Single-Particle Reconstruction of Biological Molecules-Story in a Sample (Nobel Lecture)

Seeing the Supracolloidal Assemblies in 3D: Unraveling High-Resolution Structures Using Electron Tomography

Transmission electron microscopy (TEM) imaging has revolutionized modern materials science, nanotechnology, and structural biology. Its ability to provide information about materials' structure, composition, and properties at atomic-level resolution has enabled groundbreaking discoveries and the development of innovative materials with precision and accuracy. Electron tomography, single particle reconstruction, and microcrystal electron diffraction techniques have paved the way for the three-dimensional (3D) reconstruction of biological samples, synthetic materials, and hybrid nanostructures at near atomic-level resolution. TEM tomography using a series of two-dimensional (2D) projections has been used extensively in biological science, but in recent years it has become an important method in synthetic nanomaterials and soft matter research. TEM tomography offers unprecedented morphological details of 3D objects, internal structures, packing patterns, growth mechanisms, and self-assembly pathways of self-assembled colloidal systems. It complements other analytical tools, including small-angle X-ray scattering, and provides valuable data for computational simulations for predictive design and reverse engineering of nanomaterials with the desired structure and properties. In this perspective, I will discuss the importance of TEM tomography in the structural understanding and engineering of self-assembled nanostructures with specific emphasis on colloidal capsids, composite cages, biohybrid superlattices with complex geometries, polymer assemblies, and self-assembled protein-based superstructures.

Pulsed-beam transmission electron microscopy and radiation damage

We review the use of pulsed electron-beams in transmission electron microscopes (TEMs) for the purpose of mitigating specimen damage. We begin by placing the importance of TEMs with respect to materials characterization into proper context, and we provide a brief overview of established methods for reducing or eliminating the deleterious effects of beam-induced damage. We then introduce the concept of pulsed-beam TEM, and we briefly describe the basic methods and instrument configurations used to create so-called temporally structured electron beams. Following a brief overview of the use of high-dose-rate pulsed-electron beams in cancer radiation therapy, we review historical speculations and more recent compelling but mostly anecdotal findings of a pulsed-beam TEM damage effect. This is followed by an in-depth technical review of recent works seeking to establish cause-and-effect relationships, to conclusively uncover the presence of an effect, and to explore the practicality of the approach. These studies, in particular, provide the most compelling evidence to date that using a pulsed electron beam in the TEM is indeed a viable way to mitigate damage. Throughout, we point out current gaps in understanding, and we conclude with a brief perspective of current needs and future directions.

Simple and Effective Conformational Sampling Strategy for Intrinsically Disordered Proteins Using the UNRES Web Server

Intrinsically disordered proteins (IDPs) contain more charged amino acids than folded proteins, resulting in a lack of hydrophobic core(s) and a tendency to adopt rapidly interconverting structures rather than well-defined structures. The structural heterogeneity of IDPs, encoded by the amino acid sequence, is closely related to their unique roles in biological pathways, which require them to interact with different binding partners. Recently, Robustelli and co-workers have demonstrated that a balanced all-atom force field can be used to sample heterogeneous structures of disordered proteins ( Proc. Natl. Acad. Sci. U.S.A. 2018, 115, E4758-E4766). However, such a solution requires extensive computational resources, such as Anton supercomputers. Here, we propose a simple and effective solution to sample the conformational space of IDPs using a publicly available web server, namely, the UNited-RESidue (UNRES) web server. Our proposed solution requires no investment in computational resources and no prior knowledge of UNRES. UNRES Replica Exchange Molecular Dynamics (REMD) simulations were carried out on a set of eight disordered proteins at temperatures spanning from 270 to 430 K. Utilizing the latest UNRES force field designed for structured proteins, with proper selections of temperatures, we were able to produce comparable results to all-atom force fields as reported in work done by Robustelli and co-workers. In addition, NMR observables and the radius of gyration calculated from UNRES ensembles were directly compared with the experimental data to further evaluate the accuracy of the UNRES model at all temperatures. Our results suggest that carrying out the UNRES simulations at optimal temperatures using the UNRES web server can be a good alternative to sample heterogeneous structures of IDPs.

