Identification and quantification of trace metal(loid)s in water-extractable road dust nanoparticles using SP-ICP-MS

Resuspension of road dust is a major source of airborne particulate matter (PM) in urban environments. Inhalation of ultrafine particles (UFP; < 0.1 μm) represents a health concern due to their ability to reach the alveoli and be translocated into the blood stream. It is therefore important to characterize chemical properties of UFPs associated with vehicle emissions. We investigated the capability of Single-Particle ICP-MS (SP-ICP-MS) to quantify key metal(loid)s in nanoparticles (NPs; < 0.1 μm) isolated from road dust collected in Toronto, Canada. Water extraction was performed to separate the <1-μm fraction from two different road dust samples (local road vs. arterial road) and a multi-element SP-ICP-MS analysis was then conducted on the samples' supernatants. Based on the particle number concentrations obtained for both supernatants, the metal(loid)-containing NPs could be grouped in the following categories: high (Cu and Zn, > 1.3 × 1011 particles/L), medium (V, Cr, Ba, Pb, Sb, Ce, La), low (As, Co, Ni, < 4.6 × 109 particles/L). The limit of detection for particle number concentration was below 5.5 × 106 particles/L for most elements, except for Cu, Co, Ni, Cr, and V (between 0.9 and 7.7 × 107 particles/L). The results demonstrate that road dust contains a wide range of readily mobilizable metal(loid)-bearing NPs and that NP numbers may vary as a function of road type. These findings have important implications for human health risk assessments in urban areas. Further research is needed, however, to comprehensively assess the NP content of road dust as influenced by various factors, including traffic volume and speed, fleet composition, and street sweeping frequency. The described method can quickly characterize multiple isotopes per sample in complex matrices, and offers the advantage of rapid sample scanning for the identification of NPs containing potentially toxic transition metal(loid)s at a low detection limit.

Bacterial selenocysteine synthase structure revealed by single-particle cryoEM

The 21st amino acid, selenocysteine (Sec), is synthesized on its dedicated transfer RNA (tRNASec). In bacteria, Sec is synthesized from Ser-tRNA[Ser]Sec by Selenocysteine Synthase (SelA), which is a pivotal enzyme in the biosynthesis of Sec. The structural characterization of bacterial SelA is of paramount importance to decipher its catalytic mechanism and its role in the regulation of the Sec-synthesis pathway. Here, we present a comprehensive single-particle cryo-electron microscopy (SPA cryoEM) structure of the bacterial SelA with an overall resolution of 2.69 Å. Using recombinant Escherichia coli SelA, we purified and prepared samples for single-particle cryoEM. The structural insights from SelA, combined with previous in vivo and in vitro knowledge, underscore the indispensable role of decamerization in SelA's function. Moreover, our structural analysis corroborates previous results that show that SelA adopts a pentamer of dimers configuration, and the active site architecture, substrate binding pocket, and key K295 catalytic residue are identified and described in detail. The differences in protein architecture and substrate coordination between the bacterial enzyme and its counterparts offer compelling structural evidence supporting the independent molecular evolution of the bacterial and archaea/eukarya Ser-Sec biosynthesis present in the natural world.

Deep generative priors for biomolecular 3D heterogeneous reconstruction from cryo-EM projections

Cryo-electron microscopy has become a powerful tool to determine three-dimensional (3D) structures of rigid biological macromolecules from noisy micrographs with single-particle reconstruction. Recently, deep neural networks, e.g., CryoDRGN, have demonstrated conformational and compositional heterogeneity of complexes. However, the lack of ground-truth conformations poses a challenge to assess the performance of heterogeneity analysis methods. In this work, variational autoencoders (VAE) with three types of deep generative priors were learned for latent variable inference and heterogeneous 3D reconstruction via Bayesian inference. More specifically, VAEs with "Variational Mixture of Posteriors" priors (VampPrior-SPR), non-parametric exemplar-based priors (ExemplarPrior-SPR) and priors from latent score-based generative models (LSGM-SPR) were quantitatively compared with CryoDRGN. We built four simulated datasets composed of hypothetical continuous conformation or discrete states of the hERG K + channel. Empirical and quantitative comparisons of inferred latent representations were performed with affine-transformation-based metrics. These models with more informative priors gave better regularized, interpretable factorized latent representations with better conserved pairwise distances, less deformed latent distributions and lower within-cluster variances. They were also tested on experimental datasets to resolve compositional and conformational heterogeneity (50S ribosome assembly, cowpea chlorotic mottle virus, and pre-catalytic spliceosome) with comparable high resolution. Codes and data are available: https://github.com/benjamin3344/DGP-SPR.

