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https://www.readbyqxmd.com/read/28968848/a-comprehensive-assessment-of-long-intrinsic-protein-disorder-from-the-disprot-database
#1
Marco Necci, Damiano Piovesan, Zsuzsanna Dosztanyi, 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...
September 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453683/mobidb-lite-fast-and-highly-specific-consensus-prediction-of-intrinsic-disorder-in-proteins
#2
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://www.readbyqxmd.com/read/28328918/simultaneous-quantification-of-protein-order-and-disorder
#3
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://www.readbyqxmd.com/read/28292960/degrons-in-cancer
#4
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://www.readbyqxmd.com/read/28104628/mobidb-lite-fast-and-highly-specific-consensus-prediction-of-intrinsic-disorder-in-proteins
#5
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://www.readbyqxmd.com/read/27965415/disprot-7-0-a-major-update-of-the-database-of-disordered-proteins
#6
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://www.readbyqxmd.com/read/27899635/interpro-in-2017-beyond-protein-family-and-domain-annotations
#7
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 (http://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://www.readbyqxmd.com/read/27899601/disprot-7-0-a-major-update-of-the-database-of-disordered-proteins
#8
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://www.readbyqxmd.com/read/27150584/systematic-analysis-of-somatic-mutations-driving-cancer-uncovering-functional-protein-regions-in-disease-development
#9
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)...
2016: Biology Direct
https://www.readbyqxmd.com/read/26538579/systematic-discovery-of-linear-binding-motifs-targeting-an-ancient-protein-interaction-surface-on-map-kinases
#10
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
https://www.readbyqxmd.com/read/25502193/prediction-and-analysis-of-intrinsically-disordered-proteins
#11
REVIEW
Marco Punta, István Simon, Zsuzsanna Dosztányi
Intrinsically disordered proteins and protein regions (IDPs/IDRs) do not adopt a well-defined folded structure under physiological conditions. Instead, these proteins exist as heterogeneous and dynamical conformational ensembles. IDPs are widespread in eukaryotic proteomes and are involved in fundamental biological processes, mostly related to regulation and signaling. At the same time, disordered regions often pose significant challenges to the structure determination process, which generally requires highly homogeneous proteins samples...
2015: Methods in Molecular Biology
https://www.readbyqxmd.com/read/23418572/the-n-terminal-intrinsically-disordered-domain-of-mgm101p-is-localized-to-the-mitochondrial-nucleoid
#12
David C Hayward, Zsuzsanna Dosztányi, George Desmond Clark-Walker
The mitochondrial genome maintenance gene, MGM101, is essential for yeasts that depend on mitochondrial DNA replication. Previously, in Saccharomyces cerevisiae, it has been found that the carboxy-terminal two-thirds of Mgm101p has a functional core. Furthermore, there is a high level of amino acid sequence conservation in this region from widely diverse species. By contrast, the amino-terminal region, that is also essential for function, does not have recognizable conservation. Using a bioinformatic approach we find that the functional core from yeast and a corresponding region of Mgm101p from the coral Acropora millepora have an ordered structure, while the N-terminal domains of sequences from yeast and coral are predicted to be disordered...
2013: PloS One
https://www.readbyqxmd.com/read/23203878/d%C3%A2-p%C3%A2-database-of-disordered-protein-predictions
#13
Matt E Oates, Pedro Romero, Takashi Ishida, Mohamed Ghalwash, Marcin J Mizianty, Bin Xue, Zsuzsanna Dosztányi, Vladimir N Uversky, Zoran Obradovic, Lukasz Kurgan, A Keith Dunker, Julian Gough
We present the Database of Disordered Protein Prediction (D(2)P(2)), available at http://d2p2.pro (including website source code). A battery of disorder predictors and their variants, VL-XT, VSL2b, PrDOS, PV2, Espritz and IUPred, were run on all protein sequences from 1765 complete proteomes (to be updated as more genomes are completed). Integrated with these results are all of the predicted (mostly structured) SCOP domains using the SUPERFAMILY predictor. These disorder/structure annotations together enable comparison of the disorder predictors with each other and examination of the overlap between disordered predictions and SCOP domains on a large scale...
