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Cobalamin decyanation by the membrane transporter BtuM Structure (IF 5.7) Pub Date : 2024-05-10 Jose M. Martínez Felices, Yan Borges Barreto, Chancievan Thangaratnarajah, Jacob J. Whittaker, Adriano M. Alencar, Albert Guskov, Dirk J. Slotboom
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Polymorphic residues in HLA-B that mediate HIV control distinctly modulate peptide interactions with both TCR and KIR molecules Structure (IF 5.7) Pub Date : 2024-05-10 Rhoda Tano-Menka, Nishant K. Singh, Itai Muzhingi, Xiaolong Li, Michael V. Mandanas, Clarety Kaseke, Charles R. Crain, Angela Zhang, Funsho J. Ogunshola, Liza Vecchiarello, Alicja Piechocka-Trocha, Arman Bashirova, Michael E. Birnbaum, Mary Carrington, Bruce D. Walker, Gaurav D. Gaiha
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αMI-domain of integrin Mac-1 binds the cytokine pleiotrophin using multiple mechanisms Structure (IF 5.7) Pub Date : 2024-05-09 Hoa Nguyen, Nataly P. Podolnikova, Tatiana P. Ugarova, Xu Wang
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Custom protein nanoparticles for targeted drug delivery Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-05-09
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Computational design of non-porous pH-responsive antibody nanoparticles Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-05-09 Erin C. Yang, Robby Divine, Marcos C. Miranda, Andrew J. Borst, Will Sheffler, Jason Z. Zhang, Justin Decarreau, Amijai Saragovi, Mohamad Abedi, Nicolas Goldbach, Maggie Ahlrichs, Craig Dobbins, Alexis Hand, Suna Cheng, Mila Lamb, Paul M. Levine, Sidney Chan, Rebecca Skotheim, Jorge Fallas, George Ueda, Joshua Lubner, Masaharu Somiya, Alena Khmelinskaia, Neil P. King, David Baker
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Cryo-EM structure of the Rev1–Polζ holocomplex reveals the mechanism of their cooperativity in translesion DNA synthesis Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-05-08 Radhika Malik, Robert E. Johnson, Iban Ubarretxena-Belandia, Louise Prakash, Satya Prakash, Aneel K. Aggarwal
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Illuminating cortactin structure and function at actin filament branches Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-05-07 Klemens Rottner, Peter Bieling
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The risky business of ADP-ribosylating telomeric DNA Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-05-07 Ylli Doksani, Francisca Lottersberger
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Deregulated DNA ADP-ribosylation impairs telomere replication Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-05-07 Anne R. Wondisford, Junyeop Lee, Robert Lu, Marion Schuller, Josephine Groslambert, Ragini Bhargava, Sandra Schamus-Haynes, Leyneir C. Cespedes, Patricia L. Opresko, Hilda A. Pickett, Jaewon Min, Ivan Ahel, Roderick J. O’Sullivan
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Target-based discovery of a broad-spectrum flukicide Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-05-07 Daniel J. Sprague, Sang-Kyu Park, Svenja Gramberg, Lisa Bauer, Claudia M. Rohr, Evgeny G. Chulkov, Emery Smith, Louis Scampavia, Timothy P. Spicer, Simone Haeberlein, Jonathan S. Marchant
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Slower CDK4 and faster CDK2 activation in the cell cycle Structure (IF 5.7) Pub Date : 2024-05-03 Wengang Zhang, Yonglan Liu, Hyunbum Jang, Ruth Nussinov
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Structural elucidation of the mesothelin-mucin-16/CA125 interaction Structure (IF 5.7) Pub Date : 2024-05-03
Mesothelin (MSLN) is a cell-surface glycoprotein expressed at low levels on normal mesothelium but overexpressed in many cancers. Mesothelin has been …
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Cryo-EM structure reveals how SID-1 recognizes dsRNA that initiates systemic RNAi Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-05-03
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Simulations predict preferred Mg2+ coordination in a nonenzymatic primer-extension reaction center Biophys. J. (IF 3.4) Pub Date : 2024-05-03 Shriyaa Mittal, Collin Nisler, Jack W. Szostak
The mechanism by which genetic information was copied prior to the evolution of ribozymes is of great interest because of its importance to the origin of life. The most effective known process for the nonenzymatic copying of an RNA template is primer extension by a two-step pathway in which 2-aminoimidazole-activated nucleotides first react with each other to form an imidazolium-bridged intermediate
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A role for conformational changes in enzyme catalysis Biophys. J. (IF 3.4) Pub Date : 2024-05-03 Olivier Rivoire
