Exploring Protein Intrinsic Disorder with MobiDB.

Nowadays, it is well established that many proteins or regions under physiological conditions lack a fixed three-dimensional structure and are intrinsically disordered. MobiDB is the main repository of protein disorder and mobility annotations, combining different data sources to provide an exhaustive overview of intrinsic disorder. MobiDB includes curated annotations from other databases, indirect disorder evidence from structural data, and disorder predictions from protein sequences. It provides an easy-to-use web server to visualize and explore disorder information. This chapter describes the data available in MobiDB, emphasizing how to use and access the intrinsic disorder data. MobiDB is available at URL http://mobidb.bio.unipd.it .

[1]  Christopher J. Oldfield,et al.  Classification of Intrinsically Disordered Regions and Proteins , 2014, Chemical reviews.

[2]  István Simon,et al.  Preformed structural elements feature in partner recognition by intrinsically unstructured proteins. , 2004, Journal of molecular biology.

[3]  Toby J. Gibson,et al.  The eukaryotic linear motif resource – 2018 update , 2017, Nucleic Acids Res..

[4]  Silvio C. E. Tosatto,et al.  ESpritz: accurate and fast prediction of protein disorder , 2012, Bioinform..

[5]  Roberta Pierattelli,et al.  Recent progress in NMR spectroscopy: Toward the study of intrinsically disordered proteins of increasing size and complexity , 2012, IUBMB life.

[6]  Sonia Longhi,et al.  DisProt 7.0: a major update of the database of disordered proteins , 2016, Nucleic Acids Res..

[7]  B. Rost,et al.  Protein disorder--a breakthrough invention of evolution? , 2011, Current opinion in structural biology.

[8]  William I. Weis,et al.  Three-Dimensional Structure of the Armadillo Repeat Region of β-Catenin , 1997, Cell.

[9]  Jie J. Zheng,et al.  Crystal structure of a full-length beta-catenin. , 2008, Structure.

[10]  Peter Tompa,et al.  Intrinsically disordered proteins: emerging interaction specialists. , 2015, Current opinion in structural biology.

[11]  Silvio C. E. Tosatto,et al.  Where differences resemble: sequence-feature analysis in curated databases of intrinsically disordered proteins , 2018, Database J. Biol. Databases Curation.

[12]  Silvio C. E. Tosatto,et al.  MobiDB: a comprehensive database of intrinsic protein disorder annotations , 2012, Bioinform..

[13]  David S Wishart,et al.  A simple method to predict protein flexibility using secondary chemical shifts. , 2005, Journal of the American Chemical Society.

[14]  Silvio C. E. Tosatto,et al.  The RING 2.0 web server for high quality residue interaction networks , 2016, Nucleic Acids Res..

[15]  Geng Wu,et al.  Structure of a -TrCP1-Skp1--Catenin Complex , 2003 .

[16]  Silvio C. E. Tosatto,et al.  MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins , 2017, Nucleic Acids Res..

[17]  K. Grzeschik,et al.  Localization of the human beta-catenin gene (CTNNB1) to 3p21: a region implicated in tumor development. , 1994, Genomics.

[18]  David A. Lee,et al.  Gene3D: Extensive prediction of globular domains in proteins , 2017, Nucleic Acids Res..

[19]  N. Sonenberg,et al.  Translational homeostasis via the mRNA cap-binding protein, eIF4E. , 2012, Molecular cell.

[20]  Michele Vendruscolo,et al.  Accurate random coil chemical shifts from an analysis of loop regions in native states of proteins. , 2009, Journal of the American Chemical Society.

[21]  A. Dunker,et al.  Understanding protein non-folding. , 2010, Biochimica et biophysica acta.

[22]  Aidan Budd,et al.  Short linear motifs: ubiquitous and functionally diverse protein interaction modules directing cell regulation. , 2014, Chemical reviews.

[23]  Zheng Rong Yang,et al.  RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins , 2005, Bioinform..

[24]  Gary D Bader,et al.  Bringing order to protein disorder through comparative genomics and genetic interactions , 2011, Genome Biology.

[25]  Albert J. Vilella,et al.  EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. , 2009, Genome research.

[26]  Silvio C. E. Tosatto,et al.  FELLS: fast estimator of latent local structure , 2017, Bioinform..

[27]  E. Callaway.  The revolution will not be crystallized: a new method sweeps through structural biology , 2015, Nature.

[28]  P. Radivojac,et al.  Protein flexibility and intrinsic disorder , 2004, Protein science : a publication of the Protein Society.

[29]  B. Schuler,et al.  Single-Molecule FRET Spectroscopy and the Polymer Physics of Unfolded and Intrinsically Disordered Proteins. , 2016, Annual review of biophysics.

[30]  P. Romero,et al.  Sequence complexity of disordered protein , 2001, Proteins.

[31]  R. Pappu,et al.  Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues , 2013, Proceedings of the National Academy of Sciences.

[32]  Zsuzsanna Dosztányi,et al.  Prediction of Protein Binding Regions in Disordered Proteins , 2009, PLoS Comput. Biol..

[33]  J. S. Sodhi,et al.  Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. , 2004, Journal of molecular biology.

[34]  Sven Berg,et al.  A repeating amino acid motif shared by proteins with diverse cellular roles , 1994, Cell.

