Spline-based image-to-volume registration for three-dimensional electron microscopy

Identification of incorrectly oriented particles in cryo-EM single particle analysis

The quality of a 3D map produced by the single-particle analysis method is highly dependent on an accurate assignment of orientations to the many experimental images. However, the problem's complexity implies the presence of several local minima in the optimized goal functions. Consequently, validation methods to confirm the angular assignment are very useful to yield higher-resolution 3D maps. In this work, we present a graph-signal-processing-based methodology that analyzes the correlation landscape as a function of the orientation, an approach allowing the estimation of the assigned orientations' reliability. Using this method, we may identify low-reliability images that probably incorrectly contribute to the final 3D reconstruction.

Hybrid Electron Microscopy Normal Mode Analysis with Scipion

Hybrid Electron Microscopy Normal Mode Analysis (HEMNMA) method was introduced in 2014. HEMNMA computes normal modes of a reference model (an atomic structure or an electron microscopy map) of a molecular complex and uses this model and its normal modes to analyze single-particle images of the complex to obtain information on its continuous conformational changes, by determining the full distribution of conformational variability from the images. An advantage of HEMNMA is a simultaneous determination of all parameters of each image (particle conformation, orientation, and shift) through their iterative optimization, which allows applications of HEMNMA even when the effects of conformational changes dominate those of orientational changes. HEMNMA was first implemented in Xmipp and was using MATLAB for statistical analysis of obtained conformational distributions and for fitting of underlying trajectories of conformational changes. A HEMNMA implementation independent of MATLAB is now available as part of a plugin of Scipion V2.0 (http://scipion.i2pc.es). This plugin, named ContinuousFlex, can be installed by following the instructions at https://pypi.org/project/scipion-em-continuousflex. In this article, we present this new HEMNMA software, which is user-friendly, totally free, and open-source. STATEMENT FOR A BROADER AUDIENCE: This article presents Hybrid Electron Microscopy Normal Mode Analysis (HEMNMA) software that allows analyzing single-particle images of a complex to obtain information on continuous conformational changes of the complex, by determining the full distribution of conformational variability from the images. The HEMNMA software is user-friendly, totally free, open-source, and available as part of ContinuousFlex plugin (https://pypi.org/project/scipion-em-continuousflex) of Scipion V2.0 (http://scipion.i2pc.es).

Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy

Single-particle analysis by electron microscopy is a well established technique for analyzing the three-dimensional structures of biological macromolecules. Besides its ability to produce high-resolution structures, it also provides insights into the dynamic behavior of the structures by elucidating their conformational variability. Here, the different image-processing methods currently available to study continuous conformational changes are reviewed.

Gaussian mixture model for coarse-grained modeling from XFEL

We explore the advantage of Gaussian mixture model (GMM) for interpretation of single particle diffraction patterns from X-ray free electron laser (XFEL) experiments. GMM approximates a biomolecular shape by the superposition of Gaussian distributions. As the Fourier transformation of GMM can be quickly performed, we can efficiently simulate XFEL diffraction patterns from approximated structure models. We report that the resolution that GMM can accurately reproduce is proportional to the cubic root of the number of Gaussians used in the modeling. This behavior can be attributed to the correspondence between the number of adjustable parameters in GMM and the amount of sampling points in diffraction space. Furthermore, GMMs can successfully be used to perform angular assignment and to detect conformational variation. These results demonstrate that GMMs serve as useful coarse-grained models for hybrid approach in XFEL single particle experiments.

Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol

This article presents an integral graphical interface to the Hybrid Electron Microscopy Normal Mode Analysis (HEMNMA) approach that was developed for capturing continuous motions of large macromolecular complexes from single-particle EM images. HEMNMA was shown to be a good approach to analyze multiple conformations of a macromolecular complex but it could not be widely used in the EM field due to a lack of an integral interface. In particular, its use required switching among different software sources as well as selecting modes for image analysis was difficult without the graphical interface. The graphical interface was thus developed to simplify the practical use of HEMNMA. It is implemented in the open-source software package Xmipp 3.1 (http://xmipp.cnb.csic.es) and only a small part of it relies on MATLAB that is accessible through the main interface. Such integration provides the user with an easy way to perform the analysis of macromolecular dynamics and forms a direct connection to the single-particle reconstruction process. A step-by-step HEMNMA protocol with the graphical interface is given in full details in Supplementary material. The graphical interface will be useful to experimentalists who are interested in studies of continuous conformational changes of macromolecular complexes beyond the modeling of continuous heterogeneity in single particle reconstruction.

Image processing for electron microscopy single-particle analysis using XMIPP

We describe a collection of standardized image processing protocols for electron microscopy single-particle analysis using the XMIPP software package. These protocols allow performing the entire processing workflow starting from digitized micrographs up to the final refinement and evaluation of 3D models. A particular emphasis has been placed on the treatment of structurally heterogeneous data through maximum-likelihood refinements and self-organizing maps as well as the generation of initial 3D models for such data sets through random conical tilt reconstruction methods. All protocols presented have been implemented as stand-alone, executable python scripts, for which a dedicated graphical user interface has been developed. Thereby, they may provide novice users with a convenient tool to quickly obtain useful results with minimum efforts in learning about the details of this comprehensive package. Examples of applications are presented for a negative stain random conical tilt data set on the hexameric helicase G40P and for a structurally heterogeneous data set on 70S Escherichia coli ribosomes embedded in vitrified ice.

Cryo-EM image alignment based on nonuniform fast Fourier transform

In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform fast Fourier transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis.

3D electron microscopy of biological nanomachines: principles and applications

Transmission electron microscopy is a powerful technique for studying the three-dimensional (3D) structure of a wide range of biological specimens. Knowledge of this structure is crucial for fully understanding complex relationships among macromolecular complexes and organelles in living cells. In this paper, we present the principles and main application domains of 3D transmission electron microscopy in structural biology. Moreover, we survey current developments needed in this field, and discuss the close relationship of 3D transmission electron microscopy with other experimental techniques aimed at obtaining structural and dynamical information from the scale of whole living cells to atomic structure of macromolecular complexes.