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Automated orthogonal tRNA generation Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-12-20 Martin Spinck, Amir Guppy, Jason W. Chin
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Author Correction: Targeting colorectal cancer with small-molecule inhibitors of ALDH1B1 Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-12-09 Zhiping Feng, Marisa E. Hom, Thomas E. Bearrood, Zachary C. Rosenthal, Daniel Fernández, Alison E. Ondrus, Yuchao Gu, Aaron K. McCormick, Madeline G. Tomaske, Cody R. Marshall, Toni Kline, Che-Hong Chen, Daria Mochly-Rosen, Calvin J. Kuo, James K. Chen
Correction to: Nature Chemical Biology https://doi.org/10.1038/s41589-022-01048-w, published online 4 July 2022.
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Detecting features of antibody structure through their mediator-accessible redox activities Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-12-02 Dana Motabar, Eunkyoung Kim, Jinyang Li, Zhiling Zhao, Trina Mouchahoir, D. Travis Gallagher, John E. Schiel, Mamatha Garige, Carole Sourbier, Gregory F. Payne, William E. Bentley
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Mitochondria-localized MBD2c facilitates mtDNA transcription and drug resistance Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-11-28 Yijie Hao, Zilong Zhou, Rui Liu, Shengqi Shen, Haiying Liu, Yingli Zhou, Yuchen Sun, Qiankun Mao, Tong Zhang, Shi-Ting Li, Zhaoji Liu, Yiyang Chu, Linchong Sun, Ping Gao, Huafeng Zhang
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How nature ties peptide knots Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-11-26 Andrew G. Roberts, Jessica M. J. Swanson
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Discovery and mechanism of K63-linkage-directed deubiquitinase activity in USP53 Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-11-25 Kim Wendrich, Kai Gallant, Sarah Recknagel, Stavroula Petroulia, Nafizul Haque Kazi, Jan André Hane, Siska Führer, Karel Bezstarosti, Rachel O’Dea, Jeroen Demmers, Malte Gersch
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A key to sperm–egg union Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-11-18 Gene Chong
The fusion of egg and sperm requires an egg surface protein, JUNO in mammals or Bouncer in fish, and several conserved sperm surface proteins, including IZUMO1, SPACA6, DCST1 and DCST2. The binding of JUNO and IZUMO1 is known but is not sufficient for fusion, and the specific roles of SPACA6 and DCST1/DCST2 remain unclear. Deneke, Blaha et al. have now identified a conserved sperm complex that includes
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Assembly-activated aggregation Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-11-18 Yiyun Song
The aberrant aggregation of the presynaptic protein α-synuclein (α-syn) is a hallmark of synucleinopathies, which include Parkinson’s disease, dementia with Lewy bodies, and multiple system atrophy. Previous studies have suggested that α-syn can undergo liquid–liquid phase separation (LLPS) and transition from a liquid to a solid state, which contributes to aggregation and fibril formation. However
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Guiding the pioneer Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-11-18 Grant Miura
Forkhead box protein A1 (FOXA1) is a pioneer transcription factor that binds to chromatin at a canonical DNA motif. This binding promotes the opening of chromatin, providing access to additional transcription factors. Targeting transcription factors such as FOXA1 with small molecules can serve as a useful tool to elucidate the rapid dynamics of transcriptional regulation, but remains difficult owing
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Spatiotemporal control of subcellular O-GlcNAc signaling using Opto-OGT Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-11-14 Qunxiang Ong, Ler Ting Rachel Lim, Cameron Goh, Yilie Liao, Sher En Chan, Crystal Jing Yi Lim, Valerie Kam, Jerome Yap, Tiffany Tseng, Reina Desrouleaux, Loo Chien Wang, Siok Ghee Ler, Siew Lan Lim, Sun-Yee Kim, Radoslaw M. Sobota, Anton M. Bennett, Weiping Han, Xiaoyong Yang
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Open-ended molecular recording of sequential cellular events into DNA Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-11-14 Theresa B. Loveless, Courtney K. Carlson, Catalina A. Dentzel Helmy, Vincent J. Hu, Sara K. Ross, Matt C. Demelo, Ali Murtaza, Guohao Liang, Michelle Ficht, Arushi Singhai, Marcello J. Pajoh-Casco, Chang C. Liu
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Author Correction: Evybactin is a DNA gyrase inhibitor that selectively kills Mycobacterium tuberculosis Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-11-08 Yu Imai, Glenn Hauk, Jeffrey Quigley, Libang Liang, Sangkeun Son, Meghan Ghiglieri, Michael F. Gates, Madeleine Morrissette, Negar Shahsavari, Samantha Niles, Donna Baldisseri, Chandrashekhar Honrao, Xiaoyu Ma, Jason J. Guo, James M. Berger, Kim Lewis
Correction to: Nature Chemical Biology https://doi.org/10.1038/s41589-022-01102-7, published online 22 August 2022.