Expression, Purification, and Nanodisc Reconstitution of Connexin-43 Hemichannels for Structural Characterization by Cryo-Electron Microscopy

Connexins are polytopic domain membrane proteins that form hexameric hemichannels (HCs) which can assemble into gap junction channels (GJCs) at the interface of two neighboring cells. The HCs may be involved in ion and small-molecule transport across the cellular plasma membrane in response to various stimuli. Despite their importance, relatively few structures of connexin HCs are available to date, compared to the structures of the GJCs. Here, we describe a protocol for expression, purification, and nanodisc reconstitution of connexin-43 (Cx43) HCs, which we have recently structurally characterized using cryo-EM analysis. Application of similar protocols to other connexin family members will lead to breakthroughs in the understanding of the structure and function of connexin HCs.

Determining Macromolecular Structures Using Cryo-Electron Microscopy

Structural insights into macromolecular and protein complexes provide key clues about the molecular basis of the function. Cryogenic electron microscopy (cryo-EM) has emerged as a powerful structural biology method for studying protein and macromolecular structures at high resolution in both native and near-native states. Despite the ability to get detailed structural insights into the processes underlying protein function using cryo-EM, there has been hesitancy amongst plant biologists to apply the method for biomolecular interaction studies. This is largely evident from the relatively fewer structural depositions of proteins and protein complexes from plant origin in electron microscopy databank. Even though the progress has been slow, cryo-EM has significantly contributed to our understanding of the molecular biology processes underlying photosynthesis, energy transfer in plants, besides viruses infecting plants. This chapter introduces sample preparation for both negative-staining electron microscopy (NSEM) and cryo-EM for plant proteins and macromolecular complexes and data analysis using single particle analysis for beginners.

Use of Localized Reconstruction to Visualize the Shigella Phage Sf6 Tail Apparatus

Cryogenic electron microscopy (cryo-EM) single-particle analysis has revolutionized the structural analysis of icosahedral viruses, including tailed bacteriophages. In recent years, localized (or focused) reconstruction has emerged as a powerful data analysis method to capture symmetry mismatches and resolve asymmetric features in icosahedral viruses. Here, we describe the methods used to reconstruct the 2.65-MDa tail apparatus of the Shigella phage Sf6, a representative member of the Podoviridae superfamily.

Nanoparticle Spikes Enhance Cellular Uptake via Regulating Myosin IIA Recruitment

Spike-like nanostructures are omnipresent in natural and artificial systems. Although biorecognition of nanostructures to cellular receptors has been indicated as the primary factor for virus infection pathways, how the spiky morphology of DNA-modified nanoparticles affects their cellular uptake and intracellular fate remains to be explored. Here, we design dually emissive gold nanoparticles with varied spikiness (from 0 to 2) to probe the interactions of spiky nanoparticles with cells. We discovered that nanospikes at the nanoparticle regulated myosin IIA recruitment at the cell membrane during cellular uptake, thereby enhancing cellular uptake efficiency, as revealed by dual-modality (plasmonic and fluorescence) imaging. Furthermore, the spiky nanoparticles also exhibited facilitated endocytosis dynamics, as revealed by real-time dark-field microscopy (DFM) imaging and colorimetry-based classification algorithms. These findings highlight the crucial role of the spiky morphology in regulating the intracellular fate of nanoparticles, which may shed light on engineering theranostic nanocarriers.

Basic and advanced spectrometric methods for complete nanoparticles characterization in bio/eco systems: current status and future prospects

The use of engineered nanoparticles in the environment and human life has increased in the last 20 years. The risk assessment concerning application of nanomaterials in biological systems requires their thorough characterization. Understanding the correlations between physicochemical properties of nanoparticles concerning not only the size, particle size distribution, number concentration, degree of aggregation, or agglomeration but also solubility, stability, binding affinity, surface activity, chemical composition, and nanoparticle synthesis yield allows their reliable characterization. Thus, to find the structure-function/property relationship of nanoparticles, multifaceted characterization approach based on more than one analytical technique is required. On the other hand, the increasing demand for identification and characterization of nanomaterials has contributed to the continuous development of spectrometric techniques which enables for their qualitative and quantitative analysis in complex matrices giving reproducible and reliable results. This review is aimed at providing a discussion concerning four main aspects of nanoparticle characterization: nanoparticle synthesis yield, particle size and number concentration, elemental and isotopic composition of nanoparticles, and their surface properties. The conventional and non-conventional spectrometric techniques such as spectrophotometry UV-Vis, mass spectrometric techniques working in conventional and single-particle mode, or those based on optical emission detection systems are described with special emphasis paid on their advantages and drawbacks. The application and recent advances of these methods are also comprehensively reviewed and critically discussed.

