keyword
https://read.qxmd.com/read/31713636/disprot-intrinsic-protein-disorder-annotation-in-2020
#21
JOURNAL ARTICLE
András Hatos, Borbála Hajdu-Soltész, Alexander M Monzon, Nicolas Palopoli, Lucía Álvarez, Burcu Aykac-Fas, Claudio Bassot, Guillermo I Benítez, Martina Bevilacqua, Anastasia Chasapi, Lucia Chemes, Norman E Davey, Radoslav Davidović, A Keith Dunker, Arne Elofsson, Julien Gobeill, Nicolás S González Foutel, Govindarajan Sudha, Mainak Guharoy, Tamas Horvath, Valentin Iglesias, Andrey V Kajava, Orsolya P Kovacs, John Lamb, Matteo Lambrughi, Tamas Lazar, Jeremy Y Leclercq, Emanuela Leonardi, Sandra Macedo-Ribeiro, Mauricio Macossay-Castillo, Emiliano Maiani, José A Manso, Cristina Marino-Buslje, Elizabeth Martínez-Pérez, Bálint Mészáros, Ivan Mičetić, Giovanni Minervini, Nikoletta Murvai, Marco Necci, Christos A Ouzounis, Mátyás Pajkos, Lisanna Paladin, Rita Pancsa, Elena Papaleo, Gustavo Parisi, Emilie Pasche, Pedro J Barbosa Pereira, Vasilis J Promponas, Jordi Pujols, Federica Quaglia, Patrick Ruch, Marco Salvatore, Eva Schad, Beata Szabo, Tamás Szaniszló, Stella Tamana, Agnes Tantos, Nevena Veljkovic, Salvador Ventura, Wim Vranken, Zsuzsanna Dosztányi, Peter Tompa, Silvio C E Tosatto, Damiano Piovesan
The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website. The website includes a redesigned graphical interface, a better search engine, a clearer API for programmatic access and a new annotation interface that integrates text mining technologies...
November 12, 2019: Nucleic Acids Research
https://read.qxmd.com/read/31612960/phasepro-the-database-of-proteins-driving-liquid-liquid-phase-separation
#22
JOURNAL ARTICLE
Bálint Mészáros, Gábor Erdős, Beáta Szabó, Éva Schád, Ágnes Tantos, Rawan Abukhairan, Tamás Horváth, Nikoletta Murvai, Orsolya P Kovács, Márton Kovács, Silvio C E Tosatto, Péter Tompa, Zsuzsanna Dosztányi, Rita Pancsa
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), a process that relies on multivalent weak interactions of the constituent proteins and other macromolecules. Since the first discoveries of certain proteins being able to drive LLPS, it emerged as a general mechanism for the effective organization of cellular space that is exploited in all kingdoms of life...
October 15, 2019: Nucleic Acids Research
https://read.qxmd.com/read/31415767/sequential-structural-and-functional-properties-of-protein-complexes-are-defined-by-how-folding-and-binding-intertwine
#23
JOURNAL ARTICLE
Bálint Mészáros, László Dobson, Erzsébet Fichó, Gábor E Tusnády, Zsuzsanna Dosztányi, István Simon
Intrinsically disordered proteins (IDPs) fulfill critical biological roles without having the potential to fold on their own. While lacking inherent structure, the majority of IDPs do reach a folded state via interaction with a protein partner, presenting a deep entanglement of the folding and binding processes. Protein disorder has been recognized as a major determinant in several properties of proteins, such as sequence, adopted structure upon binding and function. However, the way the binding process is reflected in these features in general lacks a detailed description...
