Biology subjects

Pancsa, R.

Publications and source records attributed to Pancsa, R..

11 recordsLinked to original sources

bioRxiv2026

Positive selection tends to act on exposed extracellular regions and delineate interaction modules targeted by pathogens

Background: Positive selection shapes protein function by favoring amino acid substitutions that increase fitness. Although numerous studies have identified positively selected genes (PSGs), the structural principles underlying residue-level positive selection remain incompletely understood and previous studies have produced conflicting conclusions, particularly regarding the role of intrinsically disordered regions. In order to resolve these issues and to better understand the driving forces underlying positive selection in human proteins in general, we performed a comprehensive analysis on a manually curated, high quality collection of PSGs and positively selected residues (PSRs) as well as on a large-scale PSR dataset restricted to proteins with experimental structures. Results: Human PSRs were significantly enriched in secreted and cell membrane proteins and preferentially localized to extracellular regions, solvent-exposed surfaces, coil structures, and protein-protein interaction interfaces, whereas neither domains nor intrinsically disordered regions showed an enrichment. Spatial clustering analysis reinforced that PSRs accumulate within localized surface patches. Integration of host-pathogen interaction data highlighted that adaptive changes preferentially affect extracellular molecular recognition surfaces, recurrently appearing in certain pathogen-interacting membrane protein families and particular domain types. Additionally, PSRs showed an enrichment in the residues of human-pathogen interaction interfaces that are in direct contact with pathogenic proteins, implying that neutralizing pathogen attacks is one of the driving forces behind the adaptive evolution of human proteins. By analysing human variation data we found that PSRs are enriched in benign but depleted in pathogenic substitutions, extending previous observations that positively selected genes contain elevated levels of missense variation. Notably, PSGs of the large-scale dataset were also enriched among clinical-stage drug targets, suggesting a potential link between positive selection and pharmacological relevance. Conclusion: Together, our results provide a refined structural model of adaptive evolution in human proteins and identify extracellular exposed molecular recognition surfaces and human-pathogen interaction interfaces as recurrent hotspots of positive selection. Our results point to the direction that precise identification of human PSRs could delineate important host-pathogen interfaces that exert evolutionary selection pressure on humans and appoint novel targets with therapeutic potential.

molecular biology↗

bioRxiv2026

Binding of long non-coding RNAs within the androgen receptor N-terminal tail modulates interdomain communication and liquid-liquid phase separation

The androgen receptor (AR) is a transcription factor whose overactivation is a primary driver of prostate cancer. Although AR interactions with several long non-coding RNAs (lncRNAs) have been implicated in castration-resistant prostate cancer, their underlying molecular mechanisms and functional consequences remain poorly understood. Here, we identify the N-terminal 37 residues of the intrinsically disordered AR N-terminal domain as the primary RNA-binding region that mediates selective interactions with the lncRNAs HOTAIR and SLNCR1. Residue-level mapping and mutational analysis define Y11, R13, and Q24 as key determinants of RNA recognition. This RNA-binding region partially overlaps with the F23QNLF27 motif, previously shown to mediate N/C interdomain communication with the ligand-binding domain through folding upon binding. We observe a partner-dependent binding mode in which this motif remains dynamically disordered upon RNA binding. LncRNA binding promotes phase separation of the N-terminal domain, indicating that lncRNAs upregulated in late-stage prostate cancer may lower the threshold for AR condensate formation and contribute to ligand-independent AR signaling. LncRNAs modulate communication between the N-terminal and ligand-binding domains within condensates, suggesting that lncRNA binding may tune hormone-dependent full-length AR signaling. These findings provide a mechanistic framework for AR-lncRNA regulation, laying the groundwork for future therapeutic strategies against advanced prostate cancer. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC="FIGDIR/small/728402v1_ufig1.gif" ALT="Figure 1000"> View larger version (22K): org.highwire.dtl.DTLVardef@bee76dorg.highwire.dtl.DTLVardef@14bb6edorg.highwire.dtl.DTLVardef@1d693b5org.highwire.dtl.DTLVardef@7b70d1_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

