ArticlebioRxiv : the preprint server for biology2026
An Investigation of the Conformational Dynamics of ABC Exporter PCAT1 using Microsecond-Level MD Simulations.
Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Peptidase-containing ATP-binding cassette transporters (PCATs) couple ATP hydrolysis with proteolytic processing and export of cargo peptides across cellular membranes. Despite their importance in bacterial secretion systems, the molecular determinants governing nucleotide binding and stabilization in PCAT transporters remain incompletely understood. In particular, recent experimental observations suggest that PCAT1 may display altered nucleotide preferences compared with canonical ABC transporters. Here, we employed microsecond-scale all-atom molecular dynamics simulations combined with free energy perturbation (FEP) calculations to characterize nucleotide binding, protein stability, and conformational dynamics of PCAT1 across multiple biochemical conditions. Simulations were performed for inward-facing (IF) and outward-facing (OF) conformations in the presence or absence of Mg
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