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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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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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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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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
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DNA double-strand break–capturing nuclear envelope tubules drive DNA repair Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-17 Mitra Shokrollahi, Mia Stanic, Anisha Hundal, Janet N. Y. Chan, Defne Urman, Chris A. Jordan, Anne Hakem, Roderic Espin, Jun Hao, Rehna Krishnan, Philipp G. Maass, Brendan C. Dickson, Manoor P. Hande, Miquel A. Pujana, Razqallah Hakem, Karim Mekhail
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HS-AFM single-molecule structural biology uncovers basis of transporter wanderlust kinetics Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-17 Yining Jiang, Atsushi Miyagi, Xiaoyu Wang, Biao Qiu, Olga Boudker, Simon Scheuring
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Molecular basis of Gabija anti-phage supramolecular assemblies Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-16 Xiao-Yuan Yang, Zhangfei Shen, Jiale Xie, Jacelyn Greenwald, Ila Marathe, Qingpeng Lin, Wen Jun Xie, Vicki H. Wysocki, Tian-Min Fu
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A structure-based computational model of IP3R1 incorporating Ca and IP3 regulation Biophys. J. (IF 3.4) Pub Date : 2024-04-16 D’Artagnan Greene, Yohannes Shiferaw
The inositol 1,4,5-triphosphate receptor (IPR) mediates Ca release in many cell types and is pivotal to a wide range of cellular processes. High-resolution cryoelectron microscopy studies have provided new structural details of IPR type 1 (IPR1), showing that channel function is determined by the movement of various domains within and between each of its four subunits. Channel properties are regulated
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Characteristic fingerprint spectrum of α-synuclein mutants on terahertz time-domain spectroscopy Biophys. J. (IF 3.4) Pub Date : 2024-04-16 Xiaofang Zhao, Chenlong Yang, Xin Chen, Yu Sun, Weihai Liu, Qinggang Ge, Jun Yang
-Synuclein, a presynaptic neuronal protein encoded by the gene, is involved in the pathogenesis of Parkinson’s disease. Point mutations and multiplications of -synuclein (A30P and A53T) are correlated with early-onset Parkinson’s disease characterized by rapid progression and poor prognosis. Currently, the clinical identification of variants, especially disease-related A30P and A53T mutants, remains
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Molecular basis for pH sensing in the KDEL trafficking receptor Structure (IF 5.7) Pub Date : 2024-04-15 Zhiyi Wu, Kathryn Smith, Andreas Gerondopoulos, Tomoaki Sobajima, Joanne L. Parker, Francis A. Barr, Simon Newstead, Philip C. Biggin
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Structural basis for the immune recognition and selectivity of the immune receptor PVRIG for ligand Nectin-2 Structure (IF 5.7) Pub Date : 2024-04-15 Songtao Hu, Pu Han, Meiyu Wang, Xiaoqing Cao, Hao Liu, Shuailong Zhang, Shuijun Zhang, Jun Liu, Yi Han, Jinhe Xiao, Qiang Chen, Kai Miao, Jianxun Qi, Shuguang Tan, George Fu Gao, Han Wang
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DNA and mRNA as molecular speed bumps in Escherichia coli’s cytoplasm Biophys. J. (IF 3.4) Pub Date : 2024-04-15 Arnold J. Boersma
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Optimizing properties of translocation-enhancing transmembrane proteins Biophys. J. (IF 3.4) Pub Date : 2024-04-13 Ladislav Bartoš, Martina Drabinová, Robert Vácha
Cell membranes act as semi-permeable barriers, often restricting the entry of large or hydrophilic molecules. Nonetheless, certain amphiphilic molecules, such as antimicrobial and cell-penetrating peptides, can cross these barriers. In this study, we demonstrate that specific properties of transmembrane proteins/peptides can enhance membrane permeation of amphiphilic peptides. Using coarse-grained
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Scaling and merging macromolecular diffuse scattering with mdx2 Acta Cryst. D (IF 2.2) Pub Date : 2024-04-12 Meisburger, S.P., Ando, N.
