bioRxiv : the preprint server for biology最新文献

{"title":"Dual-specific autophosphorylation of kinase IKK2 enables phosphorylation of substrate IκBα through a phosphoenzyme intermediate.","authors":"Prateeka Borar, Tapan Biswas, Ankur Chaudhuri, Pallavi Rao T, Swasti Raychaudhuri, Tom Huxford, Saikat Chakrabarti, Gourisankar Ghosh, Smarajit Polley","doi":"10.1101/2023.06.27.546692","DOIUrl":"10.1101/2023.06.27.546692","url":null,"abstract":"<p><p>Rapid and high-fidelity phosphorylation of serine residues at positions 32 and 36 of IκBα by IKK2, a prototypical Ser/Thr kinase, is critical for canonical NF-κB activation. Here, we report that IKK2 not only phosphorylates substrate serine residues and autophosphorylates its own activation loop, but also autophosphorylates at a tyrosine residue proximal to the active site and is, therefore, a dual-specificity kinase. We observed that mutation of Y169, an autophosphorylatable tyrosine located at the DFG+1 (DLG in IKK1) position, to phenylalanine renders IKK2 incapable of catalyzing phosphorylation at S32 within its IκBα substrate. We also observed that mutation of the phylogenetically conserved ATP-contacting residue K44 in IKK2 to methionine converts IKK2 to an enzyme that no longer catalyzes specific phosphorylation of IκBα at S32 or S36, but rather directs phosphorylation of IκBα at other residues. Lastly, we report evidence of a phospho-relay from autophosphorylated IKK2 to IκBα in the presence of ADP. These observations suggest an unusual evolution of IKK2, in which autophosphorylation of tyrosine(s) in the activation loop, and the conserved ATP-contacting K44 residue provide its signal-responsive substrate specificity and ensure fidelity during NF-κB activation.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10508718/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41175010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Immunotherapy for ovarian cancer is improved by tumor-targeted delivery of a neoantigen surrogate.","authors":"Lauren Rose Scanlon, Lisa Gabor, Olivia Khouri, Shahbaz Ahmad, Evan Levy, Elizabeth Buckley, Ariene Ouedraogo, Dennis Yi-Shin Kuo, Ken Lin, Nicole Nevadunsky, Sara Isani, Shixiang Sun, Claudia Gravekamp","doi":"10.1101/2023.10.11.561944","DOIUrl":"10.1101/2023.10.11.561944","url":null,"abstract":"<p><p>Ovarian cancer is known for its poor neoantigen expression and strong immunosuppression. Here, we utilized an attenuated non-pathogenic bacterium <i>Listeria monocytogenes</i> to deliver a highly immunogenic Tetanus Toxoid protein (Listeria-TT), as a neoantigen surrogate, into tumor cells through infection in a metastatic mouse ovarian cancer model (Id8p53-/-Luc). Gemcitabine (GEM) was added to reduce immune suppression. Listeria-TT+GEM treatments resulted in tumors expressing TT and reactivation of pre-existing CD4 and CD8 memory T cells to TT (generated early in life). These T cells were then attracted to the TT-expressing tumors now producing perforin and granzyme B. This correlated with a strong reduction in tumor burden, and significant improvement of the survival time compared to all control groups. Checkpoint inhibitors have little effect on ovarian cancer partly because of low neoantigen expression. Here we demonstrated that Listeria-TT+GEM+anti-PD1 was significantly more effective (efficacy and survival) than anti-PD1 or Listeria-TT+GEM alone. Of clinical interest, high doses of anti-PD1 (PD1H) (when added to Listeria-TT+GEM) were less effective than the low doses (PD1L). IHC and ELISPOT demonstrated that high doses of anti-PD1 inhibited T cell function in the TME. Using RNAseq, Differentially Expressed Genes (DEG) analysis and Genes Set Enrichment Analysis (GSEA) showed that gene expression levels and biological pathways were predominantly upregulated in the PD1H compared to the PD1L group, in correlation with low immune infiltration in tumors, more immune suppression, and more aggressive ovarian cancer. In summary, this study suggests that our approach may benefit ovarian cancer patients.</p><p><strong>Abstract figure: </strong></p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10592780/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49694752","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular signature and functional properties of human pluripotent stem cell-derived brain pericytes.","authors":"Ruslan Rust, Abhay P Sagare, Kassandra Kisler, Youbin Kim, Mingzi Zhang, Casey Griffin, Yaoming Wang, Veronica Clementel, Carina Torres-Sepulveda, Julia Tcw, Berislav V Zlokovic, Marcelo P Coba","doi":"10.1101/2023.06.26.546577","DOIUrl":"10.1101/2023.06.26.546577","url":null,"abstract":"<p><p>Brain pericytes maintain the blood-brain barrier (BBB), secrete neurotrophic factors and clear toxic proteins. Their loss in neurological disorders leads to BBB breakdown, neuronal dysfunction, and cognitive decline. Therefore, cell therapy to replace lost pericytes holds potential to restore impaired cerebrovascular and brain functions. However, the molecular composition and function of human iPSC-derived brain pericytes (iPSC-PC) remains poorly characterized. Here, we show by a quantitative analysis of 8,344 proteins and 20,572 phosphopeptides that iPSC-PC share 96% of total proteins and 98% of protein phosphorylation sites with primary human brain pericytes. This includes cell adhesion and tight junction proteins, transcription factors, and different protein kinase families of the human kinome. In pericyte-deficient mice, iPSC-PC home to host brain capillaries to form hybrid human-mouse microvessels with ligand-receptor associations. They repair BBB leaks and protect against neuron loss, which we show requires PDGRFB and pleiotrophin. They also clear Alzheimer's amyloid-β and tau neurotoxins via lipoprotein receptor. Thus, iPSC-PC may have potential as a replacement therapy for pericyte-deficient neurological disorders.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12026417/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82085031","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stable isotope tracing in human plasma-like medium reveals metabolic and immune modulation of the glioblastoma microenvironment.","authors":"Milan R Savani, Mohamad El Shami, Lauren C Gattie, Bailey C Smith, William H Hicks, Skyler S Oken, Lauren G Zacharias, Misty S Martin-Sandoval, Eric Y Montgomery, Yi Xiao, Diana D Shi, Jeremy N Rich, Timothy E Richardson, Pascal O Zinn, Bradley C Lega, Thomas P Mathews, Ralph J DeBerardinis, Samuel K McBrayer, Kalil G Abdullah","doi":"10.1101/2023.05.29.542774","DOIUrl":"10.1101/2023.05.29.542774","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;In vivo stable isotope tracing is useful for natively surveying glioma metabolism but can be difficult to implement. Stable isotope tracing is tractable using in vitro glioma models, but most models lack nutrient conditions and cell populations relevant to human gliomas. This limits our ability to study glioma metabolism in the presence of an intact tumor microenvironment (TME) and immune-metabolic crosstalk.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;We optimized an in vitro stable isotope tracing approach for human glioma explants and glioma stem-like cell (GSC) lines that integrates human plasma-like medium (HPLM). We performed &lt;sup&gt;15&lt;/sup&gt; N &lt;sub&gt;2&lt;/sub&gt; -glutamine tracing in GSC monocultures and human IDH-wildtype glioblastoma explants and developed an analytical framework to evaluate microenvironment-dependent metabolic features that distinguish them. We also conducted spatial transcriptomics to assess transcriptional correlates to metabolic activities.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;HPLM culture preserved glioma explant viability and stemness while unmasking metabolic and immune programs suppressed by conventional culture conditions. Stable isotope tracing in HPLM revealed TME-dependent and TME-independent features of tumor metabolism. Tissue explants recapitulated tumor cell-intrinsic metabolic activities, such as synthesis of immunomodulatory purines. Unlike GSC monocultures, tissue explants captured tumor cell- extrinsic activities associated with stromal cell metabolism, as exemplified by astrocytic GDP- mannose production in heterocellular explants. Finally, glioma explants displayed tumor subtype-specific metabolic reprogramming, including robust pyrimidine degradation in mesenchymal cells.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;We present a tractable approach to assess glioma metabolism in vitro under physiological nutrient levels and in the presence of an intact TME. This platform opens new avenues to interrogate glioma metabolism and its interplay with the immune microenvironment.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance of the study: &lt;/strong&gt;Metabolic reprogramming is a hallmark of tumor biology, but in vitro studies of glioma metabolism often fail to replicate the nutrient complexity and cellular heterogeneity of the TME. We developed a method to perform stable isotope tracing in glioma explants grown in HPLM to analyze metabolism in a nutrient context that reflects in vivo conditions. By comparing metabolic activities between glioma cell monocultures and explanted tumor tissues, our approach captures features of tumor metabolism that are driven by the microenvironment. We show that HPLM not only sustains cell fitness and identity in tumor explants but also evokes distinct metabolic patterns and immune activation signatures repressed by standard culture conditions. Our approach offers a tractable and scalable way to study tumor cell intrinsic and microenvironmental metabolism in faithful tissue culture glioma models, comple","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10312566/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9761035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optogenetic Stimulation of Single Ganglion Cells in the Living Primate Fovea.","authors":"Peter J Murphy, Juliette E McGregor, Zhengyang Xu, Qiang Yang, William Merigan, David R Williams","doi":"10.1101/2023.07.21.550081","DOIUrl":"10.1101/2023.07.21.550081","url":null,"abstract":"<p><p>Though