Biology subjects

Katona, G.

Publications and source records attributed to Katona, G..

12 recordsLinked to original sources

bioRxiv2025

Functional Group Composition: The Blueprint for Protein Interactions

Understanding the complex landscape of protein interactions, especially those involving intrinsically disordered proteins (IDPs), is fundamental yet challenging due to their structural heterogeneity and flexibility. Traditional sequence-based homology methods frequently fall short in characterizing IDP functions and interactions. Here, we present a novel approach leveraging supervised and unsupervised machine learning techniques, focusing exclusively on the compositional features of proteins. An Edmond-Ogston-inspired mixing model can reliably predict the degree of survivin (BIRC5) binding as a function of peptide composition alone, revealing a first interesting connection with the composition diagrams of chemical thermodynamics. By representing protein sequences through their functional group compositions, we demonstrate that specific compositions robustly predict binding interactions with survivin, an important human protein in cellular regulation pathways. Experimental validation via peptide microarray confirms the predictive power of our simplified compositional model, independent of exact amino acid sequences. Extending this method across the human proteome, we identified distinct compositional signatures correlating with survivin interactions and revealed fine grained biologically meaningful functional clusters based on compositional similarity. Our findings suggest a compositional blueprint underpinning protein interactions, offering a powerful, simplified framework to decode complex biological networks.

systems biology↗

bioRxiv2025

Insulin exerts epigenetic control of joint-specific memory T cells in rheumatoid arthritis

BackgroundInsulin has epigenetic effect influencing gene expression. High peripheral insulin concentrations promote insulin resistance in autoimmunity. Oncoprotein survivin/BIRC5 modulates glucose metabolism through chromatin binding and propagates IFNg effects in CD4+ cells. In this study, we explored how insulin influences chromatin binding and metabolic activity in autoimmune CD4+ cells of patients with rheumatoid arthritis (RA). MethodsWe profiled the metabolic activity of CD4+ cell clusters using single-cell transcriptome analysis in blood, synovial fluid and synovial tissue of RA patients. Through chromatin immunoprecipitation and sequencing, we identified the genes controlled by deposition of survivin and acetylated lysine 27 on histone H3 (H3K27ac) in CD4+ cells. Treating CD4+ cells with insulin and histone deacetylase inhibitors (HDACi), we identified changes in H3K27ac, linked those to transcription of the H3K27-survivin-controlled genes and the pathogenic phenotype of CD4+ cells using flow cytometry. Finally, we explored if anti-diabetic and anti-rheumatic drugs affect the metabolic profile and memory phenotype of the metabolic active CD4+ cells. ResultsTranscription of survivin/BIRC5 and histone acetylation enzymes strongly correlate with active metabolism in blood CD4+ cells of RA patients. In RA synovial tissue, these BIRC5hi active T cell clusters are inflammatory, exhausted, and memory-like. Genome co-deposition of H3K27ac-survivin pinpointed the insulin-dependent genes in metabolic active CD4+ cells. These genes favored histone acetylation by suppressing methylating enzymes EZH2 and KMT2A, and T cell development by activating CD27, CD3G, and SCIMP. Inhibition of histone deacetylation reverted these transcriptional effects and supported cellular sensitivity to insulin. Insulin stimulation increased H3K27ac and together with HDACi, suppressed PDCD1 and IFNg transcription and production in CD4+CD27+CD45RO+ memory T cells. Immune modulation impacted metabolic activity and synergized with the effect of histone acetylation on insulin responsiveness in RA patients. ConclusionsRA synovia is enriched with the metabolic active BIRC5hiCD4+ T cell clusters. The metabolic activity of these cells is histone acetylation-dependent and mediates insulin effects through the H3K27ac-survivin epigenetic mechanism. Increasing plasma insulin levels when combined with insulin sensitivity, can be protective in RA dearmoring effector T cell function. Hence, increasing the insulin sensitivity by enabling histone acetylation presents a reasonable interventional goal to restore immune cell homeostasis in RA.

immunology↗

bioRxiv2024

Femtosecond X-ray snapshots reveal correlated displacements of specific distal atoms in a protein crystal

