Tordai, Hedvig;
Suhajda, Erzsebet;
Sillitoe, Ian;
Nair, Sreenath;
Varadi, Mihaly;
Hegedus, Tamas;
(2022)
Comprehensive Collection and Prediction of ABC Transmembrane Protein Structures in the AI Era of Structural Biology.
International Journal of Molecular Sciences
, 23
(16)
, Article 8877. 10.3390/ijms23168877.
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Abstract
The number of unique transmembrane (TM) protein structures doubled in the last four years, which can be attributed to the revolution of cryo-electron microscopy. In addition, AlphaFold2 (AF2) also provided a large number of predicted structures with high quality. However, if a specific protein family is the subject of a study, collecting the structures of the family members is highly challenging in spite of existing general and protein domain-specific databases. Here, we demonstrate this and assess the applicability and usability of automatic collection and presentation of protein structures via the ABC protein superfamily. Our pipeline identifies and classifies transmembrane ABC protein structures using the PFAM search and also aims to determine their conformational states based on special geometric measures, conftors. Since the AlphaFold database contains structure predictions only for single polypeptide chains, we performed AF2-Multimer predictions for human ABC half transporters functioning as dimers. Our AF2 predictions warn of possibly ambiguous interpretation of some biochemical data regarding interaction partners and call for further experiments and experimental structure determination. We made our predicted ABC protein structures available through a web application, and we joined the 3D-Beacons Network to reach the broader scientific community through platforms such as PDBe-KB.
| Type: | Article |
|---|---|
| Title: | Comprehensive Collection and Prediction of ABC Transmembrane Protein Structures in the AI Era of Structural Biology |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.3390/ijms23168877 |
| Publisher version: | https://doi.org/10.3390/ijms23168877 |
| Language: | English |
| Additional information: | This is an open access article distributed under the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
| Keywords: | protein structure; protein complex; ABC transporters; AlphaFold2; AF-multimer; structure database; 3D-Beacons |
| UCL classification: | UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Structural and Molecular Biology UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10154175 |
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