Zinc Binding Properties of Engineered RING Finger Domain of Arkadia E3 Ubiquitin Ligase by Christos T. Chasapis, Ariadni K. Loutsidou, Malvina G. Orkoula, Georgios A. Spyroulias

“…Atomic absorption measurements and preliminary NMR data analysis reveal that the C955R point mutation in the RING Finger domain of Arkadia diminishes dramatically the zinc binding affinity, leading to the breakdown of the global structural integrity of the RING construct.…”
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The nucleoid protein Dps binds genomic DNA of Escherichia coli in a non-random manner. by S S Antipov, M N Tutukina, E V Preobrazhenskaya, F A Kondrashov, M V Patrushev, S V Toshchakov, I Dominova, U S Shvyreva, V V Vrublevskaya, O S Morenkov, N A Sukharicheva, V V Panyukov, O N Ozoline

“…In most cases this can be explained by the relieved interference with Dps for nucleoid proteins exploiting sequence-specific modes of DNA binding. Thus, protecting bacterial cells from different stresses during exponential growth, Dps can modulate transcriptional integrity of the bacterial chromosome hampering RNA biosynthesis from some genes via competition with RNA polymerase or, vice versa, competing with inhibitors to activate transcription.…”
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The Replicative Consequences of Papillomavirus E2 Protein Binding to the Origin Replication Factor ORC2. by Marsha DeSmet, Sriramana Kanginakudru, Anne Rietz, Wai-Hong Wu, Richard Roden, Elliot J Androphy

“…To initiate its replication, the viral E2 protein binds to and recruits the E1 DNA helicase at the viral origin. …”
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The RNA Binding Protein Bcas2 is Required for Antibody Class Switch in Activated‐B Cells by Yu Chen, Siyuan Sun, Chenxu Lu, Yixuan Li, Bing Fang, Xiangfeng Tang, Xuepeng Li, Weiru Yu, Yumei Lei, Longjie Sun, Ming Zhang, Jiazeng Sun, Ping Liu, Yongting Luo, Xingwang Zhao, Jing Zhan, Libing Liu, Rong Liu, Jiaqiang Huang, Ziwei Yi, Yifei Yu, Weihan Xiao, Zheng Ding, Lei Li, Dan Su, Fazheng Ren, Changchang Cao, Ran Wang, Wenbiao Shi, Juan Chen

“…The antibody diversity is partially determined by the alternative splicing (AS) in the germline, which is mainly regulated by RNA‐binding proteins, including Breast cancer amplified sequence 2 (Bcas2). …”
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Binding Affinity Prediction for Pancreatic Ductal Adenocarcinoma Using Drug-Target Descriptors and Artificial Intelligence by Pragya, A. Amalin Prince, Jac Fredo Agastinose Ronickom

“…This study addresses the gap in disease-specific binding affinity prediction by integrating PDAC-derived targets with diverse molecular descriptors and artificial intelligence (AI) models, enabling more accurate therapeutic profiling. …”
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A Novel CTC-Binding Probe: Enzymatic vs. Shear Stress-Based Detachment Approaches by Sophia Krakowski, Sara Campos, Henri Wolff, Gabi Bondzio, Felix Hehnen, Michael Lommel, Ulrich Kertzscher, Paul Friedrich Geus

“…The influence on the integrity and viability of cells must, however, be considered.…”
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Generation of recombinant rabies virus ERA strain applied to virus tracking in cell infection by Dan-dan ZHAO, Lei SHUAI, Jin-ying GE, Jin-liang WANG, Zhi-yuan WEN, Ren-qiang LIU, Chong WANG, Xi-jun WANG, Zhi-gao BU

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SNX27-Retromer directly binds ESCPE-1 to transfer cargo proteins during endosomal recycling. by Boris Simonetti, Qian Guo, Manuel Giménez-Andrés, Kai-En Chen, Edmund R R Moody, Ashley J Evans, Mintu Chandra, Chris M Danson, Tom A Williams, Brett M Collins, Peter J Cullen

“…Coat complexes coordinate cargo recognition through cargo adaptors with biogenesis of transport carriers during integral membrane protein trafficking. Here, we combine biochemical, structural, and cellular analyses to establish the mechanistic basis through which SNX27-Retromer, a major endosomal cargo adaptor, couples to the membrane remodeling endosomal SNX-BAR sorting complex for promoting exit 1 (ESCPE-1). …”
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LABind: identifying protein binding ligand-aware sites via learning interactions between ligand and protein by Zhijun Zhang, Lijun Quan, Junkai Wang, Liangchen Peng, Qiufeng Chen, Bei Zhang, Lexin Cao, Yelu Jiang, Geng Li, Liangpeng Nie, Tingfang Wu, Qiang Lyu

“…Further analysis validates that LABind can effectively integrate ligand information to predict binding sites. …”
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Perturbation of EPHA2 and EFNA1 trans binding amplifies inflammatory response in airway epithelial cells by Ryosuke Fukuda, Shiori Beppu, Daichi Hinata, Yuka Kamada, Tsukasa Okiyoneda

