New Hunt's House, King's College London, Guy's Campus, London, SE1 1UL, UK.
Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
Sci Rep. 2022 Sep 8;12(1):15201. doi: 10.1038/s41598-022-18890-6.
Multidomain proteins composed of individual domains connected by flexible linkers pose a challenge for structural studies due to their intrinsic conformational dynamics. Integrated modelling approaches provide a means to characterise protein flexibility by combining experimental measurements with molecular simulations. In this study, we characterise the conformational dynamics of the catalytic RBR domain of the E3 ubiquitin ligase HOIP, which regulates immune and inflammatory signalling pathways. Specifically, we combine small angle X-ray scattering experiments and molecular dynamics simulations to generate weighted conformational ensembles of the HOIP RBR domain using two different approaches based on maximum parsimony and maximum entropy principles. Both methods provide optimised ensembles that are instrumental in rationalising observed differences between SAXS-based solution studies and available crystal structures and highlight the importance of interdomain linker flexibility.
由通过柔性接头连接的单个结构域组成的多结构域蛋白由于其内在的构象动力学，给结构研究带来了挑战。综合建模方法通过将实验测量与分子模拟相结合，为研究蛋白质的柔性提供了一种手段。在这项研究中，我们对调节免疫和炎症信号通路的 E3 泛素连接酶 HOIP 的催化 RBR 结构域的构象动力学进行了研究。具体来说，我们结合小角度 X 射线散射实验和分子动力学模拟，使用基于最大简约和最大熵原理的两种不同方法，为 HOIP RBR 结构域生成加权构象集合。这两种方法都提供了优化的集合，有助于合理地解释基于 SAXS 的溶液研究和现有晶体结构之间的差异，并强调了结构域间连接区柔性的重要性。
