Biology subjects

Xue, W.

Publications and source records attributed to Xue, W..

At least 19 recordsLinked to original sources

bioRxiv2026

The vagus nerve drives cognitive function through the default mode network

The afferent vagus nerve transmits interoceptive signals to the brain but a systematic understanding of how vagal signals affect brain-wide neuronal dynamics remains elusive. Here, comprehensive spatiotemporal analyses across the entire mouse brain revealed that vagus nerve stimulation activated neuronal ensembles within the default mode network (DMN). In contrast, vagal-independent mechanisms predominantly affected the salience network. The vagal-DMN association was mediated by locus coeruleus neuronal subpopulations. Selective activation or silencing of vagal-responsive DMN neuronal ensembles replicated or abolished VNS-induced enhancement of cognitive behaviors and progressive problem-solving behaviors. These findings establish a unifying framework for how the vagus nerve drives cognitive functions by engaging the DMN.

neuroscience↗

bioRxiv2026

Coronavirus papain-like protease antagonizes innate immunity by cleaving Importin α1 to disrupt nuclear transport

The Importin family, as key mediators of nucleocytoplasmic transport, represents a common target for viral immune evasion. However, whether coronaviruses directly manipulate Importin to disrupt nuclear trafficking and suppress antiviral immunity has remained unclear. In this study, we identify a previously unrecognized mechanism by which coronaviruses from all four genera subvert host innate immunity through the proteolytic inactivation of Importin 1, a key mediator of nuclear import of cargo proteins. We demonstrate that the membrane-associated papain-like protease (PLpro-TM) directly cleaves Importin 1 at specific glycine residues, G129 for PEDV and IBV PLpro, and G119 for MHV and PDCoV PLpro, thereby disrupting its nuclear import function. This cleavage impairs the nuclear translocation of multiple transcription factors (IRF3, STAT1, STAT2, and p65) and suppresses the expression of downstream antiviral genes, including IFN-{beta} and IFN-stimulated genes (ISGs). Importantly, cleavage-resistant mutants of Importin 1 (G129A or G119A) restore nuclear import capability and rescue IFN-{beta} signaling. Consequently, they exert a more potent inhibitory effect on viral replication than the wild-type Importin 1, fulfilling an antiviral role. Our work establishes PLpro-TM-mediated cleavage of Importin 1 as a conserved immune evasion strategy across coronaviruses and highlights this interaction as a potential target for broad-spectrum antiviral intervention. Author summaryThe nuclear transport of transcription factors is a critical checkpoint for the initiation of innate antiviral immunity. Here, we identify the PLpro-TM protein as a pan-coronavirus antagonist of nucleocytoplasmic trafficking and innate immune response. We demonstrate that PLpro-TM from four distinct coronavirus genera directly cleaves Importin 1 at specific glycine residues, thereby disabling its ability to mediate the nuclear import of key transcription factors and subsequent transcription of anti-viral genes. This work reveals a previously unrecognized, evolutionarily conserved immune evasion strategy shared across , {beta}, {gamma}, and {delta} coronaviruses. By uncovering the proteolytic inactivation of Importin 1 targeting by PLpro-TM, our findings not only resolve a long-standing question about how coronaviruses disrupt nuclear trafficking, but also establish PLpro-TM and Importin 1 as promising targets for the development of broad-spectrum antiviral therapeutics against current and emerging coronaviruses.

microbiology↗

bioRxiv2026

Potential risk for hearing from prolonged exposure to sound at conversation levels

Prolonged exposure to loud and moderate noise impairs hearing; the lower the noise level, the lower risk of hearing loss is. To date, little is known about how low the noise level can be safe to hearing. This study investigated the risk of exposure to tone at typical conversational levels by measuring auditory brainstem response (ABR). We show that exposing C57 mice to continuous pure tone at 65 dB SPL for 1 hour (TE65) leads to an increase in ABR threshold that is specific to the exposure frequency. Tone exposure also increased the latencies and decreased the amplitude in Waves I and II but not in Waves III and V. Significantly, the changes in amplitude and latency were highly correlated in Wave I and such correlation gradually degraded from Wave I through to Wave V. Our findings suggest that exposure to low level sound can impair hearing and alter the auditory information process in the brain if it is persistent and presented over a sufficient period of time. Significant StatementOur findings established the risk of hearing impairment following the exposure to continuous tone at normal or conversational voice levels. This finding challenges current public health guidelines for hearing protection. Although further clarification is required, our studies prompt that the regular use of ABR testing is a potential protocol for diagnosing hearing impairment in patients experiencing hidden hearing loss (HHL).