Structure and function meet at the nicotinic acetylcholine receptor-lipid interface

The nicotinic acetylcholine receptor (nAChR) is a transmembrane protein that mediates fast intercellular communication in response to the endogenous neurotransmitter acetylcholine. It is the best characterized and archetypal molecule in the superfamily of pentameric ligand-gated ion channels (pLGICs). As a typical transmembrane macromolecule, it interacts extensively with its vicinal lipid microenvironment. Experimental evidence provides a wealth of information on receptor-lipid crosstalk: the nAChR exerts influence on its immediate membrane environment and conversely, the lipid moiety modulates ligand binding, affinity state transitions and gating of ion translocation functions of the receptor protein. Recent cryogenic electron microscopy (cryo-EM) studies have unveiled the occurrence of sites for phospholipids and cholesterol on the lipid-exposed regions of neuronal and electroplax nAChRs, confirming early spectroscopic and affinity labeling studies demonstrating the close contact of lipid molecules with the receptor transmembrane segments. This new data provides structural support to the postulated "lipid sensor" ability displayed by the outer ring of M4 transmembrane domains and their modulatory role on nAChR function, as we postulated a decade ago. Borrowing from the best characterized nAChR, the electroplax (muscle-type) receptor, and exploiting new structural information on the neuronal nAChR, it is now possible to achieve an improved depiction of these sites. In combination with site-directed mutagenesis, single-channel electrophysiology, and molecular dynamics studies, the new structural information delivers a more comprehensive portrayal of these lipid-sensitive loci, providing mechanistic explanations for their ability to modulate nAChR properties and raising the possibility of targetting them in disease.

DNA Stability in Biodosimetry, Pharmacy and DNA Based Data-Storage: Optimal Storage and Handling Conditions

DNA long-term stability and integrity is of importance for applications in DNA based bio-dosimetry, data-storage, pharmaceutical quality-control, donor insemination and DNA based functional nanomaterials. Standard protocols for these applications involve repeated freeze-thaw cycles of the DNA, which can cause detrimental damage to the nucleobases, as well as the sugar-phosphate backbone and therefore the whole molecule. Throughout the literature three hypotheses can be found about the underlying mechanisms occurring during freeze-thaw cycles. It is hypothesized that DNA single-strand breaks during freezing can be induced by mechanical stress leading to shearing of the DNA molecule, by acidic pH causing damage through depurination and beta elimination or by the presence of metal ions catalyzing oxidative damage via reactive oxygen species (ROS). Here we test these hypotheses under well defined conditions with plasmid DNA pUC19 in high-purity buffer (1xPBS) at physiological salt and pH 7.4 conditions, under pH 6 and in the presence of metal ions in combination with the radical scavengers DMSO and Ectoine. The results show for the 2686 bp long plasmid DNA, that neither mechanical stress, nor pH 6 lead to degradation during repeated freeze-thaw cycles. In contrast, the presence of metal ions (Fe2+ ) leads to degradation of DNA via the production of radical species.

Prion strains viewed through the lens of cryo-EM

Mammalian prions are lethal transmissible pathogens that cause fatal neurodegenerative diseases in humans and animals. They consist of fibrils of misfolded, host-encoded prion protein (PrP) which propagate through templated protein polymerisation. Prion strains produce distinct clinicopathological phenotypes in the same host and appear to be encoded by distinct misfolded PrP conformations and assembly states. Despite fundamental advances in our understanding of prion biology, key knowledge gaps remain. These include precise delineation of prion replication mechanisms, detailed explanation of the molecular basis of prion strains and inter-species transmission barriers, and the structural definition of neurotoxic PrP species. Central to addressing these questions is the determination of prion structure. While high-resolution definition of ex vivo prion fibrils once seemed unlikely, recent advances in cryo-electron microscopy (cryo-EM) and computational methods for 3D reconstruction of amyloids have now made this possible. Recently, near-atomic resolution structures of highly infectious, ex vivo prion fibrils from hamster 263K and mouse RML prion strains were reported. The fibrils have a comparable parallel in-register intermolecular β-sheet (PIRIBS) architecture that now provides a structural foundation for understanding prion strain diversity in mammals. Here, we review these new findings and discuss directions for future research.

Recovery of Conformational Continuum From Single-Particle Cryo-EM Images: Optimization of ManifoldEM Informed by Ground Truth

This work is based on the manifold-embedding approach to study biological molecules exhibiting continuous conformational changes. Previous work established a method-now termed ManifoldEM-capable of reconstructing 3D movies and accompanying free-energy landscapes from single-particle cryo-EM images of macromolecules exercising multiple conformational degrees of freedom. While ManifoldEM has proven its viability in several experimental studies, critical limitations and uncertainties have been found throughout its extended development and use. Guided by insights from studies with cryo-EM ground-truth data, simulated from atomic structures undergoing conformational changes, we have built a novel framework, ESPER, able to retrieve the free-energy landscape and respective 3D Coulomb potential maps for all states simulated. As shown by a direct comparison of ground truth vs. recovered maps, and analysis of experimental data from the 80S ribosome and ryanodine receptor, ESPER offers substantial improvements relative to the previous work.

