Evaluation of charging on macromolecules in electron cryomicroscopy

Electron Imaging of Nanoscale Charge Distributions Induced by Femtosecond Light Pulses

Surface charging is ubiquitously observable during in situ transmission electron microscopy of nonconducting specimens as a result of electron beam/sample interactions or optical stimuli and often limits the achievable image stability and spatial or spectral resolution. Here, we report on the electron-optical imaging of surface charging on a nanostructured surface following femtosecond multiphoton photoemission. By quantitatively extracting the light-induced electrostatic potential and studying the charging dynamics on relevant time scales, we gain insights into the details of the multiphoton photoemission process in the presence of an electrostatic background field. We study the interaction of the charge distribution with the high-energy electron beam and secondary electrons and propose a simple model to describe the interplay of electron- and light-induced processes. In addition, we demonstrate how to mitigate sample charging by simultaneously optically illuminating the sample.

Time-resolved imaging and analysis of the electron beam-induced formation of an open-cage metallo-azafullerene

The visualization of single-molecule reactions provides crucial insights into chemical processes, and the ability to do so has grown with the advances in high-resolution transmission electron microscopy. There is currently a limited mechanistic understanding of chemical reactions under the electron beam. However, such reactions may enable synthetic methodologies that cannot be accessed by traditional organic chemistry methods. Here we demonstrate the synthetic use of the electron beam, by in-depth single-molecule, atomic-resolution, time-resolved transmission electron microscopy studies, in inducing the formation of a doubly holed fullerene-porphyrin cage structure from a well-defined benzoporphyrin precursor deposited on graphene. Through real-time imaging, we analyse the hybrid's ability to host up to two Pb atoms, and subsequently probe the dynamics of the Pb-Pb binding motif in this exotic metallo-organic cage structure. Through simulation, we conclude that the secondary electrons, which accumulate in the periphery of the irradiated area, can also initiate chemical reactions. Consequently, designing advanced carbon nanostructures by electron-beam lithography will depend on the understanding and limitations of molecular radiation chemistry.

Charging of Vitreous Samples in Cryogenic Electron Microscopy Mitigated by Graphene

Cryogenic electron microscopy can provide high-resolution reconstructions of macromolecules embedded in a thin layer of ice from which atomic models can be built de novo. However, the interaction between the ionizing electron beam and the sample results in beam-induced motion and image distortion, which limit the attainable resolutions. Sample charging is one contributing factor of beam-induced motions and image distortions, which is normally alleviated by including part of the supporting conducting film within the beam-exposed region. However, routine data collection schemes avoid strategies whereby the beam is not in contact with the supporting film, whose rationale is not fully understood. Here we characterize electrostatic charging of vitreous samples, both in imaging and in diffraction mode. We mitigate sample charging by depositing a single layer of conductive graphene on top of regular EM grids. We obtained high-resolution single-particle analysis (SPA) reconstructions at 2 Å when the electron beam only irradiates the middle of the hole on graphene-coated grids, using data collection schemes that previously failed to produce sub 3 Å reconstructions without the graphene layer. We also observe that the SPA data obtained with the graphene-coated grids exhibit a higher b factor and reduced particle movement compared to data obtained without the graphene layer. This mitigation of charging could have broad implications for various EM techniques, including SPA and cryotomography, and for the study of radiation damage and the development of future sample carriers. Furthermore, it may facilitate the exploration of more dose-efficient, scanning transmission EM based SPA techniques.

Cryogenic electron ptychographic single particle analysis with wide bandwidth information transfer

Advances in cryogenic transmission electron microscopy have revolutionised the determination of many macromolecular structures at atomic or near-atomic resolution. This method is based on conventional defocused phase contrast imaging. However, it has limitations of weaker contrast for small biological molecules embedded in vitreous ice, in comparison with cryo-ptychography, which shows increased contrast. Here we report a single-particle analysis based on the use of ptychographic reconstruction data, demonstrating that three dimensional reconstructions with a wide information transfer bandwidth can be recovered by Fourier domain synthesis. Our work suggests future applications in otherwise challenging single particle analyses, including small macromolecules and heterogeneous or flexible particles. In addition structure determination in situ within cells without the requirement for protein purification and expression may be possible.

CryoFIB milling large tissue samples for cryo-electron tomography

Cryo-electron tomography (cryoET) is a powerful tool for exploring the molecular structure of large organisms. However, technical challenges still limit cryoET applications on large samples. In particular, localization and cutting out objects of interest from a large tissue sample are still difficult steps. In this study, we report a sample thinning strategy and workflow for tissue samples based on cryo-focused ion beam (cryoFIB) milling. This workflow provides a full solution for isolating objects of interest by starting from a millimeter-sized tissue sample and ending with hundred-nanometer-thin lamellae. The workflow involves sample fixation, pre-sectioning, a two-step milling strategy, and localization of the object of interest using cellular secondary electron imaging (CSEI). The milling strategy consists of two steps, a coarse milling step to improve the milling efficiency, followed by a fine milling step. The two-step milling creates a furrow-ridge structure with an additional conductive Pt layer to reduce the beam-induced charging issue. CSEI is highlighted in the workflow, which provides on-the-fly localization during cryoFIB milling. Tests of the complete workflow were conducted to demonstrate the high efficiency and high feasibility of the proposed method.

