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JOURNAL ARTICLE
Mátyás Pajkos, Gábor Erdős, Zsuzsanna Dosztányi
Disorder prediction methods that can discriminate between ordered and disordered regions have contributed fundamentally to our understanding of the properties and prevalence of intrinsically disordered proteins (IDPs) in proteomes as well as their functional roles. However, a recent large-scale assessment of the performance of these methods indicated that there is still room for further improvements, necessitating novel approaches to understand the strengths and weaknesses of individual methods. In this study, we compared two methods, IUPred and disorder prediction, based on the pLDDT scores derived from AlphaFold2 (AF2) models...
September 25, 2023: Biomolecules
#2
REVIEW
Lukasz Kurgan, Gang Hu, Kui Wang, Sina Ghadermarzi, Bi Zhao, Nawar Malhis, Gábor Erdős, Jörg Gsponer, Vladimir N Uversky, Zsuzsanna Dosztányi
Intrinsic disorder is instrumental for a wide range of protein functions, and its analysis, using computational predictions from primary structures, complements secondary and tertiary structure-based approaches. In this Tutorial, we provide an overview and comparison of 23 publicly available computational tools with complementary parameters useful for intrinsic disorder prediction, partly relying on results from the Critical Assessment of protein Intrinsic Disorder prediction experiment. We consider factors such as accuracy, runtime, availability and the need for functional insights...
September 22, 2023: Nature Protocols
#3
REVIEW
Bálint Mészáros, András Hatos, Nicolas Palopoli, Federica Quaglia, Edoardo Salladini, Kim Van Roey, Haribabu Arthanari, Zsuzsanna Dosztányi, Isabella C Felli, Patrick D Fischer, Jeffrey C Hoch, Cy M Jeffries, Sonia Longhi, Emiliano Maiani, Sandra Orchard, Rita Pancsa, Elena Papaleo, Roberta Pierattelli, Damiano Piovesan, Iva Pritisanac, Luiggi Tenorio, Thibault Viennet, Peter Tompa, Wim Vranken, Silvio C E Tosatto, Norman E Davey
An unambiguous description of an experiment, and the subsequent biological observation, is vital for accurate data interpretation. Minimum information guidelines define the fundamental complement of data that can support an unambiguous conclusion based on experimental observations. We present the Minimum Information About Disorder Experiments (MIADE) guidelines to define the parameters required for the wider scientific community to understand the findings of an experiment studying the structural properties of intrinsically disordered regions (IDRs)...
July 3, 2023: Nature Methods
#4
JOURNAL ARTICLE
Elizabeth Martínez-Pérez, Mátyás Pajkos, Silvio C E Tosatto, Toby J Gibson, Zsuzsanna Dosztanyi, Cristina Marino-Buslje
BACKGROUND: DisProt is the primary repository of Intrinsically Disordered Proteins (IDPs). This database is manually curated and the annotations there have strong experimental support. Currently, DisProt contains a relatively small number of proteins highlighting the importance of transferring annotations regarding verified disorder state and corresponding functions to homologous proteins in other species. In such a way, providing them with highly valuable information to better understand their biological roles...
May 11, 2023: Protein Science
#5
REVIEW
Anthony W Ashton, Harpreet K Dhanjal, Benjamin Rossner, Huma Mahmood, Vivek I Patel, Mohammad Nadim, Manpreet Lota, Farhan Shahid, Zhiping Li, David Joyce, Matyas Pajkos, Zsuzsanna Dosztányi, Xuanmao Jiao, Richard G Pestell
Lysine acetylation is a common reversible post-translational modification of proteins that plays a key role in regulating gene expression. Nuclear receptors (NRs) include ligand-inducible transcription factors and orphan receptors for which the ligand is undetermined, which together regulate the expression of genes involved in development, metabolism, homeostasis, reproduction, and human diseases including cancer. Since the original finding that the ERα, AR, and HNF4 are acetylated, we now understand that the vast majority of NRs are acetylated and that this modification has profound effects on NR function...
