Conformational Landscape of the Di- and Tripeptide Permease A Transport Cycle

Dipeptide and tripeptide permease A (DtpA) transporter is a bacterial homologue of the human PepT that is responsible for the uptake of di- and tripeptides from the small intestine and transports them across the cell membrane utilizing an inward-directed proton electrochemical gradient. Despite its importance, the structural dynamics governing the conformational transitions of DtpA remain poorly understood. In this study, we employed Adaptive Bandit enhanced sampling molecular dynamics simulations to investigate the five major conformational states of DtpA adopted during the transport cycle. We identified key metastable states and transitions underlying the transport cycle using Markov State Models (MSMs). Our findings reveal that intra- and interhelical interactions drive conformational changes by inducing bending and rotation of helices lining the pore, resulting in its opening and closure. This study explains the substrate transport mechanism in DtpA, enhancing our understanding of bacterial proton-dependent oligopeptide transporters (POTs) and opening new drug design and development opportunities.