neuroscience↗

bioRxiv2026

Evolutionary dynamics of insect odorant receptors reveal ecological tuning shaping olfactory perception

Insect olfaction is facilitated by a heterotetrameric odorant receptor-odorant receptor co-receptor (OR-Orco) complex, which is distinct from that of vertebrate ORs. However, extreme sequence divergence among insect ORs has hindered a unified understanding of their evolutionary history and ecological importance. In this study, we present a multiscale analysis of OR genes across 115 insect species. We overcome the limitations of traditional phylogenetic approaches by applying a protein similarity network-based strategy and introduce a "trunk-branch" framework to systematically describe the evolutionary trajectories of insect ORs across sequence, structural, and predicted olfactory potential levels. Although they possess different sequences and structural communities, all sampled insect orders contained ORs assigned to all six docking-derived functional communities. Notably, extant insect lineages with order-level origins spanning the end-Permian mass extinction (EPME) differed in docking-derived functional OR repertoires, and early-and late-diverging lineages differed in OR sequence-community diversity. The emergence of Orco represents a key evolutionary transition point, marking the shift from a homomeric to a heteromeric complex accompanied by specialization of the extracellular domain and binding pocket. Furthermore, we established robust associations between potential olfactory recognition breadth and ecological variables, including diet, circadian rhythm, and habitat. Our findings provide a class-level framework for investigating insect OR evolution and generate testable hypotheses about how receptor repertoire diversification may relate to ecological adaptation.

evolutionary biology↗

bioRxiv2026

Glucokinase links metabolism and lineage plasticity in neuroendocrine prostate cancer via interaction with AKT1

Cancer cells frequently rewire their metabolism to sustain growth and survival under stress. Despite the critical role of metabolic adaptation in tumorigenesis, how specific metabolic enzymes regulate lineage plasticity remains unclear. Here, through FDG-PET imaging and transcriptomic analyses, we reveal markedly elevated glucose uptake in neuroendocrine prostate cancer (NEPC) and identify glucokinase (GCK) as a MYCN-induced metabolic enzyme. Beyond its metabolic role, GCK is indispensable for maintaining the neuroendocrine lineage of prostate cancer cells by establishing a functional circuit with AKT1 through reciprocal regulation--AKT1 binds and phosphorylates GCK at S373, whereas GCK phosphorylates AKT1 at S473. Pharmacological disruption of this AKT1-GCK axis suppresses tumor growth in NEPC mouse models and patient-derived xenografts. Altogether, our findings uncover both the metabolic and noncanonical kinase functions of GCK and establish the AKT1-GCK axis as a key link between metabolic reprogramming and neuroendocrine lineage transition in prostate cancer.

cancer biology↗

bioRxiv2026

Abalone genomics reveals an ancient asymmetry axis and the multifunctionality of the mantle

Gastropod diversification represents one of the most spectacular evolutionary radiations, underpinned by a fundamentally asymmetric body plan and diverse pigmentation patterns. To understand the genetic underpinnings of these cardinal traits, we constructed a chromosome-level genome assembly for the rainbow abalone, Haliotis iris. Integrating systematic genomics, histoembryology, and molecular assays, we uncover an ancient regulatory axis, conserved for over 544 million years, in which the long non-coding RNA lncRNA1 functions as a competing endogenous RNA to shield pitx transcripts from miRNA-mediated degradation, thereby driving the establishment of asymmetric body patterning, including the mantle. Furthermore, we identify a wnt-mitf-tyr cascade as the driver of melanogenesis and demonstrate that the mantle is the primary site of melanin synthesis. Concurrently, we reveal the mantle as a multifunctional organ possessing mechanosensory capabilities. These findings elucidate the ancient genetic toolkit governing trait evolution in gastropods. TeaserA deeply conserved RNA switch directs gastropod body plans and reveals the mantles hidden talents.

genomics↗

bioRxiv2025

Lattice Instability Drives Formation of Protofilament Clusters at the Microtubule Plus End Tips