[35]  Tom Lenaerts,et al.  From protein sequence to dynamics and disorder with DynaMine , 2013, Nature Communications.

[36]  Silvio C. E. Tosatto,et al.  The Pfam protein families database in 2019 , 2018, Nucleic Acids Res..

[37]  Srinivasaraghavan Kannan,et al.  Long range recognition and selection in IDPs: the interactions of the C-terminus of p53 , 2016, Scientific Reports.

[38]  Robert B. Russell,et al.  GlobPlot: exploring protein sequences for globularity and disorder , 2003, Nucleic Acids Res..

[39]  Yifan Cheng.  Single-Particle Cryo-EM at Crystallographic Resolution , 2015, Cell.

[40]  Silvio C. E. Tosatto,et al.  Mobi 2.0: an improved method to define intrinsic disorder, mobility and linear binding regions in protein structures , 2018, Bioinform..

[41]  A. Dunker,et al.  Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life , 2012, Journal of biomolecular structure & dynamics.

[42]  Xi He,et al.  Developmental Cell Review Wnt / b-Catenin Signaling : Components , Mechanisms , and Diseases , 2022 .

[43]  Silvio C. E. Tosatto,et al.  Comprehensive large-scale assessment of intrinsic protein disorder , 2015, Bioinform..

[44]  Norman E. Davey,et al.  The functional importance of structure in unstructured protein regions. , 2019, Current opinion in structural biology.

[45]  T. Gibson,et al.  Protein disorder prediction: implications for structural proteomics. , 2003, Structure.

[46]  V. Uversky,et al.  Why are “natively unfolded” proteins unstructured under physiologic conditions? , 2000, Proteins.

[47]  Jaime Prilusky,et al.  Assessment of disorder predictions in CASP8 , 2009, Proteins.

[48]  Silvio C. E. Tosatto,et al.  MOBI: a web server to define and visualize structural mobility in NMR protein ensembles , 2010, Bioinform..

[49]  Christopher J. Oldfield,et al.  Evolutionary Rate Heterogeneity in Proteins with Long Disordered Regions , 2002, Journal of Molecular Evolution.

[50]  E. Wieschaus,et al.  The segment polarity gene armadillo interacts with the wingless signaling pathway in both embryonic and adult pattern formation. , 1991, Development.

[51]  Márton Miskei,et al.  FuzDB: database of fuzzy complexes, a tool to develop stochastic structure-function relationships for protein complexes and higher-order assemblies , 2016, Nucleic Acids Res..

[52]  Vladimir N Uversky,et al.  What does it mean to be natively unfolded? , 2002, European journal of biochemistry.

[53]  Silvio C. E. Tosatto,et al.  MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins , 2014, Nucleic Acids Res..

[54]  Motonori Ota,et al.  IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners , 2013, Nucleic Acids Res..

[55]  John C. Wootton,et al.  Non-globular Domains in Protein Sequences: Automated Segmentation Using Complexity Measures , 1994, Comput. Chem..

[56]  Erzsébet Fichó,et al.  MFIB: a repository of protein complexes with mutual folding induced by binding , 2017, Bioinform..

[57]  Zsuzsanna Dosztányi,et al.  IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content , 2005, Bioinform..

[58]  Carlo Camilloni,et al.  Determination of secondary structure populations in disordered states of proteins using nuclear magnetic resonance chemical shifts. , 2012, Biochemistry.

[59]  Philipp Selenko,et al.  Structural disorder of monomeric α-synuclein persists in mammalian cells , 2016, Nature.

[60]  Norbert Perrimon,et al.  dishevelled and armadillo act in the Wingless signalling pathway in Drosophila , 1994, Nature.

[61]  Zsuzsanna Dosztányi,et al.  DIBS: a repository of disordered binding sites mediating interactions with ordered proteins , 2017, Bioinform..

[62]  Sonia Longhi,et al.  Simultaneous quantification of protein order and disorder. , 2017, Nature chemical biology.

[63]  María Martín,et al.  Activities at the Universal Protein Resource (UniProt) , 2013, Nucleic Acids Res..

[64]  G. Wagner,et al.  The interaction of eIF4E with 4E‐BP1 is an induced fit to a completely disordered protein , 1998, Protein science : a publication of the Protein Society.

[65]  Geng Wu,et al.  Structure of a beta-TrCP1-Skp1-beta-catenin complex: destruction motif binding and lysine specificity of the SCF(beta-TrCP1) ubiquitin ligase. , 2003, Molecular cell.

[66]  S. Vucetic,et al.  Flavors of protein disorder , 2003, Proteins.

[67]  Zoran Obradovic,et al.  Length-dependent prediction of protein intrinsic disorder , 2006, BMC Bioinformatics.

[68]  Cristian Oscar Rohr,et al.  CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state , 2016, Database J. Biol. Databases Curation.

[69]  The translation initiation factor eIF-4E binds to a common motif shared by the translation factor eIF-4 gamma and the translational repressors 4E-binding proteins. , 1995, Molecular and cellular biology.

[70]  David T. Jones,et al.  Getting the most from PSI-BLAST. , 2002, Trends in biochemical sciences.

[71]  Silvio C. E. Tosatto,et al.  MobiDB‐lite: fast and highly specific consensus prediction of intrinsic disorder in proteins , 2017, Bioinform..

[72]  P. Tompa,et al.  Structural Disorder in Eukaryotes , 2012, PloS one.