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Author Correction: ML-enhanced peroxisome capacity enables compartmentalization of multienzyme pathway Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-11-08 Jordan J. Baker, Jie Shi, Shangying Wang, Elena M. Mujica, Simone Bianco, Sara Capponi, John E. Dueber
Correction to: Nature Chemical Biology https://doi.org/10.1038/s41589-024-01759-2, published online 14 October 2024.
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Engineering a xylose fermenting yeast for lignocellulosic ethanol production Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-11-04 Yi-Wen Zhang, Jun-Jie Yang, Feng-Hui Qian, Kate Brandon Sutton, Carsten Hjort, Wen-Ping Wu, Yu Jiang, Sheng Yang
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A multiplex single-cell RNA-Seq pharmacotranscriptomics pipeline for drug discovery Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-31 Alice Dini, Harlan Barker, Emilia Piki, Subodh Sharma, Juuli Raivola, Astrid Murumägi, Daniela Ungureanu
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Carbonic anhydrase inhibition ameliorates tau toxicity via enhanced tau secretion Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-31 Ana Lopez, Farah H. Siddiqi, Julien Villeneuve, Rodrigo Portes Ureshino, Hee-Yeon Jeon, Philippos Koulousakis, Sophie Keeling, William A. McEwan, Angeleen Fleming, David C. Rubinsztein
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Evading resistance at the double Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-30 Mohamed I. Barmada, Graeme L. Conn
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Protein Degradation in Focus Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-29 David Zollman, Kirsten McAulay
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Genes and crystals are not so separate Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-28 Peter G. Vekilov
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Selective bioorthogonal probe for N-glycan hybrid structures Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-28 Mana Mohan Mukherjee, Devin Biesbrock, Lara K. Abramowitz, Matteo Pavan, Bhoj Kumar, Peter J. Walter, Parastoo Azadi, Kenneth A. Jacobson, John A. Hanover
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Cracking the diversity of sweet drugs Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-24 Sharon Yehuda, Vered Padler-Karavani
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Stressing out with electrophiles Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-24 Caroline Stanton, Kayla Nutsch, Michael J. Bollong
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Delineating cysteine-reactive compound modulation of cellular proteostasis processes Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-24 Ashley R. Julio, Flowreen Shikwana, Cindy Truong, Nikolas R. Burton, Emil R. Dominguez, Alexandra C. Turmon, Jian Cao, Keriann M. Backus
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In vivo manipulation of human gut Bacteroides fitness by abiotic oligosaccharides Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-23 Darryl A. Wesener, Zachary W. Beller, Megan F. Hill, Han Yuan, David B. Belanger, Cheryl Frankfater, Nicolas Terrapon, Bernard Henrissat, Dmitry A. Rodionov, Semen A. Leyn, Andrei Osterman, Johan E. T. van Hylckama Vlieg, Jeffrey I. Gordon
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Bridging the gap in protein targeting Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-22 Irene Serrano
Targeted protein degradation has emerged as a highly promising therapeutic approach to modulate proteins that are difficult to target with conventional small molecules. This approach has recently been expanded to include alteration of extracellular protein levels and activity — including both secreted and membrane proteins. Now, Zhang et al. have exploited the upregulation of cell surface transferrin
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Forming folate-fortified rice Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-22 Francesco Zamberlan
Folates are a group of water-soluble B vitamins that are essential for all organisms. Although plants and microbes can synthesize them, humans cannot, and insufficient intake of folates can lead to several disorders. It is therefore important to find folate sources that can help alleviate folate malnutrition. Cereals are poor sources of folates but contain high levels of MeFox, a pyrazino-s-triazine
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Molecular glue modulates mitochondria Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-22 Engi Hassaan
Early-onset Parkinson’s disease (EOPD) is a movement disorder caused by loss of specific neurons in the midbrain that are responsible for fine motor control. Mutations in the ubiquitin ligase parkin and the kinase PINK1 (which work together to target degradation of damaged mitochondria) cause EOPD, as mitochondrial homeostasis is crucial for neuronal survival. Upon mitochondrial damage, PINK1 accumulates
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A cerium-dependent photoenzyme Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-22 Majda Bratovič
Enzymes efficiently catalyze numerous reactions, but re-engineering them to speed up reactions that are not known in nature is challenging. Lanthanides, particularly cerium complexes, have previously been used in photocatalytic transformations that proceed via radical species. However, these radical reactions are rarely stereoselective. In an effort to address this, Klein, Leiss-Maier et al. developed
