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Biomolecules
Special Issues
Integrative Approaches Based on Cryo-EM and Cryo-ET in Biological Applications
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Integrative Approaches Based on Cryo-EM and Cryo-ET in Biological Applications

A special issue of Biomolecules (ISSN 2218-273X).

Deadline for manuscript submissions: closed (31 August 2022) | Viewed by 5462

Special Issue Editors

Dr. Hélène Démèné

E-Mail Website
Guest Editor
Centre de Biochimie Structurale (CBS), INSERM, CNRS, Univ Montpellier, 34090 Montpellier, France
Interests: Cryo-EM; Structural Biology; Molecular Dynamics; NMR
Dr. Nadia Izadi-Pruneyre

E-Mail Website
Guest Editor
Department of Structural Biology and Chemistry Institut Pasteur, CNRS UMR 3528, 75015 Paris, France
Interests: structural biology; NMR; molecular interactions; integrative approach; dynamics; bacterial membrane systems

Special Issue Information

Dear Colleagues,

The unprecedented growth of cryo-electron microscopy (cryo-EM) in recent years has promoted this method as one of the most powerful in structural and cell biology. Single-particle analysis of purified macromolecular complexes allows us to elucidate their structure at near-atomic resolution. Their visualization and study in the cellular context at an unprecedented resolution have become possible by cryo-electron tomography (cryo-ET). However, there are still pitfalls related to the resolutions available for a number of biological objects. These limitations can be overcome by using an integrative approach combining cryo-EM and cryo-ET data with complementary biochemical and structural techniques, such as copurification of macromolecular complexes, NMR, X-ray crystallography, SAXS, cross-linking and hydrogen-deuterium exchange mass spectrometry, light scattering, molecular modeling as well as mutagenesis and functional assays. The information at different resolutions then completes the interpretation of cryo-EM/cryo-ET data and allows the identification of different components, the determination of their conformation(s), and molecular interactions at atomic or molecular levels. This allows the understanding of biological processes at the highest spatial and temporal resolution possible. In this Special Issue, we will report integrative studies with mechanistic and functional insights, as well as new methods for significant advances in the field.

Dr. Hélène Démèné
Dr. Nadia Izadi-Pruneyre
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. Biomolecules is an international peer-reviewed open access monthly 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-EM
  • cryo-ET
  • integrative structural biology
  • NMR, mass-spectrometry
  • modeling
  • light scattering

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Published Papers (2 papers)

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15 pages, 15065 KiB  
Article
Building Protein Atomic Models from Cryo-EM Density Maps and Residue Co-Evolution
by Guillaume Bouvier, Benjamin Bardiaux, Riccardo Pellarin, Chiara Rapisarda and Michael Nilges
Biomolecules 2022, 12(9), 1290; https://doi.org/10.3390/biom12091290 - 13 Sep 2022
Cited by 1 | Viewed by 2316
Abstract
Electron cryo-microscopy (cryo-EM) has emerged as a powerful method by which to obtain three-dimensional (3D) structures of macromolecular complexes at atomic or near-atomic resolution. However, de novo building of atomic models from near-atomic resolution (3–5 Å) cryo-EM density maps is a challenging task, [...] Read more.
Electron cryo-microscopy (cryo-EM) has emerged as a powerful method by which to obtain three-dimensional (3D) structures of macromolecular complexes at atomic or near-atomic resolution. However, de novo building of atomic models from near-atomic resolution (3–5 Å) cryo-EM density maps is a challenging task, in particular because poorly resolved side-chain densities hamper sequence assignment by automatic procedures at a lower resolution. Furthermore, segmentation of EM density maps into individual subunits remains a difficult problem when the structure of the subunits is not known, or when significant conformational rearrangement occurs between the isolated and associated form of the subunits. To tackle these issues, we have developed a graph-based method to thread most of the C-α trace of the protein backbone into the EM density map. The EM density is described as a weighted graph such that the resulting minimum spanning tree encompasses the high-density regions of the map. A pruning algorithm cleans the tree and finds the most probable positions of the C-α atoms, by using side-chain density when available, as a collection of C-α trace fragments. By complementing experimental EM maps with contact predictions from sequence co-evolutionary information, we demonstrate that this approach can correctly segment EM maps into individual subunits and assign amino acid sequences to backbone traces to generate atomic models. Full article
(This article belongs to the Special Issue Integrative Approaches Based on Cryo-EM and Cryo-ET in Biological Applications)
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17 pages, 2595 KiB  
Article
Beyond the Backbone: The Next Generation of Pathwalking Utilities for Model Building in CryoEM Density Maps
by Corey F. Hryc and Matthew L. Baker
Biomolecules 2022, 12(6), 773; https://doi.org/10.3390/biom12060773 - 2 Jun 2022
Cited by 6 | Viewed by 2202
Abstract
Single-particle electron cryomicroscopy (cryoEM) has become an indispensable tool for studying structure and function in macromolecular assemblies. As an integral part of the cryoEM structure determination process, computational tools have been developed to build atomic models directly from a density map without structural [...] Read more.
Single-particle electron cryomicroscopy (cryoEM) has become an indispensable tool for studying structure and function in macromolecular assemblies. As an integral part of the cryoEM structure determination process, computational tools have been developed to build atomic models directly from a density map without structural templates. Nearly a decade ago, we created Pathwalking, a tool for de novo modeling of protein structure in near-atomic resolution cryoEM density maps. Here, we present the latest developments in Pathwalking, including the addition of probabilistic models, as well as a companion tool for modeling waters and ligands. This software was evaluated on the 2021 CryoEM Ligand Challenge density maps, in addition to identifying ligands in three IP3R1 density maps at ~3 Å to 4.1 Å resolution. The results clearly demonstrate that the Pathwalking de novo modeling pipeline can construct accurate protein structures and reliably localize and identify ligand density directly from a near-atomic resolution map. Full article
(This article belongs to the Special Issue Integrative Approaches Based on Cryo-EM and Cryo-ET in Biological Applications)
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