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)
Review
Biochemistry & Molecular Biology
Emma Danelius, Steve Halaby, Wilfred A. van der Donk, Tamir Gonen
Summary: The MicroED method allows high-resolution structural data to be collected from vanishingly small crystals, originally developed for studying proteins, it is also powerful for smaller systems like natural products, with promising impact on the field of small molecule research.
NATURAL PRODUCT REPORTS
(2021)
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
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
Chemistry, Multidisciplinary
Emma Danelius, Nicholas J. Porter, Johan Unge, Frances H. Arnold, Tamir Gonen
Summary: Microcrystal electron diffraction (MicroED) is a promising technique for determining chemical and biological molecular structures. In this study, the first structure of an Aeropyrum pernix protoglobin variant was determined by MicroED using an AlphaFold2 model for phasing. The structure revealed that directed evolution mutations enhance carbene transfer activity by reorienting an alpha helix into a dynamic loop. Additionally, the reactive iron-carbenoid intermediate involved in the engineered ApePgb's new-to-nature activity was trapped, providing insights into the catalytic mechanism.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Chuanxu Ma, Zhongcan Xiao, Peter Bonnesen, Liangbo Liang, Alexander A. Puretzky, Jingsong Huang, Marek Kolmer, Bobby G. Sumpter, Wenchang Lu, Kunlun Hong, Jerzy Bernholc, An-Ping Li
Summary: This study investigates the cyclodehydrogenation reaction mechanism in the on-surface synthesis of graphene nanoribbons using isotopic labeling. A reaction pathway involving conrotatory electrocyclization and a [1,9]-sigmatropic D shift, followed by H/D eliminations, is identified and substantiated by experiments and simulations. The research not only helps clarify the reaction process in GNR synthesis, but also presents a rational strategy for designing precise hydrogen/deuterium isotope labeling patterns in on-surface reactions.
Article
Biochemistry & Molecular Biology
Michael W. Martynowycz, Tamir Gonent
Summary: By soaking ligands into protein microcrystals on TEM grids simultaneously, a high-resolution structure with high occupancy of four ligands was successfully determined, demonstrating efficient uptake of ligands into protein microcrystals. The number of ligands bound and their occupancy was higher compared to larger crystals treated similarly and investigated by X-ray crystallography.
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.
Article
Chemistry, Multidisciplinary
Jong-Duk Park, Yuchen Li, Kyuho Moon, Esther J. Han, Seoung Rak Lee, Mohammad R. Seyedsayamdost
Summary: The study reports eight novel and architecturally unusual secondary metabolites synthesized by the bacterial symbiont Phaeobacter inhibens, which may originate from their algal hosts in a natural setting. Some of these metabolites exhibit potent algaecidal activity, providing important implications for the parasitic phase of algal-bacterial symbiotic interactions.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Tatiana E. Gorelik, Kamaleddin H. M. E. Tehrani, Tim Gruene, Thomas Monecke, Dierk Niessing, Ute Kaiser, Wulf Blankenfeldt, Rolf Mueller
Summary: The crystal structure of natural product argyrin D was determined using 3D electron diffraction data. The newly determined molecular conformation is similar to that of other argyrins, and its exceptional stability is attributed to an extended intramolecular hydrogen-bonding network.
Article
Materials Science, Multidisciplinary
P. Thunstroem, K. Held
Summary: The study shows that SmB6 is a strongly correlated topological insulator, and not a Kondo insulator. Through a symmetry analysis of the pole extended Hamiltonian, it fully captures the effect of the self-energy arising from the strong electron-electron correlation within the Sm 4f orbitals.
Article
Biochemistry & Molecular Biology
Emma Danelius, Khushboo Patel, Brenda Gonzalez, Tamir Gonen
Summary: The cryo-electron microscopy (cryo-EM) method microcrystal electron diffraction (MicroED) was first described in 2013 and has recently gained attention as an emerging technique for drug discovery research. Compared to other structural biology methods, MicroED has advantages in using nanocrystalline material for investigations. This review discusses recent advancements in MicroED and presents important examples of small molecule, peptide, and protein structures that contribute to the current development of MicroED as a crucial tool in drug discovery.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Sho Ito, Fraser J. White, Eiji Okunishi, Yoshitaka Aoyama, Akihito Yamano, Hiroyasu Sato, Joseph D. Ferrara, Michal Jasnowski, Mathias Meyer
Summary: 3D electron diffraction/Micro electron diffraction techniques have expanded the possibilities of crystallography for determining three-dimensional molecular structures from sub-micrometer microcrystals. However, current measurements using advanced electron microscopes require expertise in both electron microscopy and crystallography, making it challenging for researchers. The newly developed electron diffractometer offers an easier path for many researchers to determine crystal structures smaller than 1 micrometer in size.
