Biology subjects

Liu, X.

Publications and source records attributed to Liu, X..

At least 505 records · Page 28Linked to original sources

bioRxiv2025

Deciphering the Sequence Basis and Application of Transcriptional Initiation Regulation in Plant Genomes Through Deep Learning

Transcription initiation is a critical regulatory step in plant gene expression, yet its sequence determinants remain largely elusive. Here we introduce GenoRetriever, an interpretable deep learning model that deciphers the sequence basis of transcriptional initiation regulation across plant genomes. Trained on STRIPE-seq data from 16 soybean tissues and six other crop species, GenoRetriever identifies 27 core sequence motifs that govern transcription start site (TSS) selection and usage. The model predicts TSS locations and usage levels with high accuracy, as validated by in silico motif insertions, saturation mutagenesis, and CRISPR-Cas9 promoter editing. It further reveals that 31.85% of natural variation between wild and domesticated soybean drives shifts in promoter motif usage during domestication, and uncovers lineage-specific motif effects between monocots and dicots. This interpretable model and its user-friendly web server for promoter analysis and design make GenoRetriever both a methodological innovation and practical tool for plant functional genomics and crop improvement.

plant biology↗

bioRxiv2025

Predicting Early Transitions in Respiratory Virus Infections via Critical Transient Gene Interactions

Early detection of respiratory virus infections, such as influenza A (H3N2), is critical for timely intervention and disease management. Conventional biomarkers often overlook the complex and dynamic nature of gene regulatory changes, while existing predictive models frequently lack automation and robust external validation. Thus, we present CRISGI (Critical tran-Sient Gene Interaction), a computational framework that detects early-warning signals of infection by identifying dynamic changes in gene-gene interactions--termed critical transient interactions--from bulk RNA-seq data. CRISGI leverages critical transition (CT) theory to capture a GRNs unstable intermediate state, known as the CT stage, before irreversible phenotypic shifts. Applied to a human challenge study with H3N2, CRISGI identified 128 critical transition edges (128-TER). These were used to train predictive models capable of forecasting symptom status and onset timing. 128-TER was then validated across six temporal transcriptomic datasets involving three respiratory viruses (H3N2, H1N1, HRV). The 128-TER consistently distinguished symptomatic individuals, predicted infection onset, and revealed phenotype-specific enrichment patterns. Notably, CRISGI captured immune-related transitions involving interferon-stimulated genes (e.g., IFIT1, CXCL10), underscoring their role in early host defense. CRISGI advances early-warning biomarker discovery by integrating interaction-level dynamics and predictive modeling. Its reproducibility across viruses highlights shared immune activation pathways, supporting its utility in both research and clinical contexts.

bioinformatics↗

bioRxiv2025

Ploidy and neuron size impact nervous system development and function in Xenopus

Neuron size varies significantly over evolution, contributing to diverse nervous systems of variable complexity, while aberrant neuron size is associated with neurodevelopmental and degenerative diseases. How do neuron cell body and neurite size and organization impact nervous system development and function? To systematically study effects of neuron size on the vertebrate nervous system, we characterized triploid Xenopus tadpoles that possess a 1.5-fold increase in genome size compared to diploids. Triploids displayed a linear increase in total neuronal volume and a superlinear increase in membrane surface area. Imaging, flow cytometry, and RNA-seq analyses revealed that triploid brains were morphologically and transcriptionally similar to diploid brains, but less proliferative, containing fewer neurons and displaying increased global activity. Interestingly, physiological differences at the neuron and nervous system levels affected swimming behavior in tadpoles. Our findings thus establish a framework to link genome size, neuron size, and nervous system development and function in vertebrates.

cell biology↗

bioRxiv2025

Catastrophic drought effects on water quality and phytoplankton biomass in Nanwan Reservoir (Xinyang, China)

Climate change has led to increasingly frequent and unpredictable droughts and high-temperature events, creating extreme conditions that profoundly impact the productivity of freshwater ecosystems. This study investigates the Nanwan Reservoir, a large and deep reservoir in Xinyang, China, to evaluate the effects of extreme drought events on water quality and phytoplankton production. Field investigations were conducted during both high-temperature and drought (HTD) conditions in 2019, and during non-high-temperature and drought (NHTD) conditions in 2020. Results showed that HTD conditions significantly disrupted the thermocline and oxycline structures, leading to prolonged stratification during the HTD period. Although phosphorus concentrations remained relatively stable across both periods, nitrogen levels were markedly lower during HTD events--likely due to uptake by phytoplankton--indicating a shift in nutrient limitation from phosphorus to nitrogen. Additionally, a complex relationship between environmental variables and phytoplankton biomass was observed under HTD conditions. These findings advance our understanding of primary production responses to extreme weather events in the Nanwan Reservoir and highlight the importance of incorporating such knowledge into water resource management and ecological conservation strategies.

