Biology subjects

Cha, S.

Publications and source records attributed to Cha, S..

14 recordsLinked to original sources

bioRxiv2026

Systematic exploration of predicted quaternary structures within pandemic-relevant viral proteomes

Mechanistic understanding of viral protein-protein interactions enables global health security and pandemic preparedness, yet experimental characterisation remains difficult, costly, and often restricted to specialised laboratories. Here, we describe an in silico campaign using AlphaFold2 and AlphaFold-Multimer to predict monomers and dimer structures within 2,812 viral proteomes from 23 viral families relevant to human health. We report high-confidence predicted structures of 5,279 hetero-, and 2,749 homo-dimers. Structural clustering of interfaces reduces the set fivefold to 1,598 consolidated by form and function, of which 471 (29.5%) lacked detectable similarity to experimentally determined interfaces in the PDB. These clusters yielded two notable findings: new data on vaccinology-relevant glycoproteins, and accurate prediction of the specificity and cleavage-site recognition of viral proteases, which are targets for anti-viral development. Viral monomers and high-confidence dimers are available for interactive browsing in the Pandemic Preparedness Portal of the AlphaFold Database (https://alphafold.ebi.ac.uk/), and the full dataset is available for bulk download.

bioinformatics↗

bioRxiv2026

Latent generative search unlocks de novo design of untapped biomolecular interactions at scale

De novo protein design has advanced rapidly, yet designing binders to polar, solvent-exposed epitopes and small, flexible ligands remains challenging. Such hydrated surfaces and flexible molecules, including carbohydrates, provide few of the hydrophobic contacts favoured by current methods and have largely resisted de novo binders. To address this challenge, here we introduce latent generative search for binder design, a novel framework that uses reward-guided search at inference time to steer the Proteina-Complexa generative model. The model codesigns sequence and structure - generating them together in a continuous latent space - and thereby removes the inverse-folding step on which current methods rely. In a screen of more than one million designs by multiplexed phage display, latent generative search produced more validated binders than every other method tested, its codesigned sequences surpassing post hoc redesign. It delivered high-affinity binders across therapeutic receptors, a viral attachment protein and intracellular signalling targets. Our approach also accessed previously untapped biology, generating the first de novo proteins that bind a free carbohydrate, including one that discriminates between blood-group antigens - a polar, flexible target class beyond the reach of current design methods.

bioengineering↗

bioRxiv2026

Foldseek-Interface reveals a protein interface universe far from complete

Protein-protein interactions mediate a vast range of cellular functions, requiring diverse modes of binding. While recent years have seen major efforts to chart and classify the protein structure universe, we lack comparable methods to assess and cluster that diversity in interface structure at interactome scale. Here, we present Foldseek-Interface, a method that converts 3D interface structures into searchable sequences to enable fast alignment and clustering of protein interaction interfaces. It matches the accuracy of state-of-the-art tools while running up to 230 times faster. Applying it to all biological assemblies in the PDB, we cluster 3.1 million dimers into 77{,}167 interface clusters and use this resource to characterise interface diversity, evolution, and pathogen mimicry. Application of Foldseek-Interface to resources of predicted protein complex structures rapidly revealed putatively novel interface types worth further experimental interrogation. Foldseek-Interface and the interface cluster resource are freely available as webservers for search https://search.foldseek.com/interface and exploration https://interface.foldseek.com.

bioinformatics↗

bioRxiv2026

AlphaFold Database expands to proteome-scale quaternary structures

Protein function is governed by molecular interactions, yet structural coverage of these interactions remains sparse. The AlphaFold Protein Structure Database (AFDB) transformed access to accurate monomeric protein structures at scale. Here, we expand the AFDB to quaternary structures by predicting 31M candidate homo- and heterodimeric protein complexes, compiled from 4,777 proteomes, including model- and global health organisms. We established confidence criteria via analysis of experimentally determined structures, resulting in 1.81M high-confidence predictions. These models enabled the discovery of emergent structures and topologies not present in monomeric predictions. Additionally, the top 1% of structural clusters accounted for [~]44% of all complexes, and [~]8.3% of clusters were conserved across multiple domains of life, pointing to a substantial fraction of ancient, universally retained assemblies. Structural search highlighted that high-confidence predictions are anchored in experimental multimer space, yet 31.3% extend beyond detectable PDB coverage. These freely accessible proteome-scale predictions facilitate functional and mechanistic hypothesis generation across biology.

