Energetics of substrate transport in proton-dependent oligopeptide transporters
Abstract The PepTSo transporter mediates the transport of peptides across biological membranes. Despite advancements in structural biology, including cryogenic electron microscopy structures resolving PepTSo in different states, the molecular basis of peptide recognition and transport by PepTSo is n...
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Nature Portfolio
2024-12-01
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| Series: | Communications Chemistry |
| Online Access: | https://doi.org/10.1038/s42004-024-01398-7 |
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| author | Balaji Selvam Nicole Chiang Diwakar Shukla |
| author_facet | Balaji Selvam Nicole Chiang Diwakar Shukla |
| author_sort | Balaji Selvam |
| collection | DOAJ |
| description | Abstract The PepTSo transporter mediates the transport of peptides across biological membranes. Despite advancements in structural biology, including cryogenic electron microscopy structures resolving PepTSo in different states, the molecular basis of peptide recognition and transport by PepTSo is not fully elucidated. In this study, we used molecular dynamics simulations, Markov State Models (MSMs), and Transition Path Theory (TPT) to investigate the transport mechanism of an alanine-alanine peptide (Ala-Ala) through the PepTSo transporter. Our simulations revealed conformational changes and key intermediate states involved in peptide translocation. We observed that the presence of the Ala-Ala peptide substrate lowers the free energy barriers associated with transition to the inward-facing state. We also show a proton transport model and analyzed the pharmacophore features of intermediate states, providing insights for rational drug design. These findings highlight the significance of substrate binding in modulating the conformational dynamics of PepTSo and identify critical residues that facilitate transport. |
| format | Article |
| id | doaj-art-f0e9f3ade38949ad93c1a6a7df1e0865 |
| institution | Kabale University |
| issn | 2399-3669 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Chemistry |
| spelling | doaj-art-f0e9f3ade38949ad93c1a6a7df1e08652025-01-05T12:10:52ZengNature PortfolioCommunications Chemistry2399-36692024-12-01711910.1038/s42004-024-01398-7Energetics of substrate transport in proton-dependent oligopeptide transportersBalaji Selvam0Nicole Chiang1Diwakar Shukla2Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-ChampaignDepartment of Chemical and Biomolecular Engineering, University of Illinois at Urbana-ChampaignDepartment of Chemical and Biomolecular Engineering, University of Illinois at Urbana-ChampaignAbstract The PepTSo transporter mediates the transport of peptides across biological membranes. Despite advancements in structural biology, including cryogenic electron microscopy structures resolving PepTSo in different states, the molecular basis of peptide recognition and transport by PepTSo is not fully elucidated. In this study, we used molecular dynamics simulations, Markov State Models (MSMs), and Transition Path Theory (TPT) to investigate the transport mechanism of an alanine-alanine peptide (Ala-Ala) through the PepTSo transporter. Our simulations revealed conformational changes and key intermediate states involved in peptide translocation. We observed that the presence of the Ala-Ala peptide substrate lowers the free energy barriers associated with transition to the inward-facing state. We also show a proton transport model and analyzed the pharmacophore features of intermediate states, providing insights for rational drug design. These findings highlight the significance of substrate binding in modulating the conformational dynamics of PepTSo and identify critical residues that facilitate transport.https://doi.org/10.1038/s42004-024-01398-7 |
| spellingShingle | Balaji Selvam Nicole Chiang Diwakar Shukla Energetics of substrate transport in proton-dependent oligopeptide transporters Communications Chemistry |
| title | Energetics of substrate transport in proton-dependent oligopeptide transporters |
| title_full | Energetics of substrate transport in proton-dependent oligopeptide transporters |
| title_fullStr | Energetics of substrate transport in proton-dependent oligopeptide transporters |
| title_full_unstemmed | Energetics of substrate transport in proton-dependent oligopeptide transporters |
| title_short | Energetics of substrate transport in proton-dependent oligopeptide transporters |
| title_sort | energetics of substrate transport in proton dependent oligopeptide transporters |
| url | https://doi.org/10.1038/s42004-024-01398-7 |
| work_keys_str_mv | AT balajiselvam energeticsofsubstratetransportinprotondependentoligopeptidetransporters AT nicolechiang energeticsofsubstratetransportinprotondependentoligopeptidetransporters AT diwakarshukla energeticsofsubstratetransportinprotondependentoligopeptidetransporters |