The role played by conformational changes in enzyme catalysis is controversial. In addition to examining specific enzymes, studying formal models can help identify the conditions under which conformational changes promote catalysis. Here, we present a model demonstrating how conformational changes can break a generic trade-off due to the conflicting requirements of successive steps in catalytic cycles
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OrganL: Dynamic triangulation of biomembranes using curved elements Biophys. J. (IF 3.4) Pub Date : 2024-05-03 Christoph Allolio, Balázs Fábián, Mark Dostalík
We describe a method for simulating biomembranes of arbitrary shape. In contrast to other dynamically triangulated surface (DTS) algorithms, our method provides a rich, -tangent-continuous, yet local description of the surface. We use curved Nagata triangles, which we generalize to cubic order to achieve the requisite flexibility. The resulting interpolation can be constructed locally without iterations
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DR-BERT: A protein language model to annotate disordered regions Structure (IF 5.7) Pub Date : 2024-05-02 Ananthan Nambiar, John Malcolm Forsyth, Simon Liu, Sergei Maslov
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Structural and biochemical characterization of a nucleotide hydrolase from Streptococcus pneumonia Structure (IF 5.7) Pub Date : 2024-05-02 Yuping Jin, Jiyuan Ke, Peiyi Zheng, Haiyan Zhang, Zhongliang Zhu, Liwen Niu
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Introducing: Ulrich J. Lorenz, Radoslav I. Enchev, Clare F. Megarity, Helen Ginn, Patrick Rabe, Alice R. Walker, and Kartik Ayyer Structure (IF 5.7) Pub Date : 2024-05-02
In this Voices article we introduce seven impressive young group leaders who spoke at the recent Ringberg Workshop on Structural Biology organized by …
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The critical importance of conditions: Reconciling GPCR functionality and biophysical findings Structure (IF 5.7) Pub Date : 2024-05-02 Melissa A. Reith, Jan K. Rainey
G-protein-coupled receptor (GPCR) activation relies on conformational sampling, a nuanced but functionally key behavior well suited to elucidation by nuclear magnetic resonance (NMR) spectroscopy. In this issue of Structure, Thakur et al.1 demonstrate that judicious choice of experimental conditions for 19F NMR studies of a GPCR enables rationalization of functional and pharmacological behavior, leading
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Enzyme engineering lets us play with new building blocks in non-ribosomal peptide synthesis Structure (IF 5.7) Pub Date : 2024-05-02 Minuri S. Ratnayake, Mathias H. Hansen, Max J. Cryle
In a recent issue of Nature Chemical Biology, Folger et al. demonstrated a high-throughput approach for engineering peptide bond forming domains from non-ribosomal peptide synthesis. A non-ribosomal peptide synthetase module from surfactin biosynthesis was reprogrammed to accept a fatty acid substrate into peptide biosynthesis, thus illustrating the potential of this approach for generating novel bioactive
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Structural basis of TRPV1 modulation by endogenous bioactive lipids Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-05-02 William R. Arnold, Adamo Mancino, Frank R. Moss, Adam Frost, David Julius, Yifan Cheng
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Structural determinants for activity of the antidepressant vortioxetine at human and rodent 5-HT3 receptors Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-05-02 Uriel López-Sánchez, Lachlan Jake Munro, Lucy Kate Ladefoged, Anders Juel Pedersen, Christian Colding Brun, Signe Meisner Lyngby, Delphine Baud, Céline Juillan-Binard, Miriam Grønborg Pedersen, Sarah C. R. Lummis, Benny Bang-Andersen, Birgit Schiøtt, Christophe Chipot, Guy Schoehn, Jacques Neyton, Francois Dehez, Hugues Nury, Anders S. Kristensen
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Protein condensates in the secretory pathway: Deciphering biophysical interactions and functional significance Biophys. J. (IF 3.4) Pub Date : 2024-05-02 Felix Campelo, Javier Vera Lillo, Julia von Blume
The emergence of phase separation phenomena among macromolecules has identified biomolecular condensates as fundamental cellular organizers. These condensates concentrate specific components and accelerate biochemical reactions without relying on membrane boundaries. Although extensive studies have revealed a large variety of nuclear and cytosolic membraneless organelles, we are witnessing a surge
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Cryo-EM images of phase-separated lipid bilayer vesicles analyzed with a machine-learning approach Biophys. J. (IF 3.4) Pub Date : 2024-04-30 Karan D. Sharma, Milka Doktorova, M. Neal Waxham, Frederick A. Heberle
