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Open access publications by faculty, postdocs, and graduate students in the Department of Chemistry and Biochemistry.

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    Coupling Novel Probes with Molecular Localization Microscopy Reveals Cell Wall Homeostatic Mechanisms in Staphylococcus aureus
    (ACS Chemical Biology, 2022-11-22) Lund, Victoria A.; Gangotra, Haneesh; Zhao, Zhen; Sutton, Joshua A. F.; Wacnik, Katarzyna; DeMeester, Kristen; Liang, Hai; Santiago, Cintia; Grimes, Catherine Leimkuhler; Jones, Simon; Foster, Simon J.
    Bacterial cell wall peptidoglycan is essential for viability, and its synthesis is targeted by antibiotics, including penicillin. To determine how peptidoglycan homeostasis controls cell architecture, growth, and division, we have developed novel labeling approaches. These are compatible with super-resolution fluorescence microscopy to examine peptidoglycan synthesis, hydrolysis, and the localization of the enzymes required for its biosynthesis (penicillin binding proteins (PBPs)). Synthesis of a cephalosporin-based fluorescent probe revealed a pattern of PBPs at the septum during division, supporting a model of dispersed peptidoglycan synthesis. Metabolic and hydroxylamine-based probes respectively enabled the synthesis of glycan strands and associated reducing termini of the peptidoglycan to be mapped. Foci and arcs of reducing termini appear as a result of both synthesis of glycan strands and glucosaminidase activity of the major peptidoglycan hydrolase, SagB. Our studies provide molecular level details of how essential peptidoglycan dynamics are controlled during growth and division.
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    Matrix Adhesiveness Regulates Myofibroblast Differentiation from Vocal Fold Fibroblasts in a Bio-orthogonally Cross-linked Hydrogel
    (ACS Applied Materials and Interfaces, 2022-11-23) Song, Jiyeon; Gao, Hanyuan; Zhang, He; George, Olivia J.; Hillman, Ashlyn S.; Fox, Joseph M.; Jia, Xinqiao
    Repeated mechanical and chemical insults cause an irreversible alteration of extracellular matrix (ECM) composition and properties, giving rise to vocal fold scarring that is refractory to treatment. Although it is well known that fibroblast activation to myofibroblast is the key to the development of the pathology, the lack of a physiologically relevant in vitro model of vocal folds impedes mechanistic investigations on how ECM cues promote myofibroblast differentiation. Herein, we describe a bio-orthogonally cross-linked hydrogel platform that recapitulates the alteration of matrix adhesiveness due to enhanced fibronectin deposition when vocal fold wound healing is initiated. The synthetic ECM (sECM) was established via the cycloaddition reaction of tetrazine (Tz) with slow (norbornene, Nb)- and fast (trans-cyclooctene, TCO)-reacting dienophiles. The relatively slow Tz–Nb ligation allowed the establishment of the covalent hydrogel network for 3D cell encapsulation, while the rapid and efficient Tz–TCO reaction enabled precise conjugation of the cell-adhesive RGDSP peptide in the hydrogel network. To mimic the dynamic changes of ECM composition during wound healing, RGDSP was conjugated to cell-laden hydrogel constructs via a diffusion-controlled bioorthognal ligation method 3 days post encapsulation. At a low RGDSP concentration (0.2 mM), fibroblasts residing in the hydrogel remained quiescent when maintained in transforming growth factor beta 1 (TGF-β1)-conditioned media. However, at a high concentration (2 mM), RGDSP potentiated TGF-β1-induced myofibroblast differentiation, as evidenced by the formation of an actin cytoskeleton network, including F-actin and alpha-smooth muscle actin. The RGDSP-driven fibroblast activation to myofibroblast was accompanied with an increase in the expression of wound healing-related genes, the secretion of profibrotic cytokines, and matrix contraction required for tissue remodeling. This work represents the first step toward the establishment of a 3D hydrogel-based cellular model for studying myofibroblast differentiation in a defined niche associated with vocal fold scarring.
