Review
Biochemistry & Molecular Biology
Xuelang Mu, Cody Gillman, Chi Nguyen, Tamir Gonen
Summary: The determination of chemical compounds, peptides, and proteins structures plays a crucial role in drug discovery and understanding cellular function. MicroED, with its ability to expand the application of cryo-electron microscopy to samples of various sizes, is an important addition to the existing biophysical toolkit, providing new opportunities for structural biology and drug discovery.
ANNUAL REVIEW OF BIOCHEMISTRY, VOL 90, 2021
(2021)
Article
Multidisciplinary Sciences
Michael W. W. Martynowycz, Anna Shiriaeva, Max T. B. Clabbers, William J. J. Nicolas, Sara J. J. Weaver, Johan Hattne, Tamir Gonen
Summary: In this study, the authors demonstrate a method for milling vitrified biological material and collecting MicroED data for the adenosine receptor. They use an integrated fluorescence light microscope inside a focused ion beam and scanning electron microscope to identify and mill fluorescently labeled GPCR crystals. Plasma ion-beam milling is shown to be a powerful tool for preparing biological lamellae.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Jingjing Zhao, Hongyi Xu, Hugo Lebrette, Marta Carroni, Helena Taberman, Martin Hogbom, Xiaodong Zou
Summary: Preassis is a pressure-assisted method for the preparation of MicroED specimens, capable of handling a wide range of protein crystal suspensions under different buffer conditions, including samples with high viscosity and low crystal concentrations.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Bo Wang, Yiqing Lin
Summary: In this study, we used MicroED analysis with kinematical refinement and the recently developed dynamical refinement approach to determine the absolute configuration of a drug candidate, SMTP-7, which bears five chiral centers. This method demonstrated its utility in unambiguously assigning absolute configuration for molecules that are hard to crystallize, complex, and limited in quantity.
CHEMICAL COMMUNICATIONS
(2022)
Review
Chemistry, Multidisciplinary
Max T. B. Clabbers, Anna Shiriaeva, Tamir Gonen
Summary: This article documents a keynote seminar presented at the IUCr Congress in Prague, 2021, discussing the method of cryo-EM microcrystal electron diffraction and its application in macromolecular electron crystallography. It also provides an outlook on future developments.
Article
Chemistry, Multidisciplinary
Jieye Lin, Johan Unge, Tamir Gonen
Summary: This study uses MicroED to determine the 3D crystal structure of meclizine dihydrochloride and reveals its binding mechanism with the histamine H1 receptor. The research demonstrates the potential of MicroED and molecular docking in unraveling drug structures and protein-drug interactions.
Review
Biochemistry & Molecular Biology
Marc J. Gallenito, Tamir Gonen
Summary: The structural investigation of biological macromolecules is crucial for understanding disease mechanisms. MicroED is an effective technique for solving difficult sample structures, but membrane proteins remain a challenge.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2022)
Article
Clinical Neurology
Marta Montero-Crespo, Marta Dominguez-Alvaro, Lidia Alonso-Nanclares, Javier DeFelipe, Lidia Blazquez-Llorca
Summary: Alzheimer's disease is a common form of dementia characterized by persistent and progressive impairment of cognitive functions. Early-stage cases show normal synaptic morphology, but late-stage cases experience decreased synaptic density and morphological alterations.
Article
Clinical Neurology
Marta Montero-Crespo, Marta Dominguez-Alvaro, Lidia Alonso-Nanclares, Javier DeFelipe, Lidia Blazquez-Llorca
Summary: Alzheimer's disease is a common form of dementia characterized by cognitive impairment, with extracellular protein deposits and abnormal protein accumulation in neurons. Synaptic alterations were found in different stages of the disease, with more severe changes observed in late-stage cases.
Article
Chemistry, Organic
Yoshihiro Watanabe, Shuhei Takahashi, Sho Ito, Toshiyuki Tokiwa, Yoshihiko Noguchi, Haruki Azami, Hiroki Kojima, Mayuka Higo, Sayaka Ban, Kenichiro Nagai, Tomoyasu Hirose, Toshiaki Sunazuka, Takashi Yaguchi, Kenichi Nonaka, Masato Iwatsuki
Summary: A new polyketide compound, hakuhybotrol (1), was discovered, along with six known analogs, showing antifungal activity against Aspergillus spp. and Candida auris, which are causative agents of mycosis. This suggests mycoparasitic fungi as potential sources of antifungal drug lead compounds, and the effectiveness of 3D ED/MicroED for structure elucidation of natural products.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Patrick R. Gleason, Brent L. Nannenga, Jeremy H. Mills
Summary: The study utilized MicroED to analyze the structure of an enzymatic reaction product, identifying an isomer of 24DHPA and establishing its structure model. The MicroED method can provide valuable structural information in a short amount of time.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Cell Biology
Maryna Ivanchenko, Artur A. Indzhykulian, David P. Corey
Summary: Hair cells in the vertebrate inner ear have actin-filled protrusions called stereocilia which mediate mechanosensitivity. Hereditary deafness is often linked to abnormalities in stereocilia bundles, making them essential for understanding genetic hearing loss models. Electron microscopy techniques, such as TEM and SEM, are crucial for studying stereocilia morphology and protein localization.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Michael W. Martynowycz, Tamir Gonen
Summary: The detailed protocol for preparing small molecule samples for microcrystal electron diffraction (MicroED) experiments is described in this article, which has been developed to solve structures of proteins and small molecules using standard electron cryo-microscopy equipment. Recent advancements have shown that this method can be applied to a variety of small molecules and protein structures.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Biochemical Research Methods
Max T. B. Clabbers, Hongyi Xu
Summary: Microcrystal electron diffraction (MicroED) has emerged as a promising method for macromolecular structure determination in structural biology, showing capabilities in revealing atomic structures, solving new protein structures, visualizing ligand-binding interactions, and determining membrane-protein structures. Further development and optimization are needed to make MicroED experiments more accurate and accessible, but it is anticipated to become a robust method complementing existing methods in structural biology.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2021)
Article
Materials Science, Multidisciplinary
Xiangli Zhong, Philip J. Withers, Yi Guo, Xiaorong Zhou, Ivan S. Cole
Summary: Through large area crystallographic analysis and topographic analysis, the crystallographic and topographic characteristics of corrosion on zinc are identified. The surface is dominated by striated domains, resulting from preferential dissolution of non-basal planes. Three corrosion layers, including a highly porous outer layer, a densified intermediate layer, and an attacked layer, are found.