Single-particle assessment of six different drug-loading strategies for incorporating doxorubicin into small extracellular vesicles

Extracellular vesicles (EVs) have emerged as an attractive drug delivery system owing to their natural roles in intercellular communication. On account of the large intrinsic heterogeneity of EVs, it is highly desirable to evaluate not only the encapsulation efficiency but also the alteration of biological functionality after the drug-loading process at the single-particle level. However, the nanoscale size of EVs poses a great challenge. Taking advantage of nano-flow cytometry (nFCM) in the multiparameter analysis of single EVs as small as 40 nm, six commonly used drug-loading strategies (coincubation, electroporation, extrusion, freeze-thawing, sonication, and surfactant treatment) were exploited by employing doxorubicin (Dox) as the model drug. Encapsulation ratio, EV concentration, drug content, and membrane proteins of Dox-loaded EVs were measured at the single-particle level. Our data indicated that coincubation and electroporation outperformed other methods with an encapsulation ratio of approximately 45% and a higher Dox content in single EVs. Interestingly, the labeling ratios of membrane proteins indicated that varying degrees of damage to the surface proteins of EVs occurred upon extrusion, freeze-thawing, sonication, and surfactant treatment. Confocal fluorescence microscopy and flow cytometry analysis revealed that Dox-loaded EVs prepared by electroporation induced the strongest apoptosis followed by coincubation. These results correlated well with their cellular uptake rate and fundamentally with the Dox encapsulation efficiency of single EVs. nFCM provides a rapid and sensitive platform for single-particle assessment of drug-loading strategies for incorporating drugs into EVs.

Purification and Structural Analysis of the Gliding Motility Machinery in Mycoplasma mobile

Isolating functional units from large insoluble protein complexes are a complex but valuable approach for quantitative and structural analysis. Mycoplasma mobile, a gliding bacterium, contains a large insoluble protein complex called gliding machinery. The machinery contains several chain structures formed by motors that are evolutionarily related to the F₁-ATPase. Recently, we developed a method to purify functional motors and their chain structures using Triton X-100 and a high salt concentration buffer and resolved their structures using electron microscopy. In this chapter, we describe the processes of purification and structural analysis of functional motors for the gliding of M. mobile using negative-staining electron microscopy.

Near-Atomic Resolution Cryo-EM Image Reconstruction of RNA

The rapid development of cryogenic electron microscopy (cryo-EM) enables the structure determination of macromolecules without the need for crystallization. Protein, protein-lipid, and protein-nucleic acid complexes can now be routinely resolved by cryo-EM single-particle analysis (SPA) to near-atomic or atomic resolution. Here we describe the structure determination of pure RNAs by SPA, from cryo-specimen preparation to data collection and 3D reconstruction. This protocol is useful to yield many cryo-EM structures of RNA, here exemplified by the Tetrahymena L-21 ScaI ribozyme at 3.1-Å resolution.

Detection of magnetic iron nanoparticles by single-particle ICP-TOFMS: case study for a magnetic filtration medical device

Nanoparticles are increasingly used in medical products and devices. Their properties are critical for such applications, as particle characteristics determine their interaction with the biological system, and, therefore, the performance and safety of the final product. Among the most important nanoparticle characteristics and parameters are particle mass distribution, composition, total particle mass, and number concentration. In this study, we utilize single-particle inductively coupled plasma time-of-flight mass spectrometry (spICP-TOFMS) for the characterization of inorganic nanoparticles in complex biological fluids. We report online microdroplet calibration for reference-nanomaterial-free and matrix-matched calibration of carbon-coated iron carbide nanoparticles (C/Fe₃C NPs). As a case study, we analyze C/Fe₃C NPs designed for targeted blood purification. Through the analysis of NP mass distributions, we study the effect of the NP surface modification on aggregation of C/Fe₃C NPs in whole blood. We also demonstrate the efficiency of removal of coated C/Fe₃C NP from saline by magnetically enhanced filters. Magnetic filtering is shown to reduce the mass concentration of detectable C/Fe₃C NPs by 99.99 ± 0.01% in water.

Development and single-particle analysis of hybrid extracellular vesicles fused with liposomes using viral fusogenic proteins

Extracellular vesicles (EVs) have potential biomedical applications, particularly as a means of transport for therapeutic agents. There is a need for rapid and efficient EV‐liposome membrane fusion that maintains the integrity of hybrid EVs. We recently described Sf9 insect cell‐derived EVs on which functional membrane proteins were presented using a baculovirus‐expression system. Here, we developed hybrid EVs by membrane fusion of small liposomes and EVs equipped with baculoviral fusogenic proteins. Single‐particle analysis of EV‐liposome complexes revealed controlled introduction of liposome components into EVs. Our findings and methodology will support further applications of EV engineering in biomedicine.

High-resolution structure of phosphoketolase from Bifidobacterium longum determined by cryo-EM single-particle analysis

In bifidobacteria, phosphoketolase (PKT) plays a key role in the central hexose fermentation pathway called "bifid shunt." The three-dimensional structure of PKT from Bifidobacterium longum with co-enzyme thiamine diphosphate (ThDpp) was determined at 2.1 Å resolution by cryo-EM single-particle analysis using 196,147 particles to build up the structural model of a PKT octamer related by D4 symmetry. Although the cryo-EM structure of PKT was almost identical to the X-ray crystal structure previously determined at 2.2 Å resolution, several interesting structural features were observed in the cryo-EM structure. Because this structure was solved at relatively high resolution, it was observed that several amino acid residues adopt multiple conformations. Among them, Q546-D547-H548-N549 (the QN-loop) demonstrate the largest structural change, which seems to be related to the enzymatic function of PKT. The QN-loop is at the entrance to the substrate binding pocket. The minor conformer of the QN-loop is similar to the conformation of the QN-loop in the crystal structure. The major conformer is located further from ThDpp than the minor conformer. Interestingly, the major conformer in the cryo-EM structure of PKT resembles the corresponding loop structure of substrate-bound Escherichia coli transketolase. That is, the minor and major conformers may correspond to "closed" and "open" states for substrate access, respectively. Moreover, because of the high-resolution analysis, many water molecules were observed in the cryo-EM structure of PKT. Structural features of the water molecules in the cryo-EM structure are discussed and compared with water molecules observed in the crystal structure.

