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A proteome-wide structural systems approach reveals insights into protein families of all human herpesviruses. | LitMetric

AI Article Synopsis

  • Structure predictions are essential tools in understanding protein structures, but important viral proteins are missing from the AlphaFold database.
  • This study presents structure predictions for all nine human herpesviruses, revealing significant clusters like the HCMV UL112-113.
  • The findings suggest that these predictions can uncover similarities between viral proteins and their cellular counterparts, offering insights into their potential functions, with a new database called HerpesFolds made available to the public.

Article Abstract

Structure predictions have become invaluable tools, but viral proteins are absent from the EMBL/DeepMind AlphaFold database. Here, we provide proteome-wide structure predictions for all nine human herpesviruses and analyze them in depth with explicit scoring thresholds. By clustering these predictions into structural similarity groups, we identified new families, such as the HCMV UL112-113 cluster, which is conserved in alpha- and betaherpesviruses. A domain-level search found protein families consisting of subgroups with varying numbers of duplicated folds. Using large-scale structural similarity searches, we identified viral proteins with cellular folds, such as the HSV-1 US2 cluster possessing dihydrofolate reductase folds and the EBV BMRF2 cluster that might have emerged from cellular equilibrative nucleoside transporters. Our HerpesFolds database is available at https://www.herpesfolds.org/herpesfolds and displays all models and clusters through an interactive web interface. Here, we show that system-wide structure predictions can reveal homology between viral species and identify potential protein functions.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11599850PMC
http://dx.doi.org/10.1038/s41467-024-54668-2DOI Listing

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