Article
Chemistry, Multidisciplinary
Nesrine Aissaoui, Josephine Lai-Kee-Him, Allan Mills, Nathalie Declerck, Zakia Morichaud, Konstantin Brodolin, Sonia Baconnais, Eric Le Cam, Jean Baptiste Charbonnier, Remy Sounier, Sebastien Granier, Virginie Ropars, Patrick Bron, Gaetan Bellot
Summary: Technological breakthroughs in electron microscopy have made it possible to study biological macromolecular complexes with novel challenges, such as sample preparation and heterogeneous macromolecular assemblies. In this study, a V-shaped DNA origami template was used to position proteins, demonstrating a new approach for characterizing mechanosensitive proteins and expanding the range of potential targets for single-particle EM investigation. Validation with RNAP protein showed compatibility with cryo-EM sample preparation.
Article
Microbiology
Takuma Toyonaga, Takayuki Kato, Akihiro Kawamoto, Noriyuki Kodera, Tasuku Hamaguchi, Yuhei O. Tahara, Toshio Ando, Keiichi Namba, Makoto Miyata
Summary: The study isolated a protein complex from Mycoplasma cells and supported the conclusion that it contains detailed structures with common and novel features related to F-1-ATPase.
Review
Biochemistry & Molecular Biology
Sepideh Valimehr, Ashish Sethi, Manjari Shukla, Sudipta Bhattacharyya, Mohsen Kazemi, Isabelle Rouiller
Summary: p97/VCP, a highly conserved AAA+ ATPase, is a significant therapeutic target in the treatment of neurodegenerative diseases and cancer. This review provides an understanding of p97's molecular mechanism during the ATPase cycle and its regulation by cofactors and inhibitors. It compares structural information obtained in different nucleotide states and discusses the impact of pathogenic mutations on p97's conformational changes. Overall, the review emphasizes how the mechanistic knowledge of p97 contributes to the design of pathway-specific modulators and inhibitors.
Article
Multidisciplinary Sciences
Joshua B. R. White, Daniel P. Maskell, Andrew Howe, Martin Harrow, Daniel K. Clare, C. Alistair Siebert, Emma L. Hesketh, Rebecca F. Thompson
Summary: Cryo-electron microscopy is a powerful technique for structure determination of macromolecular complexes through single particle analysis, involving vitrification, specimen screening, data collection, and image processing, with options for user modification and common troubleshooting. Variations on imaging protocols to assist users in efficient operation and imaging when physical access to the microscope is limited are being developed due to remote microscope operation becoming standard.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Chemistry, Physical
Jin-Hu Dou, Maxx Q. Arguilla, Yi Luo, Jian Li, Weizhe Zhang, Lei Sun, Jenna L. Mancuso, Luming Yang, Tianyang Chen, Lucas R. Parent, Grigorii Skorupskii, Nicole J. Libretto, Chenyue Sun, Min Chieh Yang, Phat Vinh Dip, Edward J. Brignole, Jeffrey T. Miller, Jing Kong, Christopher H. Hendon, Junliang Sun, Mircea Dinca
Summary: Researchers have successfully grown single crystals of 2D metal-organic frameworks up to 200 µm in size by balancing in-plane and out-of-plane interactions, revealing anisotropic transport and a clear correlation between conductivity and the nature of the metal cation in the sheets.
