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Results for “Molecular Biology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2018

A synthetic non-histone substrate provides insight into substrate targeting by the Gcn5 HAT and sirtuin HDACs

Gcn5 and sirtuins are highly conserved HAT and HDAC enzymes that were first characterised as regulators of gene expression. Although histone tails are important substrates of these enzymes, these proteins also target many non-histone substrates that participate in diverse biological processes. The mechanisms used by these enzymes to choose their non-histone substrates is unclear. In this work, we use a unique synthetic biology approach in S. cerevisiae to demonstrate that a shared target sequence can act as a determinant of substrate selection for Gcn5 and sirtuins. We also exploit this system to define specific subunits of the Gcn5-containing ADA complex as regulators of non-histone acetylations proteome-wide.

molecular biology↗

bioRxiv2020

A multifaceted microRNA turnover complex from Caenorhabditis elegans

microRNAs are known to regulate expression of more than two third of all the eukaryotic genes by post-transcriptional means, and regulation of these tiny regulators play an important role in determining their activities. Here, we report a macromolecular microRNA turnover complex, whose components are crucial to microRNA homeostasis and development in Caenorhabditis elegans. Biochemical investigations with the purified complex in an isolated system not only unfolded the roles of the individual subunits critical for the functionality of the complex, but also unraveled the different modes of operations and regulatability of this biological machine. Our results reveal that this complex is highly receptive and capable of switching between an ATP-dependent and ATP-independent mode of operation depending on the availability of ATP in its environment, which might allow the complex to function dynamically during different physiological conditions.

molecular biology↗

bioRxiv2021

Golden Gate Assembly of Aerobic and Anaerobic Microbial Bioreporters

Microbial bioreporters provide direct insight into cellular processes by producing a quantifiable signal dictated by reporter gene expression. The core of a bioreporter is a genetic circuit in which a reporter gene (or operon) is fused to promoter and regulatory sequences that govern its expression. In this study, we develop a system for constructing novel Escherichia coli bioreporters based on Golden Gate assembly, a synthetic biology approach for the rapid and seamless fusion of DNA fragments. Gene circuits are generated by fusing promoter and reporter sequences encoding yellow fluorescent protein, mCherry, bacterial luciferase, and an anaerobically active flavin-based fluorescent protein. We address a barrier to the implementation of Golden Gate assembly by designing a series of compatible destination vectors that can accommodate the assemblies. We validate the approach by measuring the activity of constitutive bioreporters and mercury and arsenic biosensors in quantitative exposure assays. We also demonstrate anaerobic quantification of mercury and arsenic in biosensors that produce flavin-based fluorescent protein, highlighting the expanding range of redox conditions that can be examined by microbial bioreporters. IMPORTANCEMicrobial bioreporters are versatile genetic tools with wide-ranging applications, particularly in the field of environmental toxicology. For example, biosensors that produce a signal output in the presence of a specific analyte offer less costly alternatives to analytical methods for the detection of environmental toxins such as mercury and arsenic. Biosensors of specific toxins can also be used to test hypotheses regarding mechanisms of uptake, toxicity, and biotransformation. In this study, we develop an assembly platform that uses a synthetic biology technique to streamline construction of novel Escherichia coli bioreporters that produce fluorescent or luminescent signals. We validate the approach by synthesizing and testing an array of bioreporters, including arsenic and mercury biosensors, that produce signal outputs in environments ranging from aerobic to highly reduced anaerobic growth conditions.

molecular biology↗

bioRxiv2023

Exploring G-quadruplex structure in PRCC-TFE3 fusion Oncogene: Plausible use as anti cancer therapy for translocation Renal cell carcinoma (tRCC)

The TFE3 fusion gene, byproduct of Xp11.2 translocation, is the diagnostic marker for translocation renal cell carcinoma (tRCC). Absence of any clinically recognized therapy for tRCC, pressing a need to create novel and efficient therapeutic approaches. Previous studies shown that stabilization of the G-quadruplex structure in oncogenes suppresses their expression machinery. To combat the oncogenesis caused by fusion genes, our objective is to locate and stabilize the G-quadruplex structure within the PRCC-TFE3 fusion gene. Using the Quadruplex- forming G Rich Sequences (QGRS) mapper and the Non-B DNA motif search tool (nBMST) online server, we found putative G-quadruplex forming sequences (PQS) in the PRCC-TFE3 fusion gene. Circular dichroism demonstrating a parallel G-quadruplex in the targeted sequence. Fluorescence and UV-vis spectroscopy results suggest that pyridostatin binds to this newly discovered G-quadruplex. The PCR stop assay, as well as transcriptional or translational inhibition by PQS, revealed that stable G-quadruplex formation affects biological processes. Confocal microscopy of HEK293T cells transfected with the fusion transcript confirmed G- quadruplexes formation in cell. This investigation may shed light on G-quadruplexs functions in fusion genes and may help in the development of therapies specifically targeted against fusion oncogenes, which would enhance the capability of current tRCC therapy approach.

