Article
Computer Science, Artificial Intelligence
Tamir Bendory, Nicolas Boumal, William Leeb, Eitan Levin, Amit Singer
Summary: Single-particle cryo-electron microscopy (cryo-EM), together with X-ray crystallography and NMR spectroscopy, is a high-resolution structural method for studying biological macromolecules. However, the standard techniques of cryo-EM face challenges in detecting small molecules due to high noise levels. This paper proposes a new approach that directly reconstructs the structure from the micrographs without intermediate detection, aiming to make cryo-EM more applicable to small molecules. The authors introduce an autocorrelation analysis technique that allows for online processing and discuss future challenges in implementing this approach.
SIAM JOURNAL ON IMAGING SCIENCES
(2023)
Article
Neurosciences
Vladan Lucic
Summary: This article reviews the importance of electron microscopy in the study of neuronal synapse structures and discusses the use of image processing software methods. Special attention is given to the application of recent cryo-electron microscopy and tomography methods in molecular level analysis.
CURRENT OPINION IN NEUROBIOLOGY
(2022)
Article
Chemistry, Physical
Yohei Suzuki, Fumiaki Makino, Tomoko Miyata, Hideaki Tanaka, Keiichi Namba, Kenji Kano, Keisei Sowa, Yuki Kitazumi, Osamu Shirai
Summary: In this study, the Flavin adenine dinucleotide-dependent d-fructose dehydrogenase (FDH) from Gluconobacter japonicus NBRC3260 was investigated from the perspectives of structural biology, bioelectrochemistry, and protein engineering. The researchers discovered the electron transfer pathway during the catalytic oxidation process and identified the crucial amino acid residues and electrode-active site. Site-directed mutagenesis experiments revealed the impact of certain amino acids on the DET-type activity of FDH.
Article
Chemistry, Physical
Yohei Suzuki, Fumiaki Makino, Tomoko Miyata, Hideaki Tanaka, Keiichi Namba, Kenji Kano, Keisei Sowa, Yuki Kitazumi, Osamu Shirai
Summary: In this study, the flavin adenine dinucleotide-dependent d-fructose dehydrogenase (FDH) from Gluconobacter japonicus NBRC3260 was investigated using structural biology, bioelectrochemistry, and protein engineering. The FDH showed intense direct electron transfer (DET)-type catalytic activity, making it a promising enzyme for biosensors. Structural analysis and mutagenesis experiments revealed the electron transfer pathway and the key residues involved in the DET-type activity of FDH.
Review
Biochemistry & Molecular Biology
Miguel Ricardo Leung, Tzviya Zeev-Ben-Mordehai
Summary: The different oligomeric forms of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) have defined cellular and subcellular distributions. While crystal structures of AChE and BChE have been available for many years, structures of the physiologically relevant cholinesterase tetramer were only recently solved by cryo-electron microscopy (cryo-EM). The next frontier in cholinesterase structural biology is to image membrane-anchored ChE oligomers directly in their native environment - the cell.
JOURNAL OF NEUROCHEMISTRY
(2021)
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
Biochemistry & Molecular Biology
Jie E. Yang, Matthew R. Larson, Bryan S. Sibert, Samantha Shrum, Elizabeth R. Wright
Summary: Cryo-correlative light and electron microscopy (CLEM) combines the advantages of fluorescence light microscopy (FLM) and cryo-electron microscopy (cryo-EM) for high-resolution ultrastructure analysis of biological samples. Challenges lie in implementing correlation workflows and software tools on different microscope platforms to support automated cryo-EM data acquisition. CorRelator is an open-source desktop application that bridges between cryo-FLM and real-time cryo-EM/ET automated data collection, providing flexible and high accuracy correlation for cryo-CLEM workflows.