synthetic biology↗

bioRxiv2026

StrucTTY: An Interactive, Terminal-Native Protein Structure Viewer

Terminal-based workflows are central to large-scale structural biology, particularly in high-performance computing (HPC) environments and SSH sessions. Yet no existing tool enables real-time, interactive visualization of protein backbone structures directly within a text-only terminal. To address this gap, we present StrucTTY, a fully interactive, terminal-native protein structure viewer. StrucTTY is a single self-contained executable that loads mulitple PDB and mmCIF files, normalizes three-dimensional coordinates, and renders protein structures as ASCII graphics. Users can rotate, translate, and zoom in on structures, adjust visualization modes, inspect chain-level features and view secondary structure assignments. The tool supports simultaneous visualization of up to nine protein structures and can directly display structural alignments using Foldseeks output, enabling rapid comparative analysis in headless environments. The source code is available at https://github.com/steineggerlab/StrucTTY. O_TEXTBOXKey MessagesO_LIReal-time, interactive protein structure visualization directly within text-only terminals C_LIO_LIASCII-based, depth-aware rendering of PDB and mmCIF backbone structures C_LIO_LIMulti-structure comparison with direct application of Foldseek alignment transformations C_LIO_LIDesigned for headless workflows on remote servers and HPC systems C_LI C_TEXTBOX

bioinformatics↗

bioRxiv2024

Skeletal Muscle Mitochondrial Dysfunction Mediated by Pseudomonas aeruginosa Quorum Sensing Transcription Factor MvfR: Reversing Effects with Anti-MvfR and Mitochondrial-Targeted Compounds

Sepsis and chronic infections with Pseudomonas aeruginosa, a leading "ESKAPE" bacterial pathogen, are associated with increased morbidity and mortality and skeletal muscle atrophy. The actions of this pathogen on skeletal muscle remain poorly understood. In skeletal muscle, mitochondria serve as a crucial energy source, which may be perturbed by infection. Here, using the well-established backburn and infection model of murine P. aeruginosa infection, we deciphered the systemic impact of the quorum sensing (QS) transcription factor MvfR by interrogating five days post-infection its effect on mitochondrial-related functions in the gastrocnemius skeletal muscle and the outcome of the pharmacological inhibition of MvfR function and that of the mitochondrial-targeted peptide, Szeto-Schiller 31 (SS-31). Our findings show that the MvfR perturbs ATP generation, oxidative phosphorylation (OXPHOS), and antioxidant response, elevates the production of reactive oxygen species, and promotes oxidative damage of mitochondrial DNA in the gastrocnemius muscle of infected mice. These impairments in mitochondrial-related functions were corroborated by the alteration of key mitochondrial proteins involved in electron transport, mitochondrial biogenesis, dynamics and quality control, and mitochondrial uncoupling. Pharmacological inhibition of MvfR using the potent anti-MvfR lead, D88, we developed, or the mitochondrial-targeted peptide SS-31 rescued the MvfR- mediated alterations observed in mice infected with the wild-type strain PA14. Our study provides insights into the actions of MvfR in orchestrating mitochondrial dysfunction in the skeletal murine muscle, and it presents novel therapeutic approaches for optimizing clinical outcomes in affected patients.

microbiology↗

bioRxiv2024

SLIRP mediates nuclear-mitochondrial communication during antiviral signaling to promote robust interferon response

The abnormal innate immune response is a prominent feature underlying autoimmune diseases. One emerging factor that can trigger dysregulated immune activation is cytosolic mitochondrial double-stranded RNAs (mt-dsRNAs). However, the mechanism by which mt-dsRNAs stimulate immune responses remains poorly understood. Here, we discover SRA stem-loop interacting RNA binding protein (SLIRP) as a key amplifier of mt-dsRNA-triggered antiviral signals. In autoimmune diseases, SLIRP is commonly upregulated, and targeted knockdown of SLIRP dampens the interferon response. We find that the activation of melanoma differentiation-associated gene 5 (MDA5) by exogenous dsRNAs upregulates SLIRP, which then stabilizes mt-dsRNAs and promotes their cytosolic release to activate MDA5 further, augmenting the interferon response. Furthermore, the downregulation of SLIRP partially rescues the abnormal interferon-stimulated gene expression in autoimmune patients primary cells and makes cells vulnerable to certain viral infections. Our study unveils SLIRP as a pivotal mediator of interferon response through positive feedback amplification of antiviral signaling.

molecular biology↗

bioRxiv2024

The Bacterial Quorum-Sensing Signal 2-Aminoacetophenone Rewires Immune Cell Bioenergetics through the PGC-1α/ERRα Axis to Mediate Tolerance to Infection