molecular biology↗

bioRxiv2024

Multi omics aided small RNA profiling of wheat rhizosphere and their potential targets in contrasting soils for Rhizoctonia solani-AG8 suppression

Next-generation sequencing helps describe microbial communities in rhizosphere environments, but understanding rhizosphere-plant interactions synergistic effects on plant traits and health outcomes remains challenging. This study analyses rhizosphere sRNAs ability to manipulate host gene targets in plants grown in suppressive (SP) and non-suppressive (NSP) soils with an integrated multi omics dataset. The results showed that rhizosphere sRNAs exhibited specific compositional features that may be important for rhizosphere-plant interaction. Small RNAs, less than 30 nt in size, were predominant in both samples, with a 5-prime bias towards cytosine enrichment, suggesting potential association with wheat specific argonauts. Mapping of sRNA reads to microbial metagenomes assembled draft genomes from SP and NSP soils showed sRNA loci were differentially expressed (DE) between the soils with contrasting disease suppressive capacities. In total, 96 and 132 non redundant rhizosphere sRNAs were abundant in SP and NSP rhizosphere communities, respectively. While 55 known bacterial sRNA loci were predicted from both SP and NSP metagenomes, 127 sRNAs originated from these loci were differentially expressed. Global wheat target prediction and functional analysis from DE rhizosphere sRNAs showed both soil type specific and common pathways. Upregulated NSP sRNAs target metabolic pathways, secondary metabolite biosynthesis, MAPK signalling, while SP sRNAs target glycerophospholipid metabolism, pathways such as polycomb repressive complex, starch/sucrose metabolism, and plant-pathogen interactions were targeted by both sets of sRNAs. This is the first study showing evidence for rhizosphere sRNAs and their corresponding plant transcripts in the context of biological disease suppression in agricultural soils. ImportanceSmall RNAs (sRNAs) have gained attention in host-microbe interactions due to their diverse roles in controlling biological processes. Studies have identified numerous sRNAs with novel functions across various organisms. Echoing growing evidence of sRNAs in different plant-microbe interaction, we show an evidence of rhizosphere sRNAs regulating wheat genes in soil disease suppression context. This understanding could significantly enhance our comprehension of gene regulation in biological functions, potentially paving the way for the development of microbiome-based methods to influence host traits. Understanding the microbiome communitys mechanisms in different environments offers opportunities to modify them for agriculture, including modifying farming practices, host genetics/immunity, and synthetic communities for disease suppression.

molecular biology↗

bioRxiv2019

Digital polymerase chain reaction in an array of microfluidic printed droplets

Digital polymerase chain reaction (PCR) is a fast-developed technology, which makes it possible to provide absolute quantitative results. However, this technology has not been widely used in research field or clinical diagnostics. Although digital PCR has been born for two decades, the products on this subject still suffer from either high cost or cumbersome user experience, hence very few labs have the willingness or budget to routinely use such product; On the other hand, the unique sensitivity of dPCR over traditional qPCR shows great potential applications. Here, a cost-effective digital PCR method based on a microfluidic printing system was introduced, trying to overcome those shortcomings. The microfluidic droplet printing technology was utilized in this study to directly generate droplet array containing PCR reaction solution onto the simple glass substrate for the subsequent PCR and imaging, which could be done with any regular flat-panel PCR machine and microscope. The method introduces a new perspective in droplet-based digital PCR in that the droplets generated with this method aligns well in an array without touch with each other, therefore the regular glass and oil could be used without any special surfactant. With simple analysis, the data generated with this method showed reliable quality, which followed the Poisson distribution trend. Compared with other expensive digital PCR methods, this system is more affordable and simpler to integrate, especially for those biological or medical labs which are in need for the digital PCR options but short in budget. Therefore, this method is believed to have the great potential in the future market application.

