Rethinking protein aggregation and drug discovery in neurodegenerative diseases: Why we need to embrace complexity?

More than a century has passed since pathological protein aggregates were first identified in the brains of patients with neurodegenerative diseases (NDDs). Yet, we still do not have effective therapies to treat or slow the progression of these devastating diseases or diagnostics for early detection and monitoring disease progression. Herein, I reflect on recent findings that are challenging traditional views about the composition, ultrastructural properties, and diversity of protein pathologies in the brain, their mechanisms of formation and how we investigate and model pathological aggregation processes in the laboratory today. This article is an invitation to embrace the complexity of proteinopathies as an essential step to understanding the molecular mechanisms underpinning NDDs and to advance translational research and drug discovery in NDDs.     

Tuning of the Zernike phase-plate for visualization of detailed ultrastructure in complex biological specimens

In order to acquire phase-contrast images with adequate contrast, conventional TEM requires large amount of defocus. Increasing the defocus improves the low-frequency components but attenuates the high-frequency ones. On the other hand, Zernike phase-contrast TEM (ZPC-TEM) can recover low-frequency components without losing the high-frequency ones under in-focus conditions. ZPC-TEM however, has another problem, especially in imaging of complex biological specimens such as cells and tissues; strong halos appear around specimen structures, and these halos hinder the interpretation of images. Due to this problem, the application of ZPC-TEM has been restricted to imaging of smaller particles. In order to improve the halo appearance, we fabricated a new quarter-wave thin film phase-plate with a smaller central hole and tested it on vitreous biological specimens. ZPC-TEM with the new plate could successfully visualize, in in-focus images, the intracellular fine features of cultured cells and brain tissues. This result indicates that reduction of the central hole diameter makes ZPC-TEM applicable on size scales ranging from protein particles to tissue sections. The application of ZPC-TEM to vitreous biological specimens will be a powerful method to advance the new field of imaging science for ultrastructures in close-to-physiological state.     

Heterogeneity in E. coli RecBCD Helicase-DNA Binding and Base Pair Melting

E. coli RecBCD, a helicase/nuclease involved in double stranded (ds) DNA break repair, binds to a dsDNA end and melts out several DNA base pairs (bp) using only its binding free energy. We examined RecBCD-DNA initiation complexes using thermodynamic and structural approaches. Measurements of enthalpy changes for RecBCD binding to DNA ends possessing pre-melted ssDNA tails of increasing length suggest that RecBCD interacts with ssDNA as long as 17–18 nucleotides and can melt at least 10–11 bp upon binding a blunt DNA end. Cryo-EM structures of RecBCD alone and in complex with a blunt-ended dsDNA show significant conformational heterogeneities associated with the RecB nuclease domain (RecB^Nuc) and the RecD subunit. In the absence of DNA, 56% of RecBCD molecules show no density for the RecB nuclease domain, RecB^Nuc, and all RecBCD molecules show only partial density for RecD. DNA binding reduces these conformational heterogeneities, with 63% of the molecules showing density for both RecD and RecB^Nuc. This suggests that the RecB^Nuc domain is dynamic and influenced by DNA binding. The major RecBCD-DNA structural class in which RecB^Nuc is docked onto RecC shows melting of at least 11 bp from a blunt DNA end, much larger than previously observed. A second structural class in which RecB^Nuc is not docked shows only four bp melted suggesting that RecBCD complexes transition between states with different extents of DNA melting and that the extent of melting regulates initiation of helicase activity.     

How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM

The atomic coordinates derived from cryo-electron microscopy (cryo-EM) maps can be inaccurate when the voxel scaling factors are not properly calibrated. Here, we describe a method for correcting relative voxel scaling factors between pairs of cryo-EM maps for the same or similar structures that are expanded or contracted relative to each other. We find that the correction of scaling factors reduces the amplitude differences of Fourier-inverted structure factors from voxel-rescaled maps by up to 20–30%, as shown by two cryo-EM maps of the SARS-CoV-2 spike protein measured at pH 4.0 and pH 8.0. This allows for the calculation of the difference map after properly scaling, revealing differences between the two structures for individual amino acid residues. Unexpectedly, the analysis uncovers two previously overlooked differences of amino acid residues in structures and their local structural changes. Furthermore, we demonstrate the method as applied to two cryo-EM maps of monomeric apo-photosystem II from the cyanobacteria Synechocystis sp. PCC 6803 and Thermosynechococcus elongatus. The resulting difference maps reveal many changes in the peripheral transmembrane PsbX subunit between the two species.     