Temporal dynamics of charge buildup in cryo-electron microscopy

It is well known that insulating samples can accumulate electric charges from exposure to an electron beam. How the accumulation of charge affects imaging parameters and sample stability in transmission electron microscopy is poorly understood. To quantify these effects, it is important to know how the charge is distributed within the sample and how it builds up over time. In the present study, we determine the spatial distribution and temporal dynamics of charge accumulation on vitreous ice samples with embedded proteins through a combination of modeling and Fresnel diffraction experiments. Our data reveal a rapid evolution of the charge state on ice upon initial exposure to the electron beam accompanied by charge gradients at the interfaces between ice and carbon films. We demonstrate that ice film movement and charge state variations occur upon electron beam exposure and are dose-rate dependent. Both affect the image defocus through a combination of sample height changes and lensing effects. Our results may be used as a guide to improve sample preparation, data collection, and data processing for imaging of dose-sensitive samples.

Developing Graphene Grids for Cryoelectron Microscopy

Cryogenic electron microscopy (cryo-EM) single particle analysis has become one of the major techniques used to study high-resolution 3D structures of biological macromolecules. Specimens are generally prepared in a thin layer of vitrified ice using a holey carbon grid. However, the sample quality using this type of grid is not always ideal for high-resolution imaging even when the specimens in the test tube behave ideally. Various problems occur during a vitrification procedure, including poor/nonuniform distribution of particles, preferred orientation of particles, specimen denaturation/degradation, high background from thick ice, and beam-induced motion, which have become important bottlenecks in high-resolution structural studies using cryo-EM in many projects. In recent years, grids with support films made of graphene and its derivatives have been developed to efficiently solve these problems. Here, the various advantages of graphene grids over conventional holey carbon film grids, functionalization of graphene support films, production methods of graphene grids, and origins of pristine graphene contamination are reviewed and discussed.

Conquer by cryo-EM without physically dividing

This mini-review provides an update regarding the substantial progress that has been made in using single-particle cryo-EM to obtain high-resolution structures for proteins and other macromolecules whose particle sizes are smaller than 100 kDa. We point out that establishing the limits of what can be accomplished, both in terms of particle size and attainable resolution, serves as a guide for what might be expected when attempting to improve the resolution of small flexible portions of a larger structure using focused refinement approaches. These approaches, which involve computationally ignoring all but a specific, targeted region of interest on the macromolecules, is known as 'masking and refining,' and it thus is the computational equivalent of the 'divide and conquer' approach that has been used so successfully in X-ray crystallography. The benefit of masked refinement, however, is that one is able to determine structures in their native architectural context, without physically separating them from the biological connections that they require for their function. This mini-review also compares where experimental achievements currently stand relative to various theoretical estimates for the smallest particle size that can be successfully reconstructed to high resolution. Since it is clear that a substantial gap still remains between the two, we briefly recap the areas in which further improvement seems possible, both in equipment and in methods.

Application of Monolayer Graphene and Its Derivative in Cryo-EM Sample Preparation

Cryo-electron microscopy (Cryo-EM) has become a routine technology for resolving the structure of biological macromolecules due to the resolution revolution in recent years. The specimens are typically prepared in a very thin layer of vitrified ice suspending in the holes of the perforated amorphous carbon film. However, the samples prepared by directly applying to the conventional support membranes may suffer from partial or complete denaturation caused by sticking to the air-water interface (AWI). With the application in materials, graphene has also been used recently to improve frozen sample preparation instead of a suspended conventional amorphous thin carbon. It has been proven that graphene or graphene oxide and various chemical modifications on its surface can effectively prevent particles from adsorbing to the AWI, which improves the dispersion, adsorbed number, and orientation preference of frozen particles in the ice layer. Their excellent properties and thinner thickness can significantly reduce the background noise, allowing high-resolution three-dimensional reconstructions using a minimum data set.