molecular biology↗

bioRxiv2023

Rapid cloning-free mutagenesis of new SARS-CoV-2 variants using a novel reverse genetics platform

Reverse genetic systems enable the engineering of RNA virus genomes and are instrumental in studying RNA virus biology. With the recent outbreak of the COVID-19 pandemic, already established methods were challenged by the large genome of SARS-CoV-2. Herein we present an elaborated strategy for the rapid and straightforward rescue of recombinant plus-stranded RNA viruses with high sequence fidelity, using the example of SARS-CoV-2. The strategy called CLEVER (CLoning-free and Exchangeable system for Virus Engineering and Rescue) is based on the intracellular recombination of transfected overlapping DNA fragments allowing the direct mutagenesis within the initial PCR-amplification step. Furthermore, by introducing a linker fragment - harboring all heterologous sequences - viral RNA can directly serve as a template for manipulating and rescuing recombinant mutant virus, without any cloning step. Overall, this strategy will facilitate recombinant SARS-CoV-2 rescue and accelerate its manipulation. Using our protocol, newly emerging variants can quickly be engineered to further elucidate their biology. To demonstrate its potential as a reverse genetics platform for plus-stranded RNA viruses, the protocol has been successfully applied for the cloning-free rescue of recombinant Chikungunya and Dengue virus.

molecular biology↗

bioRxiv2024

Rapid UPF1 depletion illuminates the temporal dynamics of the NMD-regulated transcriptome in human cells

The helicase UPF1 acts as the central essential factor in human nonsense-mediated mRNA decay (NMD) and is involved in various other mRNA degradation processes. Given its multifunctionality, distinguishing between mRNAs regulated directly and indirectly by UPF1 remains a critical challenge. We engineered two different conditional degron tags into endogenous UPF1 in human cell lines to probe the consequences of UPF1 rapid depletion. UPF1 degradation inhibits NMD within hours and strongly stabilizes endogenous NMD substrates, which can be classified into different groups based on their expression kinetics. Extended UPF1 depletion results in massive transcript and isoform alterations, partially driven by secondary effects. We define a high-confidence UPF1-regulated core set of transcripts, which consists mostly of NMD substrates. NMD-regulated genes are involved in brain development and the integrated stress response, among other biological processes. In summary, UPF1 degron systems rapidly inhibit NMD, providing valuable insights into its roles across various experimental systems.

molecular biology↗

bioRxiv2025

Serotonin signaling modulates growth and motility in juvenile Fasciola hepatica

Fasciola hepatica causes fasciolosis, a parasitic disease that poses significant animal and human health challenges. Control relies on flukicides, most of which are adulticides, with only triclabendazole effective against the pathogenic migratory juvenile. Classical neurotransmitter pathways are widely targeted by anthelmintics yet remain underexplored for flukicide development. Here we explore the importance of serotonin (5-HT) signaling in juvenile fluke. In silico analyses confirmed all F. hepatica life stages express a complete 5-HT signaling pathway encompassing genes encoding proteins for 5-HT synthesis, transport, and reuptake, as well as five putative 5-HT G protein-coupled receptors (GPCRs). Homology and binding motif analyses supported the presence of two 5-HT1 (Fh5HT1A, Fh5HT1B) and three 5-HT7 (Fh5HT7A, -7B, -7C) GPCRs. Immunocytochemistry and in situ hybridization revealed widespread neuronal expression of 5-HT, its synthetic enzyme tryptophan hydroxylase (FhTPH), and the GPCR Fh5HT7C. 5-HT addition stimulated juvenile fluke motility; consistent with this observation, serotonin reuptake inhibition, which causes 5-HT persistence at synaptic junctions, also enhanced juvenile movement. Silencing of FhTPH, a key enzyme in 5-HT synthesis, blunted juvenile motility, a phenotype reversed by the addition of 5-HT. Silencing the fluke vesicular monoamine transporter (FhVMAT), which packages 5-HT into synaptic vesicles, reduced juvenile motility, whilst silencing the 5-HT reuptake transporter (FhSERT) which recycles synaptic 5-HT increased juvenile motility and growth, consistent with 5-HT accumulation enhancing effects. Whilst combinatorial silencing of Fh5HT1 receptors reduced fluke motility, silencing Fh5HT7 receptors led to a greater reduction in motility. Exogenous addition of 5-HT partially rescued motility deficits of juveniles with silenced Fh5HT1 receptors, but 5-HT excitation was abolished in Fh5HT7-RNAi juveniles, exposing their importance to fluke motility. Notably, sustained 5-HT exposure promoted juvenile growth, but these effects were not blunted by receptor-RNAi. The findings emphasize a central role of serotonin signaling in both juvenile motility and growth, exposing novel aspects of receptor function and encouraging therapeutic exploitation for liver fluke control. Author SummaryThe liver fluke, Fasciola hepatica, causes fasciolosis, a neglected tropical disease that poses a significant burden on human and animal health. There is no vaccine for fasciolosis and treatment relies on a single drug, triclabendazole, to control the early stages of infection which cause liver pathology whilst migrating through the mammalian host. Single drug reliance has increased the incidence of drug resistance in both human and animal populations, such that there is a pressing need for the characterization of novel drug targets and development of new anthelmintics targeting liver fluke. The focus of this research is to examine the role of the serotonin signaling system of liver fluke, bridging a gap in knowledge to enable the exploitation of this signaling pathway for flatworm drug development. Here, bioinformatic analysis has characterized the pathway components and receptors in multiple clinically relevant flatworm parasite species. Chemical and functional genomic methods have been used to prove the integral function of serotonin in liver fluke biology, regulating motility and growth, both essential for parasite infection and survival. This work provides data that help validate the serotonergic system of liver fluke as a potential target for future anthelmintic development.

