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1. DNP-assisted solid-state NMR enables detection of proteins at nanomolar concentrations in fully protonated cellular milieu

   https://doi.org/10.1007/s10858-024-00436-9  

   Costello, Whitney N; Xiao, Yiling; Mentink-Vigier, Frederic; Kragelj, Jaka; Frederick, Kendra K (June 2024, Journal of Biomolecular NMR)

   With the sensitivity enhancements conferred by dynamic nuclear polarization (DNP), magic angle spinning (MAS) solid state NMR spectroscopy experiments can attain the necessary sensitivity to detect very low concentrations of proteins. This potentially enables structural investigations of proteins at their endogenous levels in their biological contexts where their native stoichiometries with potential interactors is maintained. Yet, even with DNP, experiments are still sensitivity limited. Moreover, when an isotopically-enriched target protein is present at physiological levels, which typically range from low micromolar to nanomolar concentrations, the isotope content from the natural abundance isotopes in the cellular milieu can outnumber the isotope content of the target protein. Using isotopically enriched yeast prion protein, Sup35NM, diluted into natural abundance yeast lysates, we optimized sample composition. We found that modest cryoprotectant concentrations and fully protonated environments support efficient DNP. We experimentally validated theoretical calculations of the limit of specificity for an isotopically enriched protein in natural abundance cellular milieu. We establish that, using pulse sequences that are selective for adjacent NMR-active nuclei, proteins can be specifically detected in cellular milieu at concentrations in the hundreds of nanomolar. Finally, we find that maintaining native stoichiometries of the protein of interest to the components of the cellular environment may be important for proteins that make specific interactions with cellular constituents. 

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2. Structural Diversity and Distribution of Nuclear Matrix Constituent Protein Class Nuclear Lamina Proteins in Streptophytic Algae

   https://doi.org/10.1093/gbe/evae244  

   Kosztyo, Brendan S; Richards, Eric J (November 2024, Genome Biology and Evolution)

   Archibald, John (Ed.)

   Abstract Nuclear matrix constituent proteins in plants function like animal lamins, providing the structural foundation of the nuclear lamina and regulating nuclear organization and morphology. Although they are well characterized in angiosperms, the presence and structure of nuclear matrix constituent proteins in more distantly related species, such as streptophytic algae, are relatively unknown. The rapid evolution of nuclear matrix constituent proteins throughout the plant lineage has caused a divergence in protein sequence that makes similarity-based searches less effective. Structural features are more likely to be conserved compared to primary amino acid sequence; therefore, we developed a filtration protocol to search for diverged nuclear matrix constituent proteins based on four physical characteristics: intrinsically disordered content, isoelectric point, number of amino acids, and the presence of a central coiled-coil domain. By setting parameters to recognize the properties of bona fide nuclear matrix constituent protein proteins in angiosperms, we filtered eight complete proteomes from streptophytic algae species and identified strong nuclear matrix constituent protein candidates in six taxa in the Classes Zygnematophyceae, Charophyceae, and Klebsormidiophyceae. Through analysis of these proteins, we observed structural variance in domain size between nuclear matrix constituent proteins in algae and land plants, as well as a single block of amino acid conservation. Our analysis indicates that nuclear matrix constituent proteins are absent in the Mesostigmatophyceae. The presence versus absence of nuclear matrix constituent protein proteins does not correlate with the distribution of different forms of mitosis (e.g. closed/semi-closed/open) but does correspond to the transition from unicellularity to multicellularity in the streptophytic algae, suggesting that a nuclear matrix constituent protein-based nucleoskeleton plays important roles in supporting cell-to-cell interactions. 