January 2013: Nucleic Acids Research
https://www.readbyqxmd.com/read/23056474/disordered-binding-regions-and-linear-motifs-bridging-the-gap-between-two-models-of-molecular-recognition
#14
Bálint Mészáros, Zsuzsanna Dosztányi, István Simon
Intrinsically disordered proteins (IDPs) exist without the presence of a stable tertiary structure in isolation. These proteins are often involved in molecular recognition processes via their disordered binding regions that can recognize partner molecules by undergoing a coupled folding and binding process. The specific properties of disordered binding regions give way to specific, yet transient interactions that enable IDPs to play central roles in signaling pathways and act as hubs of protein interaction networks...
2012: PloS One
https://www.readbyqxmd.com/read/21918772/is-there-a-biological-cost-of-protein-disorder-analysis-of-cancer-associated-mutations
#15
Mátyás Pajkos, Bálint Mészáros, István Simon, Zsuzsanna Dosztányi
As many diseases can be traced back to altered protein function, studying the effect of genetic variations at the level of proteins can provide a clue to understand how changes at the DNA level lead to various diseases. Cellular processes rely not only on proteins with well-defined structure but can also involve intrinsically disordered proteins (IDPs) that exist as highly flexible ensembles of conformations. Disordered proteins are mostly involved in signaling and regulatory processes, and their functional repertoire largely complements that of globular proteins...
January 2012: Molecular BioSystems
https://www.readbyqxmd.com/read/21814507/proteins-with-complex-architecture-as-potential-targets-for-drug-design-a-case-study-of-mycobacterium-tuberculosis
#16
Bálint Mészáros, Judit Tóth, Beáta G Vértessy, Zsuzsanna Dosztányi, István Simon
Lengthy co-evolution of Homo sapiens and Mycobacterium tuberculosis, the main causative agent of tuberculosis, resulted in a dramatically successful pathogen species that presents considerable challenge for modern medicine. The continuous and ever increasing appearance of multi-drug resistant mycobacteria necessitates the identification of novel drug targets and drugs with new mechanisms of action. However, further insights are needed to establish automated protocols for target selection based on the available complete genome sequences...
July 2011: PLoS Computational Biology
https://www.readbyqxmd.com/read/21572179/the-expanding-view-of-protein-protein-interactions-complexes-involving-intrinsically-disordered-proteins
#17
REVIEW
Bálint Mészáros, István Simon, Zsuzsanna Dosztányi
A frequently neglected aspect of protein-protein interactions is flexibility. Small-scale fluctuations are present even in globular proteins, and alternative conformations can have a significant influence on the binding process. However, flexibility becomes highly prominent in complexes involving intrinsically disordered proteins. The importance of disordered regions in protein interactions has been recognized only relatively recently. In this survey we examine the basic properties of the complexes of disordered and ordered proteins from three different directions...
June 2011: Physical Biology
https://www.readbyqxmd.com/read/20007729/bioinformatical-approaches-to-characterize-intrinsically-disordered-unstructured-proteins
#18
REVIEW
Zsuzsanna Dosztányi, Bálint Mészáros, István Simon
Intrinsically disordered/unstructured proteins exist without a stable three-dimensional (3D) structure as highly flexible conformational ensembles. The available genome sequences revealed that these proteins are surprisingly common and their frequency reaches high proportions in eukaryotes. Due to their vital role in various biological processes including signaling and regulation and their involvement in various diseases, disordered proteins and protein segments are the focus of many biochemical, molecular biological, pathological and pharmaceutical studies...
March 2010: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/19717576/anchor-web-server-for-predicting-protein-binding-regions-in-disordered-proteins
#19
Zsuzsanna Dosztányi, Bálint Mészáros, István Simon
UNLABELLED: ANCHOR is a web-based implementation of an original method that takes a single amino acid sequence as an input and predicts protein binding regions that are disordered in isolation but can undergo disorder-to-order transition upon binding. The server incorporates the result of a general disorder prediction method, IUPred and can carry out simple motif searches as well. AVAILABILITY: The web server is available at http://anchor.enzim.hu. The program package is freely available for academic users...
October 15, 2009: Bioinformatics
https://www.readbyqxmd.com/read/19412530/prediction-of-protein-binding-regions-in-disordered-proteins
#20
Bálint Mészáros, István Simon, Zsuzsanna Dosztányi
Many disordered proteins function via binding to a structured partner and undergo a disorder-to-order transition. The coupled folding and binding can confer several functional advantages such as the precise control of binding specificity without increased affinity. Additionally, the inherent flexibility allows the binding site to adopt various conformations and to bind to multiple partners. These features explain the prevalence of such binding elements in signaling and regulatory processes. In this work, we report ANCHOR, a method for the prediction of disordered binding regions...
May 2009: PLoS Computational Biology
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