A5007279828- Protein Structure and Dynamics
- Enzyme Structure and Function
- Machine Learning in Bioinformatics
- RNA and protein synthesis mechanisms
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Redox biology and oxidative stress
- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Metal-Catalyzed Oxygenation Mechanisms
- Cellular transport and secretion
- Ubiquitin and proteasome pathways
- Barrier Structure and Function Studies
- Fungal and yeast genetics research
- RNA modifications and cancer
- Machine Learning in Materials Science
- Cellular Mechanics and Interactions
- Hippo pathway signaling and YAP/TAZ
- Retinal Development and Disorders
- Biofuel production and bioconversion
- Peptidase Inhibition and Analysis
- RNA Research and Splicing
- Animal Ecology and Behavior Studies
- Glycosylation and Glycoproteins Research
- S100 Proteins and Annexins
Eötvös Loránd University
2017-2025
Technical University of Munich
2023
The structural states of proteins include ordered globular domains as well intrinsically disordered protein regions that exist highly flexible conformational ensembles in isolation.Various computational tools have been developed to discriminate and segments based on the amino acid sequence.However, properties IDRs can also depend various conditions, including binding partners or environmental factors, such redox potential.These cases provide further challenges for characterization...
Intrinsically disordered proteins and protein regions (IDPs/IDRs) exist without a single well-defined conformation. They carry out important biological functions with multifaceted roles which is also reflected in their evolutionary behavior. Computational methods play the characterization of IDRs. One commonly used disorder prediction IUPred, relies on an energy estimation approach. The IUPred web server takes amino acid sequence or Uniprot ID/accession as input predicts tendency for each to...
IUPred2A is a combined prediction tool designed to discover intrinsically disordered or conditionally proteins and protein regions. Intrinsically regions exist without well-defined three-dimensional structure in isolation but carry out important biological functions. Over the years, various methods have been developed characterize The existence of segments can also be dependent on different factors such as binding partners environmental traits like pH redox potential, recognizing represents...
Membraneless organelles (MOs) are dynamic liquid condensates that host a variety of specific cellular processes, such as ribosome biogenesis or RNA degradation. MOs form through liquid-liquid phase separation (LLPS), process relies on multivalent weak interactions the constituent proteins and other macromolecules. Since first discoveries certain being able to drive LLPS, it emerged general mechanism for effective organization space is exploited in all kingdoms life. While numerous...
Abstract The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository manually curated annotations intrinsically disordered proteins and regions from literature. We report here recent updates DisProt version 9, including a restyled web interface, refactored Ontology (IDPO), improvements in curation process significant content growth around 30%. Higher quality consistency provided by newly implemented reviewing training curators. increased...
Intrinsically disordered proteins and protein regions (IDPs/IDRs) carry out important biological functions without relying on a single well-defined conformation. As these are challenge to study experimentally, computational methods play roles in their characterization. One of the commonly used tools is IUPred web server which provides prediction binding sites. rooted simple biophysical model uses limited number parameters largely derived globular structures only. This enabled an incredibly...
Abstract Intrinsic disorder (ID) in proteins is well-established structural biology, with increasing evidence for its involvement essential biological processes. As measuring dynamic ID behavior experimentally on a large scale remains difficult, scores of published predictors have tried to fill this gap. Unfortunately, their heterogeneity makes it difficult compare performance, confounding biologists wanting make an informed choice. To address issue, the Critical Assessment protein Disorder...
Intrinsically disordered regions (IDRs) play critical roles in various cellular processes, often mediating interactions through binding that transition to ordered states. Experimental characterization of these functional is highly challenging, underscoring the need for fast and accurate computational tools. Despite their importance, predicting remains a significant challenge due limitations existing datasets methodologies. In this study, we introduce AIUPred-binding, novel prediction tool...
Intrinsically disordered proteins (IDPs) contain regions lacking intrinsic globular structure (intrinsically regions, IDRs). IDPs are present across the tree of life, with great variability IDR type and frequency even between closely related taxa. To investigate function IDRs, we evaluated compared distribution disorder content in 10,695 reference proteomes, confirming its high finding certain correlation along Euteleostomi (bony vertebrates) lineage to number cell types. We used comparison...
Abstract Recently developed quantitative redox proteomic studies enable the direct identification of redox‐sensing cysteine residues that regulate functional behavior target proteins in response to changing levels reactive oxygen species. At molecular level, regulation can directly modify active sites enzymes, although a growing number examples indicate importance an additional underlying mechanism involves conditionally disordered proteins. These alter their by undergoing disorder‐to‐order...
Protein-protein interactions (PPIs) formed between short linear motifs and globular domains play important roles in many regulatory signaling processes but are highly underrepresented current protein-protein interaction databases. These types of usually characterized by a specific binding motif that captures the key amino acids shared among partners. However, computational proteome-level identification partners based on known is hindered huge number randomly occurring matches from which...
Disorder prediction methods that can discriminate between ordered and disordered regions have contributed fundamentally to our understanding of the properties prevalence intrinsically proteins (IDPs) in proteomes as well their functional roles. However, a recent large-scale assessment performance these indicated there is still room for further improvements, necessitating novel approaches understand strengths weaknesses individual methods. In this study, we compared two methods, IUPred...
Protein and lipid membrane interactions play fundamental roles in a large number of cellular processes (e.g. signalling, vesicle trafficking, or viral invasion). A growing examples indicate that such can also rely on intrinsically disordered protein regions (IDRs), which form specific reversible not only with proteins but lipids. We named IDRs involved lipid-induced disorder-to-order transition as MemMoRFs, an analogy to exhibiting upon interaction partners termed Molecular Recognition...
Dynein light chain LC8 is a small dimeric hub protein that recognizes its partners through short linear motifs and commonly assumed to drive their dimerization. It has more than 100 known binding involved in wide range of cellular processes. Recent large-scale interaction studies suggested could also play role the ciliary/centrosome system. However, function this system remains elusive. In work, we characterized with centrosomal lebercilin (LCA5), which associated specific form ciliopathy....
Intrinsically disordered proteins (IDPs) play important roles in a wide range of biological processes and have been associated with various diseases, including cancer. In the last few years, cancer genome projects systematically collected genetic variations underlying multiple types. parallel, number different types characterized by experimental methods also significantly increased. Nevertheless, role IDPs is still not well understood. this work, we present DisCanVis, novel visualization...
Abstract Recently developed quantitative redox proteomic studies enable the direct identification of redox-sensing cysteine residues that regulate functional behavior target proteins in response to changing levels reactive oxygen species (ROS). At molecular level, regulation can directly modify active sites enzymes, although a growing number examples indicate importance an additional underlying mechanism involves conditionally disordered proteins. These alter their by undergoing...