Protein dynamics is shaped by interactions between thermal fluctuations, external forces, and molecular structures. Thermal fluctuations have high frequencies and are hence very challenging to quantify. We were able to record femtosecond X-ray diffraction snapshots and determine atomic displacements of crystalline bovine trypsin atoms either in the native steady state or in a transient state initiated by a short THz pulse, the results of which were interpreted with numerical simulations. In the absence of THz pulses, specific distal atoms exhibited correlated movements. Under the influence of THz fields, numerical simulations demonstrated a slight enhancement of displacement correlations. The experimental results revealed a contrasting response to short THz pulses, where the measured displacements were not solely determined by the atom position, but also influenced by the atomic type. These findings call for a reinterpretation of the dynamic properties inherent in folded protein structures and the physical principles behind the formation of protein assemblies. To this end, a theoretical model was developed for lattice deformations and local excitations entraining a (squeezed) coherent steady state, explaining the emergence of atom correlations. The model accounts for the magnitudes of atomic displacements and fluctuations through a balance between harmonic and anharmonic coupling forces.

biophysics↗

bioRxiv2024

Survivin in synergy with BAF/SWI complex binds bivalent chromatin regions and activates DNA damage response in CD4+ T cells

This study explores a regulatory role of oncoprotein survivin on the bivalent regions of chromatin (BvCR) characterized by concomitant deposition of trimethylated lysine of histone H3 at position 4 (H3K4me3) and 27 (H3K27me3). Intersect between BvCR and chromatin sequences bound to survivin demonstrated their co-localization on cis-regulatory elements of genes which execute DNA damage control in primary human CD4+ cells. Survivin anchored BRG1-complex to BvCR to repress DNA damage repair genes in IFN{gamma}-stimulated CD4+ cells. In contrast, survivin inhibition shifted the functional balance of BvCR in favor of H3K4me3, which activated DNA damage recognition and repair. Co-expression of BRG1, survivin and IFN{gamma} in CD4+ cells of patients with rheumatoid arthritis identified arthritogenic BRG1hi cells abundant in autoimmune synovia. Immunomodulating drugs inhibited the subunits anchoring BRG1-complex to BvCR, which changed the arthritogenic profile. Together, this study demonstrates the function of BvCR in DNA damage control of CD4+ cells offering an epigenetic platform for survivin and BRG1-complex targeting interventions to combat autoimmunity. SummaryThis study shows that bivalent chromatin regions accommodate survivin which represses DNA repair enzymes in IFN{gamma}-stimulated CD4+ T cells. Survivin anchors BAF/SWI complex to these regions and supports autoimmune profile of T cells, providing novel targets for therapeutic intervention.

immunology↗

bioRxiv2024

Deciphering Peptide-Protein Interactions via Composition-Based Prediction: A Case Study with Survivin/BIRC5

In the realm of atomic physics and chemistry, composition emerges as the most powerful means of describing matter. Mendeleevs periodic table and chemical formulas, while not entirely free from ambiguities, provide robust approximations for comprehending the properties of atoms, chemicals, and their collective behaviours, which stem from the dynamic interplay of their constituents. Our study illustrates that protein-protein interactions follow a similar paradigm, wherein the composition of peptides plays a pivotal role in predicting their interactions with the protein survivin, using an elegantly simple model. An analysis of these predictions within the context of the human proteome not only illuminates the known cellular locations of survivin and its interaction partners, but also introduces novel insights into biological functionality. It becomes evident that an electrostatic- and primary structure-based descriptions fall short in predictive power, leading us to speculate that protein interactions are orchestrated by the collective dynamics of functional groups.

bioinformatics↗

bioRxiv2022

Monitoring correlates of SARS-CoV-2 infection in cell culture using two-photon microscopy and a novel fluorescent calcium-sensitive dye