Preyssler-type phosphotungstate is a new family of negative-staining reagents for the TEM observation of viruses

Transmission electron microscopy (TEM) is an essential method in virology because it allows for direct visualization of virus morphology at a nanometer scale. Negative staining to coat virions with heavy metal ions must be performed before TEM observations to achieve sufficient contrast. Herein, we report that potassium salts of Preyssler-type phosphotungstates (K_(15-n)[P₅W₃₀O₁₁₀Mⁿ⁺], M = Na⁺, Ca²⁺, Ce³⁺, Eu³⁺, Bi³⁺, or Y³⁺) are high-performance negative staining reagents. Additionally, we compare the staining abilities of these salts to those of uranyl acetate and Keggin-type phosphotungstate. The potassium salt of Preyssler-type phosphotungstates has the advantage of not requiring prior neutralization because it is a neutral compound. Moreover, the potassium counter-cation can be protonated by a reaction with H⁺-resin, allowing easy exchange of protons with other cations by acid–base reaction. Therefore, the counter-cations can be changed. Encapsulated cations can also be exchanged, and clear TEM images were obtained using Preyssler-type compounds with different encapsulated cations. Preyssler-type phosphotungstates may be superior negative staining reagents for observing virus. Polyoxotungstates (tungsten-oxide molecules with diverse molecular structures and properties) are thus promising tools to develop negative staining reagents for TEM observations.

Within and Beyond the Nucleotide Addition Cycle of Viral RNA-dependent RNA Polymerases

Nucleotide addition cycle (NAC) is a fundamental process utilized by nucleic acid polymerases when carrying out nucleic acid biosynthesis. An induced-fit mechanism is usually taken by these polymerases upon NTP/dNTP substrate binding, leading to active site closure and formation of a phosphodiester bond. In viral RNA-dependent RNA polymerases, the post-chemistry translocation is stringently controlled by a structurally conserved motif, resulting in asymmetric movement of the template-product duplex. This perspective focuses on viral RdRP NAC and related mechanisms that have not been structurally clarified to date. Firstly, RdRP movement along the template strand in the absence of catalytic events may be relevant to catalytic complex dissociation or proofreading. Secondly, pyrophosphate or non-cognate NTP-mediated cleavage of the product strand 3′-nucleotide can also play a role in reactivating paused or arrested catalytic complexes. Furthermore, non-cognate NTP substrates, including NTP analog inhibitors, can not only alter NAC when being misincorporated, but also impact on subsequent NACs. Complications and challenges related to these topics are also discussed.

Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells

Cryo-electron microscopy (cryo-EM) enables macromolecular structure determination in vitro and inside cells. In addition to aligning individual particles, accurate registration of sample motion and three-dimensional deformation during exposures are crucial for achieving high-resolution reconstructions. Here we describe M, a software tool that establishes a reference-based, multi-particle refinement framework for cryo-EM data and couples a comprehensive spatial deformation model to in silico correction of electron-optical aberrations. M provides a unified optimization framework for both frame-series and tomographic tilt-series data. We show that tilt-series data can provide the same resolution as frame-series data on a purified protein specimen, indicating that the alignment step no longer limits the resolution obtainable from tomographic data. In combination with Warp and RELION, M resolves to residue level a 70S ribosome bound to an antibiotic inside intact bacterial cells. Our work provides a computational tool that facilitates structural biology in cells.

Efficient screening of ligand-receptor complex formation using fluorescence labeling and size-exclusion chromatography

Evidence of a complex formation is a crucial step in the structural studies of ligand-receptor interactions. Here we presented a simple and fast approach for qualitative screening of the complex formation between the chimeric extracellular domain of the nicotinic acetylcholine receptor (α7-ECD) and three-finger proteins. Complex formation of snake toxins α-Bgtx and WTX, as well as of recombinant analogs of human proteins Lynx1 and SLURP-1, with α7-ECD was confirmed using fluorescently labeled ligands and size-exclusion chromatography with simultaneous absorbance and fluorescence detection. WTX/α7-ECD complex formation also was confirmed by cryo-EM. The proposed approach could easily be adopted to study the interaction of other receptors with their ligands.