Thin Layer Buckling in Perovskite CsPbBr3 Nanobelts

Flexible semiconductor materials, where structural fluctuations and transformation are tolerable and have low impact on electronic properties, focus interest for future applications. Two-dimensional thin layer lead halide perovskites are hailed for their unconventional optoelectronic features. We report structural deformations via thin layer buckling in colloidal CsPbBr₃ nanobelts adsorbed on carbon substrates. The microstructure of buckled nanobelts is determined using transmission electron microscopy and atomic force microscopy. We measured significant decrease in emission from the buckled nanobelt using cathodoluminescence, marking the influence of such mechanical deformations on electronic properties. By employing plate buckling theory, we approximate adhesion forces between the buckled nanobelt and the substrate to be F_adhesion ∼ 0.12 μN, marking a limit to sustain such deformation. This work highlights detrimental effects of mechanical buckling on electronic properties in halide perovskite nanostructures and points toward the capillary action that should be minimized in fabrication of future devices and heterostructures based on nanoperovskites.

Sub-3 Å Cryo-EM Structures of Necrosis Virus Particles via the Use of Multipurpose TEM with Electron Counting Camera

During this global pandemic, cryo-EM has made a great impact on the structure determination of COVID-19 proteins. However, nearly all high-resolution results are based on data acquired on state-of-the-art microscopes where their availability is restricted to a number of centers across the globe with the studies on infectious viruses being further regulated or forbidden. One potential remedy is to employ multipurpose microscopes. Here, we investigated the capability of 200 kV multipurpose microscopes equipped with a direct electron camera in determining the structures of infectious particles. We used 30 nm particles of the grouper nerve necrosis virus as a test sample and obtained the cryo-EM structure with a resolution as high as ∼2.7 Å from a setting that used electron counting. For comparison, we tested a high-end cryo-EM (Talos Arctica) using a similar virus (Macrobrachium rosenbergii nodavirus) to obtain virtually the same resolution. Those results revealed that the resolution is ultimately limited by the depth of field. Our work updates the density maps of these viruses at the sub-3Å level to allow for building accurate atomic models from de novo to provide structural insights into the assembly of the capsids. Importantly, this study demonstrated that multipurpose TEMs are capable of the high-resolution cryo-EM structure determination of infectious particles and is thus germane to the research on pandemics.

Graphene Liquid Cell Electron Microscopy: Progress, Applications, and Perspectives

Graphene liquid cell electron microscopy (GLC-EM), a cutting-edge liquid-phase EM technique, has become a powerful tool to directly visualize wet biological samples and the microstructural dynamics of nanomaterials in liquids. GLC uses graphene sheets with a one carbon atom thickness as a viewing window and a liquid container. As a result, GLC facilitates atomic-scale observation while sustaining intact liquids inside an ultra-high-vacuum transmission electron microscopy chamber. Using GLC-EM, diverse scientific results have been recently reported in the material, colloidal, environmental, and life science fields. Here, the developments of GLC fabrications, such as first-generation veil-type cells, second-generation well-type cells, and third-generation liquid-flowing cells, are summarized. Moreover, recent GLC-EM studies on colloidal nanoparticles, battery electrodes, mineralization, and wet biological samples are also highlighted. Finally, the considerations and future opportunities associated with GLC-EM are discussed to offer broad understanding and insight on atomic-resolution imaging in liquid-state dynamics.

Direct transfer of electron microscopy samples to wetted carbon and graphene films via a support floatation block

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Design of a sample-support transfer block for negative stain and cryo-EM.

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Direct wetted transfer of 10 μL samples to carbon.

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Direct wetted transfer of 10 μL samples to graphene.

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Buffer exchange from 10 μL sample volumes in situ within the block.

Support films are commonly used during cryo-EM specimen preparation to both immobilise the sample and minimise the exposure of particles at the air-water interface. Here we report preparation protocols for carbon and graphene supported single particle electron microscopy samples using a novel 3D-printed sample transfer block to facilitate the direct, wetted, movement of both carbon and graphene supports from the substrate on which they were generated to small volumes (10 μL) of sample. These approaches are simple and inexpensive to implement, minimise hydrophobic contamination of the support films, and are widely applicable to single particle studies. Our approach also allows the direct exchange of the sample buffer on the support film in cases in which it is unsuitable for vitrification, e.g. for samples from centrifugal density gradients that help to preserve sample integrity.

Phase plates in the transmission electron microscope: operating principles and applications

In this paper, we review the current state of phase plate imaging in a transmission electron microscope. We focus especially on the hole-free phase plate design, also referred to as the Volta phase plate. We discuss the implementation, operating principles and applications of phase plate imaging. We provide an imaging theory that accounts for inelastic scattering in both the sample and in the hole-free phase plate.