Single-Particle Cryo-EM of Membrane Proteins

In the recent years, the protein databank has been fueled by the exponential growth of high-resolution electron cryo-microscopy (cryo-EM) structures. This trend will be further accelerated through the continuous software and method developments and the increasing availability of imaging centers, which will open cryo-EM to a wide array of researchers with their diverse scientific goals and questions. Especially for structural biology of membrane proteins, cryo-EM offers significant advantages as it can overcome multiple limitations of classical methods. Most importantly, in cryo-EM, the sample is prepared as a vitrified suspension, which abolishes the need for crystallization, reduces the required sample amount and allows usage of a wide arsenal of hydrophobic environments. Despite recent improvements, high-resolution cryo-EM still poses some significant challenges, and standardized procedures, especially for the characterization of membrane proteins, are missing. While there can be no ultimate recipe toward a high-resolution cryo-EM structure for every membrane protein, certain factors seem to be universally relevant. Here, we share the protocols that have been successfully used in our laboratory. We hope that this may be a useful resource to other researchers in the field and may increase their chances of success.

Cryo-EM structure of monomeric photosystem II at 2.78 Å resolution reveals factors important for the formation of dimer

Photosystem II (PSII) functions mainly as a dimer to catalyze the light energy conversion and water oxidation reactions. However, monomeric PSII also exists and functions in vivo in some cases. The crystal structure of monomeric PSII has been solved at 3.6 Å resolution, but it is still not clear which factors contribute to the formation of the dimer. Here, we solved the structure of PSII monomer at a resolution of 2.78 Å using cryo-electron microscopy (cryo-EM). From our cryo-EM density map, we observed apparent differences in pigments and lipids in the monomer-monomer interface between the PSII monomer and dimer. One β-carotene and two sulfoquinovosyl diacylglycerol (SQDG) molecules are found in the monomer-monomer interface of the dimer structure but not in the present monomer structure, although some SQDG and other lipid molecules are found in the analogous region of the low-resolution crystal structure of the monomer, or cryo-EM structure of an apo-PSII monomer lacking the extrinsic proteins from Synechocystis sp. PCC 6803. In the current monomer structure, a large part of the PsbO subunit was also found to be disordered. These results indicate the importance of the β-carotene, SQDG and PsbO in formation of the PSII dimer.

Single-Particle Kinetics of Immobilized Enzymes by Harnessing the Autofluorescence of Co-Immobilized Cofactors

The co-immobilized enzymes and cofactors onto porous microparticles work as self-sufficient heterogeneous biocatalysts whose catalytic activity can be easily monitored by means of the cofactors autofluorescence. The reduction step of some cofactors as NAD⁺ and FAD⁺ to NADH and FADH₂, respectively, involves an increase of its autofluorescence. This phenomenon is harnessed to image and analyze the enzymatic reactions catalyzed by cofactor-dependent enzymes at real time and single-particle level during the operational process. Due to the universality and highly accessibility of fluorescence microscopy, the strategy described here allows a straightforward and more accurate analysis at micro-scale of heterogeneous biocatalysts. These studies promote and support the rational design and optimization of biocatalysts toward highly efficient heterogeneous biocatalytic reactions.

ENRICH: A fast method to improve the quality of flexible macromolecular reconstructions

Cryo-electron microscopy using single particle analysis requires the computational averaging of thousands of projection images captured from identical macromolecules. However, macromolecules usually present some degree of flexibility showing different conformations. Computational approaches are then required to classify heterogeneous single particle images into homogeneous sets corresponding to different structural states. Nonetheless, sometimes the attainable resolution of reconstructions obtained from these smaller homogeneous sets is compromised because of reduced number of particles or lack of images at certain macromolecular orientations. In these situations, the current solution to improve map resolution is returning to the electron microscope and collect more data. In this work, we present a fast approach to partially overcome this limitation for heterogeneous data sets. Our method is based on deforming and then moving particles between different conformations using an optical flow approach. Particles are then merged into a unique conformation obtaining reconstructions with improved resolution, contrast and signal-to-noise ratio. We present experimental results that show clear improvements in the quality of obtained 3D maps, however, there are also limits to this approach, i.e., the method is restricted to small deformations and cannot determine local patterns of flexibility of small elements, such as secondary structures, which we discuss in the manuscript.

