Division of Structural Biology, University of Oxford, Oxford, United Kingdom.
PLoS One. 2013 Nov 4;8(11):e80371. doi: 10.1371/journal.pone.0080371. eCollection 2013.
Human metapneumovirus (HMPV) of the family Paramyxoviridae is a major cause of respiratory illness worldwide. Phosphoproteins (P) from Paramyxoviridae are essential co-factors of the viral RNA polymerase that form tetramers and possess long intrinsically disordered regions (IDRs). We located the central region of HMPV P (P(ced)) which is involved in tetramerization using disorder analysis and modeled its 3D structure ab initio using Rosetta fold-and-dock. We characterized the solution-structure of P(ced) using small angle X-ray scattering (SAXS) and carried out direct fitting to the scattering data to filter out incorrect models. Molecular dynamics simulations (MDS) and ensemble optimization were employed to select correct models and capture the dynamic character of P(ced). Our analysis revealed that oligomerization involves a compact central core located between residues 169-194 (P(core)), that is surrounded by flexible regions with α-helical propensity. We crystallized this fragment and solved its structure at 3.1 Å resolution by molecular replacement, using the folded core from our SAXS-validated ab initio model. The RMSD between modeled and experimental tetramers is as low as 0.9 Å, demonstrating the accuracy of the approach. A comparison of the structure of HMPV P to existing mononegavirales P(ced) structures suggests that P(ced) evolved under weak selective pressure. Finally, we discuss the advantages of using SAXS in combination with ab initio modeling and MDS to solve the structure of small, homo-oligomeric protein complexes.
人偏肺病毒(HMPV)属于副黏液病毒科,是全球范围内引发呼吸道疾病的主要病原体之一。副黏液病毒科的磷蛋白(P)是病毒 RNA 聚合酶的必需辅助因子,它们形成四聚体并具有长的固有无序区域(IDR)。我们通过无序分析定位了 HMPV P 中参与四聚化的中央区域(P(ced)),并使用 Rosetta 折叠和对接从头开始对其三维结构进行建模。我们使用小角 X 射线散射(SAXS)对 P(ced)的溶液结构进行了表征,并对散射数据进行直接拟合,以滤除不正确的模型。分子动力学模拟(MDS)和整体优化用于选择正确的模型并捕获 P(ced)的动态特性。我们的分析表明,寡聚化涉及位于残基 169-194 之间的紧凑中央核心(P(core)),该核心被具有α-螺旋倾向的柔性区域所包围。我们对该片段进行了结晶,并使用我们的 SAXS 验证的从头模型中的折叠核心,通过分子置换以 3.1 Å 的分辨率解决了其结构。模型化和实验四聚体之间的 RMSD 低至 0.9 Å,证明了该方法的准确性。将 HMPV P 的结构与现有的单负链 RNA 病毒 P(ced)结构进行比较表明,P(ced)是在较弱的选择压力下进化而来的。最后,我们讨论了使用 SAXS 结合从头建模和 MDS 来解决小同型寡聚蛋白复合物结构的优势。