Lateral lipid heterogeneity (i.e., raft formation) in biomembranes plays a functional role in living cells. Three-component mixtures of low- and high-melting lipids plus cholesterol offer a simplified experimental model for raft domains in which a liquid-disordered (Ld) phase coexists with a liquid-ordered (Lo) phase. Using such models, we recently showed that cryogenic electron microscopy (cryo-EM)
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Structural insights into the bifunctional enzyme human FAD synthase Structure (IF 5.7) Pub Date : 2024-04-29 Giulia Leo, Piero Leone, Elham Ataie Kachoie, Maria Tolomeo, Michele Galluccio, Cesare Indiveri, Maria Barile, Stefano Capaldi
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Complementary structures of the yeast phosphate transporter Pho90 provide insights into its transport mechanism Structure (IF 5.7) Pub Date : 2024-04-29 Simon Schneider, Werner Kühlbrandt, Özkan Yildiz
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Unveiling the secrets of vimentin filament architecture relevant to human disease Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-29 Ivan B. Lomakin, Minh Ho, Christopher G. Bunick
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Structural basis of closed groove scrambling by a TMEM16 protein Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-29 Zhang Feng, Omar E. Alvarenga, Alessio Accardi
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A bupropion modulatory site in the Gloeobacter violaceus ligand-gated ion channel Biophys. J. (IF 3.4) Pub Date : 2024-04-27 Hoa Quynh Do, Elham Pirayesh, Garren Ferreira, Akash Pandhare, Zackary Ryan Gallardo, Michaela Jansen
Bupropion is an atypical antidepressant and smoking cessation drug that causes adverse effects such as insomnia, irritability, and anxiety. Bupropion inhibits dopamine and norepinephrine reuptake transporters and eukaryotic cation-conducting pentameric ligand-gated ion channels, such as nicotinic acetylcholine and serotonin type 3A receptors, at clinically relevant concentrations. Here, we demonstrate
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Mapping the contribution of the C-linker domain to gating polarity in CNBD channels Biophys. J. (IF 3.4) Pub Date : 2024-04-27 Jenna L. Lin, Yongchang Chang, Debanjan Tewari, John Cowgill, Baron Chanda
Ion channels of the cyclic-nucleotide-binding domain (CNBD) family play a crucial role in the regulation of key biological processes, such as photoreception and pacemaking activity in the heart. These channels exhibit high sequence and structural similarity but differ greatly in their functional responses to membrane potential. The CNBD family includes hyperpolarization-activated ion channels and
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Molecular simulations and NMR reveal how lipid fluctuations affect membrane mechanics Biophys. J. (IF 3.4) Pub Date : 2024-04-27 Milka Doktorova, George Khelashvili, Rana Ashkar, Michael F. Brown
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Combinatorial quantification of 5mC and 5hmC at individual CpG dyads and the transcriptome in single cells reveals modulators of DNA methylation maintenance fidelity Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-26 Alex Chialastri, Saumya Sarkar, Elizabeth E. Schauer, Shyl Lamba, Siddharth S. Dey
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Receptor-recognition and antiviral mechanisms of retrovirus-derived human proteins Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-26 Shashank Khare, Miryam I. Villalba, Juan C. Canul-Tec, Arantza Balsebre Cajiao, Anand Kumar, Marija Backovic, Felix A. Rey, Els Pardon, Jan Steyaert, Camilo Perez, Nicolas Reyes
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Constitutive activity of ionotropic glutamate receptors via hydrophobic substitutions in the ligand-binding domain Structure (IF 5.7) Pub Date : 2024-04-26 Sandra Seljeset, Oksana Sintsova, Yuhong Wang, Hassan Y. Harb, Timothy Lynagh
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Structural and functional insights into yeast Tbf1 as an atypical telomeric repeat-binding factor Structure (IF 5.7) Pub Date : 2024-04-26 Zhenfang Wu, Xin Gu, Lin Zha, Qingqiu Yang, Yuanze Zhou, Zhixiong Zeng
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Structural and functional characterization of itaconyl-CoA hydratase and citramalyl-CoA lyase involved in itaconate metabolism of Pseudomonas aeruginosa Structure (IF 5.7) Pub Date : 2024-04-26 Qin Huang, Chenxi Duan, Haichuan Ma, Cheng Nong, Qianqian Zheng, Jun Zhou, Ninglin Zhao, Xingyu Mou, Tonggen Liu, Shuang Zou, Ningchuan Yang, Aiping Tong, Wenming Qin, Rui Bao
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Illuminating the role of chaperones in spliceosome biogenesis and recycling Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-25 Suyang Zhang
