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Special Issue "Cryogenic Biomolecular Imaging and Image Analysis Techniques: Present and Future"

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: 30 November 2023 | Viewed by 2888

Special Issue Editor

CNRS, UMR7590, IMPMC, Sorbonne University, 38044 Paris, France
Interests: structural biology; image processing; electron microscopy; biomedical engineering

Special Issue Information

Dear Colleagues,

Cryogenic microscopy techniques, such as cryo-electron microscopy single particle analysis, cryo-electron tomography, cryo correlative light and electron microscopy, and cryo super-resolution fluorescence microscopy, allow a multi-scale and multi-resolution analysis of biomolecular assemblies.

Advances in instrumentation increase the amount and quality of the collected data, which opens new research avenues, including the development of new image analysis algorithms. Over the years, modeling, simulation, and deep learning have become integral parts of cryogenic biomolecular image analysis.

This Special Issue welcomes original research and review articles on advances and future directions in all techniques of cryogenic biomolecular imaging and image analysis, including modeling, simulation, and deep learning.

Dr. Slavica Jonić
Guest Editor

Manuscript Submission Information

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Published Papers (3 papers)

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Research

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Article
Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Workflow Engine Enabling Integration of Databases, Simulations and Cryo-Electron Microscopy Image Processing
Int. J. Mol. Sci. 2023, 24(18), 14245; https://doi.org/10.3390/ijms241814245 - 18 Sep 2023
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Abstract
Macromolecular assemblies, such as protein complexes, undergo continuous structural dynamics, including global reconfigurations critical for their function. Two fast analytical methods are widely used to study these global dynamics, namely elastic network model normal mode analysis and principal component analysis of ensembles of [...] Read more.
Macromolecular assemblies, such as protein complexes, undergo continuous structural dynamics, including global reconfigurations critical for their function. Two fast analytical methods are widely used to study these global dynamics, namely elastic network model normal mode analysis and principal component analysis of ensembles of structures. These approaches have found wide use in various computational studies, driving the development of complex pipelines in several software packages. One common theme has been conformational sampling through hybrid simulations incorporating all-atom molecular dynamics and global modes of motion. However, wide functionality is only available for experienced programmers with limited capabilities for other users. We have, therefore, integrated one popular and extensively developed software for such analyses, the ProDy Python application programming interface, into the Scipion workflow engine. This enables a wider range of users to access a complete range of macromolecular dynamics pipelines beyond the core functionalities available in its command-line applications and the normal mode wizard in VMD. The new protocols and pipelines can be further expanded and integrated into larger workflows, together with other software packages for cryo-electron microscopy image analysis and molecular simulations. We present the resulting plugin, Scipion-EM-ProDy, in detail, highlighting the rich functionality made available by its development. Full article
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Article
Extensive Angular Sampling Enables the Sensitive Localization of Macromolecules in Electron Tomograms
Int. J. Mol. Sci. 2023, 24(17), 13375; https://doi.org/10.3390/ijms241713375 - 29 Aug 2023
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Abstract
Cryo-electron tomography provides 3D images of macromolecules in their cellular context. To detect macromolecules in tomograms, template matching (TM) is often used, which uses 3D models that are often reliable for substantial parts of the macromolecules. However, the extent of rotational searches in [...] Read more.
Cryo-electron tomography provides 3D images of macromolecules in their cellular context. To detect macromolecules in tomograms, template matching (TM) is often used, which uses 3D models that are often reliable for substantial parts of the macromolecules. However, the extent of rotational searches in particle detection has not been investigated due to computational limitations. Here, we provide a GPU implementation of TM as part of the PyTOM software package, which drastically speeds up the orientational search and allows for sampling beyond the Crowther criterion within a feasible timeframe. We quantify the improvements in sensitivity and false-discovery rate for the examples of ribosome identification and detection. Sampling at the Crowther criterion, which was effectively impossible with CPU implementations due to the extensive computation times, allows for automated extraction with high sensitivity. Consequently, we also show that an extensive angular sample renders 3D TM sensitive to the local alignment of tilt series and damage induced by focused ion beam milling. With this new release of PyTOM, we focused on integration with other software packages that support more refined subtomogram-averaging workflows. The automated classification of ribosomes by TM with appropriate angular sampling on locally corrected tomograms has a sufficiently low false-discovery rate, allowing for it to be directly used for high-resolution averaging and adequate sensitivity to reveal polysome organization. Full article
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Review

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Review
Overview of Membrane Protein Sample Preparation for Single-Particle Cryo-Electron Microscopy Analysis
Int. J. Mol. Sci. 2023, 24(19), 14785; https://doi.org/10.3390/ijms241914785 - 30 Sep 2023
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Abstract
Single-particle cryo-electron microscopy (cryo-EM SPA) has recently emerged as an exceptionally well-suited technique for determining the structure of membrane proteins (MPs). Indeed, in recent years, huge increase in the number of MPs solved via cryo-EM SPA at a resolution better than 3.0 Å [...] Read more.
Single-particle cryo-electron microscopy (cryo-EM SPA) has recently emerged as an exceptionally well-suited technique for determining the structure of membrane proteins (MPs). Indeed, in recent years, huge increase in the number of MPs solved via cryo-EM SPA at a resolution better than 3.0 Å in the Protein Data Bank (PDB) has been observed. However, sample preparation remains a significant challenge in the field. Here, we evaluated the MPs solved using cryo-EM SPA deposited in the PDB in the last two years at a resolution below 3.0 Å. The most critical parameters for sample preparation are as follows: (i) the surfactant used for protein extraction from the membrane, (ii) the surfactant, amphiphiles, nanodiscs or other molecules present in the vitrification step, (iii) the vitrification method employed, and (iv) the type of grids used. The aim is not to provide a definitive answer on the optimal sample conditions for cryo-EM SPA of MPs but rather assess the current trends in the MP structural biology community towards obtaining high-resolution cryo-EM structures. Full article
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