Preparation of Proteins and Macromolecular Assemblies for Cryo-electron Microscopy

Cryo-electron microscopy has become popular as the penultimate step on the road to structure determination for many proteins and macromolecular assemblies. The process of obtaining high-resolution images of a purified biomolecular complex in an electron microscope often follows a long, and in many cases exhaustive screening process in which many iterative rounds of protein purification are employed and the sample preparation procedure progressively re-evaluated in order to improve the distribution of particles visualized under the electron microscope, and thus maximize the opportunity for high-resolution structure determination. Typically, negative stain electron microscopy is employed to obtain a preliminary assessment of the sample quality, followed by cryo-EM which first requires the identification of optimal vitrification conditions. The original methods for frozen-hydrated specimen preparation developed over 40 years ago still enjoy widespread use today, although recent developments have set the scene for a future where more systematic and high-throughput approaches to the preparation of vitrified biomolecular complexes may be routinely employed. Here we summarize current approaches and ongoing innovations for the preparation of frozen-hydrated single particle specimens for cryo-EM, highlighting some of the commonly encountered problems and approaches that may help overcome these.

Charging ain't all bad: Complex physics in DyScO3

Although charging is ubiquitous in electron microscopy, its effects are typically avoided or ignored. However, avoiding charging is not possible in some materials, e.g. lanthanide scandates with well-ordered surfaces positively charge immensely under electron beam illumination because of their electronic structure, and ignoring charging can leave new science undiscovered. In this work, a combination of rapidly acquired electron energy loss spectra and cross-correlation were used to understand and overcome charging effects in DyScO₃. A 5.4 eV band gap was extracted from the charging-corrected loss spectrum, in good agreement with previously reported band gaps, and a 3.8 eV in-gap peak was attributed to surface states via comparison with density functional theory calculations. Additionally, ultraviolet photoelectron spectroscopy measurements indicated that under some conditions well-annealed DyScO₃ surfaces charge negatively causing upward band bending associated with occupied surface states in the gap. As was previously found in the case of positive charging under electron beam illumination with in-situ flexoelectric bending observations, the magnitude of negative charging under ultraviolet illumination is Zener tunneling limited in well-annealed DyScO₃.

Protein denaturation at the air-water interface and how to prevent it

Electron cryo-microscopy analyzes the structure of proteins and protein complexes in vitrified solution. Proteins tend to adsorb to the air-water interface in unsupported films of aqueous solution, which can result in partial or complete denaturation. We investigated the structure of yeast fatty acid synthase at the air-water interface by electron cryo-tomography and single-particle image processing. Around 90% of complexes adsorbed to the air-water interface are partly denatured. We show that the unfolded regions face the air-water interface. Denaturation by contact with air may happen at any stage of specimen preparation. Denaturation at the air-water interface is completely avoided when the complex is plunge-frozen on a substrate of hydrophilized graphene.

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.

From Electron Crystallography to Single Particle CryoEM (Nobel Lecture)

Pictures are a key to knowledge: The development of electron microscopy from its beginnings to modern single particle cryo-EM is described by R. Henderson in his Nobel lecture. Shown is the first projection structure at 7 Å resolution of the purple membrane from October 1974.

Oxide-free aC/Zr0.65Al0.075Cu0.275/aC phase plates for transmission electron microscopy

Thin-film phase plates (PP) have become a valuable tool for the imaging of organic objects in transmission electron microscopy (TEM). The thin film usually consists of amorphous carbon (aC), which undergoes rapid aging under intense illumination with high-energy electrons. The limited lifetime of aC film PPs calls for alternative PP materials with improved material stability. This work presents thin-film PPs fabricated from the metallic glass alloy Zr_0.65Al_0.075Cu_0.275 (ZAC), which was identified as a promising PP material with beneficial properties, such as a large inelastic mean free path. An adverse effect of the ZAC alloy is the formation of a surface oxide layer in ambient air, which reduces the electrical conductivity and causes electrostatic charging in the electron beam. To avoid surface oxidation, the ZAC alloy is enclosed by thin aC layers. The resulting aC/ZAC/aC layer system is used to fabricate Zernike and Hilbert PPs. Phase-contrast TEM imaging is demonstrated for a sample of carbon nanotubes, which show strong contrast enhancement in PP TEM images.

Charge accumulation in electron cryomicroscopy

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A physical account of charge accumulation in low-dose cryoEM is presented.

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We describe electrostatic micro-lenses that are extremely sensitive charge detectors.

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These micro-lenses allow the direct measurement of charge accumulation.

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Charge build-up saturates within the first millisecond of a typical micrograph.

When irradiated in a transmission electron microscope, plunge-frozen, amorphous water ice specimens accumulate a pattern of static charge that changes dynamically as the specimen is irradiated, and which can deflect the transmitted electrons and blur the resultant micrographs. Here we provide a physical description of this charge accumulation and characterise its dynamic behaviour in the context of low-dose electron cryomicroscopy (cryoEM). We observe the accumulation of positive charge in the primary irradiation area as expected from earlier work. To our surprise, we also observed a build-up of negative charge in nearby unirradiated regions of the specimen. Using a standard carbon support foil containing a pure water ice specimen, we collect a portion of this negative charge in the micrometer sized specimen holes which act as electrostatic lenses. These unusual, diverging micro-lenses are extremely sensitive charge detectors that allow us to directly measure the magnitude and dynamics of charge accumulation and neutralisation that occur during cryoEM imaging. Using these measurements, we find that the build-up of charge on the specimen saturates to a dynamic equilibrium at an electron fluence which is orders of magnitude lower than required for a typical low-dose micrograph. The measurements here will guide the development of optimal imaging conditions for biological specimens and contribute to a complete theory of information loss in electron cryomicroscopy.