August 12, 2019: Journal of Molecular Biology
https://read.qxmd.com/read/30698641/disentangling-the-complexity-of-low-complexity-proteins
#24
JOURNAL ARTICLE
Pablo Mier, Lisanna Paladin, Stella Tamana, Sophia Petrosian, Borbála Hajdu-Soltész, Annika Urbanek, Aleksandra Gruca, Dariusz Plewczynski, Marcin Grynberg, Pau Bernadó, Zoltán Gáspári, Christos A Ouzounis, Vasilis J Promponas, Andrey V Kajava, John M Hancock, Silvio C E Tosatto, Zsuzsanna Dosztanyi, Miguel A Andrade-Navarro
There are multiple definitions for low complexity regions (LCRs) in protein sequences, with all of them broadly considering LCRs as regions with fewer amino acid types compared to an average composition. Following this view, LCRs can also be defined as regions showing composition bias. In this critical review, we focus on the definition of sequence complexity of LCRs and their connection with structure. We present statistics and methodological approaches that measure low complexity (LC) and related sequence properties...
January 30, 2019: Briefings in Bioinformatics
https://read.qxmd.com/read/30628183/large-scale-analysis-of-redox-sensitive-conditionally-disordered-protein-regions-reveals-their-widespread-nature-and-key-roles-in-high-level-eukaryotic-processes
#25
JOURNAL ARTICLE
Gábor Erdős, Bálint Mészáros, Dana Reichmann, Zsuzsanna Dosztányi
Recently developed quantitative redox proteomic studies enable the direct identification of redox-sensing cysteine residues that regulate the functional behavior of target proteins in response to changing levels of reactive oxygen species (ROS). At the molecular level, redox regulation can directly modify the active sites of enzymes, although a growing number of examples indicate the importance of an additional underlying mechanism that involves conditionally disordered proteins. These proteins alter their functional behavior by undergoing a disorder-to-order transition in response to changing redox conditions...
January 9, 2019: Proteomics
https://read.qxmd.com/read/29860432/iupred2a-context-dependent-prediction-of-protein-disorder-as-a-function-of-redox-state-and-protein-binding
#26
JOURNAL ARTICLE
Bálint Mészáros, Gábor Erdos, Zsuzsanna Dosztányi
The structural states of proteins include ordered globular domains as well as intrinsically disordered protein regions that exist as highly flexible conformational ensembles in isolation. Various computational tools have been developed to discriminate ordered and disordered segments based on the amino acid sequence. However, properties of IDRs can also depend on various conditions, including binding to globular protein partners or environmental factors, such as redox potential. These cases provide further challenges for the computational characterization of disordered segments...
July 2, 2018: Nucleic Acids Research
https://read.qxmd.com/read/29385418/dibs-a-repository-of-disordered-binding-sites-mediating-interactions-with-ordered-proteins
#27
JOURNAL ARTICLE
Eva Schad, Erzsébet Fichó, Rita Pancsa, István Simon, Zsuzsanna Dosztányi, Bálint Mészáros
Motivation: Intrinsically Disordered Proteins (IDPs) mediate crucial protein-protein interactions, most notably in signaling and regulation. As their importance is increasingly recognized, the detailed analyses of specific IDP interactions opened up new opportunities for therapeutic targeting. Yet, large scale information about IDP-mediated interactions in structural and functional details are lacking, hindering the understanding of the mechanisms underlying this distinct binding mode...
February 1, 2018: Bioinformatics
https://read.qxmd.com/read/29240760/novel-linear-motif-filtering-protocol-reveals-the-role-of-the-lc8-dynein-light-chain-in-the-hippo-pathway
#28
JOURNAL ARTICLE
Gábor Erdős, Tamás Szaniszló, Mátyás Pajkos, Borbála Hajdu-Soltész, Bence Kiss, Gábor Pál, László Nyitray, Zsuzsanna Dosztányi
Protein-protein interactions (PPIs) formed between short linear motifs and globular domains play important roles in many regulatory and signaling processes but are highly underrepresented in current protein-protein interaction databases. These types of interactions are usually characterized by a specific binding motif that captures the key amino acids shared among the interaction partners. However, the computational proteome-level identification of interaction partners based on the known motif is hindered by the huge number of randomly occurring matches from which biologically relevant motif hits need to be extracted...