Evaluating Local and Directional Resolution of Cryo-EM Density Maps

A systematic and quantitative evaluation of cryo-EM maps is necessary to judge their quality and to capture all possible sources of error. A single value for global resolution is insufficient to accurately describe the quality of a reconstructed density. We describe the estimation and evaluation of two additional resolution measures, local and directional resolution, using methods based on the Fourier shell correlation (FSC). We apply the protocol to samples that encompass different types of pathologies a user is expected to encounter and provide analyses on how to interpret the output files and resulting maps. Implementation of these tools will facilitate density interpretation and can guide the user in adapting their experiments to improve the quality of cryo-EM maps, and by extension atomic models.

Multi-body Refinement of Cryo-EM Images in RELION

Single-particle analysis of electron cryo-microscopy (cryo-EM) images allows structure determination of macromolecular complexes. But when these molecules adopt many different conformations, traditional image processing approaches often lead to blurred reconstructions. By considering complexes to be comprised of multiple, independently moving rigid bodies, multi-body refinement in RELION enables structure determination of highly flexible complexes, while at the same time providing a characterization of the motions in the complex. Here, we describe how to perform multi-body refinement in RELION using a publicly available example. We outline how to prepare the necessary files, how to run the actual multi-body calculation, and how to interpret its output. This method can be applied to any cryo-EM data set of flexible complexes that can be divided into two or more bodies, each with a minimum molecular weight of 100-150 kDa.

Localized reconstruction in Scipion expedites the analysis of symmetry mismatches in cryo-EM data

Technological advances in transmission electron microscopes and detectors have turned cryogenic electron microscopy (cryo-EM) into an essential tool for structural biology. A commonly used cryo-EM data analysis method, single particle analysis, averages hundreds of thousands of low-dose images of individual macromolecular complexes to determine a density map of the complex. The presence of symmetry in the complex is beneficial since each projection image can be assigned to multiple views of the complex. However, data processing that applies symmetry can average out asymmetric features and consequently data analysis methods are required to resolve asymmetric structural features. Scipion is a cryo-EM image processing framework that integrates functions from different image processing packages as plugins. To extend its functionality for handling symmetry mismatches, we present here a Scipion plugin termed LocalRec implementing the localized reconstruction method. When tested on an adenovirus data set, the plugin enables resolving the symmetry-mismatched trimeric fibre bound to the five-fold vertices of the capsid. Furthermore, it improves the structure determination of the icosahedral capsid by dealing with the defocus gradient across the particle. LocalRec is expected to be widely applicable in a range of cryo-EM investigations of flexible and symmetry mismatched complexes.

Fusion of DARPin to Aldolase Enables Visualization of Small Protein by Cryo-EM

Solving protein structures by single-particle cryoelectron microscopy (cryo-EM) has become a crucial tool in structural biology. While exciting progress is being made toward the visualization of small macromolecules, the median protein size in both eukaryotes and bacteria is still beyond the reach of cryo-EM. To overcome this problem, we implemented a platform strategy in which a small protein target was rigidly attached to a large, symmetric base via a selectable adapter. Of our seven designs, the best construct used a designed ankyrin repeat protein (DARPin) rigidly fused to tetrameric rabbit muscle aldolase through a helical linker. The DARPin retained its ability to bind its target: GFP. We solved the structure of this complex to 3.0 Å resolution overall, with 5-8 Å resolution in the GFP region. As flexibility in the DARPin position limited the overall resolution of the target, we describe strategies to rigidify this element.

Robustness of signal detection in cryo-electron microscopy via a bi-objective-function approach

Background

The detection of weak signals and selection of single particles from low-contrast micrographs of frozen hydrated biomolecules by cryo-electron microscopy (cryo-EM) represents a major practical bottleneck in cryo-EM data analysis. Template-based particle picking by an objective function using fast local correlation (FLC) allows computational extraction of a large number of candidate particles from micrographs. Another independent objective function based on maximum likelihood estimates (MLE) can be used to align the images and verify the presence of a signal in the selected particles. Despite the widespread applications of the two objective functions, an optimal combination of their utilities has not been exploited. Here we propose a bi-objective function (BOF) approach that combines both FLC and MLE and explore the potential advantages and limitations of BOF in signal detection from cryo-EM data.

Results

The robustness of the BOF strategy in particle selection and verification was systematically examined with both simulated and experimental cryo-EM data. We investigated how the performance of the BOF approach is quantitatively affected by the signal-to-noise ratio (SNR) of cryo-EM data and by the choice of initialization for FLC and MLE. We quantitatively pinpointed the critical SNR (~ 0.005), at which the BOF approach starts losing its ability to select and verify particles reliably. We found that the use of a Gaussian model to initialize the MLE suppresses the adverse effects of reference dependency in the FLC function used for template-matching.