Interactions between the Intrinsically Disordered Regions of hnRNP-A2 and TDP-43 Accelerate TDP-43's Conformational Transition

Most biological functions involve protein-protein interactions. Our understanding of these interactions is based mainly on those of structured proteins, because encounters between intrinsically disordered proteins (IDPs) or proteins with intrinsically disordered regions (IDRs) are much less studied, regardless of the fact that more than half eukaryotic proteins contain IDRs. RNA-binding proteins (RBPs) are a large family whose members almost all have IDRs in addition to RNA binding domains. These IDRs, having low sequence similarity, interact, but structural details on these interactions are still lacking. Here, using the IDRs of two RBPs (hnRNA-A2 and TDP-43) as a model, we demonstrate that the rate at which TDP-43's IDR undergoes the neurodegenerative disease related α-helix-to-β-sheet transition increases in relation to the amount of hnRNP-A2's IDR that is present. There are more than 1500 RBPs in human cells and most of them have IDRs. RBPs often join the same complexes to regulate genes. In addition to the structured RNA-recognition motifs, our study demonstrates a general mechanism through which RBPs may regulate each other's functions through their IDRs.

POLARIS: Path of Least Action Analysis on Energy Landscapes

Free-energy landscapes are a powerful tool for analyzing dynamical processes - capable of providing a complete mapping of a system's configurations in state space while articulating its energetics topologically in the form of sprawling hills and valleys. Within this mapping, the path of least action can be derived - representing the most probable sequence of transitions taken between any two states in the landscape. In this article, POLARIS (Path of Least Action Recursive Survey) is presented as a dynamic, global approach that efficiently automates the discovery of the least action path on previously determined 2D energy landscapes. Important built-in features of this program include plotting of landscape trajectories and transition state theory diagrams, generation of text files with least action coordinates and respective energies, and bifurcation analysis tools that provide downstream versatility for comparing most probable paths and reaction rates.

Classical pathways of gene regulation by retinoids

Retinoic acid receptors were discovered during early studies of the actions and mechanisms of essential vitamins. Vitamin A is metabolized in the body to retinoic acid (RA) which is a key compound in the control of many developmental processes in chordates. These functions are mediated by a subfamily of nuclear receptors, divided into two classes, the retinoic acid receptors (RAR) and the retinoid X receptors (RXR). Each class is encoded by three closely related genes that are located on different chromosomes. The three proteins in each class are designated α, β and γ, respectively. A wealth of structural studies have shown that they all share the same architecture including a DNA-binding domain connected by a flexible linker to the ligand and co-activator binding domain. Retinoic acid incorporation into the ligand-binding domain leads to a conformational change enabling the formation of RAR homodimers or RAR/RXR heterodimers that in turn bind specifically to target DNA sequences. The consensus sequences located on the promotors of regulated genes are known as retinoic acid response elements (RARE). The activated RAR/RXR homodimers recruit co-activators with histone acetylase activity leading to an opening of the chromatin structure and enabling downstream transcription of regulated genes. These canonical pathways describe the control mechanism for the majority of developmental processes mediated by retinoic acid and its derivatives.

Musashi-1: An Example of How Polyalanine Tracts Contribute to Self-Association in the Intrinsically Disordered Regions of RNA-Binding Proteins

RNA-binding proteins (RBPs) have intrinsically disordered regions (IDRs) whose biophysical properties have yet to be explored to the same extent as those of the folded RNA interacting domains. These IDRs are essential to the formation of biomolecular condensates, such as stress and RNA granules, but dysregulated assembly can be pathological. Because of their structural heterogeneity, IDRs are best studied by NMR spectroscopy. In this study, we used NMR spectroscopy to investigate the structural propensity and self-association of the IDR of the RBP Musashi-1. We identified two transient α-helical regions (residues ~208–218 and ~270–284 in the IDR, the latter with a polyalanine tract). Strong NMR line broadening in these regions and circular dichroism and micrography data suggest that the two α-helical elements and the hydrophobic residues in between may contribute to the formation of oligomers found in stress granules and implicated in Alzheimer’s disease. Bioinformatics analysis suggests that polyalanine stretches in the IDRs of RBPs may have evolved to promote RBP assembly.

Challenges and opportunities in cryo-EM single-particle analysis

Cryogenic electron microscopy (cryo-EM) enables structure determination of macromolecular objects and their assemblies. Although the techniques have been developing for nearly four decades, they have gained widespread attention in recent years due to technical advances on numerous fronts, enabling traditional microscopists to break into the world of molecular structural biology. Many samples can now be routinely analyzed at near-atomic resolution using standard imaging and image analysis techniques. However, numerous challenges to conventional workflows remain, and continued technical advances open entirely novel opportunities for discovery and exploration. Here, I will review some of the main methods surrounding cryo-EM with an emphasis specifically on single-particle analysis, and I will highlight challenges, open questions, and opportunities for methodology development.