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3. Charting the solid‐state NMR signals of polysaccharides: A database‐driven roadmap

   https://doi.org/10.1002/mrc.5397  

   Zhao, Wancheng; Debnath, Debkumar; Gautam, Isha; Fernando, Liyanage_D; Wang, Tuo (September 2023, Magnetic Resonance in Chemistry)

   Abstract Solid‐state nuclear magnetic resonance (ssNMR) measurements of intact cell walls and cellular samples often generate spectra that are difficult to interpret due to the presence of many coexisting glycans and the structural polymorphism observed in native conditions. To overcome this analytical challenge, we present a statistical approach for analyzing carbohydrate signals using high‐resolution ssNMR data indexed in a carbohydrate database. We generate simulated spectra to demonstrate the chemical shift dispersion and compare this with experimental data to facilitate the identification of important fungal and plant polysaccharides, such as chitin and glucans in fungi and cellulose, hemicellulose, and pectic polymers in plants. We also demonstrate that chemically distinct carbohydrates from different organisms may produce almost identical signals, highlighting the need for high‐resolution spectra and validation of resonance assignments. Our study provides a means to differentiate the characteristic signals of major carbohydrates and allows us to summarize currently undetected polysaccharides in plants and fungi, which may inspire future investigations. 

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4. Nuclear Entanglement: New Insights Into the Role of Cytoskeleton and Nucleoskeleton in Plant Nuclear Function

   https://doi.org/10.1002/cm.22048  

   Groves, Norman R; Amstutz, Katelyn; Schumacher, Lily A; Meier, Iris (June 2025, Cytoskeleton)

   ABSTRACT Of the three types of cytoskeleton known in animals—actin, microtubules, and intermediate filaments—only actin and microtubules exist in plants. Both play important roles in cellular shaping, organelle movement, organization of the endomembrane system, and cell signaling. An emerging, but often overlooked role of the plant cytoskeleton is its dynamic and mutually influential interaction with the nucleus. Here, we summarize recent advances in understanding the role of the cytoskeleton in plant nuclear movement in different biological contexts, a role for nuclear envelope‐associated proteins in reorganizing the actin and microtubule cytoskeleton, and the molecular nature of the nucleus‐cytoskeleton interface and specific proteins contributing to it. In animals, the nucleoskeleton consists of the nuclear lamina, an intermediate‐filament meshwork underlying the nuclear envelope. Plants have evolved an equivalent of this structure, built by different types of proteins. Here, we highlight recent advances in understanding its filamentous organization, newly discovered protein interactions connecting it to nuclear pores, and exciting new evidence that—just like the animal lamina—the plant lamina is involved in chromatin reorganization and epigenetic changes. Together, these new developments create new opportunities toward a deeper understanding of this important regulatory connection between the cytoskeleton and the cell's largest organelle. 

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5. Mass spectrometry-based technologies for probing the 3D world of plant proteins

   https://doi.org/10.1093/plphys/kiac039  

   Blackburn, Matthew R; Minkoff, Benjamin B; Sussman, Michael R (February 2022, Plant Physiology)

   Abstract Over the past two decades, mass spectrometric (MS)-based proteomics technologies have facilitated the study of signaling pathways throughout biology. Nowhere is this needed more than in plants, where an evolutionary history of genome duplications has resulted in large gene families involved in posttranslational modifications and regulatory pathways. For example, at least 5% of the Arabidopsis thaliana genome (ca. 1,200 genes) encodes protein kinases and protein phosphatases that regulate nearly all aspects of plant growth and development. MS-based technologies that quantify covalent changes in the side-chain of amino acids are critically important, but they only address one piece of the puzzle. A more crucially important mechanistic question is how noncovalent interactions—which are more difficult to study—dynamically regulate the proteome’s 3D structure. The advent of improvements in protein 3D technologies such as cryo-electron microscopy, nuclear magnetic resonance, and X-ray crystallography has allowed considerable progress to be made at this level, but these methods are typically limited to analyzing proteins, which can be expressed and purified in milligram quantities. Newly emerging MS-based technologies have recently been developed for studying the 3D structure of proteins. Importantly, these methods do not require protein samples to be purified and require smaller amounts of sample, opening the wider proteome for structural analysis in complex mixtures, crude lysates, and even in intact cells. These MS-based methods include covalent labeling, crosslinking, thermal proteome profiling, and limited proteolysis, all of which can be leveraged by established MS workflows, as well as newly emerging methods capable of analyzing intact macromolecules and the complexes they form. In this review, we discuss these recent innovations in MS-based “structural” proteomics to provide readers with an understanding of the opportunities they offer and the remaining challenges for understanding the molecular underpinnings of plant structure and function. 

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