How bacterial pathogens exploit host metabolism to promote immune tolerance and persist in infected hosts remains elusive. To achieve this, we show that Pseudomonas aeruginosa (PA), a recalcitrant pathogen, utilizes the quorum sensing (QS) signal 2-aminoacetophenone (2-AA). Here, we unveil how 2-AA-driven immune tolerization causes distinct metabolic perturbations in macrophages mitochondrial respiration and bioenergetics. We present evidence indicating that these effects stem from decreased pyruvate transport into mitochondria. This reduction is attributed to decreased expression of the mitochondrial pyruvate carrier (MPC1), which is mediated by diminished expression and nuclear presence of its transcriptional regulator, estrogen-related nuclear receptor alpha (ERR). Consequently, ERR exhibits weakened binding to the MPC1 promoter. This outcome arises from the impaired interaction between ERR and the peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1). Ultimately, this cascade results in diminished pyruvate influx into mitochondria and, consequently reduced ATP production in tolerized macrophages. Exogenously added ATP in infected macrophages restores the transcript levels of MPC1 and ERR- and enhances cytokine production and intracellular bacterial clearance. Consistent with the in vitro findings, murine infection studies corroborate the 2-AA-mediated long-lasting decrease in ATP and acetyl-CoA and its association with PA persistence, further supporting this QS signaling molecule as the culprit of the host bioenergetic alterations and PA persistence. These findings unveil 2-AA as a modulator of cellular immunometabolism and reveal an unprecedented mechanism of host tolerance to infection involving the PGC-1/ERR axis in its influence on MPC1/OXPHOS-dependent energy production and PA clearance. These paradigmatic findings pave the way for developing treatments to bolster host resilience to pathogen-induced damage. Given that QS is a common characteristic of prokaryotes, it is likely that 2-AA-like molecules with similar functions may be present in other pathogens.

immunology↗

bioRxiv2024

Impact of Cervical Lymphatic Obstruction on Brain Pathophysiology in Cervical Lymphedema Animal Models

BackgroundInjury to the cervical lymph nodes can lead to cervical lymphedema and subsequent fluid accumulation in the head and neck region, potentially causing pathophysiological alteration in the brain. This condition is thought to be linked with various neurological diseases, although the direct connection between cervical lymphatic obstruction and its effect on the brain has been difficult to establish. MethodsWe produced the disease animal models through lymph node dissection and radiation in fifteen male Sprague-Dawley rats aged 8 weeks and weighing 280-320 g. The models were specifically designed to induce lymphatic obstruction in the cervical region only, with no direct interventions applied to the brain. We evaluated swelling and lymphatic drainage in the head and neck for follow-up. The size of the lateral ventricles was verified through MRI, and changes in water content in brain tissue were directly measured. At 2 and 8 weeks, we observed immune cell infiltration, ventricular enlargement, and pathohistological changes in the harvested brain tissues. ResultsThe experimental animals exhibited lymphatic obstruction in the cervical region, with swelling, abnormal lymphatic drainage, and immune cell infiltration into the brains white matter, reminiscent of extremities lymphedema. MRI revealed lateral ventricular enlargement in these animals, indicative of increased cerebrospinal fluid levels compared to the control group. This increase in cerebrospinal fluid was associated with an increase in brain tissue water content, leading to pathophysiological changes akin to those seen in hydrocephalus and cerebral edema. ConclusionThe outcomes in this study underscore a significant link between lymphatic circulatory dysfunction and the onset of neurophysiological diseases. Cervical lymphedema showed pathophysiological changes similar to those seen in extremities lymphedema. However, these changes in the brain could be more critical than in the extremities. Our finding highlights the importance of understanding lymphatic system health in preventing and managing neurological conditions.

physiology↗

bioRxiv2023

Comparative study of the mechanism of natural compounds with similar structures using docking and transcriptome data for improving in silico herbal medicine experimentations