Microscopic charge fluctuations cause minimal contrast loss in cryoEM

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A physical account of charge fluctuations in low-dose cryoEM is presented.

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We quantify the bee swarm charging phenomenon on cryoEM specimen.

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We measure the envelope function caused by charge fluctuations.

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The effects of these fluctuations are negligible in cryoEM.

The fluctuating granularity or “bee swarm” effect seen in highly defocussed transmission electron micrographs is caused by microscopic charge fluctuations in the specimen created by the illuminating beam. In the field of high-resolution single particle electron cryomicroscopy (cryoEM), there has been a concern that this fluctuating charge might cause defocus-dependent Thon ring fading which would degrade the final image. In this paper, we have analysed the 2.35 Å fringes from the (111) reflection in images of gold nanoparticles embedded in amorphous ice. We show that there is a small, yet detectable amount of defocus-dependent blurring of the lattice fringes when compared with those from a pure gold foil. The transverse electric field associated with the fluctuating charges on the insulating frozen water specimen deflects the electron beam locally and causes image blurring. The perturbation is small, decreasing the amplitude of the 2.35 Å reflection at 10 µm defocus by about 7% (intensity by 14%). For smaller defocus values in the range 2–4 µm and for resolutions that are typical in cryoEM, the effects of source incoherence and the bee swarm effect are negligible for all reasonable cryoEM imaging conditions, assuming that a field emission gun (FEG) is used for illumination. This leaves physical movement of the specimen due to radiation damage as the outstanding problem and the major source of contrast loss in cryoEM micrographs.

The advent of structural biology in situ by single particle cryo-electron tomography

Single particle tomography (SPT), also known as subtomogram averaging, is a powerful technique uniquely poised to address questions in structural biology that are not amenable to more traditional approaches like X-ray crystallography, nuclear magnetic resonance, and conventional cryoEM single particle analysis. Owing to its potential for in situ structural biology at subnanometer resolution, SPT has been gaining enormous momentum in the last five years and is becoming a prominent, widely used technique. This method can be applied to unambiguously determine the structures of macromolecular complexes that exhibit compositional and conformational heterogeneity, both in vitro and in situ. Here we review the development of SPT, highlighting its applications and identifying areas of ongoing development.

Near-Atomic Resolution Structure Determination of a Cypovirus Capsid and Polymerase Complex Using Cryo-EM at 200kV

Single-particle cryo-electron microscopy (cryo-EM) allows the high-resolution structural determination of biological assemblies in a near-native environment. However, all high-resolution (better than 3.5Å) cryo-EM structures reported to date were obtained by using 300kV transmission electron microscopes (TEMs). We report here the structures of a cypovirus capsid of 750-Å diameter at 3.3-Å resolution and of RNA-dependent RNA polymerase (RdRp) complexes within the capsid at 3.9-Å resolution using a 200-kV TEM. The newly resolved structure revealed conformational changes of two subdomains in the RdRp. These conformational changes, which were involved in RdRp's switch from non-transcribing to transcribing mode, suggest that the RdRp may facilitate the unwinding of genomic double-stranded RNA. The possibility of 3-Å resolution structural determinations for biological assemblies of relatively small sizes using cryo-EM at 200kV was discussed.

Single particle electron cryomicroscopy: trends, issues and future perspective

There has been enormous progress during the last few years in the determination of three-dimensional biological structures by single particle electron cryomicroscopy (cryoEM), allowing maps to be obtained with higher resolution and from fewer images than required previously. This is due principally to the introduction of a new type of direct electron detector that has 2- to 3-fold higher detective quantum efficiency than available previously, and to the improvement of the computational algorithms for image processing. In spite of the great strides that have been made, quantitative analysis shows that there are still significant gains to be made provided that the problems associated with image degradation can be solved, possibly by minimising beam-induced specimen movement and charge build up during imaging. If this can be achieved, it should be possible to obtain near atomic resolution structures of smaller single particles, using fewer images and resolving more conformational states than at present, thus realising the full potential of the method. The recent popularity of cryoEM for molecular structure determination also highlights the need for lower cost microscopes, so we encourage development of an inexpensive, 100 keV electron cryomicroscope with a high-brightness field emission gun to make the method accessible to individual groups or institutions that cannot afford the investment and running costs of a state-of-the-art 300 keV installation. A key requisite for successful high-resolution structure determination by cryoEM includes interpretation of images and optimising the biochemistry and grid preparation to obtain nicely distributed macromolecules of interest. We thus include in this review a gallery of cryoEM micrographs that shows illustrative examples of single particle images of large and small macromolecular complexes.

