Molza Anne-Elisabeth, Westermaier Yvonne, Moutte Magali, Ducrot Pierre, Danilowicz Claudia, Godoy-Carter Veronica, Prentiss Mara, Robert Charles H, Baaden Marc, Prévost Chantal
CNRS, Université Paris-Cité, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France.
Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France.
Front Mol Biosci. 2022 Apr 11;9:826136. doi: 10.3389/fmolb.2022.826136. eCollection 2022.
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.
结构生物物理学和整合建模方法的最新进展使我们能够解析大型大分子组装体的结构。要理解其生物学功能所涉及的动力学和机制，需要对所有可用数据进行严格整合。我们开发了一套完整的建模流程，其中包括通过将自动化步骤与人工引导步骤持续结合来提取生物学重要信息的分析方法。我们用两个例子来说明这一理念。首先，我们描述兰尼碱受体，它是一种离子通道，通过在开放状态和关闭状态之间转换来控制离子穿过细胞膜的通量。与受体相当大的系统规模相比，与这些转换相关的构象变化很小；利用现有的冷冻电镜结构持续追踪这些状态具有挑战性。第二个例子涉及同源重组，其中重组酶蛋白和DNA的长丝催化同源DNA链的交换，以可靠地修复DNA双链断裂。此过程中的核蛋白丝反应中间体寿命短且具有异质性，使得它们的结构特别难以捉摸。我们所描述的流程结合了实验和理论知识以及最先进的交互式和沉浸式建模工具，有助于克服这些挑战。在这两个例子中，我们指出了这种跨学科方法对生物学过程的新见解。
