Protein Aggregation, Structural Disorder and RNA-binding Ability: a New Approach for Physico-chemical and Gene Ontology Classification of Multiple Datasets

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2015 Dec 18

PMID 26673865

Citations 9

Authors

Petr Klus

Riccardo Delli Ponti

Carmen Maria Livi

Gian Gaetano Tartaglia

Affiliations

Soon will be listed here.

Abstract

Background: Comparison between multiple protein datasets requires the choice of an appropriate reference system and a number of variables to describe their differences. Here we introduce an innovative approach to discriminate multiple protein datasets (multiCM) and to measure enrichments in gene ontology terms (cleverGO) using semantic similarities.

Results: We illustrate the powerfulness of our approach by investigating the links between RNA-binding ability and other protein features, such as structural disorder and aggregation, in S. cerevisiae, C. elegans, M. musculus and H. sapiens. Our results are in striking agreement with available experimental evidence and unravel features that are key to understand the mechanisms regulating cellular homeostasis.

Conclusions: In an intuitive way, multiCM and cleverGO provide accurate classifications of physico-chemical features and annotations of biological processes, molecular functions and cellular components, which is extremely useful for the discovery and characterization of new trends in protein datasets. The multiCM and cleverGO can be freely accessed on the Web at http://www.tartaglialab.com/cs_multi/submission and http://www.tartaglialab.com/GO_analyser/universal . Each of the pages contains links to the corresponding documentation and tutorial.

Citing Articles

Computational optimization of angiotensin-converting enzyme 2 for SARS-CoV-2 Spike molecular recognition.

Di Rienzo L, Monti M, Milanetti E, Miotto M, Boffi A, Tartaglia G Comput Struct Biotechnol J. 2021; 19:3006-3014.

PMID: 34002118 PMC: 8116125. DOI: 10.1016/j.csbj.2021.05.016.

Structural analysis of SARS-CoV-2 genome and predictions of the human interactome.

Vandelli A, Monti M, Milanetti E, Armaos A, Rupert J, Zacco E Nucleic Acids Res. 2020; 48(20):11270-11283.

PMID: 33068416 PMC: 7672441. DOI: 10.1093/nar/gkaa864.

RNA-binding and prion domains: the Yin and Yang of phase separation.

Gotor N, Armaos A, Calloni G, Torrent Burgas M, Vabulas R, Sanchez de Groot N Nucleic Acids Res. 2020; 48(17):9491-9504.

PMID: 32857852 PMC: 7515694. DOI: 10.1093/nar/gkaa681.

, and Approaches to Identify Molecular Players in Fragile X Tremor and Ataxia Syndrome.

Haify S, Botta-Orfila T, Hukema R, Tartaglia G Front Mol Biosci. 2020; 7:31.

PMID: 32219099 PMC: 7078329. DOI: 10.3389/fmolb.2020.00031.

CROSSalive: a web server for predicting the in vivo structure of RNA molecules.

Delli Ponti R, Armaos A, Vandelli A, Tartaglia G Bioinformatics. 2019; 36(3):940-941.

PMID: 31504168 PMC: 9883674. DOI: 10.1093/bioinformatics/btz666.

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