Specimen Behavior in the Electron Beam

It has long been known that cryo-EM specimens are severely damaged by a level of electron exposure that is much lower than what is needed to obtain high-resolution images from single macromolecules. Perhaps less well appreciated in the cryo-EM literature, the vitreous ice in which samples are suspended is equally sensitivity to radiation damage. This chapter provides a review of several fundamental topics such as inelastic scattering of electrons, radiation chemistry, and radiation biology, which-together-can help one to understand why radiation damage occurs so "easily." This chapter also addresses the issue of beam-induced motion that occurs at even lower levels of electron exposure. While specimen charging may be a contributor to this motion, it is argued that both radiation-induced relief of preexisting stress and damage-induced generation of additional stress may be the dominant causes of radiation-induced movement.

Progress towards an optimal specimen support for electron cryomicroscopy

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Physical principles of electron scattering govern the design of specimen supports.

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Radiation-induced motion causes loss of resolution in electron micrographs.

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Specimen supports can now be designed to reduce specimen motion.

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Tailored surfaces in the support allow control of particle distribution and orientation.

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Future developments in support technology will further improve image quality.

The physical principles of electron–specimen interaction govern the design of specimen supports for electron cryomicroscopy (cryo-EM). Supports are constructed to suspend biological samples within the vacuum of the electron microscope in a way that maximises image contrast. Although the problem of specimen motion during imaging has been known since cryo-EM was first developed, the role of the support in this movement has only been recently identified. Here we review the key technological advances in specimen supports for cryo-EM. This includes the use of graphene as a surface for the adsorption of proteins and the design of an ultrastable, all-gold substrate that reduces the motion of molecules during electron irradiation. We discuss the implications of these and other recent improvements in specimen supports on resolution, and place them in the context of important developments in structure determination by cryo-EM.

Advances in electron microscopy: A qualitative view of instrumentation development for macromolecular imaging and tomography

Macromolecular imaging and tomography of ice embedded samples has developed into a mature imaging technology, in structural biology today widely referred to simply as cryo electron microscopy.(1) While the pioneers of the technique struggled with ill-suited instruments, state-of-the-art cryo microscopes are now readily available and an increasing number of groups are producing excellent high-resolution structural data of macromolecular complexes, of cellular organelles, or the morphology of whole cells. Instrumentation developers, however, are offering yet more novel electron optical devices, such as energy filters and monochromators, aberration correctors or physical phase plates. Here we discuss how current instrumentation has already changed cryo EM, and how newly available instrumentation - often developed in other fields of electron microscopy - may further develop the use and applicability of cryo EM to the imaging of single isolated macromolecules of smaller size or molecules embedded in a crowded cellular environment.

Cryomicroscopy of radiation sensitive specimens on unmodified graphene sheets: reduction of electron-optical effects of charging

Images of radiation-sensitive specimens obtained by electron microscopy suffer a reduction in quality beyond that expected from radiation damage alone due to electron beam-induced charging or movement of the specimen. For biological specimens, charging and movement are most severe when they are suspended in an insulating layer of vitreous ice, which is otherwise optimal for preserving hydrated specimens in a near native state. We image biological specimens, including a single particle protein complex and a lipid-enveloped virus in thin, vitreous ice films over suspended sheets of unmodified graphene. We show that in such preparations, the charging of ice, as assessed by electron-optical perturbation of the imaging beam, is eliminated. We also use the same specimen supports to record high resolution images at liquid nitrogen temperature of monolayer paraffin crystals grown over graphene.

Paraxial charge compensator for electron cryomicroscopy

We describe a multi-hole condenser aperture for the production of several electron beams in the transmission electron microscope (TEM) making it possible to simultaneously image and irradiate spatially separated regions of a specimen. When the specimen is a thin film of vitreous ice suspended over a holey carbon film, simultaneous irradiation of the adjacent carbon support with the off-axis beam compensates for some of the effects of charging in the image formed by a beam irradiating only the ice. Because the intervening region is not irradiated, charge-neutralization of frozen-hydrated specimens can occur by a through-space mechanism such as the emission of secondary electrons from a grounded carbon support film. We use paraxial charge compensation (PCC) to control the amount of charge build-up on the specimen and observe the effects of charge on images. The multi-hole aperture thus provides a tool for investigating the mechanism of charging and charge mitigation during the imaging of radiation sensitive biological specimens by cryomicroscopy.