molecular biology↗

bioRxiv2019

Detection and quantification of GPCR mRNA: An assessment and implications of data from high-content methods

G protein-coupled receptors (GPCRs) are the largest family of membrane receptors and targets for approved drugs. Analysis of GPCR expression is thus important for drug discovery and typically involves mRNA-based methods. We compared transcriptomic cDNA [Affymetrix] microarrays, RNA-seq and qPCR-based TaqMan arrays for their ability to detect and quantify expression of endoGPCRs (non-chemosensory GPCRs with endogenous agonists). In human pancreatic cancer-associated fibroblasts, RNA-seq and TaqMan arrays yielded closely correlated values for GPCR number (~100) and expression levels, as validated by independent qPCR. By contrast, the microarrays failed to identify ~30 such GPCRs and generated data poorly correlated with results from those methods. RNA-seq and TaqMan arrays also yielded comparable results for GPCRs in human cardiac fibroblasts, pancreatic stellate cells, cancer cell lines and pulmonary arterial smooth muscle cells. The magnitude of mRNA expression for several Gq/11-coupled GPCRs predicted cytosolic calcium increase and cell migration by cognate agonists. RNA-seq also revealed splice variants for endoGPCRs. Thus, RNA-seq and qPCR-based arrays are better suited than microarrays for assessing GPCR expression and can yield results predictive of functional responses--findings that have implications for GPCR biology and drug discovery.\n\nAbstract Graphic\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=168 SRC=\"FIGDIR/small/734863v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (21K):\norg.highwire.dtl.DTLVardef@1a47e41org.highwire.dtl.DTLVardef@5ce56corg.highwire.dtl.DTLVardef@da5330org.highwire.dtl.DTLVardef@18b8215_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2020

Correlated motions of conserved polar motifs lay out a plausible mechanism of G protein-coupled receptor activation.

Recent advancements in the field of experimental structural biology have provided high-resolution structures of active and inactive state G protein-coupled receptors (GPCRs), a highly important pharmaceutical target family, but the process of transition between these states is poorly understood. According to the current theory, GPCRs exist in structurally distinct, dynamically interconverting functional states of which populations are shifted upon binding of ligands and intracellular signaling proteins. However, explanation of the activation mechanism on an entirely structural basis gets complicated when multiple activation pathways and active receptor states are considered. Our unbiased, atomistic molecular dynamics simulations of the mu-opioid receptor in a physiological environment revealed that external stimulus is propagated to the intracellular surface of the receptor through subtle, concerted movements of highly conserved polar amino acid side chains along the 7th transmembrane helix. To amend the widely accepted theory we suggest that the initiation event of GPCR activation is the shift of macroscopic polarization between the ortho- and allosteric binding pockets and the intracellular G protein-binding interface. O_FIG O_LINKSMALLFIG WIDTH=184 HEIGHT=200 SRC="FIGDIR/small/920769v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@102f33org.highwire.dtl.DTLVardef@8af6bforg.highwire.dtl.DTLVardef@14d9192org.highwire.dtl.DTLVardef@1903819_HPS_FORMAT_FIGEXP M_FIG Table of Contents Graphic C_FIG

molecular biology↗

bioRxiv2024

Comparative analysis of 43 distinct RNA modifications by nanopore tRNA sequencing