The organism-wide effects of viral infection SARS-CoV-2 are well studied, but little is known about the dynamics of how the infection spreads in time among or within cells due to the scarcity of suitable high-resolution experimental systems. Two-photon (2P) imaging combined with a proper subcellular staining technique has been an effective tool for studying mechanisms at such resolutions and organelle levels. Herein, we report the development of a novel calcium sensor molecule along with a 2P-technique for identifying imaging patterns associated with cellular correlates of infection damage within the cells. The method works as a cell viability assay and also provides valuable information on how the calcium level and intracellular distribution are perturbed by the virus. Moreover, it allows the quantitative analysis of infection dynamics. This novel approach facilitates the study of the infection progression and the quantification of the effects caused by viral variants and viral load.

microbiology↗

bioRxiv2022

Cortex-wide fast activation of VIP-expressing inhibitory neurons by reward and punishment

Reward and punishment powerfully inform ongoing behaviors and drive learning throughout the brain, including neocortex. Yet it remains elusive how these global signals are represented and impact local cortical computations. Previously we found that in auditory cortex, VIP-expressing interneurons are recruited by reinforcement feedback. Here, we used 3D random-access two-photon microscopy and fiber photometry to monitor VIP neural activity in dozens of cortical areas while mice learned an auditory decision task. We show that reward and punishment evoke a rapid, cortex-wide activation of most VIP interneurons. This global recruitment mode of VIP interneurons showed variations in temporal dynamics in individual neurons and across areas. Neither their weak sensory tuning in visual cortex, nor their arousal state modulation was predictive of reinforcer responses of VIP interneurons. We suggest that VIP-expressing cortical inhibitory neurons transduce global reinforcement signals to provide disinhibitory control over local circuit computations and their plasticity.

neuroscience↗

bioRxiv2022

Survivin prevents the Polycomb Repressor Complex 2 from methylating Histone 3 lysine 27

Survivin is a small protein that belongs to the inhibitor of apoptosis protein family and participates in cell division and apoptosis. It was actively studied in human cancers, inflammatory diseases and in autoimmune diseases. Here, we reveal that survivin takes part in epigenetic gene silencing by interaction with the polycomb repressive complex 2 (PRC2). PRC2 silences gene expression through tri-methylation of lysine 27 on histone 3 (H3K27). We detected differential expression of PRC2 core subunits in CD4+T cells with different survivin expression. ChIP-seq experiments indicated that survivin binds chromatin that overlap with the regions occupied by PRC2. ChIP-seq of H3K27 in CD4+T cells indicate that inhibition of survivin leads to a substantial increase in H3K27 tri-methylation by PRC2 in contrast to other histone modifications, which lends support to that survivin prevents PRC2 from functioning. Survivin binds peptides derived from PRC2 subunits EZH2, EED, SUZ12 and JARID2 in a peptide microarray that cover intersubunit interfaces, catalytic residues, and present binding sites for substrates, DNA, and regulatory proteins. Amino acid composition of the peptides has substantial predictive power for survivin interaction in the peptide microarray as determined by multilayer perceptron classification analysis. NMR experiments with 15N labelled survivin indicate that peptide colocalization does not entirely depend on binding mediated by short range interactions. These results indicate that survivin interacts with PRC2, preventing the methylation of H3K27 and specific gene silencing. This has transcriptional consequences and specific gene silencing.

molecular biology↗

bioRxiv2021

Chemical mapping exposes the importance of active site interactions in governing the temperature dependence of enzyme turnover

Uncovering the role of global protein dynamics in enzyme turnover is needed to fully understand enzyme catalysis. Recently, we have demonstrated that the heat capacity of catalysis, {Delta}CP{ddagger}, can reveal links between the protein free energy landscape, global protein dynamics and enzyme turnover, suggesting that subtle changes molecular interactions at the active site can affect long range protein dynamics and link to enzyme temperature activity. Here we use a model promiscuous enzyme (Glucose dehydrogenase from Sulfolobus Solfataricus) to chemically map how individual substrate interactions affect the temperature dependence of enzyme activity and the network of motions throughout the protein. Utilizing a combination of kinetics, REES spectroscopy and computational simulation we explore the complex relationship between enzyme-substrate interactions and the global dynamics of the protein. We find that changes in {Delta}CP{ddagger} and protein dynamics can be mapped to specific substrate-enzyme interactions. Our study reveals how subtle changes in substrate binding affect global changes in motion and flexibility extending throughout the protein.