ecology↗

bioRxiv2025

Knowledge-driven annotation for gene interaction enrichment analysis

Gene Set Enrichment Analysis (GSEA) is a cornerstone for interpreting gene expression data, yet traditional approaches overlook gene interactions by focusing solely on individual genes, limiting their ability to detect subtle or complex pathway signals. To overcome this, we present GREA (Gene Interaction Enrichment Analysis), a novel framework incorporating gene interaction data into enrichment analysis. GREA replaces the binary gene hit indicator with an interaction overlap ratio, capturing the degree of overlap between gene sets and gene interactions to enhance sensitivity and biological interpretability. It supports three enrichment metrics: Enrichment Score (ES), Enrichment Score Difference (ESD) from a Kolmogorov-Smirnov-based statistic, and Area Under the Curve (AUC) from a recovery curve. GREA evaluates statistical significance using both permutation testing and gamma distribution modeling. Benchmarking on transcriptomic datasets related to respiratory viral infections shows that GREA consistently outperforms existing tools such as blitzGSEA and GSEApy, identifying more relevant pathways with greater stability and reproducibility. By integrating gene interactions into pathway analysis, GREA offers a powerful and flexible tool for uncovering biologically meaningful insights in complex datasets. The source code is available at https://github.com/compbioclub/GREA.

bioinformatics↗

bioRxiv2025

SND1 Impairs Calcium Homeostasis in Right Ventricular Failure by Binding and Destabilizing SERCA2a in Cardiomyocytes

BackgroundRight ventricular failure (RVF) is a major contributor to a poor prognosis in patients with pulmonary arterial hypertension (PAH); however, its underlying molecular mechanisms remain incompletely understood. We identified a significant upregulation of the cardiac fetal gene SND1 in the right ventricular myocardium of RVF rats. This upregulation may be a key component of cardiac fetal reprogramming and play a critical role in RVF progression. However, the precise molecular mechanisms by which SND1 contributes to RVF remain unelucidated. MethodsRat models of PAH were established by intraperitoneal injection of monocrotaline (MCT). The pulmonary artery pressure and right ventricular function of rats were assessed using transthoracic echocardiography combined with right heart catheterization. Weighted gene co-expression network analysis (WGCNA) of proteomic data identified a significant association between SND1 upregulation and RVF progression. Calcium transient and contractility measurements in single cardiomyocytes were performed to evaluate the effect of SND1 on sarcoplasmic reticulum (SR) function. Liquid chromatography with mass spectrometry/mass spectrometry analysis combined with co-immunoprecipitation (Co-IP) was used to identify sarcoplasmic/endoplasmic reticulum Ca2+-ATPase 2A (SERCA2a) as the protein interacting with SND1. The effect of SND1 on the progression of RVF was validated using cardiomyocyte-specific SND1 conditional knockout rats. ResultsProteomic and molecular analyses revealed that the cardiac fetal gene SND1 is reactivated in RVF and may contribute to disease progression. In vitro, SND1 knockdown in neonatal rat ventricular myocytes (NRVMs) enhanced contractility, improved calcium transient amplitude and velocity, and increased cell survival under calcium overload. Mechanistically, SND1 interacts with SERCA2a and promotes its proteasomal degradation, impairing SR calcium reuptake. SND1 knockdown restored SERCA2a stability. In vivo, cardiomyocyte-specific SND1 knockout improved right ventricular function, reduced SERCA2a degradation and apoptosis, and increased survival in RVF rats. ConclusionOur study revealed that SND1 reactivation (a fetal gene) contributes to the progression of RVF by promoting SERCA2a degradation and impairing calcium handling. Targeted suppression of SND1 enhances cardiomyocyte contractility and survival, highlighting SND1 as a potential therapeutic target for improving right ventricular function in PAH. Clinical perspectiveO_ST_ABSWhat Is New?C_ST_ABSO_LIThis study identifies SND1, a reactivated fetal gene, as a key contributor to right ventricular failure (RVF) progression in pulmonary arterial hypertension (PAH). C_LIO_LISND1 interacts with SERCA2a, promoting its proteasomal degradation, which disrupts sarcoplasmic reticulum calcium reuptake and weakens cardiomyocyte contractility. C_LIO_LICardiomyocyte-specific SND1 deletion restores SERCA2a levels, improves calcium handling, enhances right ventricular function, and increases survival in RVF rats. C_LI What Are the Clinical Implications?O_LIThe reactivation of fetal genes such as SND1 is not just a marker but a pathogenic driver in maladaptive right ventricular remodeling. C_LIO_LITargeting SND1 represents a novel therapeutic approach to improve right ventricular contractility and prevent heart failure progression in patients with PAH. C_LIO_LIThese findings may inform the development of gene- or protein-targeted therapies aimed at stabilizing SERCA2a and preserving right heart function in high-risk populations. C_LI

