Instituto de Estructura de la Materia (CSIC), Serrano 121, 28006 Madrid, Spain.
Biochemistry. 2010 Jun 15;49(23):4724-31. doi: 10.1021/bi100535k.
The secondary structure of the loop IIId domain in the RNA of hepatitis C virus (HCV) is well-conserved among different genotypes of HCV, which suggests that the nucleocapsid proteins may interact with the genome RNA through this loop structure. Using infrared spectroscopy, we monitored structural changes occurring in HCV core protein and loop IIId upon formation of nucleocapsid-like particles (NLPs). The protein secondary structure of these particles involves beta-sheet enrichment in relation to its protein monomer. The phosphodiester backbone vibrations of loop IIId reflect the predominant C3'-endo conformation of the riboses involved in the RNA A-form and reveal the packaging-imposed transition of the said RNA segments toward single-stranded structure within the NLPs. Intermolecular protein-nucleic acid contacts in these particles involve RNA phosphate groups and positively charged amino acid residues such as arginine and lysine. Two-dimensional correlation spectroscopic analysis of the spectra measured in the course of deuteration shows synchronous cross-peaks correlating two bands assigned to guanine and arginine side chain, which is consistent with the presence of guanine-arginine interactions in these NLPs. This is also supported by the kinetically favored formation of NLPs having HCV core protein and guanine-enriched synthetic oligonucleotides. We also found that these NPLs are fully permeable to water molecules.
丙型肝炎病毒 (HCV) RNA 环 IIId 结构域的二级结构在 HCV 的不同基因型之间高度保守，这表明核衣壳蛋白可能通过这种环结构与基因组 RNA 相互作用。我们使用红外光谱法监测了 HCV 核心蛋白和环 IIId 在形成核衣壳样颗粒 (NLP) 时发生的结构变化。这些颗粒的蛋白质二级结构涉及到相对于其蛋白质单体的β-折叠富集。环 IIId 的磷酸二酯骨架振动反映了涉及 RNA A 构象的核糖的主要 C3'-内消旋构象，并揭示了所述 RNA 片段在 NLP 内包装诱导的向单链结构的转变。这些颗粒中分子间的蛋白质-核酸接触涉及 RNA 磷酸基团和带正电荷的氨基酸残基，如精氨酸和赖氨酸。在氘化过程中测量的光谱的二维相关光谱分析显示出与分配给鸟嘌呤和精氨酸侧链的两个带相关的同步交叉峰，这与这些 NLP 中存在鸟嘌呤-精氨酸相互作用一致。这也得到了动力学上有利于形成具有 HCV 核心蛋白和富含鸟嘌呤的合成寡核苷酸的 NLP 的支持。我们还发现这些 NLP 对水分子完全具有渗透性。