JOURNAL OF STRUCTURAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Kayo Nozawa, Yoshimasa Takizawa, Leonidas Pierrakeas, Chizuru Sogawa-Fujiwara, Kazumi Saikusa, Satoko Akashi, Ed Luk, Hitoshi Kurumizaka
Summary: The canonical nucleosome is the major packaging unit of eukaryotic chromatin, and the H3-H4 octasome is a nucleosome-like particle with alternative histone stoichiometry. The structure of the H3-H4 octasome is flexible.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Lunda Shen, Zhaoming Su, Kailu Yang, Cheng Wu, Thomas Becker, Deborah Bell-Pedersen, Junjie Zhang, Matthew S. Sachs
Summary: The study elucidated the mechanism of action of CHX in inhibiting protein synthesis by arresting the ribosome in the classical PRE translocation state, without interfering with A-site reactivity.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Xian Zhou, Chen-Jun Guo, Chia-Chun Chang, Jiale Zhong, Huan-Huan Hu, Guang-Ming Lu, Ji-Long Liu
Summary: CTPS activity is regulated by the binding of nucleotides and glutamine, with GTP directly blocking ammonia leakage and stabilizing the ammonia tunnel. Cryo-electron microscopy revealed the binding modes of substrates and analogs in Drosophila CTPS, providing insights into allosteric regulation and CTP synthesis mechanisms.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Ishika Kumar, Anju Paudyal, Anna Kadkova, Michelle Stewart, Jakob Balslev Sorensen, Julika Radecke
Summary: This article describes a straightforward method to establish a mature neuronal network on electron microscopy grids and visualize the formation of synaptic contacts.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Dominik Hrebik, Tibor Fuzik, Maria Gondova, Lenka Smerdova, Athanassios Adamopoulos, Ondrej Sedo, Zbynek Zdrahal, Pavel Plevka
Summary: This study elucidated the structure of the rhinovirus 14 complex with ICAM-1, showing how this complex is crucial for virus activation and genome release. The binding of ICAM-1 induces conformational changes in the capsid of rhinovirus 14, priming it for activation and genome release under acidic pH conditions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Editorial Material
Biochemistry & Molecular Biology
Yang Zhang, Hao Jiang, Taoyu Ye, Mario Juhas
Summary: Despite the significant interest in deep learning in microbiology, its full potential is yet to be realized. Deep-learning-based systems are believed to play a crucial role in monitoring and investigating microorganisms in the future.
TRENDS IN MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Amanda A. Riccio, Jonathan Bouvette, Matthew J. Longley, Juno M. Krahn, Mario J. Borgnia, William C. Copeland
Summary: The mitochondrial replisome is crucial for replicating mtDNA, with Twinkle helicase being a key protein component. Studying SF4 helicases helps understand common themes like self-assembly, ATP-dependent translocation, and formation of protein complexes. The methods described can support future high-resolution studies of Twinkle helicase or other SF4 helicases.
