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. 2020 Jul 2;48(W1):W77-W84.
doi: 10.1093/nar/gkaa339.

PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins

Patryk Jarnot  1 , Joanna Ziemska-Legiecka  2 , Laszlo Dobson  3   4 , Matthew Merski  5 , Pablo Mier  6 , Miguel A Andrade-Navarro  6 , John M Hancock  7 , Zsuzsanna Dosztányi  8 , Lisanna Paladin  9 , Marco Necci  9 , Damiano Piovesan  9 , Silvio C E Tosatto  9 , Vasilis J Promponas  10 , Marcin Grynberg  2 , Aleksandra Gruca  1
Affiliations

PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins

Patryk Jarnot et al. Nucleic Acids Res. .

Abstract

Low complexity regions (LCRs) in protein sequences are characterized by a less diverse amino acid composition compared to typically observed sequence diversity. Recent studies have shown that LCRs may co-occur with intrinsically disordered regions, are highly conserved in many organisms, and often play important roles in protein functions and in diseases. In previous decades, several methods have been developed to identify regions with LCRs or amino acid bias, but most of them as stand-alone applications and currently there is no web-based tool which allows users to explore LCRs in protein sequences with additional functional annotations. We aim to fill this gap by providing PlaToLoCo - PLAtform of TOols for LOw COmplexity-a meta-server that integrates and collects the output of five different state-of-the-art tools for discovering LCRs and provides functional annotations such as domain detection, transmembrane segment prediction, and calculation of amino acid frequencies. In addition, the union or intersection of the results of the search on a query sequence can be obtained. By developing the PlaToLoCo meta-server, we provide the community with a fast and easily accessible tool for the analysis of LCRs with additional information included to aid the interpretation of the results. The PlaToLoCo platform is available at: http://platoloco.aei.polsl.pl/.

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Figures

Figure 1.
Figure 1.
Layout of the results tab of the PlaToLoCo webserver. (A) summary tab, (B) sequence details, (C) amino acid frequency, (D) methods consensus, (E) Pfam and PDB details and (F) region details.
Figure 2.
Figure 2.
(A) The structure of steryl-sulfatase (PDB: 1p49). Membrane regions were predicted by CCTOP (red) (34). (B) The modelled structure of paraspeckle component multimers. Coiled-coil regions were predicted by DeepCoil (red) (35), Single-helices were predicted by CSAHdetec (yellow) (36). (C) Structure of SH3 domain and the p85 subunit of PI3-kinase. Disordered regions were predicted with IUPRED (red) (37). Blue: overlap of SEG, CAST and fLPS. Orange: overlap of CAST and fLPS – also highlighted on the structures.
Figure 3.
Figure 3.
Panel A: proportion of detected low complexity and compositionally biased regions in various proteomes and in the PDB (detected LCRs to total number of residues) for SEG, CAST and fLPS. Panel B: proportion of repeat regions in various proteomes and in the PDB (detected repeats to total number of residues) for SIMPLE and GBSC. The exact number of residues found by each method is provided in the Supplementary material 2 (Suppl2) in Supplementary Table S2.
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