Article
Chemistry, Multidisciplinary
Bo Wang, Jessica F. Bruhn, Asmerom Weldeab, Timothy S. Wilson, Philip T. McGilvray, Michael Mashore, Qiong Song, Giovanna Scapin, Yiqing Lin
Summary: Microcrystal electron diffraction (MicroED) has been established as a complementary technique to X-ray diffraction for crystal structure elucidation. However, current kinematical refinement of MicroED data lacks the differentiation power to assign the absolute structure solely based on the measured intensities. Here, we report a method for determining the absolute configuration in MicroED by employing salt formation with chiral counterions.
CHEMICAL COMMUNICATIONS
(2022)
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, Physical
Brent L. Nannenga
STRUCTURAL DYNAMICS-US
(2020)
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
Biotechnology & Applied Microbiology
Amar Thaker, Luqmanal Sirajudeen, Chad R. Simmons, Brent L. Nannenga
Summary: The study demonstrates that maltose-binding protein (MBP) can facilitate stable gold nanoparticle synthesis, with the structure of MBP in the presence of gold ions determined by X-ray crystallography. A peptide (AT1) selected and synthesized based on this structure also aids in the synthesis of stable gold nanoparticles, representing a new potential method for peptide selection in nanoparticle synthesis.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
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)
Review
Chemistry, Multidisciplinary
Lisa J. Clark, Guanhong Bu, Brent L. Nannenga, Tamir Gonen
Summary: Microcrystal electron diffraction (MicroED) is a cutting-edge technique used to determine molecular structures, particularly in drug discovery and development. It is valuable for studying protein-ligand interactions and natural product structures, with applications in rational drug design and optimization.
NATURE REVIEWS CHEMISTRY
(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
Chemistry, Physical
Sankarsan Biswas, Sayan Banerjee, Milan A. Shlain, Andrey A. Bardin, Rein Ulijn, Brent L. Nannenga, Andrew M. Rappe, Adam B. Braunschweig
Summary: Tuning solubility and mechanical activation can alter the stereoselectivity of the [2 + 2] photochemical cycloaddition reaction. The solid-state reaction and the reaction in organic solvents yield the anti and syn products, respectively. DFT calculations show that the solid-state reaction proceeds via a covalently bonded excimer, driving anti selectivity. Under photomechanochemical conditions, the noncovalently bound syn conformer experiences greater destabilization, leading to the formation of the syn product. This work demonstrates the viability of photomechanochemistry for the preparation of complex organic scaffolds.
FARADAY DISCUSSIONS
(2023)
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
Chemistry, Multidisciplinary
Xing Han, S. Ephraim Neumann, Brent L. Nannenga, Kaiyu Wang, Kelvin Kam-Yun Li, Saber Mirzaei, Xuan Yao, Chenhui Zhu, Mei-Yan Gao, Yue-Biao Zhang, Yong Cui, Omar M. Yaghi
Summary: This study demonstrates a new strategy to access 2D woven covalent organic frameworks (COFs) by controlling the angle of the linker, resulting in the successful synthesis of a 2D woven pattern based on a chain-link fence structure. The work significantly advances the concept of molecular weaving and its application in the design of complex chemical structures.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(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
Nanoscience & Nanotechnology
Sagnik Sen, Amar Thaker, Luqmanal Sirajudeen, Dewight Williams, Brent L. Nannenga
Summary: This study demonstrates the potential of cryo-EM analysis to reveal structural details of protein-nanoparticle complexes, using GroEL-PtNP and ferritin bound to iron oxide nanoparticles as model samples.
ACS APPLIED BIO MATERIALS
(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)