Conclusion

The BOF approach, which combines two distinct objective functions, provides a sensitive way to verify particles for downstream cryo-EM structure analysis. Importantly, reference dependency of the FLC does not necessarily transfer to the MLE, enabling the robust detection of weak signals. Our insights into the numerical behavior of the BOF approach can be used to improve automation efficiency in the cryo-EM data processing pipeline for high-resolution structural determination.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-2714-8) contains supplementary material, which is available to authorized users.

The cryo-electron microscopy structure of Broad Bean Stain Virus suggests a common capsid assembly mechanism among comoviruses

The Broad bean stain virus (BBSV) is a member of the genus Comovirus infecting Fabaceae. The virus is transmitted through seed and by plant weevils causing severe and widespread disease worldwide. BBSV has a bipartite, positive-sense, single-stranded RNA genome encapsidated in icosahedral particles. We present here the cryo-electron microscopy reconstruction of the BBSV and an atomic model of the capsid proteins refined at 3.22 Å resolution. We identified residues involved in RNA/capsid interactions revealing a unique RNA genome organization. Inspection of the small coat protein C-terminal domain highlights a maturation cleavage between Leu567 and Leu568 and interactions of the C-terminal stretch with neighbouring small coat proteins within the capsid pentameric turrets. These interactions previously proposed to play a key role in the assembly of the Cowpea mosaic virus suggest a common capsid assembly mechanism throughout all comovirus species.

PIXER: an automated particle-selection method based on segmentation using a deep neural network

BACKGROUND

Cryo-electron microscopy (cryo-EM) has become a widely used tool for determining the structures of proteins and macromolecular complexes. To acquire the input for single-particle cryo-EM reconstruction, researchers must select hundreds of thousands of particles from micrographs. As the signal-to-noise ratio (SNR) of micrographs is extremely low, the performance of automated particle-selection methods is still unable to meet research requirements. To free researchers from this laborious work and to acquire a large number of high-quality particles, we propose an automated particle-selection method (PIXER) based on the idea of segmentation using a deep neural network.

RESULTS

First, to accommodate low-SNR conditions, we convert micrographs into probability density maps using a segmentation network. These probability density maps indicate the likelihood that each pixel of a micrograph is part of a particle instead of just background noise. Particles selected from density maps have a more robust signal than do those directly selected from the original noisy micrographs. Second, at present, there is no segmentation-training dataset for cryo-EM. To enable our plan, we present an automated method to generate a training dataset for segmentation using real-world data. Third, we propose a grid-based, local-maximum method to locate the particles from the probability density maps. We tested our method on simulated and real-world experimental datasets and compared PIXER with the mainstream methods RELION, DeepEM and DeepPicker to demonstrate its performance. The results indicate that, as a fully automated method, PIXER can acquire results as good as the semi-automated methods RELION and DeepEM.

CONCLUSION

To our knowledge, our work is the first to address the particle-selection problem using the segmentation network concept. As a fully automated particle-selection method, PIXER can free researchers from laborious particle-selection work. Based on the results of experiments, PIXER can acquire accurate results under low-SNR conditions within minutes.

Fast multiscale reconstruction for Cryo-EM

We present a multiscale reconstruction framework for single-particle analysis (SPA). The representation of three-dimensional (3D) objects with scaled basis functions permits the reconstruction of volumes at any desired scale in the real-space. This multiscale approach generates interesting opportunities in SPA for the stabilization of the initial volume problem or the 3D iterative refinement procedure. In particular, we show that reconstructions performed at coarse scale are more robust to angular errors and permit gains in computational speed. A key component of the proposed iterative scheme is its fast implementation. The costly step of reconstruction, which was previously hindering the use of advanced iterative methods in SPA, is formulated as a discrete convolution with a cost that does not depend on the number of projection directions. The inclusion of the contrast transfer function inside the imaging matrix is also done at no extra computational cost. By permitting full 3D regularization, the framework is by itself a robust alternative to direct methods for performing reconstruction in adverse imaging conditions (e.g., heavy noise, large angular misassignments, low number of projections). We present reconstructions obtained at different scales from a dataset of the 2015/2016 EMDataBank Map Challenge. The algorithm has been implemented in the Scipion package.

Single-Particle Electron Microscopy Analysis of DNA Repair Complexes

DNA repair complexes play crucial roles in maintaining genome integrity, which is essential for the survival of an organism. The understanding of their modes of action is often obscure due to limited structural knowledge. Structural characterizations of these complexes are often challenging due to a poor protein production yield, a conformational flexibility, and a relatively high molecular mass. Single-particle electron microscopy (EM) has been successfully applied to study some of these complexes as it requires low amount of samples, is not limited by the high molecular mass of a protein or a complex, and can separate heterogeneous assemblies. Recently, near-atomic resolution structures have been obtained with EM owing to the advances in technology and image processing algorithms. In this chapter, we review the EM methodology of obtaining three-dimensional reconstructions of macromolecular complexes and provide a workflow that can be applied to DNA repair complex assemblies.