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HEIDI: an experiment-management platform enabling high-throughput fragment and compound screening Acta Cryst. D (IF 2.2) Pub Date : 2024-04-12 Metz, A., Stegmann, D.P., Panepucci, E.H., Buehlmann, S., Huang, C.-Y., McAuley, K.E., Wang, M., Wojdyla, J.A., Sharpe, M.E., Smith, K.M.L.
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STOPGAP: an open-source package for template matching, subtomogram alignment and classification Acta Cryst. D (IF 2.2) Pub Date : 2024-04-12 Wan, W., Khavnekar, S., Wagner, J.
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Structure of the γ-tubulin ring complex-capped microtubule Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-12 Amol Aher, Linas Urnavicius, Allen Xue, Kasahun Neselu, Tarun M. Kapoor
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Structure of the native γ-tubulin ring complex capping spindle microtubules Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-12 Tom Dendooven, Stanislau Yatskevich, Alister Burt, Zhuo A. Chen, Dom Bellini, Juri Rappsilber, John V. Kilmartin, David Barford
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Cryo-EM structure of flagellotropic bacteriophage Chi Structure (IF 5.7) Pub Date : 2024-04-12 Ravi R. Sonani, Nathaniel C. Esteves, Birgit E. Scharf, Edward H. Egelman
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Map conformational landscapes of intrinsically disordered proteins with polymer physics quantities Biophys. J. (IF 3.4) Pub Date : 2024-04-12 Hossain Shadman, Jesse D. Ziebarth, Caleb E. Gallops, Ray Luo, Zhengxin Li, Hai-Feng Chen, Yongmei Wang
Disordered proteins are conformationally flexible proteins that are biologically important and have been implicated in devastating diseases such as Alzheimer’s disease and cancer. Unlike stably folded structured proteins, disordered proteins sample a range of different conformations that needs to be accounted for. Here, we treat disordered proteins as polymer chains, and compute a dimensionless quantity
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Noncanonical assembly, neddylation and chimeric cullin–RING/RBR ubiquitylation by the 1.8 MDa CUL9 E3 ligase complex Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-11 Daniel Horn-Ghetko, Linus V. M. Hopf, Ishita Tripathi-Giesgen, Jiale Du, Sebastian Kostrhon, D. Tung Vu, Viola Beier, Barbara Steigenberger, J. Rajan Prabu, Luca Stier, Elias M. Bruss, Matthias Mann, Yue Xiong, Brenda A. Schulman
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Visualizing chaperone-mediated multistep assembly of the human 20S proteasome Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-10 Frank Adolf, Jiale Du, Ellen A. Goodall, Richard M. Walsh, Shaun Rawson, Susanne von Gronau, J. Wade Harper, John Hanna, Brenda A. Schulman
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Mechanism of autocatalytic activation during proteasome assembly Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-10 Benjamin Velez, Richard M. Walsh, Shaun Rawson, Aida Razi, Lea Adams, Erignacio Fermin Perez, Fenglong Jiao, Marie Blickling, Tamayanthi Rajakumar, Darlene Fung, Lan Huang, John Hanna
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Nuclear curvature determines Yes-associated protein localization and differentiation of mesenchymal stem cells Biophys. J. (IF 3.4) Pub Date : 2024-04-10 Ajinkya Ghagre, Alice Delarue, Luv Kishore Srivastava, Newsha Koushki, Allen Ehrlicher
Controlling mesenchymal stem cell (MSC) differentiation remains a critical challenge in MSCs’ therapeutic application. Numerous biophysical and mechanical stimuli influence stem cell fate; however, their relative efficacy and specificity in mechanically directed differentiation remain unclear. Yes-associated protein (YAP) is one key mechanosensitive protein that controls MSC differentiation. Previous
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A molecular switch in RCK2 triggers sodium-dependent activation of KNa1.1 (KCNT1) potassium channels Biophys. J. (IF 3.4) Pub Date : 2024-04-10 Bethan A. Cole, Antreas C. Kalli, Nadia Pilati, Stephen P. Muench, Jonathan D. Lippiat
The Na-activated K channel K1.1, encoded by the gene, is an important regulator of neuronal excitability. How intracellular Na ions bind and increase channel activity is not well understood. Analysis of K1.1 channel structures indicate that there is a large twisting of the βN-αQ loop in the intracellular RCK2 domain between the inactive and Na-activated conformations, with a lysine (K885, human subunit