cell biology↗

bioRxiv2025

Genetic and functional analysis of unproductive splicing using LeafCutter2

Alternative splicing commonly generates unproductive mRNA transcripts that harbor premature termination codons1, leading to their degradation by nonsense-mediated decay (NMD). These events reduce overall protein expression levels of affected genes, potentially contributing to gene regulation and disease mechanisms. Here, we present LeafCutter2, which enables identification and quantification of unproductive splicing from short-read RNA-seq data. LeafCutter2 requires minimal gene annotations (start and stop codons) to annotate NMD-inducing splicing events, and identifies differential unproductive splicing between groups, providing insights into its contributions to differential gene expression. Moreover, LeafCutter2 enables mapping of unproductive splicing quantitative trait loci (u-sQTLs), which often colocalize with expression QTLs and GWAS loci. Applying LeafCutter2 to RNA-seq data across human and 6 non-human species, we uncovered a broad landscape of unproductive splicing, which varies widely across tissues. Strikingly, we observed a conserved developmental-stage-specific increase in unproductive splicing during testis maturation across all species. In Alzheimers disease (AD), we analyzed RNA-seq data from the AD Functional Genomics consortium FunGen-xQTL project and identified unproductive splicing events in 18 AD risk genes, including TSPAN14, PICALM, and CASS4, likely mediating genetic effects on disease risk. We performed an integrative analysis using gene expression QTLs, protein expression QTLs, and AD GWAS data, showing that unproductive splicing provides unique regulatory insights beyond traditional approaches. Thus, LeafCutter2 represents a powerful tool for understanding the functional impact of alternative splicing on gene expression and disease mechanisms.

genomics↗

bioRxiv2025

Imputation Disparities Driven by Recent Selectionand Their Impact on Disease Risk Estimation in East and Southeast Asian Populations

Using genotype data consisting of 8,316 individuals, we systematically evaluated imputation performance across six state-of-the-art reference panels for Chinese and Thai populations. A substantial proportion of variants identified through whole-genome sequencing, especially low-frequency variants, remained undetected by existing reference panels. In the Chinese population, the TOPMed panel required an R2 threshold of 0.60-0.70 to achieve comparable imputation accuracy of the ChinaMAP panel without R2 filtering, challenging the standard practice of applying a fixed R2 threshold for downstream analyses. Regional analysis highlighted the role of recent selection in imputation discrepancies and revealed an enrichment of immune-related genes in poorly imputed regions. In addition, we showed that the selection of reference panels and R2 thresholds could significantly influence estimation of polygenic risk score for disease prediction. These findings underscore the importance of developing ancestrally diverse reference panels and provide valuable guidelines for improving genotype imputation in East and Southeast Asian populations.

genomics↗

bioRxiv2025

Population structure and domestication history of the Javan banteng (Bos javanicus javanicus)

The domestication of the banteng in Southeast Asia is one of the Worlds least known livestock domestications, yet a vital component of the agricultural system in Indonesia and surrounding countries. Here we generated the first reference genome of the banteng and used it to analyze a set of 78 resequenced wild and domesticated bantengs, including 19 newly generated whole-genome sequenced samples of which three are historical samples. We found low heterozygosity and significant differentiation, the latter primarily driven by recent genetic drift and inbreeding in two populations, and clearly attributable to anthropogenically driven founder events or ex-situ breeding. Population structure when excluding these two populations was limited, and we found that the evolutionary divergence between wild and domestic banteng is moderate (FST = 0.14), relatively young (10,356 years), and with post-divergence gene flow. We found only weak signals of a domestication bottleneck between [~]6100-2900 years ago, and genetic diversity is on average higher in domestic than in wild banteng. Despite the soft domestication history, we found 56 candidate genes under selection during domestication, with the leptin receptor gene (LEPR) of particular interest due to the robust selection signal across methods, and its known association to metabolism, obesity and energy homeostasis. Finally, genetic load estimation revealed that Bali cattle in Australia have high realized load, while Bali cattle from Bali have high masked load. These findings provide the first genomic insights into an understudied bovine that is Critically Endangered in its wild form, and agriculturally important in its domesticated form.