On the state of protein function prediction: a report on the fourth CAFA challenge

BackgroundThe Critical Assessment of Functional Annotation (CAFA) is a community effort held to understand the field of computational protein function prediction. Every three years, since 2010, the organizers initiate an experiment to collect function predictions on a large set of proteins and then evaluate the performance of predicting methods on a subset of proteins that have accumulated experimental annotations between the submission deadline and the evaluation time. CAFA provides an independent and rigorous assessment of the current state of the art, thus leveling the playing field, highlighting successes, revealing bottlenecks, and offering a forum for the exchange of ideas in protein science. Here, we report the results of the fourth CAFA experiment (CAFA4). ResultsCAFA4 featured the participation of 148 methods from 70 research groups on a total of 46,205 unique proteins over a 5-year annotation accumulation phase, the longest in any CAFA. In a comparison across CAFA2-CAFA4 methods, the prediction of Gene Ontology (GO) terms has clearly improved across all three GO aspects and traditional evaluation settings. While not achieving the first rank, several CAFA2 and CAFA3 methods featured in the top ten methods in many evaluations, suggesting that earlier methods still hold relevance. The performance is weaker in the newly introduced "partial knowledge" evaluation category (proteins with experimental annotations before submission deadline that gained additional annotations in the same GO aspect during the annotation accumulation phase), highlighting the need for a new class of methods. The rankings of the methods were stable over the years in traditional evaluation settings, but less so in the new partial knowledge evaluation. Overall, the field continues to progress with some influx of new participants. Sustained efforts will be necessary to substantially advance it.

bioinformatics↗

bioRxiv2026

Reliable prediction of short linear motifs in the human proteome

Short linear motifs (SLiMs) are small interaction modules within intrinsically disordered regions of proteins that interact with specific domains, and thereby regulate numerous biological processes. Their limited sequence information leads to frequent false positive hits in computational and experimental SLiM identification methods. We present SLiMMine, a deep learning-based method to identify SLiMs in the human proteome. By refining the annotations of known motif classes, we created a high-quality training dataset. Using protein embeddings and neural networks, SLiMMine reliably predicts novel SLiM candidates in known classes, eliminates ~80% of the pattern matching-based hits as false-positives, furthermore, it also functions as a discovery tool to find uncharacterized SLiMs based on optimal sequence environment. Finally, narrowing the broad interactor-domain definitions of known SLiM classes to specific human proteins enables more precise linking of predicted SLiMs to known protein-protein interactions. SLiMMine is available as a user-friendly, multipurpose web server at https://slimmine.pbrg.hu/.

bioinformatics↗

bioRxiv2025

Definition and discovery of tandem SH3-binding motifs interacting with members of the p47phox-related protein family

SH3 domains are widespread protein modules that mostly bind to proline-rich short linear motifs (SLiMs). Most known SH3 domain-motif interactions and canonical or non-canonical recognition specificities are described for individual SH3 domains. Although cooperation and coordinated motif binding between tandem SH3 domains has already been described for members of the p47phox-related protein family, individual cases have never been collected and analyzed collectively, which precluded the definition of the binding preferences and targeted discovery of further instances. Here, we apply an integrative approach that includes data collection, curation, bioinformatics analyses and state-of-the-art structure prediction methods to fill these gaps. We define the optimal binding preference of tandemly arranged SH3 domains as [PAVIL]PPR[PR][^DE][^DE], and propose potential new instances of this SLiM among the family members and their binding partners. Structure predictions suggest the possibility of a novel, reverse binding mode for certain motif instances. A search of the human proteome with the sequence signatures of SH3 tandemization and follow-up structure analyses suggest that SH3 tandemization could be specific for this family. In all, our comprehensive analysis of this unique SH3 binding mode enabled description of the binding preference and identification of novel interesting cases proposed for experimental validation.

molecular biology↗

bioRxiv2023

Phase-separating fusion proteins drive cancer by dysregulating transcription through ectopic condensates