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Predicting small-molecule partitioning Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-22 Russell Johnson
Biomolecular condensates perform their cellular functions via the exclusion or enrichment of molecules. Analyzing the composition of condensates is important for understanding their properties and functions. A considerable amount of work has gone into understanding the nucleic acid and protein components of condensates; however, much less is known about partitioning of small molecules and the determinants
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Studying ATP synthesis in situ Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-22 Benjamin McIlwain
Mitochondria have a crucial role in replenishing ATP, the molecule used to provide cellular energy. This is achieved by tightly coupling the movement of protons (H+) across the inner mitochondrial membrane to power the rotary action of ATP synthase in the final step of oxidative phosphorylation. Folds of the inner mitochondrial membrane called cristae provide a large, ion-impermeable surface area studded
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Targeting proteins to lysosomes with a chemical inducer of arginine methylation Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-22
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Paenilamicins bind to a unique site on the ribosome to inhibit protein synthesis Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-22
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Selective targeting of oncogenic hotspot mutations of the HER2 extracellular domain Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-22 Injin Bang, Takamitsu Hattori, Nadia Leloup, Alexis Corrado, Atekana Nyamaa, Akiko Koide, Ken Geles, Elizabeth Buck, Shohei Koide
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Designed with interactome-based deep learning Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-18 Xueying Mao, Yanyi Chu, Dongqing Wei
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Paenilamicins are context-specific translocation inhibitors of protein synthesis Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-17 Timm O. Koller, Max J. Berger, Martino Morici, Helge Paternoga, Timur Bulatov, Adriana Di Stasi, Tam Dang, Andi Mainz, Karoline Raulf, Caillan Crowe-McAuliffe, Marco Scocchi, Mario Mardirossian, Bertrand Beckert, Nora Vázquez-Laslop, Alexander S. Mankin, Roderich D. Süssmuth, Daniel N. Wilson
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Fucosylation of glycoproteins and glycolipids: opposing roles in cholera intoxication Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-16 Atossa C. Ghorashi, Andrew Boucher, Stephanie A. Archer-Hartmann, Dani Zalem, Mehrnoush Taherzadeh Ghahfarrokhi, Nathan B. Murray, Rohit Sai Reddy Konada, Xunzhi Zhang, Chao Xing, Susann Teneberg, Parastoo Azadi, Ulf Yrlid, Jennifer J. Kohler
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Methylarginine targeting chimeras for lysosomal degradation of intracellular proteins Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-16 Laurence J. Seabrook, Carolina N. Franco, Cody A. Loy, Jaida Osman, Callie Fredlender, Jan Zimak, Melissa Campos, Steven T. Nguyen, Richard L. Watson, Samantha R. Levine, Marian F. Khalil, Kaelyn Sumigray, Darci J. Trader, Lauren V. Albrecht
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A broad anti-anti-CRISPR strategy Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-15 Yi Zhang, Yue Feng
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ML-enhanced peroxisome capacity enables compartmentalization of multienzyme pathway Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-14 Jordan J. Baker, Jie Shi, Shangying Wang, Elena M. Mujica, Simone Bianco, Sara Capponi, John E. Dueber
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Mechanism of nucleosomal H2A K13/15 monoubiquitination and adjacent dual monoubiquitination by RNF168 Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-11 Huasong Ai, Zebin Tong, Zhiheng Deng, Qiang Shi, Shixian Tao, Gaoge Sun, Jiawei Liang, Maoshen Sun, Xiangwei Wu, Qingyun Zheng, Lujun Liang, Hang Yin, Jia-Bin Li, Shuai Gao, Changlin Tian, Lei Liu, Man Pan
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Sensitive fluorescent biosensor reveals differential subcellular regulation of PKC Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-10-11 Qi Su, Jing Zhang, Wei Lin, Jin-Fan Zhang, Alexandra C. Newton, Sohum Mehta, Jing Yang, Jin Zhang
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Chemical signaling in biofilm-mediated biofouling Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-30 Xiaobo Liu, Ling Zou, Boqiao Li, Patrick Di Martino, Daniel Rittschof, Jin-Long Yang, James Maki, Weijie Liu, Ji-Dong Gu
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Unlocking the electrochemical functions of biomolecular condensates Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-26 Yifan Dai, Zhen-Gang Wang, Richard N. Zare
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Direct mapping of tyrosine sulfation states in native peptides by nanopore Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-25 Hongyan Niu, Meng-Yin Li, Yan Gao, Jun-Ge Li, Jie Jiang, Yi-Lun Ying, Yi-Tao Long