CORROSION ENGINEERING SCIENCE AND TECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Johan Hattne, Dan Shi, Calina Glynn, Chih-Te Zee, Marcus Gallagher-Jones, Michael W. Martynowycz, Jose A. Rodriguez, Tamir Gonen
Article
Multidisciplinary Sciences
Jinming Ma, Hsiang-Ting Lei, Francis E. Reyes, Silvia Sanchez-Martinez, Maen F. Sarhan, Johan Hattne, Tamir Gonen
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Biochemistry & Molecular Biology
Michael W. Martynowycz, Wei Zhao, Johan Hattne, Grant J. Jensen, Tamir Gonen
Article
Microscopy
M. Jason de la Cruz, Michael W. Martynowycz, Johan Hattne, Tamir Gonen
Article
Chemistry, Multidisciplinary
Johan Hattne, Michael W. Martynowycz, Pawel A. Penczek, Tamir Gonen
Article
Biochemistry & Molecular Biology
Michael W. Martynowycz, Wei Zhao, Johan Hattne, Grant J. Jensen, Tamir Gonen
Article
Biochemistry & Molecular Biology
Michael W. Martynowycz, Johan Hattne, Tamir Gonen
Article
Biochemistry & Molecular Biology
Hsiang-Ting Lei, Xuelang Mu, Johan Hattne, Tamir Gonen
Summary: mTORC1 functions as a central hub for regulating metabolism and cellular responses, while SLC38A9 acts as a lysosomal amino acid transporter that senses arginine levels to activate mTORC1. The crystal structure of SLC38A9 revealed a significant conformational change in the N-terminal domain, suggesting a mechanism for mTORC1 activation involving N-plug insertion and Rag GTPase binding regulated by luminal arginine levels. This study provides important insights into how nutrient sensing by SLC38A9 activates the mTORC1 pathways in response to dietary amino acids.
Article
Multidisciplinary Sciences
Michael W. Martynowycz, Max T. B. Clabbers, Johan Unge, Johan Hattne, Tamir Gonen
Summary: The study analyzed the relationship between sample thickness and data quality using MicroED, revealing that structures can be reliably determined from crystalline lamellae up to twice the inelastic mean free path. Lower resolution diffraction was observed at three times the mean free path for all three accelerating voltages, but insufficient data quality prevented structure determination. No coherent diffraction was observed from lamellae thicker than four times the calculated inelastic mean free path, setting an ideal specimen thickness benchmark for cryo-EM methods.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemical Research Methods
Michael W. Martynowycz, Max T. B. Clabbers, Johan Hattne, Tamir Gonen
Summary: This article reports on the sub- and near-atomic structures of triclinic lysozyme and serine protease proteinase K, respectively, and demonstrates the successful application of ab initio phasing using electron counted MicroED data to solve macromolecular structures.
Article
Biochemistry & Molecular Biology
Max T. B. Clabbers, Michael W. Martynowycz, Johan Hattne, Brent L. Nannenga, Tamir Gonen
Summary: Microcrystal electron diffraction (MicroED) is a technique that uses electron cryo-microscopy (cryo-EM) to collect diffraction data from small crystals. In this study, the researchers used direct electron detectors, K2 and K3, to successfully determine macromolecular structures between 1.2 ? and 2.8 ? resolution. They also found that the cameras were not damaged even without using a beam stop. This study highlights the potential of using readily available cryo-EM facilities for MicroED experiments.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Michael W. W. Martynowycz, Anna Shiriaeva, Max T. B. Clabbers, William J. J. Nicolas, Sara J. J. Weaver, Johan Hattne, Tamir Gonen
Summary: In this study, the authors demonstrate a method for milling vitrified biological material and collecting MicroED data for the adenosine receptor. They use an integrated fluorescence light microscope inside a focused ion beam and scanning electron microscope to identify and mill fluorescently labeled GPCR crystals. Plasma ion-beam milling is shown to be a powerful tool for preparing biological lamellae.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Max T. B. Clabbers, Michael W. Martynowycz, Johan Hattne, Tamir Gonen
Summary: Microcrystal electron diffraction (MicroED) is a powerful technique for protein structure determination. Recent studies have shown that with high-resolution MicroED data, it is possible to accurately identify over a third of hydrogen atom positions and visualize hydrogen bonding interactions and the charged states of residues.
JOURNAL OF STRUCTURAL BIOLOGY-X
(2022)
Article
Multidisciplinary Sciences
Michael W. Martynowycz, Anna Shiriaeva, Xuanrui Ge, Johan Hattne, Brent L. Nannenga, Vadim Cherezov, Tamir Gonen
Summary: This study demonstrates how the structure of a human A2A adenosine receptor can be determined using MicroED, and lays the groundwork for future structural studies of lipid-embedded membrane proteins using single microcrystals.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