December 5, 2022: FEBS Journal
#6
JOURNAL ARTICLE
Norbert Deutsch, Mátyás Pajkos, Gábor Erdős, Zsuzsanna Dosztányi
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 have systematically collected genetic variations underlying multiple cancer types. In parallel, the number and different types of disordered proteins characterized by experimental methods have also significantly increased. Nevertheless, the role of IDPs in various types of cancer is still not well understood...
November 30, 2022: Protein Science
#7
JOURNAL ARTICLE
Kristina Kastano, Pablo Mier, Zsuzsanna Dosztányi, Vasilis J Promponas, Miguel A Andrade-Navarro
Intrinsically disordered regions (IDRs) in protein sequences are flexible, have low structural constraints and as a result have faster rates of evolution. This lack of evolutionary conservation greatly limits the use of sequence homology for the classification and functional assessment of IDRs, as opposed to globular domains. The study of IDRs requires other properties for their classification and functional prediction. While composition bias is not a necessary property of IDRs, compositionally biased regions (CBRs) have been noted as frequent part of IDRs...
October 15, 2022: Biomolecules
#8
JOURNAL ARTICLE
Tamás Szaniszló, Máté Fülöp, Mátyás Pajkos, Gábor Erdős, Réka Ágnes Kovács, Henrietta Vadászi, József Kardos, Zsuzsanna Dosztányi
Dynein light chain LC8 is a small dimeric hub protein that recognizes its partners through short linear motifs and is commonly assumed to drive their dimerization. It has more than 100 known binding partners involved in a wide range of cellular processes. Recent large-scale interaction studies suggested that LC8 could also play a role in the ciliary/centrosome system. However, the cellular function of LC8 in this system remains elusive. In this work, we characterized the interaction of LC8 with the centrosomal protein lebercilin (LCA5), which is associated with a specific form of ciliopathy...
September 16, 2022: Scientific Reports
#9
JOURNAL ARTICLE
Federica Quaglia, Bálint Mészáros, Edoardo Salladini, András Hatos, Rita Pancsa, Lucía B Chemes, Mátyás Pajkos, Tamas Lazar, Samuel Peña-Díaz, Jaime Santos, Veronika Ács, Nazanin Farahi, Erzsébet Fichó, Maria Cristina Aspromonte, Claudio Bassot, Anastasia Chasapi, Norman E Davey, Radoslav Davidović, Laszlo Dobson, Arne Elofsson, Gábor Erdős, Pascale Gaudet, Michelle Giglio, Juliana Glavina, Javier Iserte, Valentín Iglesias, Zsófia Kálmán, Matteo Lambrughi, Emanuela Leonardi, Sonia Longhi, Sandra Macedo-Ribeiro, Emiliano Maiani, Julia Marchetti, Cristina Marino-Buslje, Attila Mészáros, Alexander Miguel Monzon, Giovanni Minervini, Suvarna Nadendla, Juliet F Nilsson, Marian Novotný, Christos A Ouzounis, Nicolás Palopoli, Elena Papaleo, Pedro José Barbosa Pereira, Gabriele Pozzati, Vasilis J Promponas, Jordi Pujols, Alma Carolina Sanchez Rocha, Martin Salas, Luciana Rodriguez Sawicki, Eva Schad, Aditi Shenoy, Tamás Szaniszló, Konstantinos D Tsirigos, Nevena Veljkovic, Gustavo Parisi, Salvador Ventura, Zsuzsanna Dosztányi, Peter Tompa, Silvio C E Tosatto, Damiano Piovesan
The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisProt version 9, including a restyled web interface, refactored Intrinsically Disordered Proteins Ontology (IDPO), improvements in the curation process and significant content growth of around 30%. Higher quality and consistency of annotations is provided by a newly implemented reviewing process and training of curators...
November 25, 2021: Nucleic Acids Research
#10
JOURNAL ARTICLE
Mátyás Pajkos, Zsuzsanna Dosztányi
Protein sequences are the result of an evolutionary process that involves the balancing act of experimenting with novel mutations and selecting out those that have an undesirable functional outcome. In the case of globular proteins, the function relies on a well-defined conformation, therefore, there is a strong evolutionary pressure to preserve the structure. However, different evolutionary rules might apply for the group of intrinsically disordered regions and proteins (IDR/IDPs) that exist as an ensemble of fluctuating conformations...