evolutionary biology↗

bioRxiv2025

Adolescents with major depression featured by sensory-association subtyping show divergent information dynamics and streams

Adolescent major depressive disorder (MDD) exhibits complex and heterogeneous alterations of brain functional organization. To understand the neurobiological basis of adolescent MDD, we adopted resting-state functional MRI data and used various matrix decomposition approaches to obtain the organization gradients, temporal dynamics, and information streams. With clustering sensory-association gradient features in our exploratory sample (NMDD = 250 and NControls = 203), we identified two MDD subtypes. Subtype 1 was characterized by sensory contraction and subtype 2 was associated with association expansion. In addition, two subtypes showed divergent bottom-up and top-down information flows in sensory and association areas using temporal dynamics analysis. These subtypes exhibit distinct age-related changes and reorganization trajectories along sensory-association and auditory-visual axes, highlighting that cortical information flow patterns systematically vary and relate differently to sensory integration, cognitive complexity, and aging. These network distinctions are linked to clinical severity and molecular mechanisms. Subtype 1 is predominantly associated with early neurodevelopmental abnormalities and emotional regulation deficits, while Subtype 2 is more related to synaptic dysfunction and reduced neuronal excitability. These results could be largely replicated in another independent sample (NMDD = 73 and NControls = 28). We therefore construct a sensory-association dual functional framework to characterize MDD heterogeneity in adolescent MDD. Itl integrates cortical hierarchy, developmental trajectories, and genetic influences, offering novel insights into MDD pathophysiology and providing a theoretical foundation for precision psychiatry, facilitating personalized diagnosis and intervention strategies.

neuroscience↗

bioRxiv2025

Unfolding admixed ancestry and genomic diversity in zoo giraffes

A giraffe nicknamed Marius attracted international media attention and world-wide notoriety when euthanized by Copenhagen Zoo in 2014, deemed surplus to the European breeding program. This incident highlights the challenges of managing zoo populations to best contribute to species conservation amid limited resources. Here, we investigated the degree of admixture, genetic diversity and inbreeding in ex situ giraffes using whole genome sequencing data from Marius and 12 other zoo giraffes, leveraging a reference data set from 71 wild giraffes. We found that most zoo giraffes show admixed ancestries. Marius, and zoo individuals assigned to Reticulated giraffes, exhibits mosaic ancestry with 85% Reticulated and 15% Nubian origin. We further detected recent inbreeding in some of the zoo individuals, consistent with their studbook data. Runs of homozygosity revealed that Marius and three other zoo giraffes were more inbred than their wild counterparts, although their admixed ancestry compensates for the reduction in genetic diversity caused by inbreeding. Our findings highlight the dual challenges of admixture and inbreeding in ex situ populations of giraffe, emphasizing the need for balanced genetic management to mitigate inbreeding and outbreeding degression while preserving diversity reflective of wild populations. This study also reinforces the importance of studbooks and genomic tools in guiding ex situ conservation strategies.

evolutionary biology↗

bioRxiv2025

Iron acquisition in the weevil-farming fungus Penicillium herquei: Implications of mineral elements in insect-fungus mutualistic association