Numerous cellular processes rely on biomolecular condensates formed through liquid-liquid phase separation (LLPS), thus, perturbations of LLPS underlie various diseases. We found that proteins initiating LLPS are frequently implicated in somatic cancers, even surpassing their involvement in neurodegeneration. Cancer-associated LLPS scaffolds are connected to all cancer hallmarks and tend to be oncogenes with dominant genetic effects lacking therapeutic options. Since most of them act as oncogenic fusion proteins (OFPs), we undertook a systematic analysis of cancer driver OFPs by assessing their module-level molecular functions. We identified both known and novel combinations of molecular functions that are specific to OFPs and thus have a high potential for driving tumorigenesis. Protein regions driving condensate formation show an increased association with DNA- or chromatin-binding domains of transcription regulators within OFPs, indicating a common molecular mechanism underlying several soft tissue sarcomas and hematologic malignancies where phase-separation-prone OFPs form abnormal, ectopic condensates along the DNA, and thereby dysregulate gene expression programs.

cancer biology↗

bioRxiv2023

C9orf72-linked arginine-rich dipeptide repeats aggravate pathological phase separation of G3BP1

Ras GTPase-activating protein-binding protein 1 (G3BP1) is the key protein driving the formation of cytoplasmic stress granules (SGs) by liquid-liquid phase separation (LLPS). It is a switch-like protein held in a closed and inactive state by intramolecular electrostatic interactions competitively opened by RNA, activating the protein and initiating its LLPS. Here we show that C9orf72-derived arginine-rich dipeptide repeats PR30 and GR30 (R-DPRs) present in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), also bind to G3BP1, switching it to an LLPS-competent open state much more effectively than RNA. Whereas RNA binds G3BP1 with micromolar affinity, and cannot initiate LLPS without crowding agents, R-DPRs exhibit a thousand-fold stronger binding to G3BP1, eliciting rapid LLPS even without crowding. The pathogenic effect of R-DPRs is also underscored by the slow transition of R-DPR-G3BP1 liquid droplets to aggregated, ThS-positive states that can recruit the ALS-linked protein hnRNPA2. Deletion constructs and molecular simulations show that R-DPR binding and LLPS are mediated via binding through the negatively charged intrinsically disordered region 1 (IDR1) of the protein, allosterically regulated by the positively charged IDR3. Bioinformatic analyses point to the strong mechanistic parallels of these effects with the interaction of R-DPRs with nuclear nucleophosmin (NPM1) and also suggest that R-DPRs also interact with many other similar nucleolar and stress-granule proteins, extending the underlying mechanism of R-DPR toxicity in cells.

molecular biology↗

bioRxiv2023

The regulatory role of the CD2AP/TKS4 interaction in EMT and its potential as abiomarker for colon cancer

BackgroundColon cancer is a leading cause of death worldwide. Although several biomarkers have been developed, more sensitive and specific methods are needed for its early detection. TKS4 and CD2AP scaffold proteins have been already linked to dynamic actin assembly-related processes, such as colon cancer cell migration, although their co-instructive role during tumour-formation remains unknown. Therefore, this study was designed to validate TKS4-CD2AP interaction and study the interdependent effect of TKS4/CD2AP on oncogenic events. MethodsCD2AP was identified as a novel TKS4 interacting partner in six cell lines via co-immunoprecipitation-mass spectrometry. The interaction was validated via western blot, immunocytochemistry, DuoLink assay and peptide microarray. Gene silencing and overexpressing experiments were performed to uncover the cooperative effects of TKS4 and CD2AP in cell movement and in epithelial-mesenchymal transition (EMT). The expression levels of TKS4 and CD2AP mRNAs were quantified using a human colon cancer array, and the results were subjected to bioinformatic database analysis. ResultsThe molecular biology analysis revealed that one of the SH3-domain of CD2AP interacts with a proline-rich short linear motif in TKS4. Functional studies showed that TKS4 and CD2AP form a scaffold complex that regulates migration- and EMT-related pathways of colon cancer cells. The relative TKS4 and CD2AP expression level measurements pointed out that CD2AP/TKS4 ratio is a sensitive biomarker for the identification of tumorous colon tissue. ConclusionsThis is the first study demonstrating the TKS4-CD2AP protein-protein interaction in vitro and in vivo and their interdependent regulative effect on mesenchymal transition-like process in colon cancer. Furthermore, the results highlight that the relative expression levels of CD2AP and TKS4 might serve as a biomarker for the diagnosis of early-stage colon cancer.