December 2017: PLoS Computational Biology
https://read.qxmd.com/read/29136219/mobidb-3-0-more-annotations-for-intrinsic-disorder-conformational-diversity-and-interactions-in-proteins
#29
JOURNAL ARTICLE
Damiano Piovesan, Francesco Tabaro, Lisanna Paladin, Marco Necci, Ivan Micetic, Carlo Camilloni, Norman Davey, Zsuzsanna Dosztányi, Bálint Mészáros, Alexander M Monzon, Gustavo Parisi, Eva Schad, Pietro Sormanni, Peter Tompa, Michele Vendruscolo, Wim F Vranken, Silvio C E Tosatto
The MobiDB (URL: mobidb.bio.unipd.it) database of protein disorder and mobility annotations has been significantly updated and upgraded since its last major renewal in 2014. Several curated datasets for intrinsic disorder and folding upon binding have been integrated from specialized databases. The indirect evidence has also been expanded to better capture information available in the PDB, such as high temperature residues in X-ray structures and overall conformational diversity. Novel nuclear magnetic resonance chemical shift data provides an additional experimental information layer on conformational dynamics...
January 4, 2018: Nucleic Acids Research
https://read.qxmd.com/read/29076577/prediction-of-protein-disorder-based-on-iupred
#30
JOURNAL ARTICLE
Zsuzsanna Dosztányi
Many proteins contain intrinsically disordered regions (IDRs), functional polypeptide segments that in isolation adopt a highly flexible conformational ensemble instead of a single, well-defined structure. Disorder prediction methods, which can discriminate ordered and disordered regions from the amino acid sequence, have contributed significantly to our current understanding of the distinct properties of intrinsically disordered proteins by enabling the characterization of individual examples as well as large-scale analyses of these protein regions...
January 2018: Protein Science
https://read.qxmd.com/read/28968848/a-comprehensive-assessment-of-long-intrinsic-protein-disorder-from-the-disprot-database
#31
JOURNAL ARTICLE
Marco Necci, Damiano Piovesan, Zsuzsanna Dosztányi, Peter Tompa, Silvio C E Tosatto
Motivation: Intrinsic disorder (ID), i.e. the lack of a unique folded conformation at physiological conditions, is a common feature for many proteins, which requires specialized biochemical experiments that are not high-throughput. Missing X-ray residues from the PDB have been widely used as a proxy for ID when developing computational methods. This may lead to a systematic bias, where predictors deviate from biologically relevant ID. Large benchmarking sets on experimentally validated ID are scarce...
February 1, 2018: Bioinformatics
https://read.qxmd.com/read/28453683/mobidb-lite-fast-and-highly-specific-consensus-prediction-of-intrinsic-disorder-in-proteins
#32
JOURNAL ARTICLE
Marco Necci, Damiano Piovesan, Zsuzsanna Dosztányi, Silvio C E Tosatto
Motivation: Intrinsic disorder (ID) is established as an important feature of protein sequences. Its use in proteome annotation is however hampered by the availability of many methods with similar performance at the single residue level, which have mostly not been optimized to predict long ID regions of size comparable to domains. Results: Here, we have focused on providing a single consensus-based prediction, MobiDB-lite, optimized for highly specific (i.e. few false positive) predictions of long disorder...
May 1, 2017: Bioinformatics
https://read.qxmd.com/read/28328918/simultaneous-quantification-of-protein-order-and-disorder
#33
JOURNAL ARTICLE
Pietro Sormanni, Damiano Piovesan, Gabriella T Heller, Massimiliano Bonomi, Predrag Kukic, Carlo Camilloni, Monika Fuxreiter, Zsuzsanna Dosztanyi, Rohit V Pappu, M Madan Babu, Sonia Longhi, Peter Tompa, A Keith Dunker, Vladimir N Uversky, Silvio C E Tosatto, Michele Vendruscolo
No abstract text is available yet for this article.
