Identifying Cognate Binding Pairs Among a Large Set of Paralogs: the Case of PE/PPE Proteins of Mycobacterium Tuberculosis

Overview

Journal PLoS Comput Biol

Specialty Biology

Date 2008 Sep 13

PMID 18787688

Citations 23

Authors

Robert Riley

Matteo Pellegrini

David Eisenberg

Affiliations

Soon will be listed here.

Abstract

We consider the problem of how to detect cognate pairs of proteins that bind when each belongs to a large family of paralogs. To illustrate the problem, we have undertaken a genomewide analysis of interactions of members of the PE and PPE protein families of Mycobacterium tuberculosis. Our computational method uses structural information, operon organization, and protein coevolution to infer the interaction of PE and PPE proteins. Some 289 PE/PPE complexes were predicted out of a possible 5,590 PE/PPE pairs genomewide. Thirty-five of these predicted complexes were also found to have correlated mRNA expression, providing additional evidence for these interactions. We show that our method is applicable to other protein families, by analyzing interactions of the Esx family of proteins. Our resulting set of predictions is a starting point for genomewide experimental interaction screens of the PE and PPE families, and our method may be generally useful for detecting interactions of proteins within families having many paralogs.

Citing Articles

PE/PPE Proteome and ESX-5 Substrate Spectrum in .

Yan L, Lai H, Leung T, Cheng H, Chen X, Tsui S Int J Mol Sci. 2024; 25(17).

PMID: 39273496 PMC: 11395111. DOI: 10.3390/ijms25179550.

Immunogenicity of PE18, PE31, and PPE26 proteins from in humans and mice.

Garcia-Bengoa M, Vergara E, Tran A, Bossi L, Cooper A, Pearl J Front Immunol. 2023; 14:1307429.

PMID: 38124744 PMC: 10730732. DOI: 10.3389/fimmu.2023.1307429.

PE/PPE proteins enhance the production of reactive oxygen species and formation of neutrophil extracellular traps.

Garcia-Bengoa M, Meurer M, Stehr M, Elamin A, Singh M, Oehlmann W Front Immunol. 2023; 14:1206529.

PMID: 37675111 PMC: 10478095. DOI: 10.3389/fimmu.2023.1206529.

The rate and role of pseudogenes of the complex.

Soler-Camargo N, Silva-Pereira T, Zimpel C, Camacho M, Zelanis A, Aono A Microb Genom. 2022; 8(10).

PMID: 36250787 PMC: 9676053. DOI: 10.1099/mgen.0.000876.

The PE_PGRS Protein Family Acts as an Immunological Decoy to Subvert Host Immune Response.

Sharma T, Alam A, Ehtram A, Rani A, Grover S, Ehtesham N Int J Mol Sci. 2022; 23(1).

PMID: 35008950 PMC: 8745494. DOI: 10.3390/ijms23010525.

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