cancer biology↗

bioRxiv2022

MIADE metadata guidelines: Minimum Information About a Disorder Experiment

An unambiguous description of an experimental setup and analysis, and the subsequent biological observation is vital for accurate data interpretation and reproducible results. Consequently, experimental analyses should be described in a concise, unequivocal, and digestible manner. The aim of minimum information guidelines is to define the fundamental complement of data that can support an unambiguous conclusion on experimental observations. In this document, we present the Minimum Information About Disorder Experiments (MIADE) guidelines to define the minimal fundamental parameters required for non-experts to understand the key findings of an experiment studying intrinsically disordered proteins (IDPs) or intrinsically disordered protein regions (IDRs). MIADE guidelines provide recommendations for data producers to describe the results of their experiments at source, for curators to annotate experimental data to community resources and for database developers maintaining community resources to disseminate the data. We give examples of the application of these guidelines in common use cases and describe the implementation of an update to the DisProt IDP database to allow MIADE-compliant annotation. The MIADE guidelines will improve the interpretability of experimental results for data consumers, facilitate direct data submission, simplify data curation, improve data exchange among repositories and standardise the dissemination of the key metadata on an IDP experiment by IDP data sources.

scientific communication and education↗

bioRxiv2021

Concentration and dosage sensitivity of proteins driving liquid-liquid phase separation

Liquid-liquid phase separation (LLPS) is a molecular process that leads to the formation of membraneless organelles (MLOs), i.e. functionally specialized liquid-like cellular condensates formed by proteins and nucleic acids. Integration of data on LLPS-associated proteins from dedicated databases revealed only modest overlap between them and resulted in a confident set of 89 human LLPS driver proteins. Since LLPS is highly concentration-sensitive, the underlying experiments are often criticized for applying higher-than-physiological protein concentrations. To clarify this issue, we performed a naive comparison of in vitro applied and quantitative proteomics-derived protein concentrations and discuss a number of considerations that rationalize the choice of apparently high in vitro concentrations in most LLPS studies. The validity of in vitro LLPS experiments is further supported by in vivo phase-separation experiments and by the observation that the corresponding genes show a strong propensity for dosage sensitivity. This observation implies that the availability of the respective proteins is tightly regulated in cells to avoid erroneous condensate formation. In all, we propose that although local protein concentrations are practically impossible to determine in cells, proteomics-derived cellular concentrations should rather be considered as lower limits of protein concentrations, than strict upper bounds, to be respected by in vitro experiments.

molecular biology↗

bioRxiv2019

Phase separation by ssDNA binding protein controlled via protein-protein and protein-DNA interactions

Bacterial single stranded (ss) DNA-binding proteins (SSB) are essential for the replication and maintenance of the genome. SSBs share a conserved ssDNA-binding domain, a less conserved intrinsically disordered linker (IDL) and a highly conserved C-terminal peptide (CTP) motif that mediates a wide array of protein-protein interactions with DNA-metabolizing proteins. Here we show that the E. coli SSB protein forms liquid-liquid phase separated condensates in cellular-like conditions through multifaceted interactions involving all structural regions of the protein. SSB, ssDNA and SSB-interacting molecules are highly concentrated within the condensates, whereas phase separation is overall regulated by the stoichiometry of SSB and ssDNA. Together with recent results on subcellular SSB localization patterns, our results point to a conserved mechanism by which bacterial cells store a pool of SSB and SSB-interacting proteins. Dynamic phase separation enables rapid mobilization of this protein pool to protect exposed ssDNA and repair genomic loci affected by DNA damage.

biochemistry↗