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Cryo-EM and Hybrid Methods Development: Current Progress and Future Perspectives

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Molecular Structure".

Deadline for manuscript submissions: closed (15 September 2021) | Viewed by 3107

Special Issue Editors

Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
Interests: cryo-EM; cilia; cytoskeleton; motor proteins
Optics Deparment, Faculty of Physics, Universidad Complutense de Madrid, Plaza de Ciencias 1, 28040 Madrid, Spain
Interests: Cryo-EM; methods development; image analysis; algorithms

Special Issue Information

Dear colleagues,

The characterization of structure and associated conformational changes of biological macromolecular complexes is important for understanding how macromolecular assemblies fulfil their complex roles in the living cell. Several techniques may be used to determine their 3D macromolecular structure. X-ray crystallography may yield atomic resolution of the structure, but it requires a crystallization process, which is difficult for complexes showing conformational heterogeneity, for example. Nuclear magnetic resonance may provide unique information about dynamics and interactions, but atomic structure determination is restricted to small complexes. Cryo-electron microscopy (cryo-EM) allows studying frozen hydrated samples within a thin layer of amorphous ice, at cryogenic temperatures (generally liquid nitrogen temperatures). Cryo-EM allows the observation of biological specimens in close-to-physiological conditions as well as studying flexible complexes. Single particle analysis and single particle tomography are two cryo-EM approaches that are extensively used for obtaining 3D structural information of biological macromolecular complexes.

The cryo-EM field has been experiencing a very fast evolution in recent years. New technological developments (e.g., direct electron detector, phase plates, and new image processing methods) have opened the way to obtain quasi-atomic resolution for a large range of macromolecular complexes, including relatively small ones. Moreover, new technological developments have increased the richness of the data, requiring novel image processing methods to extract all the available structural information. Additionally, these recent developments now allow extracting information about the dynamics of complexes by exploring the conformational heterogeneity of the sample. Finally, old questions such as how to validate the reconstructed EM density map or how to measure its resolution are just as topical as ever.

This Special Issue aims at providing a platform for discussion of cutting-edge cryo-EM image analysis and 3D reconstruction methods and their structural biology and biomedical applications.

Dr. Khanh Huy Bui
Dr. Javier Vargas
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Cryo-electron microscopy
  • single particle analysis, cryo-electron tomography
  • image analysis
  • methods development

Published Papers (1 paper)

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Research

14 pages, 421 KiB  
Article
Advances in Xmipp for Cryo–Electron Microscopy: From Xmipp to Scipion
Molecules 2021, 26(20), 6224; https://doi.org/10.3390/molecules26206224 - 15 Oct 2021
Cited by 17 | Viewed by 2701
Abstract
Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and electron tomography, designed and managed by the Biocomputing Unit of the Spanish National Center for Biotechnology, although with contributions from many other developers over the [...] Read more.
Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and electron tomography, designed and managed by the Biocomputing Unit of the Spanish National Center for Biotechnology, although with contributions from many other developers over the world. During its 25 years of existence, Xmipp underwent multiple changes and updates. While there were many publications related to new programs and functionality added to Xmipp, there is no single publication on the Xmipp as a package since 2013. In this article, we give an overview of the changes and new work since 2013, describe technologies and techniques used during the development, and take a peek at the future of the package. Full article
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