Beam-induced motion of vitrified specimen on holey carbon film

The contrast observed in images of frozen-hydrated biological specimens prepared for electron cryo-microscopy falls significantly short of theoretical predictions. In addition to limits imposed by the current instrumentation, it is widely acknowledged that motion of the specimen during its exposure to the electron beam leads to significant blurring in the recorded images. We have studied the amount and direction of motion of virus particles suspended in thin vitrified ice layers across holes in perforated carbon films using exposure series. Our data show that the particle motion is correlated within patches of 0.3-0.5 μm, indicating that the whole ice layer is moving in a drum-like motion, with accompanying particle rotations of up to a few degrees. Support films with smaller holes, as well as lower electron dose rates tend to reduce beam-induced specimen motion, consistent with a mechanical effect. Finally, analysis of movies showing changes in the specimen during beam exposure show that the specimen moves significantly more at the start of an exposure than towards its end. We show how alignment and averaging of movie frames can be used to restore high-resolution detail in images affected by beam-induced motion.

The use of trehalose in the preparation of specimens for molecular electron microscopy

Biological specimens have to be prepared for imaging in the electron microscope in a way that preserves their native structure. Two-dimensional (2D) protein crystals to be analyzed by electron crystallography are best preserved by sugar embedding. One of the sugars often used to embed 2D crystals is trehalose, a disaccharide used by many organisms for protection against stress conditions. Sugars such as trehalose can also be added to negative staining solutions used to prepare proteins and macromolecular complexes for structural studies by single-particle electron microscopy (EM). In this review, we describe trehalose and its characteristics that make it so well suited for preparation of EM specimens and we review specimen preparation methods with a focus on the use of trehalose.

The surface of evaporated carbon films is an insulating, high-bandgap material

The electrical conductance and the optical density of evaporated carbon films are measured as a function of the thickness of the films. The resulting data show that up to a thickness of approximately 4 nm, carbon films are optically transparent and electrically insulating. The same data also suggest that this insulating character persists near to the surface when the overall thickness is further increased. Since a support film with poor surface conductivity is undesirable for many applications in electron microscopy, we suggest that the usefulness of evaporated carbon films in electron microscopy might be further improved by doping or by other methods that improve the electrical conductivity near the surface.

Electron cryomicroscopy of membrane proteins: specimen preparation for two-dimensional crystals and single particles

Membrane protein structure and function can be studied by two powerful and highly complementary electron cryomicroscopy (cryo-EM) methods: electron crystallography of two-dimensional (2D) crystals and single particle analysis of detergent-solubilized protein complexes. To obtain the highest-possible resolution data from membrane proteins, whether prepared as 2D crystals or single particles, cryo-EM samples must be vitrified with great care. Grid preparation for cryo-EM of 2D crystals is possible by back-injection, the carbon sandwich technique, drying in sugars before cooling in the electron microscope, or plunge-freezing. Specimen grids for single particle cryo-EM studies of membrane proteins are usually produced by plunge-freezing protein solutions, supported either by perforated or a continuous carbon film substrate. This review outlines the different techniques available and the suitability of each method for particular samples and studies. Experimental considerations in sample preparation and preservation include the protein itself and the presence of lipid or detergent. The appearance of cryo-EM samples in different conditions is also discussed.

Cryomesh: a new substrate for cryo-electron microscopy

Here we evaluate a new grid substrate developed by ProtoChips Inc. (Raleigh, NC) for cryo-transmission electron microscopy. The new grids are fabricated from doped silicon carbide using processes adapted from the semiconductor industry. A major motivating purpose in the development of these grids was to increase the low-temperature conductivity of the substrate, a characteristic that is thought to affect the appearance of beam-induced movement (BIM) in transmission electron microscope (TEM) images of biological specimens. BIM degrades the quality of data and is especially severe when frozen biological specimens are tilted in the microscope. Our results show that this new substrate does indeed have a significant impact on reducing the appearance and severity of beam-induced movement in TEM images of tilted cryo-preserved samples. Furthermore, while we have not been able to ascertain the exact causes underlying the BIM phenomenon, we have evidence that the rigidity and flatness of these grids may play a major role in its reduction. This improvement in the reliability of imaging at tilt has a significant impact on using data collection methods such as random conical tilt or orthogonal tilt reconstruction with cryo-preserved samples. Reduction in BIM also has the potential for improving the resolution of three-dimensional cryo-reconstructions in general.

Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction

Electron cryomicroscopy (cryo-EM) yields images of macromolecular assemblies and their components, from which 3D structures can be determined, by using an image processing method commonly known as "single-particle reconstruction." During the past two decades, this technique has become an important tool for 3D structure determination, but it generally has not been possible to determine atomic models. In principle, individual molecular images contain high-resolution information contaminated by a much higher level of noise. In practice, it has been unclear whether current averaging methods are adequate to extract this information from the background. We present here a reconstruction, obtained by using recently developed image processing methods, of the rotavirus inner capsid particle ("double-layer particle" or DLP) at a resolution suitable for interpretation by an atomic model. The result establishes single-particle reconstruction as a high-resolution technique. We show by direct comparison that the cryo-EM reconstruction of viral protein 6 (VP6) of the rotavirus DLP is similar in clarity to a 3.8-A resolution map obtained from x-ray crystallography. At this resolution, most of the amino acid side chains produce recognizable density. The icosahedral symmetry of the particle was an important factor in achieving this resolution in the cryo-EM analysis, but as the size of recordable datasets increases, single-particle reconstruction also is likely to yield structures at comparable resolution from samples of much lower symmetry. This potential has broad implications for structural cell biology.

A dose-rate effect in single-particle electron microscopy

A low beam intensity, low electron dose imaging method has been developed for single-particle electron cryo-microscopy (cryo-EM). Experiments indicate that the new technique can reduce beam-induced specimen movement and secondary radiolytic effects, such as "bubbling". The improvement in image quality, especially for multiple-exposure data collection, will help single-particle cryo-EM to reach higher resolution.

Automation of random conical tilt and orthogonal tilt data collection using feature-based correlation

Visualization by electron microscopy has provided many insights into the composition, quaternary structure, and mechanism of macromolecular assemblies. By preserving samples in stain or vitreous ice it is possible to image them as discrete particles, and from these images generate three-dimensional structures. This 'single-particle' approach suffers from two major shortcomings; it requires an initial model to reconstitute 2D data into a 3D volume, and it often fails when faced with conformational variability. Random conical tilt (RCT) and orthogonal tilt (OTR) are methods developed to overcome these problems, but the data collection required, particularly for vitreous ice specimens, is difficult and tedious. In this paper, we present an automated approach to RCT/OTR data collection that removes the burden of manual collection and offers higher quality and throughput than is otherwise possible. We show example datasets collected under stain and cryo conditions and provide statistics related to the efficiency and robustness of the process. Furthermore, we describe the new algorithms that make this method possible, which include new calibrations, improved targeting and feature-based tracking.

Improved specimen preparation for cryo-electron microscopy using a symmetric carbon sandwich technique

Image shift due to beam-induced specimen charging has become the most severe problem in electron microscopy for imaging two-dimensional (2D) crystals of biological macromolecules, especially in the case of highly tilted specimens. Image shift causes diffraction spots perpendicular to the tilt axis to disappear even at medium or low resolution. The yield of good images from tilted specimens prepared on a single layer of continuous carbon support film is therefore very low. In this paper, we have used 2D crystals of aquaporin-4 to investigate the effect of a carbon sandwich preparation method on specimen charging. We find that a larger number of images show sharp diffraction spots perpendicular to the tilt axis if crystals are placed in between two sheets of carbon film as compared to images taken from specimens prepared by the conventional single carbon support film technique. Our results demonstrate that the reproducible carbon sandwich preparation technique overcomes the severe specimen charging problem and thus has the potential to significantly speed up structure analysis by electron crystallography.

Experimental characterization and mitigation of specimen charging on thin films with one conducting layer

Specimen charging may be one of the most significant factors that contribute to the high variability and generally low quality of images in cryo-electron microscopy. Understanding the nature of specimen charging can help in devising methods to reduce or even avoid its effects and thus improve the rate of data collection as well as the quality of the data. We describe a series of experiments that help to characterize the charging phenomenon, which has been termed the Berriman effect. The pattern of buildup and disappearance of the charge pattern has led to several suggestions for how to alleviate the effect. Experiments are described that demonstrate the feasibility of such charge mitigation.

Specimen charging on thin films with one conducting layer: discussion of physical principles

Although the most familiar consequences of specimen charging in transmission electron microscopy can be eliminated by evaporating a thin conducting film (such as a carbon film) onto an insulating specimen or by preparing samples directly on such a conducting film to begin with, a more subtle charging effect still remains. We argue here that specimen charging is in this case likely to produce a dipole sheet rather than a layer of positive charge at the surface of the specimen. A simple model of the factors that control the kinetics of specimen charging, and its neutralization, is discussed as a guide for experiments that attempt to minimize the amount of specimen charging. Believable estimates of the electrostatic forces and the electron optical disturbances that are likely to occur suggest that specimen bending and warping may have the biggest impact on degrading the image quality at high resolution. Electron optical effects are likely to be negligible except in the case of a specimen that is tilted to high angle. A model is proposed to explain how both the mechanical and electron-optical effects of forming a dipole layer would have much greater impact on the image resolution in a direction perpendicular to the tilt axis, a well-known effect in electron microscopy of two-dimensional crystals.