Plasticity of the binding pocket in peptide transporters underpins promiscuous substrate recognition

Kotov, V.; Killer, M.; Jungnickel, K. E. J.; Lei, J.; Finocchio, G.; Steinke, J.; Bartels, K.; Strauss, J.; Dupeux, F.; Humm, A.-S.; Cornaciu, I.; Marquez, J. A.; Pardon, E.; Steyaert, J.; Loew, C.

doi:10.1101/2023.02.14.528348

bioRxiv · 10.1101/2023.02.14.528348

Plasticity of the binding pocket in peptide transporters underpins promiscuous substrate recognition

Kotov, V.·Killer, M.·Jungnickel, K. E. J.·Lei, J.·Finocchio, G.·Steinke, J.·Bartels, K.·Strauss, J.·Dupeux, F.·Humm, A.-S.·Cornaciu, I.·Marquez, J. A.·Pardon, E.·Steyaert, J.·Loew, C.

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Abstract

Proton-coupled oligopeptide transporters (POTs) are promiscuous transporters of the Major Facilitator Superfamily, that constitute the main route of entry for a wide range of dietary peptides and orally administrated peptidomimetic drugs. Given their clinical and pathophysiological relevance, several bacterial and mammalian POT homologs have been extensively studied on a structural and molecular level. However, the molecular basis of recognition and transport of the wide range of peptide substrates has remained elusive. Here we present 14 X-ray structures of the bacterial POT DtpB in complex with chemically diverse di- and tripeptides, providing novel insights into the plasticity of the conserved central binding cavity. We analyzed binding affinities for more than 80 peptides and monitored uptake by a fluorescence-based transport assay. To probe if all natural 8400 di- and tripeptides can bind to DtpB, we employed state-of-the-art molecular docking and machine learning and conclude that peptides of a specific subset with compact hydrophobic residues are the best DtpB binders.

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Kotov, V., Killer, M., Jungnickel, K. E. J., Lei, J., Finocchio, G., Steinke, J., Bartels, K., Strauss, J., Dupeux, F., Humm, A.-S., Cornaciu, I., Marquez, J. A., Pardon, E., Steyaert, J., Loew, C.. 2023-02-15. Plasticity of the binding pocket in peptide transporters underpins promiscuous substrate recognition. https://doi.org/10.1101/2023.02.14.528348

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