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1. Advances and applications of microcrystal electron diffraction (MicroED)

   https://doi.org/10.1016/j.sbi.2023.102741  

   Haymaker, Alison; Nannenga, Brent L. (February 2024, Current Opinion in Structural Biology)

   Microcrystal electron diffraction, commonly referred to as MicroED, has become a powerful tool for high-resolution structure determination. The method makes use of cryogenic transmission electron microscopes to collect electron diffraction data from crystals that are several orders of magnitude smaller than those used by other conventional diffraction techniques. MicroED has been used on a variety of samples including soluble proteins, membrane proteins, small organic molecules, and materials. Here we will review the MicroED method and highlight recent advancements to the methodology, as well as describe applications of MicroED within the fields of structural biology and chemical crystallography. 

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2. Achieving sub-0.5-angstrom–resolution ptychography in an uncorrected electron microscope

   https://doi.org/10.1126/science.adl2029  

   Nguyen, Kayla X.; Jiang, Yi; Lee, Chia-Hao; Kharel, Priti; Zhang, Yue; van der Zande, Arend M.; Huang, Pinshane Y. (February 2024, Science)

   Subangstrom resolution has long been limited to aberration-corrected electron microscopy, where it is a powerful tool for understanding the atomic structure and properties of matter. Here, we demonstrate electron ptychography in an uncorrected scanning transmission electron microscope (STEM) with deep subangstrom spatial resolution down to 0.44 angstroms, exceeding the conventional resolution of aberration-corrected tools and rivaling their highest ptychographic resolutions​. Our approach, which we demonstrate on twisted two-dimensional materials in a widely available commercial microscope, far surpasses prior ptychographic resolutions (1 to 5 angstroms) of uncorrected STEMs. We further show how geometric aberrations can create optimized, structured beams for dose-efficient electron ptychography. Our results demonstrate that expensive aberration correctors are no longer required for deep subangstrom resolution. 

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3. Cu2+-based distance measurements by pulsed EPR provide distance constraints for DNA backbone conformations in solution

   https://doi.org/10.1093/nar/gkaa133  

   Ghosh, Shreya; Lawless, Matthew J; Brubaker, Hanna J; Singewald, Kevin; Kurpiewski, Michael R; Jen-Jacobson, Linda; Saxena, Sunil (February 2020, Nucleic Acids Research)

   Abstract Electron paramagnetic resonance (EPR) has become an important tool to probe conformational changes in nucleic acids. An array of EPR labels for nucleic acids are available, but they often come at the cost of long tethers, are dependent on the presence of a particular nucleotide or can be placed only at the termini. Site directed incorporation of Cu2+-chelated to a ligand, 2,2′dipicolylamine (DPA) is potentially an attractive strategy for site-specific, nucleotide independent Cu2+-labelling in DNA. To fully understand the potential of this label, we undertook a systematic and detailed analysis of the Cu2+-DPA motif using EPR and molecular dynamics (MD) simulations. We used continuous wave EPR experiments to characterize Cu2+ binding to DPA as well as optimize Cu2+ loading conditions. We performed double electron-electron resonance (DEER) experiments at two frequencies to elucidate orientational selectivity effects. Furthermore, comparison of DEER and MD simulated distance distributions reveal a remarkable agreement in the most probable distances. The results illustrate the efficacy of the Cu2+-DPA in reporting on DNA backbone conformations for sufficiently long base pair separations. This labelling strategy can serve as an important tool for probing conformational changes in DNA upon interaction with other macromolecules. 

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4. 3D Visualization of Proteins within Metal–Organic Frameworks via Ferritin‐Enabled Electron Microscopy

   https://doi.org/10.1002/adfm.202312972  

   Dhaoui, Rakia; Cazarez, Saira L; Xing, Li; Baghdadi, Elmira; Mulvey, Justin T; Idris, Nehal S; Hurst, Paul J; Vena, M Paula; Palma, Giuseppe Di; Patterson, Joseph P (March 2024, Advanced Functional Materials)

   Abstract Electron tomography holds great promise as a tool for investigating the 3D morphologies and internal structures of metal‐organic framework‐based protein biocomposites (protein@MOFs). Understanding the 3D spatial arrangement of proteins within protein@MOFs is paramount for developing synthetic methods to control their spatial localization and distribution patterns within the biocomposite crystals. In this study, the naturally occurring iron oxide mineral core of the protein horse spleen ferritin (Fn) is leveraged as a contrast agent to directly observe individual proteins once encapsulated into MOFs by electron microscopy techniques. This methodology couples scanning electron microscopy, transmission electron microscopy, and electron tomography to garner detailed 2D and 3D structural interpretations of where proteins spatially lie in Fn@MOF crystals, addressing the significant gaps in understanding how synthetic conditions relate to overall protein spatial localization and aggregation. These findings collectively reveal that adjusting the ligand‐to‐metal ratios, protein concentration, and the use of denaturing agents alters how proteins are arranged, localized, and aggregated within MOF crystals. 

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5. New tool for kinematic regime estimation in semi-inclusive deep-inelastic scattering

   https://doi.org/10.1007/JHEP04(2022)084  

   Boglione, M.; Diefenthaler, M.; Dolan, S.; Gamberg, L.; Melnitchouk, W.; Pitonyak, D.; Prokudin, A.; Sato, N.; Scalyer, Z. (April 2022, Journal of High Energy Physics)

   A bstract We introduce a new phenomenological tool based on momentum region indicators to guide the analysis and interpretation of semi-inclusive deep-inelastic scattering measurements. The new tool, referred to as “affinity”, is devised to help visualize and quantify the proximity of any experimental kinematic bin to a particular hadron production region, such as that associated with transverse momentum dependent factorization. We apply the affinity estimator to existing HERMES and COMPASS data and expected data from Jefferson Lab and the future Electron-Ion Collider. We also provide an interactive notebook based on Machine Learning for fast evaluation of affinity. 

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