Natural products have successfully treated several diseases using a multi-component, multi-target mechanism. However, a precise mechanism of action has not been identified. Systems pharmacology methods have been used to overcome these challenges. However, there is a limitation as those similar mechanisms of similar components cannot be identified. In this study, comparisons of physicochemical descriptors, large-scale molecular docking analysis, and RNA-seq analysis were performed to compare the mechanisms of action of similar compounds and to confirm the changes observed when similar compounds were mixed and used. We propose an advanced method for in silico experiments in herbal medicine research based on the results. First, physicochemical descriptors were calculated based on the chemical structures of oleanolic acid (OA), hederagenin (HG), and gallic acid (GA). Similarities were confirmed by calculating the Euclidean, cosine, and Tanimoto distances between the descriptors. Next, the mechanisms of action of OA, HG, and GA were compared and confirmed through in silico-based systems pharmacology analysis using the BATMAN-TCM platform. The proteins interacting with the three compounds were verified through large-scale molecular docking analysis using the druggable proteome. Finally, a drug response transcriptome study was performed using OA, HG, GA, and a combination of OA and HG (COH) with similar structures.A comparison of physicochemical descriptors confirmed that OA and HG were very close. In particular, the two compounds showed a concordance rate of > 99% at cosine and Tanimoto distances. The systems pharmacology analysis results confirmed that OA and HG shared more than 86% of their predicted target proteins and differed only in GA. Systems pharmacology analysis revealed that OA and HG share the mechanisms of cardiac muscle contraction, oxidative phosphorylation, and non-alcoholic fatty liver disease. In a molecular docking analysis of the 50 major druggable proteins, OA and HG shared 38 proteins, while GA shared a few with proteins derived from the other two compounds. In addition, OA and HG were confirmed to act on gonadotropin-releasing hormone (GnRH) secretion, type 2 diabetes mellitus, cholinergic synapses, and calcium signaling pathways, and docking analysis visualization confirmed that the two components interact at the same site. RNA-seq analysis also showed that the differentially expressed genes and pathways derived from OA and HG were similar, and it was confirmed that COH had similar results to OA and HG. Our study has three novel findings. First, an advanced network pharmacology research method was suggested by partially presenting a solution to the difficulty in identifying multicomponent mechanisms. Second, a new natural product analysis method was proposed using large-scale molecular docking analysis. Finally, various biological data and analysis methods were used, such as in silico system pharmacology, docking analysis, and drug response RNA-seq. The results of this study are meaningful in that they suggest an analysis strategy that can improve existing systems pharmacology research analysis methods by showing that natural product-derived compounds with the same scaffold have the same mechanism.

bioinformatics↗

bioRxiv2022

Genetic architecture of creativity and extensive genetic overlap with psychiatric disorders revealed from genome-wide association analyses of 241,736 individuals

Creativity is heritable and exhibits familial aggregation with psychiatric disorders, but its genomic basis and genetic relationship with psychiatric disorders remain largely unknown. Here, we conducted a genome-wide association study (GWAS) using an expanded, machine learning-based definition of creativity in individuals of European ancestry from the UK Biobank (n = 241,736) and identified 25 creativity-associated loci. Extensive genetic overlap with psychiatric disorders, including schizophrenia, major depression, bipolar I disorder, attention deficit/hyperactivity disorder, and anorexia nervosa, was demonstrated by the genetic correlation, polygenic risk score, and MiXeR analyses. The condFDR and conjFDR analyses identified additional loci for creativity and psychiatric disorders, as well as shared genetic loci between creativity and psychiatric disorders. This GWAS showed significant correlations with GWASs using traditional definitions of creativity and GWASs adjusted for educational attainment. Our findings contribute to the understanding of the genetic architecture of creativity and reveal its polygenic relationships with psychiatric disorders.

genomics↗

bioRxiv2022

Highly accurate isoform identification for the human transcriptome

We explore a new hypothesis in genome annotation, namely whether computationally predicted protein structures can help to identify which of multiple possible gene isoforms represents a functional protein product. Guided by structure predictions, we evaluated over 140,000 isoforms of human protein-coding genes assembled from over 10,000 RNA sequencing experiments across many human tissues. We illustrate our new method with examples where structure provides a guide to function in combination with expression and evolutionary evidence. Additionally, we provide the complete set of structures as a resource to better understand the function of human genes and their isoforms. These results demonstrate the promise of protein structure prediction as a genome annotation tool, allowing us to refine even the most highly-curated catalog of human proteins. One-Sentence SummaryWe describe the use of 3D protein structures on a genome-wide scale to evaluate human protein isoforms for biological functionality.

genomics↗

bioRxiv2021

Targeting mitochondrial double-stranded RNAs ameliorates autoimmune characteristics of Sjogrens syndrome