Transfer RNAs are the fundamental adapter molecules of protein synthesis and the most abundant and heterogeneous class of noncoding RNA molecules in cells. The study of tRNA repertoires remains challenging, complicated by the presence of dozens of post transcriptional modifications. Nanopore sequencing is an emerging technology with promise for both tRNA sequencing and the detection of RNA modifications; however, such studies have been limited by the throughput and accuracy of direct RNA sequencing methods. Moreover, detection of the complete set of tRNA modifications by nanopore sequencing remains challenging. Here we show that recent updates to nanopore direct RNA sequencing chemistry (RNA004) combined with our own optimizations to tRNA sequencing protocols and analysis workflows enable high throughput coverage of tRNA molecules and characterization of nanopore signals produced by 43 distinct RNA modifications. We share best practices and protocols for nanopore sequencing of tRNA and further report successful detection of low abundance mitochondrial and viral tRNAs, providing proof of concept for use of nanopore sequencing to study tRNA populations in the context of infection and organelle biology. This work provides a roadmap to guide future efforts towards de novo detection of RNA modifications across multiple organisms using nanopore sequencing.

molecular biology↗

bioRxiv2025

Accurate Protein Dynamic Conformational Ensembles: Combining AlphaFold, MD and Amide 15N(1H) NMR Relaxation.

Conformational heterogeneity is critical for protein function, but the validation of dynamic ensembles remains a challenge. In this study, we introduced an approach that integrates free MD simulations, using an AlphaFold-generated structure as the starting point, with experimental relaxation data to identify biologically relevant conformational ensembles. For the extracellular region of Streptococcus pneumoniae PsrSp, we found that only certain segments of the MD long trajectory aligned well with experimental data. The defined ensembles revealed two regions with increased flexibility that play important functional roles.

molecular biology↗

bioRxiv2019

A bestiary of genetic mouse lines and related tools for inducible and reversible intersectional misexpression

Thanks to many advances in genetic manipulation, mouse models have become very powerful in their ability to interrogate biological processes. In order to precisely target expression of a gene of interest to particular cell types, intersectional genetic approaches utilizing two promoter/enhancers unique to a cell type are ideal. Within these methodologies, variants that add temporal control of gene expression are the most powerful. We describe the development, validation and application of an intersectional approach that involves three transgenes, requiring the intersection of two promoter/enhancers to target gene expression to precise cell types. Furthermore, the approach utilizes available lines expressing tTA/rTA to control timing of gene expression based on whether doxycycline is absent or present, respectively. We also show that the approach can be extended to other animal models, using chicken embryos. We generated three mouse lines targeted at the Tigre (Igs7) locus with TRE-loxP-tdTomato-loxP upstream of three genes (p21, DTA and Ctgf) and combined them with Cre and tTA/rtTA lines that target expression to the cerebellum and limbs. Our tools will facilitate unraveling biological questions in multiple fields and organisms. Summary statementAhmadzadeh et al. present a collection of four mouse lines and genetic tools for misexpression-mediated manipulation of cellular activity with high spatiotemporal control, in a reversible manner.

molecular biology↗

bioRxiv2026

Enhancing Lipid Detection and Spatial Accuracy in Carotid Plaques Using Mass Spectrometry Imaging Techniques

Matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) is a powerful technique for studying lipid distribution in carotid plaques, key to understanding atherosclerosis. This study aimed to improve sample preparation for MALDI-MSI-based spatial lipidomics of carotid plaques by improving both matrix application and tissue handling. Human carotid plaques were collected from endarterectomy patients with ethical approval and sectioned at 10 {micro}m thickness for MALDI-MSI. We compared eight sample preparation methods, including hydroxypropyl methylcellulose-polyvinylpyrrolidone (HPMC-PVP) embedding media and Cryofilm-type IMS(R) to provide support and maintain tissue structural integrity during sectioning. Methods were assessed for signal intensity, lipid diffusion, lipid coverage, tissue morphology, and image co-registration which each criterion scored from 1-3. Cryofilm-based methods scored highest for preserving tissue morphology and minimising folding artifacts (2.9-3.0) but were limited in co-registration (2.0) due to reliance on adjacent sections. Sublimation methods generally produced greater lipid coverage with reduced lateral diffusion, while automated sprayer methods scored higher in signal intensity/sensitivity (3.0) but had increased lipid delocalisation, particularly for highly hydrophobic species such as triacylglycerols and sterols. The results highlight clear trade-offs between tissue structural preservation, lipid detection sensitivity, and spatial integrity in MALDI-MSI. Because spatial integrity cannot be compromised for imaging lipids in carotid atherosclerotic plaques, Cryofilm combined with sublimation offers a clear advantage. This work strengthens MALDI-MSI workflows enabling more precise spatial mapping and deeper biological interpretation of atherosclerotic lipid distributions.

