Prediction of protein interactions with function in protein (de-)phosphorylation

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F25%3A00143909" target="_blank" >RIV/00216224:14740/25:00143909 - isvavai.cz</a>

Result on the web

<a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0319084" target="_blank" >https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0319084</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1371/journal.pone.0319084" target="_blank" >10.1371/journal.pone.0319084</a>

Result language

angličtina

Original language name

Prediction of protein interactions with function in protein (de-)phosphorylation

Original language description

Protein-protein interactions (PPIs) form a complex network called "interactome" that regulates many functions in the cell. In recent years, there is an increasing accumulation of evidence supporting the existence of a hyperbolic geometry underlying the network representation of complex systems such as the interactome. In particular, it has been shown that the embedding of the human Protein-Interaction Network (hPIN) in hyperbolic space (H2) captures biologically relevant information. Here we explore whether this mapping contains information that would allow us to predict the function of PPIs, more specifically interactions related to post-translational modification (PTM). We used a random forest algorithm to predict PTM-related directed PPIs, concretely, protein phosphorylation and dephosphorylation, based on hyperbolic properties and centrality measures of the hPIN mapped in H2. To evaluate the efficacy of our algorithm, we predicted PTM-related PPIs of ataxin-1, a protein which is responsible for Spinocerebellar Ataxia type 1 (SCA1). Proteomics analysis in a cellular model revealed that several of the predicted PTM-PPIs were indeed dysregulated in a SCA1-related disease network. A compact cluster composed of ataxin-1, its dysregulated PTM-PPIs and their common upstream regulators may represent critical interactions for disease pathology. Thus, our algorithm may infer phosphorylation activity on proteins through directed PPIs.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10600 - Biological sciences

Project

—

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2025

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

PLoS Biology

ISSN

1932-6203

e-ISSN

1932-6203

Volume of the periodical

20

Issue of the periodical within the volume

3

Country of publishing house

US - UNITED STATES

Number of pages

21

Pages from-to

1-21

UT code for WoS article

001437514700024

EID of the result in the Scopus database

2-s2.0-86000330544