The protein structurome of Orthornavirae and its dark matter

Advanced methods for protein structure prediction, such as AlphaFold2, greatly expand our capability to identify protein domains and infer their likely functions and evolutionary relationships. This is particularly pertinent for proteins encoded by viruses that are known to evolve rapidly and as a result often cannot be adequately characterized by analysis of the protein sequences. We performed an exhaustive structure prediction and comparative analysis for uncharacterized proteins and domains ("dark matter") encoded by viruses with RNA genomes. The results show the dark matter of RNA virus proteome consists mostly of disordered and all-α-helical domains that cannot be readily assigned a specific function and that likely mediate various interactions between viral proteins and between viral and host proteins. The great majority of globular proteins and domains of RNA viruses are already known although we identified several unexpected domains represented in individual viral families.

Authors

Institutions

Publication Details

Journal
mBio
Published
2024-12-23
DOI
https://doi.org/10.1128/mbio.03200-24
Citations
8
Primary Topic
Plant Virus Research Studies
Type
article
Field-Weighted Citation Impact
4.80

Funders

Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

The protein structurome of Orthornavirae and its dark matter

Yuri I. Wolf, Anamarija Butković, Mart Krupovìč, Eugene V. Koonin et al.
8 citations
mBio
Plant Virus Research Studies
4.80
article

The protein structurome of Orthornavirae and its dark matter

Yuri I. Wolf, Anamarija Butković, Mart Krupovìč, Eugene V. Koonin, Uri Neri, Antônio Pedro Camargo, Valerian V. Dolja, Pascal Mutz, Harutyun Sahakyan
article en
8 citations

Abstract

Advanced methods for protein structure prediction, such as AlphaFold2, greatly expand our capability to identify protein domains and infer their likely functions and evolutionary relationships. This is particularly pertinent for proteins encoded by viruses that are known to evolve rapidly and as a result often cannot be adequately characterized by analysis of the protein sequences. We performed an exhaustive structure prediction and comparative analysis for uncharacterized proteins and domains ("dark matter") encoded by viruses with RNA genomes. The results show the dark matter of RNA virus proteome consists mostly of disordered and all-α-helical domains that cannot be readily assigned a specific function and that likely mediate various interactions between viral proteins and between viral and host proteins. The great majority of globular proteins and domains of RNA viruses are already known although we identified several unexpected domains represented in individual viral families.

mBioVol. 16(2)
Centre National de la Recherche Scientifique (FR), National Institutes of Health (US), Oregon State University (US), Lawrence Berkeley National Laboratory (US), Institut Pasteur (FR), Joint Genome Institute (US), Université Paris Cité (FR), United States National Library of Medicine (US)
U.S. Department of Energy, Oak Ridge Associated Universities, Joint Genome Institute, National Institutes of Health, Office of Science, Oak Ridge Institute for Science and Education, U.S. National Library of Medicine
Openalex Percentile: Top 5%
Plant Virus Research Studies
4.80
DOIOpen Access PDFOpenAlex
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.