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ISWI catalyzes nucleosome sliding in condensed nucleosome arrays Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-25 Petra Vizjak, Dieter Kamp, Nicola Hepp, Alessandro Scacchetti, Mariano Gonzalez Pisfil, Joseph Bartho, Mario Halic, Peter B. Becker, Michaela Smolle, Johannes Stigler, Felix Mueller-Planitz
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Structural insights into double-stranded RNA recognition and transport by SID-1 Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-25 Jiangtao Zhang, Chunhua Zhan, Junping Fan, Dian Wu, Ruixue Zhang, Di Wu, Xinyao Chen, Ying Lu, Ming Li, Min Lin, Jianke Gong, Daohua Jiang
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Exploring the pH dependence of an improved PETase Biophys. J. (IF 3.4) Pub Date : 2024-04-25 Cyril Charlier, Sabine Gavalda, Jelena Grga, Laura Perrot, Valeria Gabrielli, Frank Löhr, Julia Schörghuber, Roman Lichtenecker, Grégory Arnal, Alain Marty, Vincent Tournier, Guy Lippens
Enzymatic recycling of plastic and especially of polyethylene terephthalate (PET) has shown great potential to reduce its negative impact on our society. PET hydrolases (PETases) have been optimized using rational design and machine learning, but the mechanistic details of the PET depolymerization process remain unclear. Belonging to the carboxylic-ester hydrolase family with a canonical Ser-His-Asp
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Directional change during active diffusion of viral ribonucleoprotein particles through cytoplasm Biophys. J. (IF 3.4) Pub Date : 2024-04-25 Kathleen C. Smith, Ryan Oglietti, Steven J. Moran, Jed C. Macosko, Douglas S. Lyles, George Holzwarth
A mesh of cytoskeletal fibers, consisting of microtubules, intermediate filaments, and fibrous actin, prevents the Brownian diffusion of particles with a diameter larger than 0.10 μm, such as vesicular stomatitis virus ribonucleoprotein (RNP) particles, in mammalian cells. Nevertheless, RNP particles do move in random directions but at a lower rate than Brownian diffusion, which is thermally driven
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New insights into the substrate recognition and transport mechanism of the human sodium-taurocholate cotransporter Biophys. J. (IF 3.4) Pub Date : 2024-04-25 Jana Shen
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The biophysical function of pulmonary surfactant Biophys. J. (IF 3.4) Pub Date : 2024-04-25 Stephen B. Hall, Yi Y. Zuo
The type II pneumocytes of the lungs secrete a mixture of lipids and proteins that together acts as a surfactant. The material forms a thin film on the surface of the liquid layer that lines the alveolar air sacks. When compressed by the decreasing alveolar surface area during exhalation, the films reduce surface tension to exceptionally low levels. Pulmonary surfactant is essential for preserving
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Mammalian PIWI–piRNA–target complexes reveal features for broad and efficient target silencing Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-24 Zhiqing Li, Zhenzhen Li, Yuqi Zhang, Lunni Zhou, Qikui Xu, Lili Li, Lin Zeng, Junchao Xue, Huilin Niu, Jing Zhong, Qilu Yu, Dengfeng Li, Miao Gui, Yongping Huang, Shikui Tu, Zhao Zhang, Chun-Qing Song, Jianping Wu, En-Zhi Shen
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Alternative splicing of CARM1 regulated by LincGET-guided paraspeckles biases the first cell fate in mammalian early embryos Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-24 Jiaqiang Wang, Yiwei Zhang, Jiaze Gao, Guihai Feng, Chao Liu, Xueke Li, Pengcheng Li, Zhonghua Liu, Falong Lu, Leyun Wang, Wei Li, Qi Zhou, Yusheng Liu
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OPUS-Rota5: A highly accurate protein side-chain modeling method with 3D-Unet and RotaFormer Structure (IF 5.7) Pub Date : 2024-04-23 Gang Xu, Zhenwei Luo, Yaming Yan, Qinghua Wang, Jianpeng Ma
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Sensing a moving target: A new model reveals how cells sense dynamic signals Biophys. J. (IF 3.4) Pub Date : 2024-04-24 Andrew Mugler
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Epigenetic marks uniquely tune the material properties of HP1α condensates Biophys. J. (IF 3.4) Pub Date : 2024-04-24 Priyasha Deshpande, Emily Prentice, Alfredo Vidal Ceballos, Patrizia Casaccia, Shana Elbaum-Garfinkle
Biomolecular condensates have emerged as a powerful new paradigm in cell biology with broad implications to human health and disease, particularly in the nucleus where phase separation is thought to underly elements of chromatin organization and regulation. Specifically, it has been recently reported that phase separation of heterochromatin protein 1alpha (HP1α) with DNA contributes to the formation
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Conformational photo-trapping in NaV1.5: Inferring local motions at the “inactivation gate” Biophys. J. (IF 3.4) Pub Date : 2024-04-24 Samuel J. Goodchild, Christopher A. Ahern