Article
Biochemistry & Molecular Biology
Linhua Tai, Guoliang Yin, Fei Sun, Yun Zhu
Summary: The nuclear pore complex (NPC) is a large protein assembly that penetrates the nuclear membrane. Recent breakthroughs in cryo-EM and artificial intelligence-based modeling have allowed for improved understanding of the complex structure of the NPC. This review article summarizes the history and latest advancements in studying the architecture of the NPC, as well as future directions for research.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Neurosciences
Michael C. Regan, Timothy Grant, Miranda J. McDaniel, Erkan Karakas, Jing Zhang, Stephen F. Traynelis, Nikolaus Grigorieff, Hiro Furukawa
Article
Biochemistry & Molecular Biology
Alberto Bartesaghi, Cecilia Aguerrebere, Veronica Falconieri, Soojay Banerjee, Lesley A. Earl, Xing Zhu, Nikolaus Grigorieff, Jacqueline L. S. Milne, Guillermo Sapiro, Xiongwu Wu, Sriram Subramaniam
Article
Multidisciplinary Sciences
William Close, Matthias Neumann, Andreas Schmidt, Manuel Hora, Karthikeyan Annamalai, Matthias Schmidt, Bernd Reif, Volker Schmidt, Nikolaus Grigorieff, Marcus Faendrich
NATURE COMMUNICATIONS
(2018)
Article
Multidisciplinary Sciences
Annapurna Vemu, Ewa Szczesna, Elena A. Zehr, Jeffrey O. Spector, Nikolaus Grigorieff, Alexandra M. Deaconescu, Antonina Roll-Mecak
Article
Microscopy
Cheng Zhang, William Cantara, Youngmin Jeon, Karin Musier-Forsyth, Nikolaus Grigorieff, Dmitry Lyumkis
Article
Multidisciplinary Sciences
Falk Liberta, Sarah Loerch, Matthies Rennegarbege, Angelika Schierhorn, Per Westermark, Gunilla T. Westermark, Bouke P. C. Hazenberg, Nikolaus Grigorieff, Marcus Faendrich, Matthias Schmidt
NATURE COMMUNICATIONS
(2019)
Article
Biochemistry & Molecular Biology
Simon Jenni, Eric N. Salgado, Tobias Herrmann, Zongli Li, Timothy Grant, Nikolaus Grigorieff, Stefano Trapani, Leandro F. Estrozi, Stephen C. Harrison
JOURNAL OF MOLECULAR BIOLOGY
(2019)
Article
Multidisciplinary Sciences
James Jung, Timothy Grant, Dennis R. Thomas, Chris W. Diehnelt, Nikolaus Grigorieff, Leemor Joshua-Tor
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Biochemical Research Methods
Kangkang Song, Zhiguo Shang, Xiaofeng Fu, Xiaochu Lou, Nikolaus Grigorieff, Daniela Nicastro
Article
Biochemistry & Molecular Biology
Johanna L. Syrjanen, Kevin Michalski, Tsung-Han Chou, Timothy Grant, Shanlin Rao, Noriko Simorowski, Stephen J. Tucker, Nikolaus Grigorieff, Hiro Furukawa
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2020)
Correction
Biochemistry & Molecular Biology
Johanna L. Syrjanen, Kevin Michalski, Tsung-Han Chou, Timothy Grant, Shanlin Rao, Noriko Simorowski, Stephen J. Tucker, Nikolaus Grigorieff, Hiro Furukawa
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2020)
Article
Cell Biology
Simon Jenni, Louis-Marie Bloyet, Ruben Diaz-Avalos, Bo Liang, Sean P. J. Whelan, Nikolaus Grigorieff, Stephen C. Harrison
Article
Biology
Chen Bao, Sarah Loerch, Clarence Ling, Andrei A. Korostelev, Nikolaus Grigorieff, Dmitri N. Ermolenko
Article
Biology
Bronwyn A. Lucas, Benjamin A. Himes, Liang Xue, Timothy Grant, Julia Mahamid, Nikolaus Grigorieff
Summary: The study emphasizes the importance of understanding molecular mechanisms within the broader context of the cell and introduces a 2D template matching method to address technical limitations. By implementing GPU acceleration in the cisTEM software, the approach becomes more scalable and accessible. Experimental results demonstrate that 2D template matching is a versatile tool for in situ visual proteomics and in situ structure determination, showcasing its precision and sensitivity in identifying molecular complexes.
Article
Chemistry, Multidisciplinary
Benjamin A. Himes, Nikolaus Grigorieff
Summary: Image simulation is crucial in the development of high-resolution electron microscopy, but challenges remain in matching contrast, modeling signal and noise accurately, and accommodating spatially variable scaling. The 'frozen plasmon' method introduces an approach to simulate spatially variable inelastic scattering processes in cryo-EM specimens, allowing for accurate amplitude contrast and incorporating radiation damage in the simulation. By quantifying these improvements using the matched filter concept, the method shows potential for accurately simulating biological specimen images.