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Enhancing micropipette aspiration with artificial-intelligence analysis Biophys. J. (IF 3.4) Pub Date : 2024-04-10 Aldo Abarca-Ortega, Blanca González-Bermúdez, Gustavo R. Plaza
The micropipette-aspiration technique is commonly used in the field of mechanobiology, offering a variety of measurement types. To extract biophysical parameters from the experiments, numerical analysis is required. Although previous works have developed techniques for the partial automation of these analyses, these approaches are relatively time consuming for the researchers. In this article, we describe
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Solving stochastic gene-expression models using queueing theory: A tutorial review Biophys. J. (IF 3.4) Pub Date : 2024-04-09 Juraj Szavits-Nossan, Ramon Grima
Stochastic models of gene expression are typically formulated using the chemical master equation, which can be solved exactly or approximately using a repertoire of analytical methods. Here, we provide a tutorial review of an alternative approach based on queueing theory that has rarely been used in the literature of gene expression. We discuss the interpretation of six types of infinite-server queues
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Structure of adenylyl cyclase 5 in complex with Gβγ offers insights into ADCY5-related dyskinesia Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-08 Yu-Chen Yen, Yong Li, Chun-Liang Chen, Thomas Klose, Val J. Watts, Carmen W. Dessauer, John J. G. Tesmer
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Transport mechanism of presynaptic high-affinity choline uptake by CHT1 Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-08 Yunlong Qiu, Yiwei Gao, Bo Huang, Qinru Bai, Yan Zhao
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Human V-ATPase function is positively and negatively regulated by TLDc proteins Structure (IF 5.7) Pub Date : 2024-04-08 Rebecca A. Oot, Stephan Wilkens
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The cryo-EM structure of trypanosome 3-methylcrotonyl-CoA carboxylase provides mechanistic and dynamic insights into its enzymatic function Structure (IF 5.7) Pub Date : 2024-04-08 Adrián Plaza-Pegueroles, Inna Aphasizheva, Ruslan Aphasizhev, Carlos Fernández-Tornero, Federico M. Ruiz
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How much does TRPV1 deviate from an ideal MWC-type protein? Biophys. J. (IF 3.4) Pub Date : 2024-04-06 Shisheng Li, Jie Zheng
Many ion channels are known to behave as an allosteric protein, coupling environmental stimuli captured by specialized sensing domains to the opening of a central pore. The classic Monod-Wyman-Changeux (MWC) model, originally proposed to describe binding of gas molecules to hemoglobin, has been widely used as a framework for analyzing ion channel gating. Here, we address the issue of how accurately
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Crystal structure of archaeal IF5A-DHS complex reveals insights into the hypusination mechanism Structure (IF 5.7) Pub Date : 2024-04-05 Mattia D'Agostino, Angelita Simonetti, Stefano Motta, Philippe Wolff, Alice Romagnoli, Astra Piccinini, Francesco Spinozzi, Daniele Di Marino, Anna La Teana, Eric Ennifar
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Cryo-EM structures reveal two allosteric inhibition modes of PI3KαH1047R involving a re-shaping of the activation loop Structure (IF 5.7) Pub Date : 2024-04-05 Xiuliang Huang, Kailiang Wang, Jing Han, Xiumei Chen, Zhenglin Wang, Tianlun Wu, Bo Yu, Feng Zhao, Xinjuan Wang, Huijuan Li, Zhi Xie, Xiaotian Zhu, Wenge Zhong, Xiaoming Ren
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SCAF1 drives the compositional diversity of mammalian respirasomes Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-04 Irene Vercellino, Leonid A. Sazanov
Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies have shown that different tissues/organs are equipped with specific sets of supercomplexes, depending on their metabolic needs, the notion that supercomplexes have a role in the regulation of metabolism has
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A rare genetic variant biases maternal meiotic recombination toward risk of pregnancy loss Nat. Struct. Mol. Biol. (IF 16.8) Pub Date : 2024-04-03 Sara A. Carioscia, Rajiv C. McCoy
Pregnancy loss is common in humans, but maternal genetic factors modulating its incidence are largely unknown. In a meta-analysis of genome-wide association studies, researchers identified a genetic variant that seems to increase risk of pregnancy loss by dysregulating meiotic recombination between homologous chromosomes during egg formation.