Article
Multidisciplinary Sciences
Arjun Saha, Arieh Warshel
Summary: This study explored the molecular basis of substrate translocation by the AAA+ motor of the 26S proteasome using simulation approaches, revealing the role of electrostatic interactions and validating the involvement of bulkier residues in pore loop 1 in substrate translocation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Joshua Pajak, Rockney Atz, Brendan J. Hilbert, Marc C. Morais, Brian A. Kelch, Paul J. Jardine, Gaurav Arya
Summary: Research has identified the crucial role of a glutamate-switch residue in coupling ATP binding to DNA gripping in viral packaging ATPases. Through molecular dynamics simulations and experimental validation, a signaling pathway mediated by the glutamate switch that regulates conformational transitions upon ATP hydrolysis has been revealed in the study.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
J. Garcia Condado, A. Munoz-Barrutia, C. O. S. Sorzano
Summary: Single-Particle Analysis by Cryo-Electron Microscopy is a technique used to determine the 3D structure of biological macromolecules. This article introduces HaPi, a method that automatically determines the handedness of macromolecule electron density maps solved by CryoEM. HaPi utilizes convolutional neural networks and a consensus strategy to determine the hand of the maps.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
J. J. Erik Maris, Freddy T. Rabouw, Bert M. Weckhuysen, Florian Meirer
Summary: Single-particle tracking is a powerful method for studying the motion of individual molecules and particles. The DiffusionLab software package provides motion analysis tools for challenging data sets, allowing trajectory classification based on motion type and computation of diffusion constants.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
C. O. S. Sorzano, D. Semchonok, S-C Lin, Y-C Lo, J. L. Vilas, A. Jimenez-Moreno, M. Gragera, S. Vacca, D. Maluenda, M. Martinez, E. Ramirez-Aportela, R. Melero, A. Cuervo, J. J. Conesa, P. Conesa, P. Losana, L. Del Cano, J. Jimenez de la Morena, Y. C. Fonseca, R. Sanchez-Garcia, D. Strelak, E. Fernandez-Gimenez, F. de Isidro, D. Herreros, P. L. Kastritis, R. Marabini, B. D. Bruce, J. M. Carazo
Summary: The presence of preferred orientations in SPA by cryoEM poses a challenge for achieving high-resolution structures, but some image processing algorithms are more robust against these detrimental conditions.
JOURNAL OF STRUCTURAL BIOLOGY
(2021)
Article
Nanoscience & Nanotechnology
Dayne F. Swearer, Stefan Fischer, Daniel K. Angell, Chris Siefe, A. Paul Alivisatos, Steven Chu, Jennifer A. Dionne
Summary: Our study involved the development of a library of 11 unique lanthanide-doped nanophosphors for high-resolution, multicolor electron microscopy. Transmission electron microscopy revealed that these nanophosphors exhibit strong cathodoluminescence spectra under electron beam, with high spatial localization characteristics.
Review
Biochemistry & Molecular Biology
Yixin Xu, Shangyu Dang
Summary: Cryo-sample preparation is a critical step in obtaining high-resolution macromolecule structures using cryo-EM, but it is often affected by high uncertainty and low reproducibility. Developing new methods to enhance cryo-sample quality is therefore an important research topic.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Agriculture, Multidisciplinary
Janja Vidmar, Luisa Haessmann, Katrin Loeschner
Summary: In this study, single-particle inductively coupled plasma-mass spectrometry (spICP-MS) was demonstrated as a potential screening technique for detecting inorganic nanoparticles in food. The method showed sensitive and interference-free detection of nanoparticles (NPs) by combining collision/reaction cell gases and microsecond dwell times. The study highlighted the importance of correctly assessing the presence of NPs in food, including setting suitable thresholds and analyzing an adequate number of blank samples to minimize false-positive results.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Chemistry, Physical
Zonglin Li, Mingxin Xie, Guozheng Nie, Junhui Wang, Lujun Huang
Summary: In this study, we developed an optical biosensor based on an all-dielectric metasurface with broken symmetry. The biosensor exhibited excellent performance, thanks to the high-Q quasi-bound states in the continuum (qBICs) and the efficient field confinement. It has potential applications in extreme biochemical sensing, such as COVID-19 detection at ultralow concentrations.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Shasha Liu, Haoran Li, Susu Fang, Weigao Xu, Wenbing Hu, Wei Wang
Summary: The Leidenfrost effect is observed when a liquid droplet is placed on a very hot surface and levitates on its own vapor layer. While the macroscopic Leidenfrost effect is well-studied, the nanoscale version of this phenomenon remains unexplored. In this study, the Leidenfrost effect was observed for single nanosized sulfur particles at room temperature using advanced dark-field optical microscopy. The nanoscale Leidenfrost effect exhibited two distinct features compared to the macroscopic effect.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)