Preparation of Tunable Microchips to Visualize Native Protein Complexes for Single-Particle Electron Microscopy

Recent advances in technology have enabled single-particle electron microscopy (EM) to rapidly progress as a preferred tool to study protein assemblies. Newly developed materials and methods present viable alternatives to traditional EM specimen preparation. Improved lipid monolayer purification reagents offer considerable flexibility, while ultrathin silicon nitride films provide superior imaging properties to the structural study of protein complexes. Here, we describe the steps for combining monolayer purification with silicon nitride microchips to create a tunable approach for the EM community.

Exploring applications of crowdsourcing to cryo-EM

Extraction of particles from cryo-electron microscopy (cryo-EM) micrographs is a crucial step in processing single-particle datasets. Although algorithms have been developed for automatic particle picking, these algorithms generally rely on two-dimensional templates for particle identification, which may exhibit biases that can propagate artifacts through the reconstruction pipeline. Manual picking is viewed as a gold-standard solution for particle selection, but it is too time-consuming to perform on data sets of thousands of images. In recent years, crowdsourcing has proven effective at leveraging the open web to manually curate datasets. In particular, citizen science projects such as Galaxy Zoo have shown the power of appealing to users’ scientific interests to process enormous amounts of data. To this end, we explored the possible applications of crowdsourcing in cryo-EM particle picking, presenting a variety of novel experiments including the production of a fully annotated particle set from untrained citizen scientists. We show the possibilities and limitations of crowdsourcing particle selection tasks, and explore further options for crowdsourcing cryo-EM data processing.

Helical reconstruction in RELION

We describe a new implementation for the reconstruction of helical assemblies in the empirical Bayesian framework of RELION. Our approach calculates optimal linear filters for the 3D reconstruction by embedding helical symmetry operators in Fourier-space, and deals with deviations from perfect helical symmetry through Gaussian-shaped priors on the orientations of individual segments. By incorporating our approach into the standard pipeline for single-particle analysis in RELION, our implementation aims to be easily accessible for non-experienced users. Although our implementation does not solve the problem that grossly incorrect structures can be obtained when the wrong helical symmetry is imposed, we show for four different test cases that it is capable of reconstructing structures to near-atomic resolution.

Reconstitution of Membrane Proteins into Nanodiscs for Single-Particle Electron Microscopy

The structure determination of integral membrane protein (IMP) in lipid environment is particularly challenging. Among emerging methods for exchanging detergent required for IMP purification by original compounds, the use of lipid nanodisc preserves a lipid environment. Compared with the classical method of proteoliposome formation, the nanodisc technology provides a better control of IMP molecules inserted in lipid membrane, therefore giving access to structural methodologies developed for soluble proteins. Here, we present the reconstitution of OprM membrane protein into nanodisc associated with a step of size-exclusion chromatography, an approach applicable to prepare IMPs for subsequent visualization by single-particle electron microscopy.

Isolation of novel PSII-LHCII megacomplexes from pea plants characterized by a combination of proteomics and electron microscopy

In higher plants, photosystem II (PSII) is a multi-subunit pigment-protein complex embedded in the thylakoid membranes of chloroplasts, where it is present mostly in dimeric form within the grana. Its light-harvesting antenna system, LHCII, is composed of trimeric and monomeric complexes, which can associate in variable number with the dimeric PSII core complex in order to form different types of PSII-LHCII supercomplexes. Moreover, PSII-LHCII supercomplexes can laterally associate within the thylakoid membrane plane, thus forming higher molecular mass complexes, termed PSII-LHCII megacomplexes (Boekema et al. 1999a, in Biochemistry 38:2233-2239; Boekema et al. 1999b, in Eur J Biochem 266:444-452). In this study, pure PSII-LHCII megacomplexes were directly isolated from stacked pea thylakoid membranes by a rapid single-step solubilization, using the detergent n-dodecyl-α-D-maltoside, followed by sucrose gradient ultracentrifugation. The megacomplexes were subjected to biochemical and structural analyses. Transmission electron microscopy on negatively stained samples, followed by single-particle analyses, revealed a novel form of PSII-LHCII megacomplexes, as compared to previous studies (Boekema et al.1999a, in Biochemistry 38:2233-2239; Boekema et al. 1999b, in Eur J Biochem 266:444-452), consisting of two PSII-LHCII supercomplexes sitting side-by-side in the membrane plane, sandwiched together with a second copy. This second copy of the megacomplex is most likely derived from the opposite membrane of a granal stack. Two predominant forms of intact sandwiched megacomplexes were observed and termed, according to (Dekker and Boekema 2005 Biochim Biophys Acta 1706:12-39), as (C2S2)4 and (C2S2 + C2S2M2)2 megacomplexes. By applying a gel-based proteomic approach, the protein composition of the isolated megacomplexes was fully characterized. In summary, the new structural forms of isolated megacomplexes and the related modeling performed provide novel insights into how PSII-LHCII supercomplexes may bind to each other, not only in the membrane plane, but also between granal stacks within the chloroplast.

