP3b macro (or "X") domain. Indeed, they are all folded in a three-layer α/β/α sandwich structure, as revealed through crystallographic structural investigation of SARS-CoV SUDs, and they have been attributed to different substrate selectivity as they selectively bind to oligonucleotides. On the other hand, the C-terminal SUD (SUD-C) exhibit much lower sequence similarities compared to the SUD-N & SUD-M, as reported in previous crystallographic and NMR studies of SARS-CoV. In the absence of the 3D structures of SARS-CoV-2, we report herein the almost complete NMR backbone and side-chain resonance assignment (H,C,N) of SARS-CoV-2 SUD-M and SUD-C proteins, and the NMR chemical shift-based prediction of their secondary structure elements. These NMR data will set the base for further understanding at the atomic-level conformational dynamics of these proteins and will allow the effective screening of a large number of small molecules as binders with potential biological impact on their function.
SARS-CoV-2 RNA，nsP3c（非结构蛋白 3c）跨越了所谓的 SARS 独特结构域（SUDs）的序列，该序列最初在 SARS-CoV 中被观察到。尽管该病毒蛋白的功能尚未完全阐明，但据信它对于复制/转录病毒复合物（RTC）的形成以及各种病毒“成分”与宿主细胞的相互作用至关重要；因此，它对于整个病毒生命周期是必不可少的。前两个 SUDs，即所谓的 SUD-N（N 末端结构域）和 SUD-M（SUD-N 后的结构域），表现出拓扑和构象特征，类似于 nsP3b 宏（或“X”）结构域。实际上，它们都折叠成三层α/β/α三明治结构，如通过 SARS-CoV SUDs 的晶体结构研究揭示的那样，并且它们被归因于不同的底物选择性，因为它们选择性地结合寡核苷酸。另一方面，与 SARS-CoV 的晶体学和 NMR 研究报告的相比，C 末端 SUD（SUD-C）与 SUD-N 和 SUD-M 的序列相似性要低得多。在缺乏 SARS-CoV-2 的 3D 结构的情况下，我们在此报告了 SARS-CoV-2 SUD-M 和 SUD-C 蛋白的几乎完整的 NMR 骨架和侧链共振分配（H，C，N），以及基于 NMR 化学位移的二级结构元素预测。这些 NMR 数据将为进一步在原子水平上理解这些蛋白质的构象动力学奠定基础，并允许有效地筛选大量小分子作为潜在具有生物学功能的结合剂。