2021: Progress in Molecular Biology and Translational Science
#11
JOURNAL ARTICLE
Gábor Erdős, Mátyás Pajkos, Zsuzsanna Dosztányi
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 important roles in the characterization of IDRs. One of the commonly used disorder prediction methods is IUPred, which relies on an energy estimation approach. The IUPred web server takes an amino acid sequence or a Uniprot ID/accession as an input and predicts the tendency for each amino acid to be in a disordered region with an option to also predict context-dependent disordered regions...
May 28, 2021: Nucleic Acids Research
#12
JOURNAL ARTICLE
Bálint Mészáros, Borbála Hajdu-Soltész, András Zeke, Zsuzsanna Dosztányi
Many proteins contain intrinsically disordered regions (IDRs) which carry out important functions without relying on a single well-defined conformation. IDRs are increasingly recognized as critical elements of regulatory networks and have been also associated with cancer. However, it is unknown whether mutations targeting IDRs represent a distinct class of driver events associated with specific molecular and system-level properties, cancer types and treatment options. Here, we used an integrative computational approach to explore the direct role of intrinsically disordered protein regions driving cancer...
March 4, 2021: Biomolecules
#13
JOURNAL ARTICLE
Marco Necci, Damiano Piovesan, Damiano Clementel, Zsuzsanna Dosztányi, Silvio C E Tosatto
MOTIVATION: The earlier version of MobiDB-lite is currently used in large-scale proteome annotation platforms to detect intrinsic disorder. However, new theoretical models allow for the classification of intrinsically disordered regions into subtypes from sequence features associated with specific polymeric properties or compositional bias. RESULTS: MobiDB-lite 3.0 maintains its previous speed and performance but also provides a finer classification of disorder by identifying regions with characteristics of polyolyampholytes, positive or negative polyelectrolytes, low complexity regions or enriched in cysteine, proline or glycine or polar residues...
December 16, 2020: Bioinformatics
#14
JOURNAL ARTICLE
Damiano Piovesan, Marco Necci, Nahuel Escobedo, Alexander Miguel Monzon, András Hatos, Ivan Mičetić, Federica Quaglia, Lisanna Paladin, Pathmanaban Ramasamy, Zsuzsanna Dosztányi, Wim F Vranken, Norman E Davey, Gustavo Parisi, Monika Fuxreiter, Silvio C E Tosatto
The MobiDB database (URL: https://mobidb.org/) provides predictions and annotations for intrinsically disordered proteins. Here, we report recent developments implemented in MobiDB version 4, regarding the database format, with novel types of annotations and an improved update process. The new website includes a re-designed user interface, a more effective search engine and advanced API for programmatic access. The new database schema gives more flexibility for the users, as well as simplifying the maintenance and updates...
November 25, 2020: Nucleic Acids Research
#15
JOURNAL ARTICLE
The MemMoRF database for recognizing disordered protein regions interacting with cellular membranes.
Georgina Csizmadia, Gábor Erdős, Hedvig Tordai, Rita Padányi, Silvio Tosatto, Zsuzsanna Dosztányi, Tamás Hegedűs
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 number of examples indicate that such interactions can also rely on intrinsically disordered protein regions (IDRs), which can form specific reversible interactions not only with proteins but also with lipids. We named IDRs involved in such membrane lipid-induced disorder-to-order transition as MemMoRFs, in an analogy to IDRs exhibiting disorder-to-order transition upon interaction with protein partners termed Molecular Recognition Features (MoRFs)...