Microtubules (MTs) are dynamic cytoskeletal filaments composed of - and {beta}-tubulin protein dimers. They are crucial for maintaining cell structure, facilitating intracellular transport, and ensuring proper chromosome segregation among other things. These biological functions are influenced by the dynamic instability of the MT plus-end tip. Recent simulations have discovered formation of protofilament (PF) clusters at the MT plus-end tip, but reliable extrapolation of PF cluster dynamics and detailed microscopic mechanism are yet to be developed to understand their behavior thoroughly. In this work, we have constructed, from "bottom up", a relatively high resolution coarse-grained (CG) molecular dynamics (MD) model for tubulins with 20 CG sites per tubulin monomer, performed extensive CG MD simulations on MT lattices with 8 and 40 layers of heterodimers, and conducted comprehensive atomistic-level analysis. Our findings demonstrate that, in both GTP and GDP states, PF clusters are stable up to tens of microseconds of CG MD simulation time during spontaneous outward bending relaxation. PF clustering is initiated by longitudinal relaxation, stabilized by residual lateral interaction in the PF clusters. This process is thermodynamically driven by intrinsic lattice instability. In longer microtubules, this instability accumulates and further facilitates PF bending and clustering at the plus-end tip, but it can also be released via lattice curvature and supertwist. GDP-MTs form more PF clusters than GTP-MT on average and undergo more lateral cleavage and faster bending relaxation due to weaker lateral interactions, which facilitates MT catastrophe. GTP-MT forms flatter and more rigid PF clusters that favor nucleotide addition. Our findings highlight the critical role of lattice instability in microtubule dynamics and offer new insights on the conformational variability of MT plus-end tips. SIGNIFICANCEThe dynamical structure and behavior of microtubule (MT) plus-end tips remains an important topic in structural and computational biophysics. For the recently discovered protofilament clusters at MT plus-end tips, this study provides a mechanism for their formation through comprehensive analyses of tubulin-tubulin interaction interfaces in all-atom simulations of complete MT lattices. This study also makes long-time predictions for the dynamics of PF clusters through a coarse-grained model for the tubulin heterodimers to extend the effective simulation time and system size, while preserving key details of the lateral and longitudinal interaction interfaces. The findings deepen understanding of the life cycle of PF clusters, while adding new insight on microtubule dynamics and the role of lattice destabilization.

biophysics↗

bioRxiv2025

Multiplexed cytokine and antigen mRNA administration generates durable anti-tumor immunity against pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) remains a devastating malignancy characterized by limited therapeutic options for advanced disease. Immunotherapy, in particular, has had dismal success rates in the PDAC due to a tumor microenvironment (TME) that contributes to immune exclusion and poor drug delivery. Many cytokines necessary for Natural Killer (NK) and T cell chemotaxis, activation, and cytotoxicity are absent in the PDAC TME. Despite their early success, cytokine therapies have largely failed in the treatment of solid tumors as a result of the lack of efficacy of single cytokine administration and toxicities from systemic delivery. To overcome these limitations, we designed multiplexed mRNA cocktails encoding diverse interleukins, chemokines, and interferons for intratumoral delivery. Administration of a cytokine-encoding mRNA mixture into mice with orthotopically transplanted PDAC tumors achieved robust yet transient cytokine expression locally in the PDAC TME, leading to NK cell and CD8+ T cell immunity and reduced tumor growth and fibrosis in multiple mouse models. Combining cytokine mRNAs with those encoding tumor-associated antigens further activated CD8+ T cell-mediated tumor control and enhanced survival after just a single dose in PDAC-bearing mice. Remarkably, lipid-based nanoparticle (NP) encapsulation of an all-in-one cytokine and antigen mRNA cocktail allowed safe systemic administration and local delivery of these immunogenic signals to autochthonous PDAC tumors in genetically engineered mouse models, culminating in complete tumor responses in 50% of animals. These results suggest that multiplexed mRNA approaches to delivering cytokine signals and antigens generally absent in the TME could pave the way for an effective immunotherapy for PDAC.

cancer biology↗

bioRxiv2025

NAPRT expression and epigenetic regulation in pediatric rhabdomyosarcoma as a potential biomarker for NAMPT inhibition

