Outer membrane β-barrel structure prediction through the lens of AlphaFold2

Topitsch, Annika and Schwede, Torsten and Pereira, Joana. (2022) Outer membrane β-barrel structure prediction through the lens of AlphaFold2.

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Official URL: https://edoc.unibas.ch/90659/

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Most proteins found in the outer membrane of Gram-negative bacteria share a common domain: the transmembrane β-barrel. These outer membrane β-barrels (OMBBs) occur in multiple sizes, and different families with a wide range of functions evolved independently by amplification from a pool of homologous ancestral ββ-hairpins. This is part of the reason why predicting their three-dimensional (3D) structure, especially by homology modeling, is a major challenge. Recently, DeepMind's AlphaFold v2 (AF2) became the first structure prediction method to reach close-to-experimental atomic accuracy in CASP even for difficult targets. However, membrane proteins, especially OMBBs, were not abundant during its training, raising the question of how accurate the predictions are for these families. In this study, we assessed the performance of AF2 in the prediction of OMBBs of various topologies using an in-house-developed tool for the analysis of OMBB 3D structures, barrOs . In agreement with previous studies on other membrane protein classes, our results indicate that AF2 predicts OMBB structures at high accuracy independently of the use of templates, even for novel topologies absent from the training set. These results provide confidence on the models generated by AF2 and open the door to the structural elucidation of novel OMBB topologies identified in high-throughput OMBB annotation studies.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Bioinformatics (Schwede)
UniBasel Contributors:Schwede, Torsten and Soares Pereira, Joana Maria and Topitsch, Annika
Item Type:Preprint
Note:Publication type according to Uni Basel Research Database: Discussion paper / Internet publication
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Last Modified:30 Nov 2022 14:07
Deposited On:30 Nov 2022 14:07

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