Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
Department of Structural Biology and Chemistry, Institut Pasteur, Université Paris Cité CNRS UMR 3528, 75015 Paris, France.
Biochemistry. 2023 Aug 15;62(16):2407-2416. doi: 10.1021/acs.biochem.3c00010. Epub 2023 Jul 21.
In recent years, major advances in cryo-electron microscopy (cryo-EM) have enabled the routine determination of complex biomolecular structures at atomistic resolution. An open challenge for this approach, however, concerns large systems that exhibit continuous dynamics. To address this problem, we developed the metadynamic electron microscopy metainference (MEMMI) method, which incorporates metadynamics, an enhanced conformational sampling approach, into the metainference method of integrative structural biology. MEMMI enables the simultaneous determination of the structure and dynamics of large heterogeneous systems by combining cryo-EM density maps with prior information through molecular dynamics, while at the same time modeling the different sources of error. To illustrate the method, we apply it to elucidate the dynamics of an amyloid fibril of the islet amyloid polypeptide (IAPP). The resulting conformational ensemble provides an accurate description of the structural variability of the disordered region of the amyloid fibril, known as fuzzy coat. The conformational ensemble also reveals that in nearly half of the structural core of this amyloid fibril, the side chains exhibit liquid-like dynamics despite the presence of the highly ordered network backbone of hydrogen bonds characteristic of the cross-β structure of amyloid fibrils.
近年来，冷冻电子显微镜（cryo-EM）技术的重大进展使得在原子分辨率下常规测定复杂生物分子结构成为可能。然而，该方法面临的一个开放性挑战是涉及具有连续动力学的大型系统。为了解决这个问题，我们开发了动态电子显微镜元推断（MEMMI）方法，该方法将元动力学（一种增强构象采样方法）纳入整合结构生物学的元推断方法中。MEMMI 通过将冷冻电子显微镜密度图与通过分子动力学获得的先验信息相结合，同时对不同来源的误差进行建模，从而实现对大型异质体系的结构和动力学的同时测定。为了说明该方法，我们将其应用于阐明胰岛淀粉样多肽（IAPP）的淀粉样纤维的动力学。所得构象集合提供了对淀粉样纤维无规区结构变异性的精确描述，称为模糊层。构象集合还表明，在该淀粉样纤维的结构核心的近一半中，尽管存在特征性的淀粉样纤维交叉-β结构的氢键高度有序网络骨架，但侧链仍表现出类液体动力学。