PurposeNew treatments are needed to improve survival in children with rhabdomyosarcoma (RMS). NAD biosynthesis, regulated by the enzymes NAPRT and NAMPT, represents a metabolic vulnerability due to high NAD turnover in cancers. Although NAMPT inhibitors (NAMPTi) show preclinical promise, clinical translation has been limited by toxicity and the lack of predictive biomarkers. Here, we evaluated NAPRT expression in RMS and its potential as an actionable biomarker to guide NAMPTi therapy. Experimental DesignNAPRT promoter methylation, transcript levels, and protein expression were assessed in RMS cells, PDXs, and primary tumors (n=109) from the Childrens Oncology Group. In vitro sensitivity to NAMPTi was tested in molecularly diverse and isogenic RMS cell lines, examining the role of NAPRT expression in mediating cytotoxicity and the ability of nicotinic acid (NA) to rescue viability. In vivo efficacy was assessed using NAPRT-isogenic orthotopic xenograft models. ResultsNAPRT promoter hypermethylation was found in a subset of RMS models and patient samples. Immunohistochemistry showed loss of NAPRT protein in 30-40% of tumors, defined as <1% tumor cell staining. Methylation modestly correlated with protein expression. NAPRT-silenced cells were highly sensitive to NAMPTi, driven by NAD depletion and not reversible with NA. In vivo, NAMPTi induced significant tumor regression, which was not abrogated with NA administration in NAPRT-silenced models. ConclusionsNAPRT loss occurs in a subset of RMS, offering a potential strategy to expand the therapeutic window of NAMPTi. Further research is needed to understand NAPRT regulation and optimize biomarker assay strategies for use in future clinical trials.

cancer biology↗

bioRxiv2025

KRAS withdrawal in Cholangiocarcinoma leads to immune infiltration and tumor regression

Background and AimsCholangiocarcinoma (CCA) is a liver cancer with poor survival rates. Current treatments, including targeted therapies for specific mutations, are limited and benefit only a small subset of patients. KRAS mutations are found in 15-40% of CCA, representing a new potential treatment target. Whether KRAS inhibition leads to CCA tumor regression is unknown partly due to the lack of conditional animal models. Approach and ResultsWe engineered a conditional KrasG12D-driven CCA mouse model by co-delivering plasmids encoding the Sleeping Beauty transposase with a luciferase reporter, a transposon-borne inducible KrasG12D transgene and Cas9 and Trp53 guide RNA into mouse liver by hydrodynamic tail-vein injection. In vivo bioluminescent imaging showed that KrasG12D withdrawal resulted in 99% tumor regression by day 7. KrasG12D withdrawal resulted in infiltration of activated CD8+ T cells by IHC and IF staining. Single cell RNA-Seq result also validated the enrichment of activated CD8+ T cells subpopulation in KrasG12D-withdrawn tumor. RNA-Seq suggested that KrasG12D withdrawal stimulated transforming growth factor beta pathway and induced senescence. We used cytokine array to characterize the secretion of pro-inflammatory factors, including IL-15 and Ccl17, upon KrasG12D withdrawal. Lentiviral overexpression of murine CCL17 delayed CCA tumor progression in a xenograft model, and overexpression of murine IL-15 resulted in tumor regression in a transplant model. Flow cytometry analysis revealed that IL-15 and CCL17 recruited and activated CD8+ T cells in CCA tumor. Expression of IL-15 resulted in blockade of tumor progression in our TKP CCA model. ConclusionsKrasG12D withdrawal results in rapid tumor regression, highlighting the importance of oncogenic Kras in CCA tumor maintenance. KrasG12D withdrawal induces p53-independent senescence, secretion of pro-inflammatory factors, and immune surveillance by activated CD8+ T cells. We identified two secreted factors IL-15 and CCL17 that could recruit and activate T cells and control CCA tumor progression. This study underscores KRAS inhibition as a potential therapeutic approach for CCA.