the responses of the rich variety of retinal ganglion cells (RGCs) reflect the totality of visual processing in the retina and provide the sole conduit for those processed responses to the brain, we have much to learn about how the brain uses these signals to guide behavior. An impediment to developing a comprehensive understanding of the role of retinal circuits in behavior is the paucity of causal studies in the intact primate visual system. Here we demonstrate the ability to optogenetically activate individual RGCs with flashes of light focused on single RGC somas <i>in vivo</i> , with no evidence for activation of neighboring cells. The ability to selectively activate specific cells is the first step toward causal experiments that directly link retinal circuits to visual experience and behavior.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/5b/fb/nihpp-2023.07.21.550081v1.PMC10401937.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10369451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impaired hippocampal circuit function underlying memory encoding and consolidation precede robust Aβ deposition in a mouse model of Alzheimer's disease.","authors":"Hanyan Li, Zhuoyang Zhao, Aline Fassini, Han K Lee, Reese J Green, Stephen N Gomperts","doi":"10.1101/2024.05.26.595168","DOIUrl":"10.1101/2024.05.26.595168","url":null,"abstract":"<p><p>Current therapeutic strategies for Alzheimer's disease (AD) target amyloid-beta (Aβ) fibrils and high molecular weight protofibrils associated with plaques, but molecular cascades associated with AD may drive neural systems failure before Aβ plaque deposition in AD. Employing hippocampal electrophysiological recordings and dynamic calcium imaging across the sleep-wake cycle in a freely behaving mouse model of AD before Aβ plaques accumulated, we detected marked impairments of hippocampal systems function: In a spatial behavioral task, phase-amplitude coupling (PAC) of the hippocampal theta and gamma oscillations was impaired and place cell calcium fluctuations were hyper-synchronized with the theta oscillation. These changes were not observed in REM sleep. In subsequent slow wave sleep (SWS), place cell reactivation was reduced. These degraded neural functions underlying memory encoding and consolidation support targeting pathological processes of the pre-plaque phase of AD to treat and prevent hippocampal impairments.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11160633/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141297436","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Expansion-assisted selective plane illumination microscopy for nanoscale imaging of centimeter-scale tissues.","authors":"Adam Glaser, Jayaram Chandrashekar, Sonya Vasquez, Cameron Arshadi, Rajvi Javeri, Naveen Ouellette, Xiaoyun Jiang, Judith Baka, Gabor Kovacs, Micah Woodard, Sharmishtaa Seshamani, Kevin Cao, Nathan Clack, Andrew Recknagel, Anna Grim, Pooja Balaram, Emily Turschak, Marcus Hooper, Alan Liddell, John Rohde, Ayana Hellevik, Kevin Takasaki, Lindsey Erion Barner, Molly Logsdon, Chris Chronopoulos, Saskia de Vries, Jonathan Ting, Steve Perlmutter, Brian Kalmbach, Nikolai Dembrow, Bosiljka Tasic, R Clay Reid, David Feng, Karel Svoboda","doi":"10.1101/2023.06.08.544277","DOIUrl":"10.1101/2023.06.08.544277","url":null,"abstract":"<p><p>Recent advances in tissue processing, labeling, and fluorescence microscopy are providing unprecedented views of the structure of cells and tissues at sub-diffraction resolutions and near single molecule sensitivity, driving discoveries in diverse fields of biology, including neuroscience. Biological tissue is organized over scales of nanometers to centimeters. Harnessing molecular imaging across intact, three-dimensional samples on this scale requires new types of microscopes with larger fields of view and working distance, as well as higher throughput. We present a new expansion-assisted selective plane illumination microscope (ExA-SPIM) with aberration-free 1.5 µm×1.5 µm×3 µm optical resolution over a large field of view (10.6×8.0 mm ² ) and working distance (35 mm) at speeds up to 946 megavoxels/sec. Combined with new tissue clearing and expansion methods, the microscope allows imaging centimeter-scale samples with 375 nm lateral and 750 nm axial resolution (4× expansion), including entire mouse brains, with high contrast and without sectioning. We illustrate ExA-SPIM by reconstructing individual neurons across the mouse brain, imaging cortico-spinal neurons in the macaque motor cortex, and visualizing axons in human white matter.