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1. L eg M uscle A rchitecture in P rimates and I ts C orrelation with L ocomotion P atterns

   https://doi.org/10.1002/ar.23745  

   Marchi, Damiano; Leischner, Carissa L; Pastor, Francisco; Hartstone‐Rose, Adam (March 2018, The Anatomical Record)

   ABSTRACT Bone biomechanical studies indicate that leg bone structure can be related to different locomotor patterns. The osteological correlates of extant primates’ locomotion patterns and substrate use are important to consider when estimating corresponding behaviors of extinct primates. Here, we test if these same patterns are seen in the differences in leg muscular architecture. Muscle mass, fascicle lengths (FL), physiological cross‐sectional area (PCSA), reduced PCSA (RPCSA) and tendon‐to‐muscle belly ratio were studied in 33 primate species (6 strepsirrhines, 14 platyrrhines and 13 catarrhines). Muscles were grouped into toe and ankle flexors and extensors and studied for phylogenetic and functional signals. All variables strongly correlate with body mass: strength variables (mass, PCSA and RPCSA) scale with positive allometry, whereas the speed/stretch measure (FL) trend toward negative allometry. Thus, larger primates are relatively stronger than smaller species, but they have relatively shorter leg muscle fibers than smaller primates. The strongest functional signal emerged when comparing belly‐muscle tendon unit (MTU) length ratio in leaping and non‐leaping primates. Leapers show significantly smaller plantarflexor belly‐MTU ratio. Surprisingly, no significant results reflect a correlation between muscle architecture and substrate and locomotor groups. However, several trends suggest that a larger sample and more fine‐grained defined categories could produce significant results. These results show the complex relation between leg bone biomechanics and muscle architecture and demand for further studies on this topic. Anat Rec, 301:515–527, 2018. © 2018 Wiley Periodicals, Inc. 

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2. 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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3. The changes in plant and soil C pools and their C : N stoichiometry control grassland N retention under elevated N inputs

   https://doi.org/10.1002/eap.2517  

   Yang, Sen; Liu, Weixing; Guo, Lulu; Wang, Chengzhang; Deng, Meifeng; Peng, Ziyang; Liu, Lingli (March 2022, Ecological Applications)
4. Open Chemistry, JupyterLab , REST , and quantum chemistry

   https://doi.org/10.1002/qua.26472  

   Hanwell, Marcus D.; Harris, Chris; Genova, Alessandro; Haghighatlari, Mojtaba; El Khatib, Muammar; Avery, Patrick; Hachmann, Johannes; Jong, Wibe Albert (January 2021, International Journal of Quantum Chemistry)

   null (Ed.)
5. 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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