biochemistry↗

bioRxiv2020

Non-linear Computation Between Neighboring Dendritic Hotspots in Rat CA1 Hippocampal Interneurons

Dendritic hotspots have been shown to play a determining role as local activity foci during sensory information coding and memory formation in cortical neurons in vivo. Here we aim to reveal the characteristics of co-activating more dendritic hotspots themselves within a dynamic time window. Using electrical stimulation and patterned two-photon uncaging for the coincident activation of two neighboring dendritic hotspots in rat hippocampal CA1 interneurons, the evoked local dendritic Ca2+ and the associated excitatory postsynaptic potentials (EPSPs) summed supralinearly. Between active hotspots, supralinearity was present in a relatively broad temporal ([~]10 ms) and spatial ([~]30 {micro}m) window, mediated by NMDA receptors. Though at larger inter-hotspot distances (>30 {micro}m) supralinear summation of EPSPs was replaced by sublinear integration, the summation of dendritic Ca2+ responses remained supralinear. The inter-hotspot integration represents a novel signal integration state, extending the interaction distance between dendritic inputs, and allowing long-range coincidence detection.

neuroscience↗

bioRxiv2018

Patterns of anisotropic temperature factors in bovine trypsin crystals with and without 0.5 THz irradiation

Vibrational oscillations in amide and side chain groups are well studied in proteins, but these are not occupied at ambient temperatures and they have a short lifespan when infrared radiation is present. Active vibrational modes in proteins lie in the terahertz (THz) range at physiological temperatures, and their experimental descriptions of them in this range are lacking. In this paper, we present the effect of 0.5 THz irradiation on atomic displacement parameters (ADP) in bovine trypsin. The crystals were subjected to terahertz radiation in an alternating manner and two states of the crystals were recovered using X-ray crystallography. The clustering of ADPs uniquely identified atoms from the different crystals. The ADP similarities tended to develop between chemically similar atoms and between atoms of the catalytic triad. This pattern of ADP similarity is likely created by delocalized polar vibration modes rather than, as frequently assumed, elastic and rigid-body motions.

biophysics↗

bioRxiv2018

Truncation and Motif Based Pan-Cancer Analysis Highlights Novel Tumor Suppressing Kinases.

A major challenge in cancer genomics is identifying driver mutations from the large number of neutral passenger mutations within a given tumor. Here, we utilize motifs critical for kinase activity to functionally filter genomic data to identify driver mutations that would otherwise be lost within mutational noise. In the first step of our screen, we define a putative tumor suppressing kinome by identifying kinases with truncation mutations occurring within or before the kinase domain. We aligned these kinase sequences and, utilizing data from the Cancer Cell Line Encyclopedia and The Cancer Genome Atlas databases, identified amino acids that represent predicted hotspots for loss-of-function mutations. The functional consequences of new LOF mutations were validated and the top 15 hotspot LOF residues were used in a pan-cancer analysis to define the tumor-suppressing kinome. A ranked list revealed MAP2K7 as a candidate tumor suppressor in gastric cancer, despite the mutational frequency of MAP2K7 falling within the mutational noise for this cancer type. The majority of mutations in MAP2K7 abolished catalytic activity compared to the wild type kinase, consistent with a tumor suppressive role for MAP2K7 in gastric cancer. Furthermore, reactivation of the JNK pathway in gastric cancer cells harboring LOF mutations in MAP2K7 or JNK1 suppresses clonogenicity and growth in soft agar, demonstrating the functional importance of inactivating the JNK pathway in gastric cancer. In summary, our data highlights a broadly applicable strategy to identify functional cancer driver mutations leading us to define the JNK pathway as tumor suppressive in gastric cancer.\n\nSummaryA unique computational pan-cancer analysis pinpoints novel tumor suppressing kinases, and highlights the power of functional genomics by defining the JNK pathway as tumor suppressive in gastric cancer.

cancer biology↗