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A glimpse into Giardia lamblia unique translational machinery Structure (IF 5.7) Pub Date : 2024-04-04 Jailson Brito Querido
Eiler et al. used cryo-electron microscopy to determine a 2.49 Å resolution structure of Giardia lamblia 80S ribosome bound to tRNA, mRNA, and the anti-protozoal drug emetine. The structure reveals some critical aspects of translation in G. lamblia, including the lack of ribosomal protein RACK1, and how emetine blocks translation by interacting with both the ribosome and mRNA.
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Structural basis for the inhibition mechanism of the DNA polymerase holoenzyme from mpox virus Structure (IF 5.7) Pub Date : 2024-04-04 Yaping Shen, Yaning Li, Renhong Yan
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MLL4 binds TET3 Structure (IF 5.7) Pub Date : 2024-04-04 Dustin C. Becht, Sk Abdul Mohid, Ji-Eun Lee, Mohamad Zandian, Caroline Benz, Soumi Biswas, Vikrant Kumar Sinha, Ylva Ivarsson, Kai Ge, Yi Zhang, Tatiana G. Kutateladze
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Full-length αIIbβ3 cryo-EM structure reveals intact integrin initiate-activation intrinsic architecture Structure (IF 5.7) Pub Date : 2024-04-04 Tong Huo, Hongjiang Wu, Zeinab Moussa, Mehmet Sen, Valerie Dalton, Zhao Wang
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AI in cellular engineering and reprogramming Biophys. J. (IF 3.4) Pub Date : 2024-04-04 Sara Capponi, Shangying Wang
During the last decade, artificial intelligence (AI) has increasingly been applied in biophysics and related fields, including cellular engineering and reprogramming, offering novel approaches to understand, manipulate, and control cellular function. The potential of AI lies in its ability to analyze complex datasets and generate predictive models. AI algorithms can process large amounts of data from
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Base pair dynamics, electrostatics, and thermodynamics at the LTR-III quadruplex:duplex junction Biophys. J. (IF 3.4) Pub Date : 2024-04-04 Haley M. Michel, Justin A. Lemkul
G-quadruplexes (GQs) play key regulatory roles within the human genome and have also been identified to play similar roles in other eukaryotes, bacteria, archaea, and viruses. Human immunodeficiency virus 1, the etiological agent of acquired immunodeficiency syndrome, can form two GQs in its long terminal repeat (LTR) promoter region, each of which act to regulate viral gene expression in opposing
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Robust spatiotemporal organization of mitotic events in mechanically perturbed C. elegans embryos Biophys. J. (IF 3.4) Pub Date : 2024-04-04 Vincent Borne, Matthias Weiss
Early embryogenesis of the nematode progresses in an autonomous fashion within a protective chitin eggshell. Cell-division timing and the subsequent mechanically guided positioning of cells is virtually invariant between individuals, especially before gastrulation. Here, we have challenged this stereotypical developmental program in early stages by mechanically perturbing the embryo without breaking