Expediting topology data gathering for the TOPDB database

Dobson, László; Langó, Tamás; Reményi, István; Tusnády, Gábor

doi:10.1093/nar/gku1119

Cited by 41 publications

(45 citation statements)

References 59 publications

(64 reference statements)

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“…Protein topology (membrane side associated with N-terminus, ‘In’ or ‘Out’) was assigned using information from UniProt, TOPDB (33), PDB and publications, including direct experimental studies of TM protein topology, locations of water-soluble domains in specific intracellular compartments and post-translational modifications.…”

Section: Protein Classification Localization and Topologymentioning

confidence: 99%

Membranome: a database for proteome-wide analysis of single-pass membrane proteins

Lomize

Krolicki

et al. 2016

Nucleic Acids Res

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The Membranome database was developed to assist analysis and computational modeling of single-pass (bitopic) transmembrane (TM) proteins and their complexes by providing structural information about these proteins on a genomic scale. The database currently collects data on >6000 bitopic proteins from Homo sapiens, Arabidopsis thaliana, Dictyostelium discoideum, Saccharomyces cerevisiae, Escherichia coli and Methanocaldococcus jannaschii. It presents the following data: (i) hierarchical classification of bitopic proteins into 15 functional classes, 689 structural superfamilies and 1404 families; (ii) 446 complexes of bitopic proteins with known three-dimensional (3D) structures classified into 129 families; (iii) computationally generated three-dimensional models of TM α-helices positioned in membranes; (iv) amino acid sequences, domain architecture, functional annotation and available experimental structures of bitopic proteins; (v) TM topology and intracellular localization, (vi) physical interactions between proteins from the database along with links to other resources. The database is freely accessible at http://membranome.org. There is a variety of options for browsing, sorting, searching and retrieval of the content, including downloadable coordinate files of TM domains with calculated membrane boundaries.

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Section: Protein Classification Localization and Topologymentioning

confidence: 99%

Membranome: a database for proteome-wide analysis of single-pass membrane proteins

Lomize

Krolicki

et al. 2016

Nucleic Acids Res

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“…To achieve the most accurate topology prediction, all predictions were enhanced with available structural and experimental information from TOPDB (28). To ensure all information is up-to-date, we updated all source databases before the creation of TSTMP or used the most up-to-date version of them.…”

Section: Resultsmentioning

confidence: 99%

TSTMP: target selection for structural genomics of human transmembrane proteins

et al. 2016

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The TSTMP database is designed to help the target selection of human transmembrane proteins for structural genomics projects and structure modeling studies. Currently, there are only 60 known 3D structures among the polytopic human transmembrane proteins and about a further 600 could be modeled using existing structures. Although there are a great number of human transmembrane protein structures left to be determined, surprisingly only a small fraction of these proteins have ‘selected’ (or above) status according to the current version the TargetDB/TargetTrack database. This figure is even worse regarding those transmembrane proteins that would contribute the most to the structural coverage of the human transmembrane proteome. The database was built by sorting out proteins from the human transmembrane proteome with known structure and searching for suitable model structures for the remaining proteins by combining the results of a state-of-the-art transmembrane specific fold recognition algorithm and a sequence similarity search algorithm. Proteins were searched for homologues among the human transmembrane proteins in order to select targets whose successful structure determination would lead to the best structural coverage of the human transmembrane proteome. The pipeline constructed for creating the TSTMP database guarantees to keep the database up-to-date. The database is available at http://tstmp.enzim.ttk.mta.hu.

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“…TOPDB database (version 2.0) [32,33] was downloaded from http://topdb.enzim.hu and each entry containing a cross reference to the PDB has been selected. These entries were filtered to 40% sequence identity by CD-HIT algorithm [34][35][36].…”

Section: Databases Determination Of Disordered Regions and Topologymentioning

confidence: 99%

“…We selected 1162 transmembrane proteins from the recently updated TOPDB database [32,33] below 40% sequence identity. 1056 of these proteins have at least one homologous structure in the PDB.…”

Section: Stringent Definition Of Disordered Regionsmentioning

confidence: 99%

Disordered regions in transmembrane proteins

Tusnády

Dobson

Tompa

2015

Biochimica et Biophysica Acta (BBA) - Biomembranes

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The functions of transmembrane proteins in living cells are widespread; they range from various transport processes to energy production, from cell-cell adhesion to communication. Structurally, they are highly ordered in their membrane-spanning regions, but may contain disordered regions in the cytosolic and extra-cytosolic parts. In this study, we have investigated the disordered regions in transmembrane proteins by a stringent definition of disordered residues on the currently available largest experimental dataset, and show a significant correlation between the spatial distributions of positively charged residues and disordered regions. This finding suggests a new role of disordered regions in transmembrane proteins by providing structural flexibility for stabilizing interactions with negatively charged head groups of the lipid molecules. We also find a preference of structural disorder in the terminal--as opposed to loop--regions in transmembrane proteins, and survey the respective functions involved in recruiting other proteins or mediating allosteric signaling effects. Finally, we critically compare disorder prediction methods on our transmembrane protein set. While there are no major differences between these methods using the usual statistics, such as per residue accuracies, Matthew's correlation coefficients, etc.; substantial differences can be found regarding the spatial distribution of the predicted disordered regions. We conclude that a predictor optimized for transmembrane proteins would be of high value to the field of structural disorder.

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Expediting topology data gathering for the TOPDB database

Cited by 41 publications

References 59 publications

Membranome: a database for proteome-wide analysis of single-pass membrane proteins

Membranome: a database for proteome-wide analysis of single-pass membrane proteins

TSTMP: target selection for structural genomics of human transmembrane proteins

Disordered regions in transmembrane proteins

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