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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
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
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
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
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 (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
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
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
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
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
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
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 The program package is freely available for academic users...
October 15, 2009: Bioinformatics
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
Eva Csosz, Peter Bagossi, Zoltan Nagy, Zsuzsanna Dosztanyi, Istvan Simon, Laszlo Fesus
Tissue transglutaminase (TG2) catalyzes the Ca(2+)-dependent posttranslational modification of proteins via formation of isopeptide bonds between their glutamine and lysine residues. Although substrate specificity of TG2 has been studied repeatedly at the sequence level, no clear consensus sequences have been determined so far. With the use of the extensive structural information on TG2 substrate proteins listed in TRANSDAB Wiki database, a slight preference of TG2 for glutamine and lysine residues situated in turns could be observed...
November 7, 2008: Journal of Molecular Biology
Zsuzsanna Dosztányi, Peter Tompa
The recent advance in our understanding of the relation of protein structure and function cautions that many proteins, or regions of proteins, exist and function without a well-defined three-dimensional structure. These intrinsically disordered/unstructured proteins (IDP/IUP) are frequent in proteomes and carry out essential functions, but their lack of stable structures hampers efforts of solving structures at high resolution by x-ray crystallography and/or NMR. Thus, filtering such proteins/regions out of high-throughput structural genomics pipelines would be of significant benefit in terms of cost and success rate...
2008: Methods in Molecular Biology
Bálint Mészáros, Peter Tompa, István Simon, Zsuzsanna Dosztányi
Thorough knowledge of the molecular principles of protein-protein recognition is essential to our understanding of protein function at the cellular level. Whereas interactions of ordered proteins have been analyzed in great detail, complexes of intrinsically unstructured/disordered proteins (IUPs) have hardly been addressed so far. Here, we have collected a database of 39 complexes of experimentally verified IUPs, and compared their interfaces with those of 72 complexes of ordered, globular proteins. The characteristic differences found between the two types of complexes suggest that IUPs represent a distinct molecular implementation of the principles of protein-protein recognition...
September 14, 2007: Journal of Molecular Biology
Veronika Csizmók, Zsuzsanna Dosztányi, István Simon, Peter Tompa
Intrinsically unstructured/disordered proteins (IUPs) and protein domains lack a well-defined three-dimensional structure under physiological conditions. Structural disorder imparts advantages in many non-conventional functions, which poses a significant challenge to our understanding of the structure-function relationship of proteins. The general appreciation of this fact, however, is hampered by the large gap in our knowledge on IUPs, as we have biophysical data on less than 500 of them, whereas bioinformatic predictions suggest at least several thousand such proteins in the human proteome alone...
April 2007: Current Protein & Peptide Science
Zsuzsanna Dosztányi, Márk Sándor, Peter Tompa, István Simon
Intrinsically disordered/unstructured proteins exist in a highly flexible conformational state largely devoid of secondary structural elements and tertiary contacts. Despite their lack of a well defined structure, these proteins often fulfill essential regulatory functions. The intrinsic lack of structure confers functional advantages on these proteins, allowing them to adopt multiple conformations and to bind to different binding partners. The structural flexibility of disordered regions hampers efforts solving structures at high resolution by X-ray crystallography and/or NMR...
April 2007: Current Protein & Peptide Science
Zsuzsanna Dosztányi, Jake Chen, A Keith Dunker, István Simon, Peter Tompa
Protein interaction networks display approximate scale-free topology, in which hub proteins that interact with a large number of other proteins determine the overall organization of the network. In this study, we aim to determine whether hubs are distinguishable from other networked proteins by specific sequence features. Proteins of different connectednesses were compared in the interaction networks of Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, and Homo sapienswith respect to the distribution of predicted structural disorder, sequence repeats, low complexity regions, and chain length...
November 2006: Journal of Proteome Research
Peter Tompa, Zsuzsanna Dosztanyi, Istvan Simon
Intrinsically unstructured proteins, which exist without a well-defined 3D structure, carry out essential functions and occur with high frequency, as predicted for genomes. The generality of this phenomenon, however, is questioned by the uncertainty of what fraction of genomes actually encodes for expressed proteins. Here, we used two independent bioinformatic predictors, PONDR VSL1, and IUPred, to demonstrate that disorder prevails in the recently characterized proteomes and essential proteins of E. coli and S...
August 2006: Journal of Proteome Research
Zsuzsanna Dosztányi, Veronika Csizmok, Peter Tompa, István Simon
Intrinsically unstructured/disordered proteins and domains (IUPs) lack a well-defined three-dimensional structure under native conditions. The IUPred server presents a novel algorithm for predicting such regions from amino acid sequences by estimating their total pairwise interresidue interaction energy, based on the assumption that IUP sequences do not fold due to their inability to form sufficient stabilizing interresidue interactions. Optional to the prediction are built-in parameter sets optimized for predicting short or long disordered regions and structured domains...
August 15, 2005: Bioinformatics
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