cancer biology↗

bioRxiv2025

Prime assembly with linear DNA donors enables large genomic insertions

Targeted insertion of large DNA fragments has promising applications for genome engineering and gene therapy1,2. Twin prime editing (PE) guide RNAs (pegRNAs) have enabled relatively large insertions, but the efficiency remains low for insertions greater than 400 base pairs3-6. Here we describe a Prime Assembly (PA) approach for the insertion of large DNA donor fragments, whose ends are designed to overlap with the flaps generated by twinPE. We used PA to insert one, two, or three overlapping DNA fragments, with total insertion sizes ranging from 0.1 to 11 kilobase pairs. An inhibitor of non-homologous end joining (NHEJ) enhanced both the efficiency and precision of insertions. PA relies on DNA templates that are easily produced and does not require co-delivery of exogenous DNA-dependent DNA polymerases. Our study demonstrates that PA can initiate "Gibson-like" assembly in cells to generate gene insertions without double-stranded DNA breaks or recombinases.

biochemistry↗

bioRxiv2025

On the Curvature and Relaxation of Microtubule Plus-endTips

Microtubules are essential cytoskeletal components with a broad range of functions in which the structure and dynamics of their plus-end tips play critical roles. Existing mechanistic models explain the tips curving dynamics in different ways: the allosteric model suggests that GTP hydrolysis induces conformational changes in tubulin subunits that destabilize the lattice, leading to protofilament curving and depolymerization, while the lattice model posits that GTP hydrolysis directly destabilizes the microtubule lattice. However, the effect of GTP hydrolysis on the curving dynamics of microtubule tips remains incompletely understood. In this study, we employed a multiscale modeling approach, combining all-atom molecular dynamics simulations with Brownian dynamics simulations, to investigate the relaxation of microtubule plus-end tips into curved configurations. Our results show that both GDP- and GTP-bound tips exhibit an outward bending of protofilaments into curved, rams horn-like structures, characterized by a linear relationship between curvature and distance from the plus-end tip. These observations align with experimental cryo-ET images of microtubule plus-end tips in different nucleotide states. Collectively, our findings suggest that the outward bending of protofilaments at the plus-end tip is an intrinsic feature of microtubules, independent of the nucleotide state. SIGNIFICANCEUnderstanding how microtubules change shape is crucial for elucidating key cellular processes such as cell division and shape maintenance, which are fundamental to both physiological function and disease progression. This study supports the concept that the microtubule plus-end tip relaxation does not align with models that couple shape changes to GTP hydrolysis, at least for the topmost tubulin heterodimers. By interfacing bottom-up multiscale modeling -- using the longest reported atomistic molecular dynamics simulations of microtubule tips-- with existing cryo-ET data, it is shown that protofilament bending operates independently of nucleotide hydrolysis and likely depolymerization. These findings highlight the need for a new conceptual framework that separates GTP hydrolysis from microtubule tip flaring.

biophysics↗

bioRxiv2025

Cell type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testicular stem cells

Stem cells have the unique ability to self-renew and differentiate into specialized cell types. Epigenetic mechanisms, including histones and their post-translational modifications, play a crucial role in regulating programs integral to a cells identity, like gene expression and DNA replication. However, the transcriptional, chromatin, and replication timing profiles of adult stem cells in vivo remain poorly understood. Containing germline stem cells (GSCs) and somatic cyst stem cells (CySCs), the Drosophila testis provides an excellent in vivo model for studying adult stem cells. However, the small number of stem cells and cellular heterogeneity of this tissue have limited comprehensive genomic studies. In this study, we developed cell type-specific genomic techniques to analyze the transcriptome, histone modification patterns, and replication timing of GSC-like and CySC-like cells. Single cell RNA sequencing validated previous findings on GSC-CySC intercellular communication and revealed high expression of chromatin regulators in GSC-like cells. To characterize chromatin landscapes, we developed a cell-type-specific chromatin profiling assay to map H3K4me3-, H3K27me3-, and H3K9me3- enriched regions, corresponding to euchromatic, facultative heterochromatic, and constitutive heterochromatic domains, respectively. Finally, we determined cell type-specific replication timing profiles, integrating our in vivo datasets with published data using cultured cell lines. Our results reveal that GSC-like cells display a distinct replication program compared to somatic lineages, that aligns with chromatin state differences. Collectively, our integrated transcriptomic, chromatin, and replication datasets provide a comprehensive framework for understanding genome regulation differences between these in vivo stem cell populations, demonstrating the power of multi-omics in uncovering cell type- specific regulatory features.

