First curated coronavirus interactome released

Artist's impression of the coronavirus interactome. Credit: Spencer Phillips

First curated coronavirus interactome released

4 Dec 2020 - 10:28

Summary 

  • The IMEx Consortium has over 15 years of experience in collecting and curating protein interaction data for the scientific community. These molecular interaction data are freely available through the IntAct database
  • Coronavirus protein interaction data – the coronavirus interactome – can now be found through the IntAct molecular interaction database
  • Identification of SARS-CoV-2 protein interactions will help researchers to understand viral infection mechanisms

1 December 2020, Cambridge – The International Molecular Exchange (IMEx) Consortium has published coronavirus protein interaction data  – the coronavirus interactome  – in the IntAct database. This dataset, complemented by an ever-growing representation of the human interactome, could help shed light on how the virus infects cells and how it replicates.

Proteins work not in isolation but as part of a network with other molecules. Mapping out protein interactions is crucial to better understand normal cellular processes. When changes, or mutations, are introduced into a protein, these interactions may be altered resulting in disease. Understanding how these protein interactions are rewired enables researchers to gain insight into disease processes.

The IMEx Consortium is an international collaboration consisting of major public interaction data providers including IntAct, The Molecular INTeraction Database (MINT), the Database of Interacting Proteins (DIP), UniProt, MatrixDB, InnateDB and many others. All of the data collected and curated by the IMEx Consortium is centralised in the IntAct database at EMBL’s European Bioinformatics Institute (EMBL-EBI). These data are readily available through IntAct and the mentha portal, maintained by the MINT group.

Protein interaction curation

Over time, researchers within the IMEx Consortium have refined and developed their curation model, which is used to score and filter protein interaction data. For each interaction recorded, the curation model collects detailed information on the host organism, experiment methodology, and contextual information known about the experiment. Their curation model has also branched out to include small molecule, carbohydrate, and nucleic acid interactions.

To understand protein function and stability in disease it is important to interpret how mutations and post translational modifications affect protein interactions. To help with this, IMEx has collected information describing the effects these alterations have on protein interactions. This includes details of the position and amino acid change of a mutation, and the effect that mutation has on the interaction.

“It’s very important that researchers can easily obtain information regarding the known effects of point mutations on protein interactions,” says Sandra Orchard, Team Leader at EMBL-EBI. “Collecting and curating this type of information has been a big step forward for the IMEx Consortium and something that is hugely beneficial to the scientific community.”

Building the coronavirus interactome

The COVID-19 pandemic has led to enormous global research efforts to better understand the biology and spread of the SARS-CoV-2 virus. To improve our molecular understanding of the virus, the IMEx Consortium has curated a dataset of protein interactions carried out by SARS-CoV-2, SARS-CoV-1 and other coronaviruses.

This coronavirus interactome comprises over 5600 interactions extracted from more than 200 publications and is freely available through the IntAct database. Identification of viral protein interactions will help researchers to understand the cellular mechanisms involved in viral infection of host cells and subsequent viral replication.

“This collaborative work carried out by the IMEx Consortium will be very beneficial for COVID-19 research,” says Pablo Porras Millan, Project Leader at EMBL-EBI. “We’ve curated a huge amount of coronavirus protein interaction data including information about the host organism, the methodology used to detect the interactions and additional details such as the effects of site-directed mutations on protein interaction.”

 

Contact the news team

Vicky Hatch | Communications Officer

vhatch@ebi.ac.uk

Oana Stroe | Senior Communications Officer

stroe@ebi.ac.uk

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