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10327101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9810185","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Submitochondrial Protein Translocation in Thermogenic Regulation.","authors":"Fahrettin Haczeyni, James M Jordan, Benjamin D Stein, Sandra Steensels, Le Li, Vincent Dartigue, Selenay S Sarklioglu, Jixuan Qiao, Xi K Zhou, Andrew J Dannenberg, Neil M Iyengar, Haiyuan Yu, Lewis C Cantley, Baran A Ersoy","doi":"10.1101/2023.05.04.539294","DOIUrl":"10.1101/2023.05.04.539294","url":null,"abstract":"<p><p>Mitochondria-rich brown adipocytes dissipate cellular energy as heat. Excessive nutrition or prolonged cold exposure suppress thermogenesis, but the mechanisms remain incompletely understood. Here we report that excessive cold or metabolic stress-induced proton leak into the matrix interface of mitochondrial innermembrane (IM) mobilizes 73 proteins from IM into matrix, which in turn alter mitochondrial bioenergetics. Interactome analysis indicates that key subunits of the electron transport chain and the mitochondrial calcium uniporter provide histidine-rich IM docking sites for 40 translocating proteins via pH-dependent protein-protein interactions. We further determine that 34% of translocating proteins correlate with obesity in human subcutaneous adipose tissue among which the top factor, acyl-CoA thioesterase 9 (ACOT9), enzymatically deactivates and prevents the utilization of acetyl-CoA in thermogenesis and promotes obesity. Overall, this study introduces stress-induced submitochondrial protein translocation as a new mitochondrial mechanism.</p><p><strong>One-sentence summary: </strong>Mitochondrial stress regulates energy utilization by forcing translocation of IM-bound proteins into the matrix.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10187325/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9544962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"T cell transcriptional landscapes are shaped by TCR sequence similarity.","authors":"Hao Wang, Zhicheng Ji","doi":"10.1101/2023.11.27.568912","DOIUrl":"10.1101/2023.11.27.568912","url":null,"abstract":"<p><p>T cells exhibit high heterogeneity in both their gene expression profiles and antigen specificities, but the precise relationship between these two features remains largely unknown. Utilizing a large-scale single-cell immune-profiling dataset that includes both T cell receptor (TCR) sequences and gene expression profiles of individual cells, we systematically investigated how the transcriptional profiles of T cells are linked to their TCR sequence similarity. We observed that T cells sharing the same clonotype often belong to the same cell type, and that gene expression similarity among T cells correlates with TCR sequence similarity. Furthermore, we identified features such as clonality, VJ gene usage, sequence motifs, and amino acid preferences that are distinctly associated with specific T cell subtypes. These findings suggest that T cell transcriptional landscapes are broadly shared and influenced by TCR sequence similarity.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10705237/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138811044","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of binding kinetics and intracellular signaling of new psychoactive substances targeting cannabinoid receptor using transition-based reweighting method.","authors":"Soumajit Dutta, Diwakar Shukla","doi":"10.1101/2023.09.29.560261","DOIUrl":"10.1101/2023.09.29.560261","url":null,"abstract":"<p><p>New psychoactive substances (NPS) targeting cannabinoid receptor 1 pose a significant threat to society as recreational abusive drugs that have pronounced physiological side effects. These greater adverse effects compared to classical cannabinoids have been linked to the higher downstream <i>β</i> -arrestin signaling. Thus, understanding the mechanism of differential signaling will reveal important structure-activity relationship essential for identifying and potentially regulating NPS molecules. In this study, we simulate the slow (un)binding process of NPS MDMB-Fubinaca and classical cannabinoid HU-210 from CB ₁ using multi-ensemble simulation to decipher the effects of ligand binding dynamics on downstream signaling. The transition-based reweighing method is used for the estimation of transition rates and underlying thermodynamics of (un)binding processes of ligands with nanomolar affinities. Our analyses reveal major interaction differences with transmembrane TM7 between NPS and classical cannabinoids. A variational autoencoder-based approach, neural relational inference (NRI), is applied to assess the allosteric effects on intracellular regions attributable to variations in binding pocket interactions. NRI analysis indicate a heightened level of allosteric control of NPxxY motif for NPS-bound receptors, which contributes to the higher probability of formation of a crucial triad interaction (Y ^7.53 -Y ^5.58 -T ^3.46 ) necessary for stronger <i>β</i> -arrestin signaling. Hence, in this work, MD simulation, data-driven statistical methods, and deep learning point out the structural basis for the heightened physiological side effects associated with NPS, contributing to efforts aimed at mitigating their public health impact.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10592854/pdf/nihpp-2023.09.29.560261v1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49694748","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}