genomics↗

bioRxiv2025

Altered auditory maturation in Fragile X syndrome and its involvement in audiogenic seizure susceptibility

BackgroundAuditory hypersensitivity is a prominent symptom in Fragile X syndrome (FXS), the most prevalent monogenic cause of autism and intellectual disability. FXS arises through the loss of the protein encoded by the FMR1 (Fragile X Messenger Ribonucleoprotein 1) gene, FMRP, required for normal neural circuit excitability. In the brainstem, FMRP is necessary for normal development of acoustic reactivity, and its loss has been implicated in audiogenic seizures (AGS) in Fmr1 knockout (KO) mice, modelling auditory hypersensitivity and seizures in FXS patients. PurposeThe present study investigated the correlation between auditory brainstem function and behavioral expression of AGS at the early (postnatal day P20, infancy) and late (P32, juvenile) stage of auditory development in Fmr1 KO mice compared with wildtype (WT) mice, and in both females and males. MethodsWe tested responsiveness to pure tones of select auditory pathway elements through auditory brainstem responses; and neural synchronization to amplitude envelopes of modulated acoustic stimuli through auditory steady-state responses. AGS behavior was categorized for severity during 5-minute exposure to loud sound. Expression of the immediate early gene cFos was quantified as a marker for neuronal activity in the inferior colliculus. ResultsDuring infancy, more severe AGS expression in Fmr1 KO mice compared with WT mice was accompanied by increased responsiveness to acoustic stimuli at the level of the superior olivary complex and inferior colliculus, and stronger neural synchronicity in subcortical auditory neurons. Fmr1 KO mice also had higher cFos positive cell counts in the inferior colliculus after exposure to loud sound. With age, both AGS susceptibility and exaggerated acoustic stimulus-evoked activity in the Fmr1 KO mice subsided. Intriguingly, Fmr1 KO mice displayed altered developmental profile in both the threshold and amplitude of auditory brainstem response. ConclusionOur findings support evidence that AGS activity relies upon hyperexcitability in the auditory system, including in the lower brainstem, possibly due to disturbed auditory maturation. Hyper-synchronization to modulated sounds in subcortical auditory neurons seemed to predict AGS severity. A better understanding of FXS-related circuit and behavioral symptoms of auditory processing across development provides the potential to identify therapeutic strategies to achieve auditory function recovery in FXS.

neuroscience↗

bioRxiv2025

CRISPR-based shuttle cloning of 1,397 human genes into UAS vectors

The construction of genome-wide DNA libraries from publicly available resources is essential for leveraging functional genomics to investigate complex biological systems. However, all existing high-throughput cloning methods for transferring DNA fragments between vectors require PCR amplification of the DNA fragments, rendering the construction of genome-wide DNA libraries labor-intensive and time-consuming. By introducing a concept of CRISPRshuttle cassette, we herein present a method named CRISPR-based shuttle cloning (CRISPRshuttle cloning). This method enables the high-throughput transfer of numerous DNA fragments from original plasmids with identical backbones to a different vector background without the need for PCR amplification of the DNA fragments. The procedure comprises two-step test tube reactions followed by bacterial transformation. Using CRISPRshuttle we successfully generated a library of GAL4/UAS-based UAS-ORF plasmids covering 1,397 human genes conserved in Drosophila. This library may serve as a valuable resource for gain-of-function screening in cultured cells and for the creation of a transgenic UAS-ORF library in Drosophila.

molecular biology↗

bioRxiv2024

Data-Driven Equation-Free Dynamics Applied to Many-Protein Complexes: The Microtubule Tip Relaxation

