DataSheet1_Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies.pdf

Recent advances in structural biophysics and integrative modelling methods now allow us to decipher the structures of large macromolecular assemblies. Understanding the dynamics and mechanisms involved in their biological function requires rigorous integration of all available data. We have developed a complete modelling pipeline that includes analyses to extract biologically significant information by consistently combining automated and interactive human-guided steps. We illustrate this idea with two examples. First, we describe the ryanodine receptor, an ion channel that controls ion flux across the cell membrane through transitions between open and closed states. The conformational changes associated with the transitions are small compared to the considerable system size of the receptor; it is challenging to consistently track these states with the available cryo-EM structures. The second example involves homologous recombination, in which long filaments of a recombinase protein and DNA catalyse the exchange of homologous DNA strands to reliably repair DNA double-strand breaks. The nucleoprotein filament reaction intermediates in this process are short-lived and heterogeneous, making their structures particularly elusive. The pipeline we describe, which incorporates experimental and theoretical knowledge combined with state-of-the-art interactive and immersive modelling tools, can help overcome these challenges. In both examples, we point to new insights into biological processes that arise from such interdisciplinary approaches.

近年来，结构生物物理学（structural biophysics）与整合建模方法的研究进展，使我们得以解析大型大分子组装体的三维结构。解析其生物学功能相关的动态过程与作用机制，需要严格整合所有可获取的实验数据。为此，我们开发了一套完整的建模流程，通过持续结合自动化操作与人工交互引导的步骤开展分析，以提取具有生物学意义的关键信息。我们通过两个实例阐释这一研究思路：其一，以ryanodine受体（ryanodine receptor）为例，该受体是一类离子通道，通过开放与关闭状态之间的构象转变，调控离子跨细胞膜的通量。相较于该受体庞大的系统尺度，构象转变伴随的结构变化幅度极小；依托现有冷冻电镜（cryo-EM）结构，难以稳定追踪这些功能相关的状态。其二，同源重组过程：重组酶蛋白与DNA组装形成的长丝状体可催化同源DNA链的交换，以此高效修复DNA双链断裂。该过程中的核蛋白丝（nucleoprotein filament）反应中间体寿命极短且具有异质性，使其结构解析极具挑战性。我们所描述的建模流程整合了实验与理论知识，并结合了当前最先进的交互式沉浸式建模工具，能够助力攻克上述难题。在两个实例中，我们均展示了此类跨学科研究方法为生物学过程研究带来的全新认知。