molecular biology↗

bioRxiv2021

Characterization of USH1C/harmonin in the human retina provides insights into pathophysiology and therapy options for Usher syndrome

Usher syndrome (USH) is the most common form of hereditary deafness-blindness in humans. USH is a complex genetic disorder, assigned to three clinical subtypes differing in onset, course, and severity, with USH1 being the most severe. Rodent USH1 models do not reflect the ocular phenotype observed in human patients to date; hence, little is known about the pathophysiology of USH1 in the human eye. One of the USH1 genes, USH1C, exhibits extensive alternative splicing and encodes numerous harmonin protein isoforms that function as scaffolds for organizing the USH interactome. RNA-seq analysis of human retinas uncovered harmonin_a1 as the most abundant transcript of USH1C. Bulk RNA-seq analysis and immunoblotting showed abundant expression of harmonin in Muller glia cells (MGCs) and retinal neurons. Furthermore, harmonin was localized in the terminal endfeet and apical microvilli of MGCs, presynaptic region (pedicle) of cones, and outer segments of rods as well as at adhesive junctions of MGCs and photoreceptors in the outer limiting membrane (OLM). Our data provide evidence for the interactions of harmonin with OLM molecules in photoreceptors (PRCs) and MGCs and rhodopsin in PRCs. Subcellular expression and colocalization of harmonin correlate with the clinical phenotype observed in USH1C patients. In addition, primary cilia defects in USH1C patient-derived fibroblasts could be reverted by the delivery of harmonin_a1 transcript isoform. Our data provide novel insights into PRC cell biology, USH1C pathophysiology, and for developing gene therapy treatment.

molecular biology↗

bioRxiv2022

A multiparametric anti-aging CRISPR screen uncovers a role for BAF in protein translation

Progeria syndromes are very rare, incurable premature aging conditions recapitulating most aging features. Here, we report the first whole genome, multiparametric CRISPR anti-aging screen, identifying 43 new genes that can reverse multiple aging phenotypes in progeria. The screen was implemented in fibroblasts from Nestor- Guillermo Progeria Syndrome (NGPS) patients, carrying a homozygous p.Ala12Thr mutation in barrier-to-autointegration factor (BAF A12T). The hits were enriched for genes involved in protein translation, protein and RNA transport and osteoclast formation. We further confirmed that BAF A12T drives increased protein translation and translational errors that could directly contribute to premature aging in patients. This work has highlighted the power of multiparametric whole genome synthetic rescue screens to identify new anti-aging genes and uncover novel biology behind progeria-associated cellular dysfunction. One-Sentence SummaryA whole genome multiparametric screen in progeria identifies new pathways that can reverse cellular aging phenotypes.

molecular biology↗

bioRxiv2023

Predicting the dynamic interaction between intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) participate in various biological processes. Interactions involving IDPs are usually dynamic and affected by their inherent conformation fluctuations. Comprehensive characterization of these interactions based on current techniques is challenging. Here, we present GSALIDP, a GraphSAGE-LSTM Network to capture the dynamic nature of IDP-involved interactions and predict their behaviors. This framework models multiple conformations of IDP as a dynamic graph which can effectively describe the fluctuation of its flexible conformation. The dynamic interaction between IDPs is studied and the datasets of IDP conformations and their interactions are obtained through atomistic molecular dynamic (MD) simulations. Residues of IDP are encoded through a series of features, including their frustration. GSALIDP can effectively predict the interaction sites of IDP and the contact residue pairs between IDPs. Its performance in predicting IDP interaction is on par with or even better than the conventional models in predicting the interaction of structural proteins. To the best of our knowledge, this is the first model to extend the protein interaction prediction to IDP-involved interactions.

molecular biology↗