Rapid and effectual inactivation in voltage-gated sodium channels is required for canonical action-potential firing. This “fast” inactivation arises from swift and reversible protein conformational changes that utilize transmembrane segments and the cytoplasmic linker between channel domains III and IV. Until recently, fast inactivation had been accepted to rely on a “ball-and-chain” mechanism whereby
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Transcription directionality is licensed by Integrator at active human promoters Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-22 Jiao Yang, Jingyang Li, Langxi Miao, Xu Gao, Wenhao Sun, Shuo Linghu, Guiping Ren, Bangya Peng, Shunkai Chen, Zhongqi Liu, Bo Wang, Ao Dong, Duo Huang, Jinrong Yuan, Yunkun Dang, Fan Lai
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Concerted SUMO-targeted ubiquitin ligase activities of TOPORS and RNF4 are essential for stress management and cell proliferation Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-22 Julio C. Y. Liu, Leena Ackermann, Saskia Hoffmann, Zita Gál, Ivo A. Hendriks, Charu Jain, Louise Morlot, Michael H. Tatham, Gian-Luca McLelland, Ronald T. Hay, Michael Lund Nielsen, Thijn Brummelkamp, Peter Haahr, Niels Mailand
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Mapping structural and dynamic divergence across the MBOAT family Structure (IF 5.7) Pub Date : 2024-04-17 T. Bertie Ansell, Megan Healy, Claire E. Coupland, Mark S.P. Sansom, Christian Siebold
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Macrophages need to release the proximal brake to degrade cellular corpses Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-18 Dimitris Typas
Writing in Nature, T. Tufan et al.1 address this gap in knowledge and provide novel functional and mechanistic insight into efferocytosis activation and execution. Assessing the RNA Polymerase II (Pol II) pausing index, the authors show that upon macrophages encountering apoptotic cells, several genes that bear high amounts of Pol II and are paused at promoter-proximal sites during the resting state
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Membrane-embedded machines Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-18
The first membrane protein structure was reported almost 40 years ago. In this issue, we are publishing a set of papers that serve to underline the incredible advances in our understanding of the biology of these multifaceted molecular machines.
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Future opportunities in solute carrier structural biology Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-18 Simon Newstead
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Kinetic cooperativity resolves bidirectional clogging within the nuclear pore complex Biophys. J. (IF 3.4) Pub Date : 2024-04-18 Tiantian Zheng, Anton Zilman
As the main gatekeeper of the nucleocytoplasmic transport in eukaryotic cells, the nuclear pore complex (NPC) faces the daunting task of facilitating the bidirectional transport of a high volume of macromolecular cargoes while ensuring the selectivity, speed, and efficiency of this process. The competition between opposing nuclear import and export fluxes passing through the same channel is expected
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Transmembrane determinants of voltage-gating differences between BK (Slo1) and Slo3 channels Biophys. J. (IF 3.4) Pub Date : 2024-04-18 Qin Li, Guanxing Chen, Jiusheng Yan
Voltage-gated potassium channels are critical in modulating cellular excitability, with Slo (slowpoke) channels forming a unique family characterized by their large conductance and dual regulation by electrical signals and intracellular messengers. Despite their structural and evolutionary similarities, Slo1 and Slo3 channels exhibit significant differences in their voltage-gating properties. This
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The volume of healthy red blood cells is optimal for advective oxygen transport in arterioles Biophys. J. (IF 3.4) Pub Date : 2024-04-18 Lucas Amoudruz, Athena Economides, Petros Koumoutsakos
Red blood cells (RBCs) are vital for transporting oxygen from the lungs to the body’s tissues through the intricate circulatory system. They achieve this by binding and releasing oxygen molecules to the abundant hemoglobin within their cytosol. The volume of RBCs affects the amount of oxygen they can carry, yet whether this volume is optimal for transporting oxygen through the circulatory system remains
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Vimentin filaments integrate low-complexity domains in a complex helical structure Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-17 Matthias Eibauer, Miriam S. Weber, Rafael Kronenberg-Tenga, Charlie T. Beales, Rajaa Boujemaa-Paterski, Yagmur Turgay, Suganya Sivagurunathan, Julia Kraxner, Sarah Köster, Robert D. Goldman, Ohad Medalia