ObjectiveSjogrens syndrome (SS) is a systemic autoimmune disease that targets the exocrine glands, resulting in impaired saliva and tear secretion. To date, type I interferons (I-IFNs) are increasingly recognized as pivotal mediators in SS, but their endogenous drivers have not been elucidated. This study investigates the role of mitochondrial double-stranded RNAs (mt-dsRNAs) in regulating I-IFN response in SS. MethodsSaliva and tear from SS patients and controls (n=73 for saliva and n=16 for tear), the salivary glands of the SS-prone-non-obese-diabetic mouse, and primary human salivary glandular cells were screened for mt-dsRNAs by RT-qPCR. The human salivary cell line (NS-SV-AC) grown as three-dimensional spheroids were subject to dsRNA stress to measure mt-dsRNA induction and recapitulation of SS glandular inflammatory features. Acetylcholine, SS-IgG, upadacitinib (JAK1 inhibitor), or 2-C'-methyladenosine (mitochondrial transcription inhibitor) were applied to characterize the roles of mt-dsRNAs. To identify endogenous dsRNA-sensor and confirm the mitochondrial origin of cytoplasmic dsRNAs, the immunoprecipitation of dsRNAs was performed. Resultsmt-dsRNAs were elevated in the SS specimens with salivary ND5 and tear CYTB1 being statistically associated with secretory dysfunction/inflammation and corneal/conjunctival damage, respectively. Stimulation of the spheroids with dsRNA stress of poly I:C induced mt-dsRNAs, p-PKR, and I-IFNS via the JAK1/STAT pathway whereas the inhibition of mt-RNA synthesis or JAK1 attenuated the glandular signature. The inhibitory effect of acetylcholine on mt-dsRNAs and I-IFNS induction was reversed by SS-IgG. Conclusionmt-dsRNAs amplify the impact of dsRNA stress on SS glandular signatures in vitro, potentially propagating a pseudo-viral signal in the SS target tissue. SummaryMitochondrial double-stranded RNA levels were elevated in the tear and saliva of SS patients, which was associated with secretory dysfunction and tissue inflammation. These RNAs amplified type I interferon signature as well as glandular phenotypes reported in SS. Inhibitors of mitochondrial RNA transcription or JAK1 in salivary gland acinar cell spheroids attenuated the mitochondrial RNA-mediated changes.

molecular biology↗

bioRxiv2019

Cost implications of a nationwide survey of schistosomiasis and other intestinal helminthiases in Sudan

BackgroundIt is vital to share details of concrete experiences of conducting a nationwide survey, so that the global health community could adapt it to expand geographic mapping programs, eventually contributing to the development of control and elimination strategies with limited resources. A nationwide survey of schistosomiasis and nine other intestinal helminthiases was conducted from December 2016 to March 2017 in Sudan. ObjectivesWe aimed to describe details of the key activities and components required for the nationwide survey of schistosomiasis and other intestinal helminthiases and to analyze its costs. MethodsWe estimated financial and economic costs from the providers perspective. Cash expenditures incurred to implement the survey were defined as financial costs. We took into account all of the resources invested in the survey for economic costs, including the components that were not paid for, such as vehicles and survey equipment provided by the Ministry of Health, Sudan and the opportunity costs of primary school teachers time spent on the survey. We ran one-way sensitivity and probabilistic analyses using Monte-Carlo methods with 10,000 draws to examine the robustness of the primary analysis results. ResultsA total of USD 1,465,902 and USD 1,516,238 was incurred for the financial and economic costs, respectively. The key cost drivers of the nationwide survey were personnel and transportation, for both financial and economic costs. Personnel and transportation accounted for around 64% and 18% of financial costs, respectively. ConclusionsThe cost is expected to vary depending on the quantity and quality of existing laboratory facilities, equipment, and consumables, and the capability of laboratory technicians and sample collectors. Establishing central-level and independent supervision mechanisms to ensure the quality of the survey is equally important. We expect the global health community to draw on this study when developing nationwide surveys of schistosomiasis and other intestinal helminthiases. Author SummaryAlthough large-scale mapping of schistosomiasis and other intestinal helminthiases has been conducted in some countries, little is known about the details of nationwide surveys, such as the necessary scale of the workforce, logistics, and the cost of conducting a nationwide survey. A nationwide survey of schistosomiasis and nine other intestinal helminthiases was conducted from December 2016 to March 2017 in Sudan. A total of 105,167 students participated in the survey from 1,772 primary schools in 183 districts of all 18 states of Sudan. Herein, we present the activities that were necessary to prepare and conduct a nationwide neglected tropical disease survey, along with details on the types and amounts of personnel, survey equipment, and consumables that are required. In addition, through an analysis of the costs of the nationwide survey, we generated average costs at the district and sub-district level. The key cost drivers were personnel and transportation, both of which were recurrent costs. Establishing a steering committee to develop and reach consensus on a survey protocol, assessing the capacities of potential staff (particularly laboratory technicians), and training laboratory technicians and data collectors were key components required to prepare a nationwide survey. If a government finds a way to mobilize existing government officials with no additional payment using the health system already in place, the cost of a nationwide survey would be remarkably lower. We expect the global health community to draw on this study to develop nationwide surveys for schistosomiasis and other intestinal helminthiases.

microbiology↗