Unlocking conformational dynamics of SapA: insights into the emphasis of ligand dependency using molecular dynamics simulation

Abstract

The Sap transport system belongs to an ATP-binding cassette importer, which is reported to render resistance against host-produced antimicrobial peptides (AMPs) amongst various Gram-negative bacteria. The Sap system imports the AMPs across the membrane into the cytoplasm, wherein they are cleaved by the proteases. The Sap system comprises five components: a substrate-binding protein (SBP, SapA), two transmembrane domains (TMDs, SapBC), and two nucleotide-binding domains (NBDs, SapDF). Interestingly, the membrane components (SapBCDF) of the Escherichia coli Sap (EcSap) system were suggested to function as a putrescine exporter. On the contrary, recent in silico reports suggested its multifaceted attributes in the uptake of dipeptides, AMPs, and heme. To establish the multifarious nature, extensive molecular dynamics simulations of EcSapA in its apo and holo (bound to dipeptides, AMPs, and heme) forms were performed to gain structural insights into its molecular plasticity. The results of this study suggest that EcSapA possesses a wide and promiscuous binding site that is favorable for accommodating varying lengths of ligands with a ligand-dependent conformational dynamics mechanism. Further, the estimated binding energies of the ligands suggest that EcSapA shows a preferential binding for cationic AMPs, followed by heme and dipeptides. In summary, the study highlights the ligand-binding dynamics within the promiscuous binding site of EcSapA, enlightening a lucrative target for drug development.