“…Summary: The interactions between EPH receptors and ephrin (EFN) ligands play a crucial role in maintaining epithelial integrity and aiding in defense against infections. …”
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Real-time monitoring of ssDNA binding using a fiber optic LSPR microfluidic platform by Vivek Semwal, Asbjørn Meldgaard Moltke, Ole Bang, Jakob Janting

“…The LSPR chip was fabricated using gold nanoparticles (AuNPs) with a diameter of 80 nm. It was integrated with a microfluidic chamber to ensure stable measurements. …”
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ELAV/Hu RNA-binding protein family: key regulators in neurological disorders, cancer, and other diseases by Huxitaer Wutikeli, Ting Xie, Wenjun Xiong, Yin Shen

“…The ELAV/Hu family represents a crucial group of RNA-binding proteins predominantly expressed in neurons, playing significant roles in mRNA transcription and translation. …”
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Discovery, Biological Evaluation and Binding Mode Investigation of Novel Butyrylcholinesterase Inhibitors Through Hybrid Virtual Screening by Lizi Li, Puchen Zhao, Can Yang, Qin Yin, Na Wang, Yan Liu, Yanfang Li

“…Fluorescence spectroscopy, molecular docking, and molecular dynamics simulations further clarified their binding modes and stability. This study provides an innovative screening strategy for the discovery of BChE inhibitors, which not only identifies promising drug candidates for the treatment of AD but also demonstrates the potential of machine learning in drug discovery.…”
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Elevated EGR1 binding at enhancers in excitatory neurons correlates with neuronal subtype-specific epigenetic regulation by Liduo Yin, Xiguang Xu, Benjamin Conacher, Yu Lin, Gabriela L. Carrillo, Yupeng Cun, Michael A. Fox, Xuemei Lu, Hehuang Xie

“…Further CUT&RUN assay confirmed that excitatory neurons exhibit more EGR1 binding sites, primarily located in enhancers. Integrative analysis demonstrated that EGR1 binding is strongly correlated with various epigenetic markers of open chromatin regions and is linked to distinct gene pathways specific to neuronal subtypes. …”
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Plasticity of BRCA2 function in homologous recombination: genetic interactions of the PALB2 and DNA binding domains. by Nicolas Siaud, Maria A Barbera, Akinori Egashira, Isabel Lam, Nicole Christ, Katharina Schlacher, Bing Xia, Maria Jasin

“…Conversely, a BRCA2 fusion peptide deleted for the PALB2 binding domain is dependent on an intact DNA binding domain, providing a role for this conserved domain in vivo; mutagenesis suggests that both single-stranded and double-stranded DNA binding activities in the DNA binding domain are required for its activity. …”
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The origin of hydroxy-cyclohexenone fatty acids from skin barrier protein and relevance to covalent binding of ceramides by Saori Noguchi, William E. Boeglin, Fumie Nakashima, Donald F. Stec, M. Wade Calcutt, Takuya Takeichi, Masashi Akiyama, Alan R. Brash

“…Lipid constituents of the skin permeability barrier include a portion of ceramides and fatty acids covalently bound to the barrier protein. The covalent binding requires enzymatic oxidation of linoleate (C18:2) esterified to skin-specific acylceramides, forming a reactive 9,10-epoxy-11E-13-keto derivative. …”
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The algebraic extended atom-type graph-based model for precise ligand–receptor binding affinity prediction by Farjana Tasnim Mukta, Md Masud Rana, Avery Meyer, Sally Ellingson, Duc D. Nguyen

“…Abstract Accurate prediction of ligand-receptor binding affinity is crucial in structure-based drug design, significantly impacting the development of effective drugs. …”
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Impact of ligand binding on VEGFR1, VEGFR2, and NRP1 localization in human endothelial cells. by Sarvenaz Sarabipour, Karina Kinghorn, Kaitlyn M Quigley, Anita Kovacs-Kasa, Brian H Annex, Victoria L Bautch, Feilim Mac Gabhann

“…The vascular endothelial growth factor receptors (VEGFRs) bind to cognate ligands to facilitate signaling pathways critical for angiogenesis, the growth of new capillaries from existing vasculature. …”
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Artificial intelligence-assisted RNA-binding protein signature for prognostic stratification and therapeutic guidance in breast cancer by Yunxia Zhao, Li Li, Shuqi Yuan, Zixin Meng, Jiayi Xu, Zhaogen Cai, Yijing Zhang, Xiaonan Zhang, Tao Wang

“…BackgroundBreast cancer is the most common malignancy in women globally, with significant heterogeneity affecting prognosis and treatment. RNA-binding proteins play vital roles in tumor progression, yet their prognostic potential remains unclear. …”
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Molecular mapping and functional validation of GLP-1R cholesterol binding sites in pancreatic beta cells by Affiong Ika Oqua, Kin Chao, Liliane El Eid, Lisa Casteller, Billy P Baxter, Alba Miguéns-Gómez, Sebastian Barg, Ben Jones, Jorge Bernardino de la Serna, Sarah L Rouse, Alejandra Tomas

“…G protein-coupled receptors (GPCRs) are integral membrane proteins which closely interact with their plasma membrane lipid microenvironment. …”
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