Article
Biochemical Research Methods
Gavin Rice, Thorsten Wagner, Markus Stabrin, Oleg Sitsel, Daniel Prumbaum, Stefan Raunser
Summary: TomoTwin is a deep metric learning-based particle picking method for cryo-electron tomograms that eliminates the need for annotating training data and retraining a picking model for each protein. It embeds tomograms in a high-dimensional space to identify proteins without manual annotation or network retraining.
Article
Chemistry, Applied
Yaping Zhang, Yi Zhou, Tu Sun, Pengyu Chen, Chengmin Li, Yoshihiro Kubota, Satoshi Inagaki, Catherine Dejoie, Alvaro Mayoral, Osamu Terasaki
Summary: This study investigated the structures of YNU-5 zeolites using various techniques, with a focus on advanced electron microscopy methods. The space group for the YNU-5 zeolites was determined to be Cmmm, showing higher symmetry than previously reported. Additionally, Rietveld refinement of synchrotron Powder X-ray diffraction data provided precise information on the framework and the location of organic species, cations, and water.
MICROPOROUS AND MESOPOROUS MATERIALS
(2021)
Article
Chemistry, Multidisciplinary
Guojun Zhou, Taimin Yang, Zhehao Huang
Summary: This study successfully determined the structure of a low-crystallinity pyrene-containing covalent organic framework using a combination of three-dimensional electron diffraction and simulated annealing.
COMMUNICATIONS CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Paul B. Klar, Yasar Krysiak, Hongyi Xu, Gwladys Steciuk, Jung Cho, Xiaodong Zou, Lukas Palatinus
Summary: Continuous-rotation 3D electron diffraction methods are used for structure analysis of small organic molecular crystals and inorganic materials. A method that considers multiple scattering effects is presented, improving accuracy and reliability of structure models and determining absolute structures.
Article
Multidisciplinary Sciences
Martin Filipovski, Jelly H. M. Soffers, Seychelle M. Vos, Lucas Farnung
Summary: This study reports the structure of a mammalian Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex and reveals the direct role of Pol II and transcription elongation factors in nucleosome retention, explaining how nucleosomes are retained to maintain the chromatin structure of actively transcribed genes.
Review
Chemistry, Multidisciplinary
Han Xue, Meng Zhang, Jianfang Liu, Jianjun Wang, Gang Ren
Summary: This article discusses how experimental parameters in cryo-electron microscopy and cryo-electron tomography affect radiation damage, and explores how to optimize experimental strategies to increase imaging dose or improve image signal-to-noise ratio without increasing radiation damage.
FRONTIERS IN CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Forrest Hoyt, Heidi G. Standke, Efrosini Artikis, Cindi L. Schwartz, Bryan Hansen, Kunpeng Li, Andrew G. Hughson, Matteo Manca, Olivia R. Thomas, Gregory J. Raymond, Brent Race, Gerald S. Baron, Byron Caughey, Allison Kraus
Summary: This study presents a high-resolution cryo-electron microscopy-based structure of infectious brain-derived fibrils of the mouse anchorless RML scrapie strain. Comparisons with the previously determined hamster 263K strain reveal both common and divergent features among these prion strains.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Nikolai N. Sluchanko, Yury B. Slonimskiy, Nikita A. Egorkin, Larisa A. Varfolomeeva, Sergey Yu Kleymenov, Mikhail E. Minyaev, Yaroslav Faletrov, Anastasia M. Moysenovich, Evgenia Yu Parshina, Thomas Friedrich, Eugene G. Maksimov, Konstantin M. Boyko, Vladimir O. Popov
Summary: In this study, the crystal structures of a carotenoid-binding protein (BmCBP) from silkworm Bombyx mori were determined, revealing the interaction between BmCBP and zeaxanthin (ZEA). The research showed structural differences in the carotenoid-binding cavity between BmCBP and human STARD3, explaining their distinct carotenoid-binding capacities. These findings provide important insights into the function of xanthophyll-binding proteins in the eye.
Article
Biochemistry & Molecular Biology
Szymon W. Manka, Adam Wenborn, Jemma Betts, Susan Joiner, Helen R. Saibil, John Collinge, Jonathan D. F. Wadsworth
Summary: Recent cryo-EM studies revealed a similar amyloid architecture in infectious prion fibrils from different strains. This study determined the cryo-EM structure of mouse prion fibrils from two prion strains, ME7 and RML, and compared their folding subdomains. The results provide a structural definition of strain-specific conformations in prion diseases.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Alexander Muhleip, Rasmus Kock Flygaard, Jana Ovciarikova, Alice Lacombe, Paula Fernandes, Lilach Sheiner, Alexey Amunts
Summary: The unique assembly of mitochondrial ATP synthase in Apicomplexa is crucial for maintaining cristae morphology, as demonstrated by the arrangement of cyclic hexamers into pentagonal pyramids in the curved apical membrane regions.
NATURE COMMUNICATIONS
(2021)
Article
Computer Science, Interdisciplinary Applications
Lorenz Lamm, Ricardo D. Righetto, Wojciech Wietrzynski, Matthias Poge, Antonio Martinez-Sanchez, Tingying Peng, Benjamin D. Engel
Summary: MemBrain is a novel deep learning-aided pipeline for automatic detection of membrane-bound protein complexes in cryo-electron tomograms, achieving high efficiency and excellent performance. The program demonstrates strong generalizability to various types of cells and tomograms, with minimal annotations required for training models.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2022)
Article
Biochemical Research Methods
Jie E. Yang, Matthew R. Larson, Bryan S. Sibert, Joseph Y. Kim, Daniel Parrell, Juan C. Sanchez, Victoria Pappas, Anil Kumar, Kai Cai, Keith Thompson, Elizabeth R. Wright
Summary: In this paper, robust tools for montage parallel array cryo-tomography (MPACT) tailored for vitrified specimens are presented, which can image large fields of view while preserving high-resolution structural information. The combination of multiple techniques in MPACT supports studies that contextually define the three-dimensional architecture of cells, and it provides flexibility and efficient data processing and analysis.
Article
Biochemistry & Molecular Biology
Xuyuan Kuang, Kyle Nunn, Jennifer Jiang, Paul Castellano, Uttara Hardikar, Arianna Horgan, Joyce Kong, Zhiqun Tan, Wei Dai
Summary: Studies have shown that mHTT can spread between cells, leading to the propagation of misfolded protein pathology. By using correlative light and electron microscopy and cryo-electron tomography, researchers identified the structure of transmissive mHTT species and highlighted the potential role of extracellular vesicles (EVs) in the transmission process.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Vasileios Rantos, Kai Karius, Jan Kosinski
Summary: Integrative modeling with Assembline enables efficient structure determination of macromolecular complexes by combining data from multiple experimental sources, including electron microscopy maps. The software package allows for exhaustive sampling of conformational space through a multistep procedure, providing new modeling restraints and a unique configuration system for setting up the modeling project.
Article
Materials Science, Multidisciplinary
Mihai M. Rusu, Adriana Vulpoi, Isabelle Maurin, Liviu C. Cotet, Lucian C. Pop, Carmen Fort, Monica Baia, Lucian Baia, Ileana Florea
Summary: Carbon xerogel nanocomposites with integrated Bi and Fe particles (C-Bi-Fe) are investigated for their potential applications as electrochemical sensors and catalysts. The catalyzed growth of nano-graphites in C-Bi-Fe systems is studied, revealing the mechanisms and constraints of this process.
MICROSCOPY AND MICROANALYSIS
(2022)