Mutualistic interactions between insects and fungi are pivotal in ecosystem dynamics, yet the underlying molecular mechanisms remain largely unexplored. This study investigates iron acquisition strategies of the weevil-farming Penicillium herquei, revealing the involvement of mineral elements in insect-fungus symbiosis. Comparative transcriptomics of weevil-farming strain (WFS) and soil free-living strain (SFS) revealed distinct transcriptional profiles, with 4,357 up-regulated genes in WFS. Enrichment analyses highlighted a significant up-regulation of genes linked to oxidoreductase activity, iron and heme binding, with a notable prevalence of Cytochrome P450 (CYP450). qRT-PCR confirmed differential expression of CYP450 and siderophore-related genes, indicating enhanced iron absorption in WFS. Comparative analysis of iron content further demonstrated significantly higher iron levels in WFS than in SFS and weevil host plant leaves, suggesting a nutritional adaptation for symbiotic lifestyle. These findings provide novel insights into the role of iron metabolism in insect-fungus mutualism, highlighting potential evolutionary mechanisms that bolster symbiotic fitness. IMPORTANCEUnraveling the complex interplay between insects and fungi is crucial for deciphering the intricate dynamics of ecosystems. In this study a notable up-regulation of genes associated with iron and heme binding, as well as a significant increase in iron content within WFS, suggesting a specialized adaptation for enhanced iron acquisition, potentially enabling the fungus to efficiently provide essential nutrients, including bioavailable iron, to weevil host. This research not only advances our understanding of the molecular mechanisms governing insect-fungus mutualism but also highlights the potential evolutionary mechanisms that bolster symbiotic fitness and contribute to the co-evolution of these interacting species.

microbiology↗

bioRxiv2025

Cortactin regulates metastatic dormancy of circulating tumor cells by suppressing mTOR-dependent senescence

Metastatic dormancy often refers to the stable cell cycle arrest of disseminated tumor cells (DTCs) at distant sites. However, whether circulating tumor cells (CTCs) in the blood microenvironment can enter a dormant state prior to extravasation and becoming DTCs remains unclear. Using patient-derived melanoma CTC lines and animal explant models (CDX), we identified a previously unrecognized role of the cytoskeletal regulator cortactin (encoded by CTTN) in controlling mTOR/p53-dependent senescence and metastatic dormancy. Cortactin was localized to Rab7-postive endosomes and engaged in late endosomal tethering and homeostasis. The depletion of cortactin resulted in the accumulation of aberrantly enlarged late endosomal aggregates that were positive for Rab7 and mTOR. The mTOR protein complex was accumulated and activated within these abnormal vesicular structures, leading to robust p53 activation through phosphorylation at serine (S) 15 and S33 sites. Consequently, melanoma CTCs underwent G0/G1 cell cycle arrest and entered cellular senescence. This unusual oncogene-induced senescence (OIS) mechanism was characterized by SASP upregulation, {beta}-galactosidase activity, depletion of Ki-67 and Lamin B1, and elevated mitochondrial ROS (mtROS) levels. Notably, a positive feedback loop between p53 and mtROS was essential for maintaining stable senescence in CTCs. In preclinical CDX mouse models, we developed a sequential therapeutic strategy combining cortactin depletion with anti-Bcl-xL senolytic drugs. Such "One-two punch" treatment strategy effectively eliminated viable CTCs and suppressed metastatic tumor growth in vivo. Thus, targeting cortactin to induce CTC senescence, followed by senolytic therapy, may represent a promising strategy to block CTC-mediated metastatic progression.

cancer biology↗

bioRxiv2025

Effects of Exercise and Konjac on Lipid Metabolism and Mechanism in Obese Rats

ObjectiveTo study the effects of exercise and konjac on body weight and lipid metabolism in obese rats, and the possible mechanism of exercise combined with konjac on body weight and lipid metabolism. MethodsFifty male Sprague Dawley rats were randomly divided into 5 groups. After six weeks of intervention, blood lipid, body weight, liver weight, inflammatory factors, oxidative stress markers and proteins were measured. ResultsWeight and liver weight in HFD group were significantly higher (P<0.05, P<0.01) than those in CON group. Compared with HFD group, blood lipid index in intervention group were significantly decreased; The levels of MDA (P<0.01, P<0.05, P<0.05) and SOD (P<0.05) in intervention group were significantly decreased; the GSH levels in HAE group and HKE group were significantly increased(P<0.01, P<0.05); the levels of IL-6, TNF-, and leptin in HAE group (P<0.05, P<0.05, P<0.01) and HKE group (P<0.01, P<0.01, P<0.05) were significantly decreased; ApoA5 in intervention group was significantly increased (P<0.01), SREBP-1c and LXR was significantly decreased (P<0.01). ConclusionKonjac or exercise alone can improve the lipid metabolism, and the comprehensive effect is better. The mechanism of regulating lipid metabolism may be related to the expression of LXR, SREBP-1c and ApoA5.

biochemistry↗

bioRxiv2025

The Golgi Rim is a Precise Tetraplex of Golgin Proteins that Can Self-Assemble into Filamentous Bands

