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1. TurboID ‐based proteomic profiling reveals proxitome of ASK1 and CUL1 of the SCF ubiquitin ligase in plants

   https://doi.org/10.1111/nph.20014  

   Sun, Fuai; Hamada, Natalie; Montes, Christian; Li, Yuanyuan; Meier, Nathan_D; Walley, Justin_W; Dinesh‐Kumar, Savithramma_P; Shabek, Nitzan (July 2024, New Phytologist)
2. Integrated structural model of the palladin–actin complex using XL ‐ MS , docking, NMR , and SAXS

   https://doi.org/10.1002/pro.70122  

   Sargent, Rachel; Liu, David H; Yadav, Rahul; Glennenmeier, Drew; Bradford, Colby; Urbina, Noely; Beck, Moriah R (May 2025, Protein Science)

   Cortajarena, Aitziber L (Ed.)

   Abstract Palladin is an actin‐binding protein that accelerates actin polymerization and is linked to the metastasis of several types of cancer. Previously, three lysine residues in an immunoglobulin‐like domain of palladin have been identified as essential for actin binding. However, it is still unknown where palladin binds to F‐actin. Evidence that palladin binds to the sides of actin filaments to facilitate branching is supported by our previous study showing that palladin was able to compensate for Arp2/3 in the formation ofListeriaactin comet tails. Here, we used chemical crosslinking to covalently link palladin and F‐actin residues based on spatial proximity. Samples were then enzymatically digested, separated by liquid chromatography, and analyzed by tandem mass spectrometry. Peptides containing the crosslinks and specific residues involved were then identified for input to the HADDOCK docking server to model the most likely binding conformation. Small‐angle x‐ray scattering was used to provide further insight into palladin flexibility and the binding interface, and NMR spectra identified potential interactions between palladin's Ig domains. Our final structural model of the F‐actin:palladin complex revealed how palladin interacts with and stabilizes F‐actin at the interface between two actin monomers. Three actin residues that were identified in this study also appear commonly in the actin‐binding interface with other proteins such as myotilin, myosin, and tropomodulin. An accurate structural representation of the complex between palladin and actin extends our understanding of palladin's role in promoting cancer metastasis through the regulation of actin dynamics. 

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3. 2.2.2-Cryptand complexes of neptunium( iii ) and plutonium( iii )

   https://doi.org/10.1039/D1CC05904A  

   Goodwin, Conrad A.; Ciccone, Sierra R.; Bekoe, Samuel; Majumdar, Sourav; Scott, Brian L.; Ziller, Joseph W.; Gaunt, Andrew J.; Furche, Filipp; Evans, William J. (January 2022, Chemical Communications)

   New coordination environments are reported for Np( iii ) and Pu( iii ) based on pilot studies of U( iii ) in 2.2.2-cryptand (crypt). The U( iii )-in-crypt complex, [U(crypt)I 2 ][I], obtained from the reaction between UI 3 and crypt, is treated with Me 3 SiOTf (OTf = O 3 SCF 3 ) in benzene to form the [U(crypt)(OTf) 2 ][OTf] complex. Similarly, the isomorphous Np( iii ) and Pu( iii ) complexes were obtained similarly starting from [AnI 3 (THF) 4 ]. All three complexes (1-An; An = U, Np, Pu) contain an encapsulated actinide in a THF-soluble complex. Absorption spectroscopy and DFT calculations are consistent with 5f 3 U( iii ), 5f 4 Np( iii ), and 5f 5 Pu( iii ) electron configurations. 

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4. Metal–ligand and hydrogen bonding in the active site of Fe( iii )-, Mn( iii )- and Co( iii )-myoglobins

   https://doi.org/10.1039/D4DT03246B  

   Freindorf, Marek; Kraka, Elfi (March 2025, Dalton Transactions)

   We investigated in this work strength of metal–ligand and hydrogen bonding in complexes formed between Fe, Mn, and Co myoglobin and molecular ligands such as methanol, water, nitrite, and azide involving ε and δ protonation forms of distal histidine. 

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5. Substrates (Acyl‐ CoA and Diacylglycerol) Entry and Products ( CoA and Triacylglycerol) Egress Pathways in DGAT1

   https://doi.org/10.1002/jcc.70108  

   Lee, Hwayoung; Im, Wonpil (April 2025, Journal of Computational Chemistry)

   ABSTRACT Diacylglycerol O‐acyltransferase 1 (DGAT1) is an integral membrane protein that uses acyl‐coenzyme A (acyl‐CoA) and diacylglycerol (DAG) to catalyze the formation of triacylglycerides (TAGs). The acyl transfer reaction occurs between the activated carboxylate group of the fatty acid and the free hydroxyl group on the glycerol backbone of DAG. However, how the two substrates enter DGAT1's catalytic reaction chamber and interact with DGAT1 remains elusive. This study aims to explore the structural basis of DGAT1's substrate recognition by investigating each substrate's pathway to the reaction chamber. Using a human DGAT1 cryo‐EM structure in complex with an oleoyl‐CoA substrate, we designed two different all‐atom molecular dynamics (MD) simulation systems: DGAT1^away(both acyl‐CoA and DAG away from the reaction chamber) and DGAT1^bound(acyl‐CoA bound in and DAG away from the reaction chamber). Our DGAT1^awaysimulations reveal that acyl‐CoA approaches the reaction chamber via interactions with positively charged residues in transmembrane helix 7. DGAT1^boundsimulations show DAGs entering into the reaction chamber from the cytosol leaflet. The bound acyl‐CoA's fatty acid lines up with the headgroup of DAG, which appears to be competent to TAG formation. We then converted them into TAG and coenzyme (CoA) and used adaptive biasing force (ABF) simulations to explore the egress pathways of the products. We identify their escape routes, which are aligned with their respective entry pathways. Visualization of the substrate and product pathways and their interactions with DGAT1 is expected to guide future experimental design to better understand DGAT1 structure and function. 

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