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Abstract: Parasites counteract host immunity by suppressing helper nucleotide binding and leucine-rich repeat (NLR) proteins that function as central nodes in immune receptor networks. Understanding the mechanisms of immunosuppression can lead to strategies for bioengineering disease resistance. Here, we show that a cyst nematode virulence effector binds and inhibits oligomerization of the helper NLR protein NRC2 by physically preventing intramolecular rearrangements required for activation. An amino acid polymorphism at the binding interface between NRC2 and the inhibitor is sufficient for this helper NLR to evade immune suppression, thereby restoring the activity of multiple disease resistance genes. This points to a potential strategy for resurrecting disease resistance in crop genomes.

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Abstract: Preventing the biogenesis of disease-relevant proteins is an attractive therapeutic strategy, but attempts to target essential protein biogenesis factors have been hampered by excessive toxicity. Here we describe KZR-8445, a cyclic depsipeptide that targets the Sec61 translocon and selectively disrupts secretory and membrane protein biogenesis in a signal peptide-dependent manner. KZR-8445 potently inhibits the secretion of pro-inflammatory cytokines in primary immune cells and is highly efficacious in a mouse model of rheumatoid arthritis. A cryogenic electron microscopy structure reveals that KZR-8445 occupies the fully opened Se61 lateral gate and blocks access to the lumenal plug domain. KZR-8445 binding stabilizes the lateral gate helices in a manner that traps select signal peptides in the Sec61 channel and prevents their movement into the lipid bilayer. Our results establish a framework for the structure-guided discovery of novel therapeutics that selectively modulate Sec61-mediated protein biogenesis.

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Abstract: γ-Amino acids can play important roles in the biological activities of natural products; however, the ribosomal incorporation of γ-amino acids into peptides is challenging. Here we report how a selection campaign employing a non-canonical peptide library containing cyclic γ2,4-amino acids resulted in the discovery of very potent inhibitors of the SARS-CoV-2 main protease (Mpro). Two kinds of cyclic γ2,4-amino acids, cis-3-aminocyclobutane carboxylic acid (γ1) and (1R,3S)-3-aminocyclopentane carboxylic acid (γ2), were ribosomally introduced into a library of thioether-macrocyclic peptides. One resultant potent Mpro inhibitor (half-maximal inhibitory concentration = 50 nM), GM4, comprising 13 residues with γ1 at the fourth position, manifests a 5.2 nM dissociation constant. An Mpro:GM4 complex crystal structure reveals the intact inhibitor spans the substrate binding cleft. The γ1 interacts with the S1′ catalytic subsite and contributes to a 12-fold increase in proteolytic stability compared to its alanine-substituted variant. Knowledge of interactions between GM4 and Mpro enabled production of a variant with a 5-fold increase in potency.

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Abstract: Topochemistry enables step-by-step conversions of solid-state materials often leading to metastable structures that retain initial structural motifs. Recent advances in this field revealed many examples where relatively bulky anionic constituents were actively involved in redox reactions during (de)intercalation processes. Such reactions are often accompanied by anion-anion bond formation, which heralds possibilities to design novel structure types disparate from known precursors, in a controlled manner. Here we present the multistep conversion of layered oxychalcogenides Sr2MnO2Cu1.5Ch2 (Ch = S, Se) into Cu-deintercalated phases where antifluorite type [Cu1.5Ch2]2.5- slabs collapsed into two-dimensional arrays of chalcogen dimers. The collapse of the chalcogenide layers on deintercalation led to various stacking types of Sr2MnO2Ch2 slabs, which formed polychalcogenide structures unattainable by conventional high-temperature syntheses. Anion-redox topochemistry is demonstrated to be of interest not only for electrochemical applications but also as a means to design complex layered architectures.

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Abstract: In this thesis, the static and dynamic properties of magnetic multilayer samples were studied using a variety of experimental techniques, based both at Exeter and the Diamond Light Source (DLS) and Advanced Light Source (ALS) synchrotron facilities. The exchange interaction, which acts to align spins, is a fundamental part in these magnetic multilayer samples. First, the glancing angle deposition (GLAD) technique was investigated as a tool for creating magnetic multilayers with exciting new exchange interactions. For this, Co thin films were grown by DC magnetron sputtering to tailor the magnetic anisotropy of the samples. These Co samples were structurally characterized using x-ray diffraction (XRD) and transmission electron microscopy (TEM). Vibrating sample magnetometry (VSM) was then performed to investigate the magnetic properties of the thin films as a result of the GLAD technique. From this, the necessary conditions for effective anisotropy control using the GLAD technique were identified. Synchrotron x-ray measurements, such as x-ray magnetic circular / linear dichroism (XMCD/XMLD) for static measurements, are vital for investigating magnetic multilayer samples with elemental resolution. To add depth-sensitivity to the synchrotron measurements, the idea of an ultra-thin Mn “spy layer” was investigated by inserting different thicknesses (tMn) of Mn into the NiFe layer in a FePt / NiFe bilayer. The effect on the static magnetic properties was studied using VSM and XMCD hysteresis loops before structural information was obtained using scanning transmission electron microscopy (STEM). The magnetization dynamics were probed using vector network analyzer ferromagnetic resonance (VNA-FMR) and element resolved x-ray ferromagnetic resonance (XFMR) measurements. From this, the ideal “spy layer” thickness of Mn was found to lie in the region 0Å < tMn < 5Å . Spin currents are a dynamic process found in magnetic multilayers and are driven by the exchange interaction. The measurement of a transverse charge current generated via the inverse spin Hall effect (ISHE) has become the principal technique for observing spin currents. During ISHE measurements, parasitic microwave effects were observed and a method to separate out the inverse spin Hall effect was identified. This method was then tested for a reference YIG / Pt bilayer. A more complex NiFe / NiO / Pd / FeCo sample was then studied using this procedure and the ISHE voltage was identified, despite the presence of additional parasitic effects. In addition to the DC spin current component, there is an AC spin current contribution. The AC spin current component was also investigated for the NiFe / NiO / Pd / FeCo sample series using XMCD, XMLD and XFMR measurements. The XMCD and XMLD data revealed the Ni and (Fe)Co spins possess perpendicular in-plane coupling relative to the magnetic moments within the NiO layer. To understand the magnetization dynamics in these samples, an evanescent spin wave model was invoked. This provides crucial insights for interpreting spin current propagation through NiO. Through the combination of work described above, new avenues for the fabrication of magnetic multilayers and the measurement of the magnetization dynamics in such systems are presented to yield a more complete understanding of the crucial role of the exchange interaction in the magnetization dynamics of magnetic multilayers.