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Orthogonal redox control Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-24 Lena M. Hümmler, Steffen N. Lindner
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Partitioning of a 2-bit hash function across 66 communicating cells Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-24 Jai P. Padmakumar, Jessica J. Sun, William Cho, Yangruirui Zhou, Christopher Krenz, Woo Zhong Han, Douglas Densmore, Eduardo D. Sontag, Christopher A. Voigt
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Functional profiling of serine, threonine and tyrosine sites Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-23 Yizhou Li, Tao Xu, Huazheng Ma, Di Yue, Qiezhong Lamao, Ying Liu, Zhuo Zhou, Wensheng Wei
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Where chemical biology meets physiology Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-20 Kimberly E. Beatty, Carsten Schultz
Research in the early days of chemical biology was mostly limited to the application of chemical tools to model cell lines grown in incubators. Now, discoveries are being made in more physiologically relevant systems, from tissues to organisms, using precisely targeted molecules. The 2023 Chemical Biology & Physiology meeting (in Portland, Oregon) discussed the latest advances in the field, with research
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Beware of extreme calculated lipophilicity when designing cyclic peptides Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-19 Vasanthanathan Poongavanam, Duc Duy Vo, Jan Kihlberg
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A tRNA modification with aminovaleramide facilitates AUA decoding in protein synthesis Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-19 Kenjyo Miyauchi, Satoshi Kimura, Naho Akiyama, Kazuki Inoue, Kensuke Ishiguro, Thien-Son Vu, Veerasak Srisuknimit, Kenta Koyama, Gosuke Hayashi, Akiko Soma, Asuteka Nagao, Mikako Shirouzu, Akimitsu Okamoto, Matthew K. Waldor, Tsutomu Suzuki
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Compact RNA editors with natural miniature Cas13j nucleases Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-19 Guo Li, Yaxian Cheng, Jingwen Yu, Yunfei Zhu, Hongru Ma, Yuqiao Zhou, Zhongji Pu, Guanglin Zhu, Yichen Yuan, Ziyue Zhang, Xinzhi Zhou, Kairen Tian, Jianjun Qiao, Xiaoxiang Hu, Xue-xin Chen, Quanjiang Ji, Xingxu Huang, Bin Ma, Yuan Yao
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Breaking down taurine Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-18 Grant Miura
N-acetyltaurine is a metabolite whose levels fluctuate with diet and exercise and that undergoes hydrolysis to form taurine and acetate. However, the enzymes that facilitate this reaction were not known. In an effort to address this, Wei et al. used liquid chromatography–mass spectrometry-based activity guided analysis of mouse tissues, detecting high N-acetyltaurine hydrolysis activity in kidney and
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Anti-aggregate activity Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-18 Russell Johnson
The formation of pathological protein aggregates occurs in many neurodegenerative diseases, such as the aggregation of the protein tau in patients with Alzheimer’s disease. Removing these aggregates offers a possible route to treat these protein misfolding diseases; however, targeting the aggregated form of a protein while sparing the monomeric form, which is required for normal cellular function,
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Sweet RNA Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-18 Yiyun Song
By coupling rPAL to enzymatic glycan cleavage and sequential window acquisition of all theoretical mass spectra (SWATH-MS), the team found that acp3U was the most enriched linker (although other putative linker substrates were identified). Importantly, knocking out DTWD2, an enzyme responsible for installing acp3U in tRNAs, reduced glycoRNA levels. This study provides not only a useful tool for glycoRNA
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An allosteric cyclin E-CDK2 site mapped by paralog hopping with covalent probes Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-18 Yuanjin Zhang, Zhonglin Liu, Marscha Hirschi, Oleg Brodsky, Eric Johnson, Sang Joon Won, Asako Nagata, Divya Bezwada, Matthew D. Petroski, Jaimeen D. Majmudar, Sherry Niessen, Todd VanArsdale, Adam M. Gilbert, Matthew M. Hayward, Al E. Stewart, Andrew R. Nager, Bruno Melillo, Benjamin F. Cravatt
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Multicellular artificial neural network-type architectures demonstrate computational problem solving Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-16 Deepro Bonnerjee, Saswata Chakraborty, Biyas Mukherjee, Ritwika Basu, Abhishek Paul, Sangram Bagh
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Biosynthesis of peptide–nucleobase hybrids in ribosomal peptides Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-16 Zeng-Fei Pei, Natalia M. Vior, Lingyang Zhu, Andrew W. Truman, Satish K. Nair
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Incorporation of nitrogen in antinutritional Solanum alkaloid biosynthesis Nat. Chem. Biol. (IF 12.9) Pub Date : 2024-09-13 Dagny Grzech, Samuel J. Smit, Ryan M. Alam, Marianna Boccia, Yoko Nakamura, Benke Hong, Ranjit Barbole, Sarah Heinicke, Maritta Kunert, Wibke Seibt, Veit Grabe, Lorenzo Caputi, Benjamin R. Lichman, Sarah E. O’Connor, Asaph Aharoni, Prashant D. Sonawane