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    Enhanced thermoelectric performance in the zintl antimonides (Ca,RE)9Cd4Sb9 (RE = rare-earth metal). Synergy between increased structural complexity and drive towards optimized chemical bonding
    (Materials Today Advances, 2022-10-27) Ogunbunmi, M. O.; Baranets, S.; Bobev, S.
    The interplay of structural complexity, high carrier mobility, and high density of states effective mass can play a pivotal role in achieving enhanced thermoelectric (TE) performance in candidate materials. In this regard, the Zintl phases represent a class of compounds that are susceptible to harboring these key ingredients. This, in addition to their amenability to various forms of chemical substitution mechanisms makes them a good choice of systems to explore systematically. Here we demonstrate the role-play of these ingredients in achieving excellent TE properties on single-crystals of Ca9–xREyCd4+δSb9 (RE = Ce, Pr, Nd, Sm, Gd, Tb; x ≈ 0.5–0.8, y ≈ 0.5–0.7, δ ≈ 0.25). These phases represent a new addition to the “9–4–9” family with intricate chemical bonding arising from both a purposely introduced disorder on Ca sites and the inherent presence of interstitial Cd positions. Many of the newly synthesized and characterized phases show moderate values of the Seebeck coefficient, lying in the range of 71–116 μV/K at 600 K and evolving as degenerate semiconductors. Simultaneously, the electrical resistivity ρ(T) of the measured samples can be as low as 0.18 mΩ cm at this temperature. As a result, the observed TE power factors in the Ce-, Nd-, and Sm-samples are in the range 6–46 μW/cm.K2. For Ca9–xCexCd4+δSb9, the estimated thermoelectric quality factor B > 0.4 at 300 K, which corresponds to a figure of merit zT ≥ 1. Calculations based on the single parabolic band (SPB) model show that the optimum region for thermoelectric performance requires carrier concentration n = 2–6 × 1019 cm−3 thus providing for an open window to further tune the TE properties.
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    Recent Developments with Icetexane Natural Products
    (Chemistry and Biodiversity, 2022-10-10) Naeini, Ali Amiri; Ziegelmeier, Alexandre A.; Chain, William J.
    Icetexane diterpenoids are a diverse family of natural products sourced from several species of terrestrial plants. Icetexanes exhibit a broad array of biological activities and together with their complex 6-7-6 tricyclic scaffolds, they have piqued the interest of synthetic organic chemists, natural products chemists, and biological investigators over the past four decades and were reviewed 13 years ago. This review summarizes icetexane natural products isolated since 2009, provides an overview of new synthetic approaches to the icetexane problem, and proposes an additional classification of icetexanes based on novel structures that are unlike previously isolated materials.
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    Proline C–H bonds as loci for proline assembly via C–H/O interactions
    (ChemBioChem, 2022-09-21) Daniecki, Noah J.; Bhatt, Megh R.; Yap, Glenn P. A.; Zondlo, Neal Joseph
    Proline residues within proteins lack a traditional hydrogen bond donor. However, the hydrogens of proline are all sterically accessible, with polarized C–H bonds that can be sites for molecular recognition. C–H/O interactions, between proline C–H bonds and oxygen lone pairs, have been previously identified as modes of recognition in proteins. A series of proline derivatives was synthesized, including 4R-hydroxyproline nitrobenzoate methyl ester, acylated on the proline nitrogen with bromoacetyl and glycolyl groups, and Boc-4S-(4-iodophenyl)hydroxyproline methyl amide. All three derivatives exhibited multiple close intermolecular C–H/O interactions in the crystallographic state, with H•••O distances as close as 2.3 Å. These observed distances are well below the 2.72 Å sum of the van der Waals radii of H and O. We further analyzed the role of C–H/O interactions in all previously crystallized derivatives of these amino acids, and found that all 26 structures exhibited close intermolecular C–H/O interactions. Finally, we analyzed all proline residues in the Cambridge Structural Database. The majority of these structures exhibited intermolecular C–H/O interactions at proline C–H bonds, suggesting that C–H/O interactions are an inherent and important mode for recognition of and higher-order assembly at proline residues. Due to steric accessibility and multiple polarized C–H bonds, proline residues are uniquely positioned as sites for binding and recognition via C–H/O interactions.
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