30nm染色质纤维结构与表观遗传调控

真核生物的DNA以染色质形式通过逐级折叠压缩形成高级结构存在于细胞核中。染色质高级结构直接参与了真核基因的转录调控和其它与DNA相关的生物学事件,因此研究染色质高级结构对了解表观遗传学分子机制有着至关重要的作用。近些年,研究者们针对30 nm染色质高级结构提出了两个模型:螺线管模型和Zig-Zag模型。2014年,我们利用体外染色质组装体系重建了30 nm染色质纤维,运用高精度冷冻电镜技术得到了分辨率为11?的30 nm染色质纤维的精细结构,提出了30 nm染色质高级结构的左手双螺旋Zig-Zag模型。本文综述了30 nm染色质纤维结构研究方面的相关进展,并对30 nm染色质高级结构的表观遗传调控机理以及单分子成像和操纵技术在研究30 nm染色质高级结构中潜在的应用作出讨论和展望。     

26S蛋白酶体的结构生物学研究进展

26S蛋白酶体是真核细胞内负责蛋白质降解的主要分子机器,通过特异性降解目的蛋白质,几乎参与了生物体的绝大多数生命活动.26S蛋白酶体在结构上可分为19S调节颗粒和20S核心颗粒两部分.19S调节颗粒负责识别带有泛素链标记的蛋白质底物及对其进行去折叠,并最终将去折叠的蛋白质底物传送至20S核心颗粒中进行降解.由于26S蛋白酶体的结构组成复杂,分子量十分巨大,现有的X-ray技术和NMR技术对其完整结构的解析都无能为力,仅能解析出部分单个蛋白成员或分子量较低的亚复合物晶体结构.而冷冻电镜技术在相当一段时间内处于发展的初级阶段,导致其三维结构的研究进展曾经十分缓慢,严重阻碍了人们对其结构和功能的了解.近年来,随着在X-ray技术领域对大分子复合物结构解析的经验积累和冷冻电镜技术领域的技术革命,完整的26S蛋白酶体三维结构解析取得了飞速的发展.本文回顾了近几年在26S蛋白酶体结构生物学领域的重要进展,并展望了该领域未来的发展及面临的挑战.     

Marker-free method for accurate alignment between correlated light,cryo-light,and electron cryo-microscopy data using sample support features

Combining fluorescence microscopy with electron cryo-tomography allows, in principle, spatial localization of tagged macromolecular assemblies and structural features within the cellular environment. To allow precise localization and scale integration between the two disparate imaging modalities, accurate alignment procedures are needed. Here, we describe a marker-free method for aligning images from light or cryo-light fluorescence microscopy and from electron cryo-microscopy that takes advantage of sample support features, namely the holes in the carbon film. We find that the accuracy of this method, as judged by prediction errors of the hole center coordinates, is better than 100?nm.     

From Bench to Biomolecular Simulation: Phospholipid Modulation of Potassium Channels

Potassium (K⁺) ion channels are crucial in numerous cellular processes as they hyperpolarise a cell through K⁺ conductance, returning a cell to its resting potential. K⁺ channel mutations result in multiple clinical complications such as arrhythmia, neonatal diabetes and migraines. Since 1995, the regulation of K⁺ channels by phospholipids has been heavily studied using a range of interdisciplinary methods such as cellular electrophysiology, structural biology and computational modelling. As a result, K⁺ channels are model proteins for the analysis of protein-lipid interactions. In this review, we will focus on the roles of lipids in the regulation of K⁺ channels, and how atomic-level structures, along with experimental techniques and molecular simulations, have helped guide our understanding of the importance of phospholipid interactions.     

Revelation of an enigmatic signaling machinery—First insights into the mammalian TRPC architecture

Canonical TRP channels (TRPCs) are a particularly enigmatic family of signaling molecules with multimodal sensing features, being involved in a wide range of biological functions. Until very recently, the main hurdle towards comprehensive mechanistic understanding of TRPC signaling has been the lack of structural information. This has changed early this year by several reports on TRPC architectures resolved by single particle cryo-EM analysis. These studies confirmed recently elaborated concepts on TRPC structure-function relations, and unveiled unanticipated features and complexity in the TRPC sensing machinery.     

Rapid tilt-series acquisition for electron cryotomography

Using a new Titan Krios stage equipped with a single-axis holder, we developed two methods to accelerate the collection of tilt-series. We demonstrate a continuous-tilting method that can record a tilt-series in seconds, but with loss of details finer than ～4?nm. We also demonstrate a fast-incremental method that can record a tilt-series several-fold faster than current methods and with similar resolution. We characterize the utility of both methods in real biological electron cryotomography workflows. We identify opportunities for further improvements in hardware and software and speculate on the impact such advances could have on structural biology.