March 22, 2017: Nature Chemical Biology
https://read.qxmd.com/read/28292960/degrons-in-cancer
#34
REVIEW
Bálint Mészáros, Manjeet Kumar, Toby J Gibson, Bora Uyar, Zsuzsanna Dosztányi
Degrons are the elements that are used by E3 ubiquitin ligases to target proteins for degradation. Most degrons are short linear motifs embedded within the sequences of modular proteins. As regulatory sites for protein abundance, they are important for many different cellular processes, such as progression through the cell cycle and monitoring cellular hypoxia. Degrons enable the elimination of proteins that are no longer required, preventing their possible dysfunction. Although the human genome encodes ~600 E3 ubiquitin ligases, only a fraction of these enzymes have well-defined target degrons...
March 14, 2017: Science Signaling
https://read.qxmd.com/read/28104628/mobidb-lite-fast-and-highly-specific-consensus-prediction-of-intrinsic-disorder-in-proteins
#35
JOURNAL ARTICLE
Marco Necci, Damiano Piovesan, Zsuzsanna Dosztányi, Silvio C E Tosatto
MOTIVATION: Intrinsic disorder (ID) is established as an important feature of protein sequences. Its use in proteome annotation is however hampered by the availability of many methods with similar performance at the single residue level, which have mostly not been optimized to predict long ID regions of size comparable to domains. Here, we have focused on providing a single consensus-based prediction, MobiDB-lite, optimized for highly specific (i.e. few false positive) predictions of long disorder...
January 18, 2017: Bioinformatics
https://read.qxmd.com/read/27965415/disprot-7-0-a-major-update-of-the-database-of-disordered-proteins
#36
JOURNAL ARTICLE
Damiano Piovesan, Francesco Tabaro, Ivan Mičetić, Marco Necci, Federica Quaglia, Christopher J Oldfield, Maria Cristina Aspromonte, Norman E Davey, Radoslav Davidović, Zsuzsanna Dosztányi, Arne Elofsson, Alessandra Gasparini, András Hatos, Andrey V Kajava, Lajos Kalmar, Emanuela Leonardi, Tamas Lazar, Sandra Macedo-Ribeiro, Mauricio Macossay-Castillo, Attila Meszaros, Giovanni Minervini, Nikoletta Murvai, Jordi Pujols, Daniel B Roche, Edoardo Salladini, Eva Schad, Antoine Schramm, Beata Szabo, Agnes Tantos, Fiorella Tonello, Konstantinos D Tsirigos, Nevena Veljković, Salvador Ventura, Wim Vranken, Per Warholm, Vladimir N Uversky, A Keith Dunker, Sonia Longhi, Peter Tompa, Silvio C E Tosatto
No abstract text is available yet for this article.
January 4, 2017: Nucleic Acids Research
https://read.qxmd.com/read/27899635/interpro-in-2017-beyond-protein-family-and-domain-annotations
#37
JOURNAL ARTICLE
Robert D Finn, Teresa K Attwood, Patricia C Babbitt, Alex Bateman, Peer Bork, Alan J Bridge, Hsin-Yu Chang, Zsuzsanna Dosztányi, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft, Gemma L Holliday, Hongzhan Huang, Xiaosong Huang, Ivica Letunic, Rodrigo Lopez, Shennan Lu, Aron Marchler-Bauer, Huaiyu Mi, Jaina Mistry, Darren A Natale, Marco Necci, Gift Nuka, Christine A Orengo, Youngmi Park, Sebastien Pesseat, Damiano Piovesan, Simon C Potter, Neil D Rawlings, Nicole Redaschi, Lorna Richardson, Catherine Rivoire, Amaia Sangrador-Vegas, Christian Sigrist, Ian Sillitoe, Ben Smithers, Silvano Squizzato, Granger Sutton, Narmada Thanki, Paul D Thomas, Silvio C E Tosatto, Cathy H Wu, Ioannis Xenarios, Lai-Su Yeh, Siew-Yit Young, Alex L Mitchell
InterPro (https://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and nucleic acid sequences to be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with InterPro and its associated software, including the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation and prediction of intrinsic disorder...