Microtubules (MTs) constitute the largest components of the eukaryotic cytoskeleton and play crucial roles in various cellular processes, including mitosis and intracellular transport. The property allowing MTs to cater to such diverse roles is attributed to dynamic instability, which is coupled to the hydrolysis of GTP (guanosine-5-triphosphate) to GDP (guanosine-5-diphosphate) within the {beta}-tubulin monomers. Understanding the equilibrium dynamics and the structural features of both GDP- and GTP-complexed MT tips, especially at an all-atom level, remains challenging for both experimental and computational methods because of their dynamic nature and the prohibitive computational demands of simulating large, many-protein systems. This study employs the "equation-free" multiscale computational method to accelerate the relaxation of all-atom simulations of MT tips toward their putative equilibrium conformation. Using large MT lattice systems (14 protofilaments x 8 heterodimers) comprising [~]21-38 million atoms, we applied this multiscale approach to leapfrog through time and nearly double the computational efficiency in realizing relaxed all-atom conformations of GDP- and GTP-complexed MT tips. Commencing from an initial 4 s unbiased all-atom simulation, we interleave coarse projective "equation-free" jumps with short bursts of all-atom molecular dynamics simulation to realize an additional effective simulation time of 1.875 s. Our 5.875 s of effective simulation trajectories for each system expose the subtle yet essential differences in the structures of MT tips as a function of whether {beta}-tubulin monomer is complexed with GDP or GTP, as well as the lateral interactions within the MT tip, offering a refined understanding of features underlying MT dynamic instability. The approach presents a robust and generalizable framework for future explorations of large biomolecular systems at atomic resolution. SIGNIFICANCEThe dynamic instability of microtubules (MTs) is essential for a plethora of biological functions, from cell division to intracellular transport. Despite their importance, current computational models often struggle to handle the large-scale, long-term dynamics of all-atom simulations. This computational study employs the "equation-free" method to accelerate relaxation of the all-atom structures of MT tips in both GDP and GTP states which nearly halves the computational demands of simulating very large biomolecular systems. Our findings expose subtle but crucial structural differences between GDP-bound and GTP-bound MTs, particularly in the number of protofilament clusters, and is consistent with a relatively stronger lateral interactions in GTP-bound MT tips.

biophysics↗

bioRxiv2024

ConoDL: A Deep Learning Framework for Rapid Generation and Prediction of Conotoxins

Conotoxins, being small disulfide-rich and bioactive peptides, manifest notable pharmacological potential and find extensive applications. However, the exploration of conotoxins vast molecular space using traditional methods is severely limited, necessitating the urgent need of developing novel approaches. Recently, deep learning (DL)-based methods have advanced to the molecular generation of proteins and peptides. Nevertheless, the limited data and the intricate structure of conotoxins constrain the application of deep learning models in the generation of conotoxins. We propose ConoDL, a framework for the generation and prediction of conotoxins, comprising the end-to-end conotoxin generation model (ConoGen) and the conotoxin prediction model (ConoPred). ConoGen employs transfer learning and a large language model (LLM) to tackle the challenges in conotoxin generation. Meanwhile, ConoPred filters artificial conotoxins generated by ConoGen, narrowing down the scope for subsequent research. A comprehensive evaluation of the peptide properties at both sequence and structure levels indicates that the artificial conotoxins generated by ConoDL exhibit a certain degree of similarity to natural conotoxins. Furthermore, ConoDL has generated artificial conotoxins with novel cysteine scaffolds. Therefore, ConoDL may uncover new cysteine scaffolds and conotoxin molecules, facilitating further exploration of the molecular space of conotoxins and the discovery of pharmacologically active variants. The code is available at https://github.com/xueww/ConoDL.The supplementary material and model are available at https://zenodo.org/records/10679280.

bioinformatics↗

bioRxiv2024

Emergence of alternative stable states in gene exchange communities

Microbial communities living in the same environment often display alternative stable states, each characterized by a unique composition of species. Understanding the origin and determinants of microbiome multistability has broad implications in environments, human health and microbiome engineering. However, despite its conceptual importance, how multistability emerges in complex communities remains largely unknown. Here, we focused on the role of horizontal gene transfer (HGT), one important aspect mostly overlooked in previous studies, on the stability landscape of microbial populations. Combining mathematical modeling and numerical simulations, we demonstrate that, when mobile genes only affect bacterial growth rates, increasing HGT rate in general promote the emergence of alternative stable states in complex microbiota. We further extend our analysis to scenarios where HGT changes interspecies interactions, microbial communities are subjected to strong environmental selections and microbes live in metacommunities consisting of multiple local habitats. We also discuss the role of different mechanisms, including interspecies interaction strength, the growth rate effects of MGEs, MGE epistasis and microbial death rates in shaping the multistability of microbial communities undergoing HGT. These results reveal how different dynamic processes collectively shape community multistability and diversity. Our results provide key insights for the predictive control and engineering of complex microbiota.

systems biology↗