Single-Particle Refinement and Variability Analysis in EMAN2.1

CryoEM single-particle reconstruction has been growing rapidly over the last 3 years largely due to the development of direct electron detectors, which have provided data with dramatic improvements in image quality. It is now possible in many cases to produce near-atomic resolution structures, and yet 2/3 of published structures remain at substantially lower resolutions. One important cause for this is compositional and conformational heterogeneity, which is both a resolution-limiting factor and presenting a unique opportunity to better relate structure to function. This manuscript discusses the canonical methods for high-resolution refinement in EMAN2.12, and then considers the wide range of available methods within this package for resolving structural variability, targeting both improved resolution and additional knowledge about particle dynamics.

Processing of Structurally Heterogeneous Cryo-EM Data in RELION

This chapter describes algorithmic advances in the RELION software, and how these are used in high-resolution cryo-electron microscopy (cryo-EM) structure determination. Since the presence of projections of different three-dimensional structures in the dataset probably represents the biggest challenge in cryo-EM data processing, special emphasis is placed on how to deal with structurally heterogeneous datasets. As such, this chapter aims to be of practical help to those who wish to use RELION in their cryo-EM structure determination efforts.

Single-particle cryoEM analysis at near-atomic resolution from several thousand asymmetric subunits

A single-particle cryoEM reconstruction of the large ribosomal subunit from Saccharomyces cerevisiae was obtained from a dataset of ∼75,000 particles. The gold-standard and frequency-limited approaches to single-particle refinement were each independently used to determine orientation parameters for the final reconstruction. Both approaches showed similar resolution curves and nominal resolution values for the 60S dataset, estimated at 2.9 Å. The amount of over-fitting present during frequency-limited refinement was quantitatively analyzed using the high-resolution phase-randomization test, and the results showed no apparent over-fitting. The number of asymmetric subunits required to reach specific resolutions was subsequently analyzed by refining subsets of the data in an ab initio manner. With our data collection and processing strategies, sub-nanometer resolution was obtained with ∼200 asymmetric subunits (or, equivalently for the ribosomal subunit, particles). Resolutions of 5.6 Å, 4.5 Å, and 3.8 Å were reached with ∼1000, ∼1600, and ∼5000 asymmetric subunits, respectively. At these resolutions, one would expect to detect alpha-helical pitch, separation of beta-strands, and separation of Cα atoms, respectively. Using this map, together with strategies for ab initio model building and model refinement, we built a region of the ribosomal protein eL6, which was missing in previous models of the yeast ribosome. The relevance for more routine high-resolution structure determination is discussed.

Semi-automated selection of cryo-EM particles in RELION-1.3

The selection of particles suitable for high-resolution cryo-EM structure determination from noisy micrographs may represent a tedious and time-consuming step. Here, a semi-automated particle selection procedure is presented that has been implemented within the open-source software RELION. At the heart of the procedure lies a fully CTF-corrected template-based picking algorithm, which is supplemented by a fast sorting algorithm and reference-free 2D class averaging to remove false positives. With only limited user-interaction, the proposed procedure yields results that are comparable to manual particle selection. Together with an improved graphical user interface, these developments further contribute to turning RELION from a stand-alone refinement program into a convenient image processing pipeline for the entire single-particle approach.

Electron microscopy and in vitro deneddylation reveal similar architectures and biochemistry of isolated human and Flag-mouse COP9 signalosome complexes

The COP9 signalosome (CSN) is a regulator of the ubiquitin (Ub) proteasome system (UPS). In the UPS, proteins are Ub-labeled for degradation by Ub ligases conferring substrate specificity. The CSN controls a large family of Ub ligases called cullin-RING ligases (CRLs), which ubiquitinate cell cycle regulators, transcription factors and DNA damage response proteins. The CSN possesses structural similarities with the 26S proteasome Lid complex and the translation initiation complex 3 (eIF3) indicating similar ancestry and function. Initial structures were obtained 14years ago by 2D electron microscopy (EM). Recently, first 3D molecular models of the CSN were created on the basis of negative-stain EM and single-particle analysis, mostly with recombinant complexes. Here, we compare deneddylating activity and structural features of CSN complexes purified in an elaborate procedure from human erythrocytes and efficiently pulled down from mouse Flag-CSN2 B8 fibroblasts. In an in vitro deneddylation assay both the human and the mouse CSN complexes deneddylated Nedd8-Cul1 with comparable rates. 3D structural models of the erythrocyte CSN as well as of the mouse Flag-CSN were generated by negative stain EM and by cryo-EM. Both complexes show a central U-shaped segment from which several arms emanate. This structure, called the horseshoe, is formed by the PCI domain subunits. CSN5 and CSN6 point away from the horseshoe. Compared to 3D models of negatively stained CSN complexes, densities assigned to CSN2 and CSN4 are better defined in the cryo-map. Because biochemical and structural results obtained with CSN complexes isolated from human erythrocytes and purified by Flag-CSN pulldown from mouse B8 fibroblasts are very similar, Flag-CSN pulldowns are a proper alternative to CSN preparation from erythrocytes.