Fully automated, sequential tilt-series acquisition with Leginon

Electron tomography has become a uniquely powerful tool for investigating the structures of individual cells, viruses, and macromolecules. Data collection is, however, time consuming and requires expensive instruments. To optimize productivity, we have incorporated one of the existing tilt-series acquisition programs, UCSF Tomo, into the well-developed automatic electron microscopy data collection package Leginon to enable fully automatic, sequential tilt-series acquisition. Here we describe how UCSF Tomo was integrated into Leginon, what users must do to set up a data collection session, how the automatic collection proceeds, how archived data about the process can be accessed and used, and how the software has been tested

Structure-based vaccine design by electron microscopy

Modern vaccine design relies on multiscale, interdisciplinary efforts that take advantage of innovative technologies such as in silico identification of antigens, high throughput screening of antigen immunogenicity, and gene expression profiling to predict host immune responses. In recent years, structural analysis has played an increasingly important role in vaccine development as a means to improve antigen stability, immunogenicity and large scale production. Transmission electron microscopy (TEM), and in particular cryo-TEM, is an established and powerful imaging technique applicable to many specimens, including the three-dimensional (3D) reconstruction of macromolecules and their associated complexes to high resolution. The technique is parsimonious in its material requirements and captures the specimens in their fully hydrated state, close to their native environment. The resolution of cryo-TEM reconstructions was limited to the subnanometer range until the recent development of direct electron detectors and improvements in image processing software, which has led to a so-called “resolution revolution” in the cryo-TEM field. Several protein structures have now been solved at near atomic resolution, establishing the technique as a viable alternative to X-ray analysis for high resolution structure determination. We have determined several structures with and without bound compounds at 2.9 Å – 3.6 Å resolution, which are being integrated into drug discovery and development workflows by our clients. Here we present the 2.4Å resolution structure of apoferritin determined with our Titan Krios electron microscope as an example of the cryo-TEM services available at NIS. These services are significantly enhanced with unique access by NIS to a new instrument, Spotiton, a robotic device that dispenses picoliter-volumes of sample onto a self-blotting nanowire grid as it flies past en route to vitrification. This provides several advantages over standard vitrification methods, including more automated and reproducible preparation of specimens and reducing the deleterious effects of particles interacting with the air-water interface. While high resolution 3D structure determination by cryo-TEM is at the forefront of structural biology, averages of 2D projection images at moderate resolution in negative stain or vitreous ice can also provide a wealth of information that may be difficult to obtain using other methods. This is illustrated in a number of case studies, including (1) mapping of neutralizing epitopes on the CMV pentameric glycoprotein complex; (2) mapping of neutralizing epitopes on the HIV-1 envelope glycoprotein trimer; (3) assessment of structure and conformational stability of pre- and post-fusion RSV-F protein; (4) characterization of novel adjuvants and protein delivery systems. In summary, both the moderate resolution TEM and high resolution cryo-TEM methods are well suited to extensively characterize antigen structure-function relationships, some of which may be refractory to other experimental methods

Routine single particle CryoEM sample and grid characterization by tomography

Single particle cryo-electron microscopy (cryoEM) is often performed under the assumption that particles are not adsorbed to the air-water interfaces and in thin, vitreous ice. In this study, we performed fiducial-less tomography on over 50 different cryoEM grid/sample preparations to determine the particle distribution within the ice and the overall geometry of the ice in grid holes. Surprisingly, by studying particles in holes in 3D from over 1000 tomograms, we have determined that the vast majority of particles (approximately 90%) are adsorbed to an air-water interface. The implications of this observation are wide-ranging, with potential ramifications regarding protein denaturation, conformational change, and preferred orientation. We also show that fiducial-less cryo-electron tomography on single particle grids may be used to determine ice thickness, optimal single particle collection areas and strategies, particle heterogeneity, and de novo models for template picking and single particle alignment

An Integrated Micro- and Macroarchitectural Analysis of the Drosophila Brain by Computer-Assisted Serial Section Electron Microscopy

A new software package allows for dense electron microscopy reconstructions of neuronal networks in the fruit fly brain, and reveals specific differences in microcircuits between insects and vertebrates

Bootstrap resampling for voxel-wise variance analysis of three-dimensional density maps derived by image analysis of two-dimensional crystals

Difference density maps are commonly used in structural biology for identifying conformational changes in macromolecular complexes. For interpretation of the results, it is essential to estimate the variance or standard deviation of the difference density and the distribution of errors in space. In order to compare three-dimensional density maps of gap junction channels with and without the C-terminal regulatory domain, we developed a bootstrap resampling method for estimation of the voxel-wise standard deviation. The bootstrap approach has been successfully used for estimating the sampling distribution from a limited data set and for estimating the statistical properties of the derived quantities [Efron, B., 1979. Bootstrap methods: another look at the jackknife. Ann. Stat. 7, 1–26]. In our application, the standard deviation map can be estimated by bootstrapping the images. Our results show that, apart from the symmetry axes and small regions bordering the lumen of the extracellular vestibule, difference maps normalized by the mean of the standard deviation map can be used as a good approximation of the t-test map of the gap junction crystals

A graphical representation of image quality for three-dimensional structure analysis of two-dimensional crystals

Electron crystallography of two-dimensional (2D) crystals is a powerful approach for the analysis of membrane protein structure. Three-dimensional (3D) structures are derived by merging data from 2D crystals at varying tilt axes and tilt angles. A graphical representation was developed that incorporates the tilt geometry to display the quality of each image. Information that can be extracted from the plot includes a symbol for each image that reflects the completeness of the data for that crystal. The polar plot also includes a novel parameter that reflects the minimal variation in tilt axis to ensure overlap of data points in reciprocal space between images at the same tilt angle. The tilt geometry and image quality plot is especially useful for tracking the progress of data collection and for assessing the completeness of two data sets prior to determination of difference maps