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The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes

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Názov: The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes
Autori: Odai, Roni, Leemann, Michèle, Al-Murad, Tamim, Abdullah, Minhal, Shyrokova, Lena, Tenson, Tanel, Hauryliuk, Vasili, Durairaj, Janani, Pereira, Joana, Atkinson, Gemma C
Prispievatelia: Lund University, Faculty of Medicine, Department of Experimental Medical Science, Protein Evolution, Lunds universitet, Medicinska fakulteten, Institutionen för experimentell medicinsk vetenskap, Proteinevolution, Originator, Lund University, Profile areas and other strong research environments, Strategic research areas (SRA), eSSENCE: The e-Science Collaboration, Lunds universitet, Profilområden och andra starka forskningsmiljöer, Strategiska forskningsområden (SFO), eSSENCE: The e-Science Collaboration, Originator, Lund University, Faculty of Medicine, Department of Experimental Medical Science, Molecular Enzymology, Lunds universitet, Medicinska fakulteten, Institutionen för experimentell medicinsk vetenskap, Molekylär enzymologi, Originator, Lund University, Faculty of Medicine, Department of Clinical Sciences, Lund, Infect@LU, Lunds universitet, Medicinska fakulteten, Institutionen för kliniska vetenskaper, Lund, Infect@LU, Originator, Lund University, Profile areas and other strong research environments, Strategic research areas (SRA), NanoLund: Centre for Nanoscience, Lunds universitet, Profilområden och andra starka forskningsmiljöer, Strategiska forskningsområden (SFO), NanoLund: Centre for Nanoscience, Originator, Lund University, Faculty of Engineering, LTH, LTH Profile areas, LTH Profile Area: Nanoscience and Semiconductor Technology, Lunds universitet, Lunds Tekniska Högskola, LTH profilområden, LTH profilområde: Nanovetenskap och halvledarteknologi, Originator, Lund University, Profile areas and other strong research environments, Lund University Profile areas, LU Profile Area: Proactive Ageing, Lunds universitet, Profilområden och andra starka forskningsmiljöer, Lunds universitets profilområden, LU profilområde: Proaktivt åldrande, Originator
Zdroj: Science Advances. 11(40):1-14
Predmety: Natural Sciences, Biological Sciences, Bioinformatics and Computational Biology, Naturvetenskap, Biologi, Bioinformatik och beräkningsbiologi
Popis: Viruses are the most abundant and genetically diverse entities on Earth, yet the functions and evolution of most viral proteins remain poorly understood. Their rapid evolution often obscures evolutionary relationships, limiting the ability to assign functions using sequence-based methods. Although the conservation of protein fold can reveal deep homologies, viral proteins remain underrepresented in structural databases. We address this by clustering viral sequences from RefSeq and predicting the structures of ~27,000 representative proteins using AlphaFold2 to create the Viral AlphaFold Database (VAD). We uncover conserved folds in diverse viruses infecting bacteria, archaea, and eukaryotes. We predict homodimers and make comparisons to the Protein Data Bank, providing data on oligomerization potential. We reveal considerable functional darkness in the viral protein universe and report the discovery and validation of an uncharacterized toxin-antitoxin system. The VAD provides a foundation for exploring viral structure-function relationships, including ancient folds shaping viral interactions across all life.
Prístupová URL adresa: https://doi.org/10.1126/sciadv.adz8560
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  Data: The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes
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  Data: Viruses are the most abundant and genetically diverse entities on Earth, yet the functions and evolution of most viral proteins remain poorly understood. Their rapid evolution often obscures evolutionary relationships, limiting the ability to assign functions using sequence-based methods. Although the conservation of protein fold can reveal deep homologies, viral proteins remain underrepresented in structural databases. We address this by clustering viral sequences from RefSeq and predicting the structures of ~27,000 representative proteins using AlphaFold2 to create the Viral AlphaFold Database (VAD). We uncover conserved folds in diverse viruses infecting bacteria, archaea, and eukaryotes. We predict homodimers and make comparisons to the Protein Data Bank, providing data on oligomerization potential. We reveal considerable functional darkness in the viral protein universe and report the discovery and validation of an uncharacterized toxin-antitoxin system. The VAD provides a foundation for exploring viral structure-function relationships, including ancient folds shaping viral interactions across all life.
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