Golgin proteins have long been suspected to be organizers of the Golgi stack. Using three-dimensional super-resolution microscopy, we comprehensively localize the human golgin family at the rim of the Golgi apparatus at 10-20 nm resolution in situ. Unexpectedly, we find that the golgins are precisely organized into a tetraplex with four discrete layers, each containing a specific set of rim golgins. We observe no golgins inside the stack between its membrane-bound cisternae. Biochemically characterizing most of the golgins as isolated proteins, we find that they form anti-parallel dimers and further self-assemble into bands of multi-micron-long filaments. Based on our findings, we propose an "outside-in" physical model, the Golgin Organizer Hypothesis, in which the Golgi stack of cisternae and its overall ribbon morphology directly result from bending circumferential bands of rim golgin filaments onto a membrane surface, explaining stack formation without the need for special "stacking proteins."

cell biology↗

bioRxiv2025

A pan-positive allosteric modulator that mediates sustainable GPCR activation

Approximately 1/3 of all clinical drugs exert their therapeutic effects by modulating the activity of G protein-coupled receptors (GPCRs). Thus, there is a constant interest in finding novel ways to modulate GPCR activity. In this work, through a newly established Survival Pressure Selection (SPS) method for high-throughput screening of GPCR agonists, we discover that atazanavir functions as an agonist for GPR119. Further studies suggest that atazanavir is capable of activating a number of Family A GPCRs, including the {beta}1 adrenergic receptor ({beta}1AR), the {beta}2 adrenergic receptor ({beta}2AR) and the opoioid receptor (OR). Cryo-EM structures reveal that atazanavir binds to an allosteric pocket near TM6/7 in both GPR119 and the {beta}1AR. Pharmacological studies suggest that atazanavir mediates non-canonical signaling of Family A GPCRs. During this process, G protein and {beta}-arrestin are spatially close, but {beta}-arrestin forms a complex with the receptor and G protein instead of desensitizing G protein signaling, thus resulting in sustained G protein signaling. The work expands the signal transduction modes and pharmacological properties of allosteric modulators for GPCRs and provides a general starting point for developing therapeutics targeting this allosteric site.

biochemistry↗

bioRxiv2025

A GPCR-G protein-β-arrestin megacomplex induced by an allosteric modulator

GPCRs signal through both G protein pathways and {beta}-arrestin pathways. Previous work suggests that {beta}-arrestins bind to GPCRs through different modes, including core engagement and tail engagement. Core engagement competes with G proteins and terminates G protein signaling, while tail engagement can coexist with G proteins, mediating sustained intracellular activation of the receptor - a process dependent on the high affinity between {beta}-arrestin and the phosphorylated C-terminus of the receptor. In this study, we determined the structure of a GPCR - G protein - {beta}-arrestin-1 complex stabilized by an allosteric modulator. The compound, atazanavir, acts like molecular glue to anchor {beta}-arrestin-1 to the receptors TM6 and TM7 regions. This pendulum binding mode is structurally compatible with simultaneous G protein binding. We further demonstrate that the atazanavir-mediated {beta}-arrestin recruitment does not require the receptors C-terminal region. This work illustrates a novel paradigm of GPCR-G protein-{beta}-arrestin1 megacomplex assembly and opens up new avenues for modulating GPCR function.

biochemistry↗

bioRxiv2025

Extracellular Nanobody Screening using Conformationally Stable GPCR

G protein-coupled receptors (GPCRs) are prominent drug targets that have attracted intensive efforts in drug screening. Binding-based screening methods for GPCR ligands often require conformationally stable, purified receptors. However, obtaining large quantities of GPCRs in stable states, particularly with unoccupied extracellular ligand-binding pockets and especially in their active conformations, remains challenging due to the inherent dynamic nature of these receptors. To address this challenge, we propose a universal approach for stabilizing GPCRs in specific conformations. Using the M1 muscarinic acetylcholine receptor (M1R) as a model, we successfully stabilized M1R in its active conformation through de novo design of a fusion protein. We screened a synthetic yeast display library of nanobodies against both the stabilized active-state and previously reported inactive-state M1R, identifying several nanobodies that specifically recognize each conformation. This method not only facilitates the stabilization of GPCRs in desired states but also provides valuable tools for developing more selective therapeutic agents, enhancing drug discovery efficiency and specificity.

biochemistry↗