October 29, 2020: Nucleic Acids Research
#16
JOURNAL ARTICLE
Kristina Kastano, Gábor Erdős, Pablo Mier, Gregorio Alanis-Lobato, Vasilis J Promponas, Zsuzsanna Dosztányi, Miguel A Andrade-Navarro
Intrinsically disordered proteins (IDPs) contain regions lacking intrinsic globular structure (intrinsically disordered regions, IDRs). IDPs are present across the tree of life, with great variability of IDR type and frequency even between closely related taxa. To investigate the function of IDRs, we evaluated and compared the distribution of disorder content in 10,695 reference proteomes, confirming its high variability and finding certain correlation along the Euteleostomi (bony vertebrates) lineage to number of cell types...
October 6, 2020: Biomolecules
#17
JOURNAL ARTICLE
Mátyás Pajkos, András Zeke, Zsuzsanna Dosztányi
Cancer is a heterogeneous genetic disease that alters the proper functioning of proteins involved in key regulatory processes such as cell cycle, DNA repair, survival, or apoptosis. Mutations often accumulate in hot-spots regions, highlighting critical functional modules within these proteins that need to be altered, amplified, or abolished for tumor formation. Recent evidence suggests that these mutational hotspots can correspond not only to globular domains, but also to intrinsically disordered regions (IDRs), which play a significant role in a subset of cancer types...
July 28, 2020: Biomolecules
#18
JOURNAL ARTICLE
Patryk Jarnot, Joanna Ziemska-Legiecka, Laszlo Dobson, Matthew Merski, Pablo Mier, Miguel A Andrade-Navarro, John M Hancock, Zsuzsanna Dosztányi, Lisanna Paladin, Marco Necci, Damiano Piovesan, Silvio C E Tosatto, Vasilis J Promponas, Marcin Grynberg, Aleksandra Gruca
Low complexity regions (LCRs) in protein sequences are characterized by a less diverse amino acid composition compared to typically observed sequence diversity. Recent studies have shown that LCRs may co-occur with intrinsically disordered regions, are highly conserved in many organisms, and often play important roles in protein functions and in diseases. In previous decades, several methods have been developed to identify regions with LCRs or amino acid bias, but most of them as stand-alone applications and currently there is no web-based tool which allows users to explore LCRs in protein sequences with additional functional annotations...
May 18, 2020: Nucleic Acids Research
#19
JOURNAL ARTICLE
Gábor Erdős, Zsuzsanna Dosztányi
IUPred2A is a combined prediction tool designed to discover intrinsically disordered or conditionally disordered proteins and protein regions. Intrinsically disordered regions exist without a well-defined three-dimensional structure in isolation but carry out important biological functions. Over the years, various prediction methods have been developed to characterize disordered regions. The existence of disordered segments can also be dependent on different factors such as binding partners or environmental traits like pH or redox potential, and recognizing such regions represents additional computational challenges...
June 2020: Current Protocols in Bioinformatics
#20
JOURNAL ARTICLE
Norman E Davey, M Madan Babu, Martin Blackledge, Alan Bridge, Salvador Capella-Gutierrez, Zsuzsanna Dosztanyi, Rachel Drysdale, Richard J Edwards, Arne Elofsson, Isabella C Felli, Toby J Gibson, Aleksandras Gutmanas, John M Hancock, Jen Harrow, Desmond Higgins, Cy M Jeffries, Philippe Le Mercier, Balint Mészáros, Marco Necci, Cedric Notredame, Sandra Orchard, Christos A Ouzounis, Rita Pancsa, Elena Papaleo, Roberta Pierattelli, Damiano Piovesan, Vasilis J Promponas, Patrick Ruch, Gabriella Rustici, Pedro Romero, Sirarat Sarntivijai, Gary Saunders, Benjamin Schuler, Malvika Sharan, Denis C Shields, Joel L Sussman, Jonathan A Tedds, Peter Tompa, Michael Turewicz, Jiri Vondrasek, Wim F Vranken, Bonnie Ann Wallace, Kanin Wichapong, Silvio C E Tosatto
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments in the field of IDP research within the ELIXIR framework. The goal of these developments is to drive the creation of high-quality tools and resources to support the identification, analysis and functional characterisation of IDPs. The roadmap is the result of a workshop titled "An intrinsically disordered protein user community proposal for ELIXIR" held at the University of Padua...
2019: F1000Research
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