January 4, 2017: Nucleic Acids Research
https://read.qxmd.com/read/27899601/disprot-7-0-a-major-update-of-the-database-of-disordered-proteins
#38
JOURNAL ARTICLE
Damiano Piovesan, Francesco Tabaro, Ivan Mičetić, Marco Necci, Federica Quaglia, Christopher J Oldfield, Maria Cristina Aspromonte, Norman E Davey, Radoslav Davidović, Zsuzsanna Dosztányi, Arne Elofsson, Alessandra Gasparini, András Hatos, Andrey V Kajava, Lajos Kalmar, Emanuela Leonardi, Tamas Lazar, Sandra Macedo-Ribeiro, Mauricio Macossay-Castillo, Attila Meszaros, Giovanni Minervini, Nikoletta Murvai, Jordi Pujols, Daniel B Roche, Edoardo Salladini, Eva Schad, Antoine Schramm, Beata Szabo, Agnes Tantos, Fiorella Tonello, Konstantinos D Tsirigos, Nevena Veljković, Salvador Ventura, Wim Vranken, Per Warholm, Vladimir N Uversky, A Keith Dunker, Sonia Longhi, Peter Tompa, Silvio C E Tosatto
The Database of Protein Disorder (DisProt, URL: www.disprot.org) has been significantly updated and upgraded since its last major renewal in 2007. The current release holds information on more than 800 entries of IDPs/IDRs, i.e. intrinsically disordered proteins or regions that exist and function without a well-defined three-dimensional structure. We have re-curated previous entries to purge DisProt from conflicting cases, and also upgraded the functional classification scheme to reflect continuous advance in the field in the past 10 years or so...
January 4, 2017: Nucleic Acids Research
https://read.qxmd.com/read/27150584/systematic-analysis-of-somatic-mutations-driving-cancer-uncovering-functional-protein-regions-in-disease-development
#39
JOURNAL ARTICLE
Bálint Mészáros, András Zeke, Attila Reményi, István Simon, Zsuzsanna Dosztányi
BACKGROUND: Recent advances in sequencing technologies enable the large-scale identification of genes that are affected by various genetic alterations in cancer. However, understanding tumor development requires insights into how these changes cause altered protein function and impaired network regulation in general and/or in specific cancer types. RESULTS: In this work we present a novel method called iSiMPRe that identifies regions that are significantly enriched in somatic mutations and short in-frame insertions or deletions (indels)...
May 5, 2016: Biology Direct
https://read.qxmd.com/read/26538579/systematic-discovery-of-linear-binding-motifs-targeting-an-ancient-protein-interaction-surface-on-map-kinases
#40
JOURNAL ARTICLE
András Zeke, Tomas Bastys, Anita Alexa, Ágnes Garai, Bálint Mészáros, Klára Kirsch, Zsuzsanna Dosztányi, Olga V Kalinina, Attila Reményi
Mitogen-activated protein kinases (MAPK) are broadly used regulators of cellular signaling. However, how these enzymes can be involved in such a broad spectrum of physiological functions is not understood. Systematic discovery of MAPK networks both experimentally and in silico has been hindered because MAPKs bind to other proteins with low affinity and mostly in less-characterized disordered regions. We used a structurally consistent model on kinase-docking motif interactions to facilitate the discovery of short functional sites in the structurally flexible and functionally under-explored part of the human proteome and applied experimental tools specifically tailored to detect low-affinity protein-protein interactions for their validation in vitro and in cell-based assays...
November 2015: Molecular Systems Biology
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