Joachim Frank's Binding with the Ribosome

With recent technological advancements, single-particle cryogenic electron microscopy (cryo-EM) is now the technique of choice to study structure and function of biological macromolecules at near-atomic resolution. Many single-particle EM reconstruction methods necessary for these advances were pioneered by Joachim Frank, and were optimized using the ribosome as a benchmark specimen. In doing so, he made several landmark contributions to the understanding of the structure and function of ribosomes. These include the first 3D visualization of ribosome-bound transfer RNAs, the first experimentally derived structures of the primary complexes formed during the bacterial translation elongation cycle, and the critical ribosomal conformational transitions required for translation. Over the years, his laboratory studied many important functional complexes of the ribosome from both eubacterial and eukaryotic systems, including ribosomes from pathogenic organisms. This article presents a brief account of the contributions made by Joachim Frank to the ribosome field.

Advances in domain and subunit localization technology for electron microscopy

The award of the 2017 Nobel Prize in chemistry, 'for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution', was recognition that this method, and electron microscopy more generally, represent powerful techniques in the scientific armamentarium for atomic level structural assessment. Technical advances in equipment, software, and sample preparation, have allowed for high-resolution structural determination of a range of complex biological machinery such that the position of individual atoms within these mega-structures can be determined. However, not all targets are amenable to attaining such high-resolution structures and some may only be resolved at so-called intermediate resolutions. In these cases, other tools are needed to correctly characterize the domain or subunit orientation and architecture. In this review, we will outline various methods that can provide additional information to help understand the macro-level organization of proteins/biomolecular complexes when high-resolution structural description is not available. In particular, we will discuss the recent development and use of a novel protein purification approach, known as the the PA tag/NZ-1 antibody system, which provides numberous beneficial properties, when used in electron microscopy experimentation.

Dissecting diverse functions of NMDA receptors by structural biology

N-Methyl-d-aspartate receptors (NMDARs) are glutamate-gated ion channels, which are critically involved in brain development, learning and memory, cognition, as well as a number of neurological diseases and disorders. Structural biology of NMDARs has been challenging due to technical difficulties associated with assembling a number of different membrane protein subunits. Here, we review historical X-ray crystallographic studies on isolated extracellular domains, which are still the most effective mean to delineate compound binding modes, as well as the most recent studies using electron cryo-microscopy (cryo-EM). A number of NMDAR structures accumulated over the past 15 years provide insights into the hetero-tetrameric assembly pattern, pharmacological specificities elicited by subtypes and alternative splicing, and potential patterns of conformational dynamics; however, many more important unanswered questions remain.

Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach

Outlier analyses are central to scientific data assessments. Conventional outlier identification methods do not work effectively for Protein Data Bank (PDB) data, which are characterized by heavy skewness and the presence of bounds and/or long tails. We have developed a data-driven nonparametric method to identify outliers in PDB data based on kernel probability density estimation. Unlike conventional outlier analyses based on location and scale, Probability Density Ranking can be used for robust assessments of distance from other observations. Analyzing PDB data from the vantage points of probability and frequency enables proper outlier identification, which is important for quality control during deposition-validation-biocuration of new three-dimensional structure data. Ranking of Probability Density also permits use of Most Probable Range as a robust measure of data dispersion that is more compact than Interquartile Range. The Probability-Density-Ranking approach can be employed to analyze outliers and data-spread on any large data set with continuous distribution.

ColorEM: analytical electron microscopy for element-guided identification and imaging of the building blocks of life

Nanometer-scale identification of multiple targets is crucial to understand how biomolecules regulate life. Markers, or probes, of specific biomolecules help to visualize and to identify. Electron microscopy (EM), the highest resolution imaging modality, provides ultrastructural information where several subcellular structures can be readily identified. For precise tagging of (macro)molecules, electron-dense probes, distinguishable in gray-scale EM, are being used. However, practically these genetically-encoded or immune-targeted probes are limited to three targets. In correlated microscopy, fluorescent signals are overlaid on the EM image, but typically without the nanometer-scale resolution and limited to visualization of few targets. Recently, analytical methods have become more sensitive, which has led to a renewed interest to explore these for imaging of elements and molecules in cells and tissues in EM. Here, we present the current state of nanoscale imaging of cells and tissues using energy dispersive X-ray analysis (EDX), electron energy loss spectroscopy (EELS), cathodoluminescence (CL), and touch upon secondary ion mass spectroscopy at the nanoscale (NanoSIMS). ColorEM is the term encompassing these analytical techniques the results of which are then displayed as false-color at the EM scale. We highlight how ColorEM will become a strong analytical nano-imaging tool in life science microscopy.