Abstract
ABC transporters are a large family of membrane proteins involved in a variety of cellular processes, including multidrug and tumor resistance and ion channel regulation. Advances in the structural and functional understanding of ABC transporters have revealed that hydrolysis at the two canonical nucleotide-binding sites (NBSs) is co-operative and non-simultaneous. A conserved core architecture of bacterial and eukaryotic ABC exporters has been established, as exemplified by the crystal structure of the homodimeric multidrug exporter Sav1866. Currently, it is unclear how sequential ATP hydrolysis arises in a symmetric homodimeric transporter, since it implies at least transient asymmetry at the NBSs. We show by molecular dynamics simulation that the initially symmetric structure of Sav1866 readily undergoes asymmetric transitions at its NBSs in a pre-hydrolytic nucleotide configuration. MgATP-binding residues and a network of charged residues at the dimer interface are shown to form a sequence of putative molecular switches that allow ATP hydrolysis only at one NBS. We extend our findings to eukaryotic ABC exporters which often consist of two non-identical half-transporters, frequently with degeneracy substitutions at one of their two NBSs. Interestingly, many residues involved in asymmetric conformational switching in Sav1866 are substituted in degenerate eukaryotic NBS. This finding strengthens recent suggestions that the interplay of a consensus and a degenerate NBS in eukaroytic ABC proteins pre-determines the sequence of hydrolysis at the two NBSs.
Highlights
ATP-binding cassette (ABC) transporters are a large family of membrane proteins that use MgATP hydrolysis to drive the import or export of solutes to or from the cytoplasm
Most ABC transporters consist of two transmembrane domains (TMDs) that provide a pathway across the membrane for the transported substrate, and two nucleotide-binding domains (NBDs) which form two nucleotide-binding sites (NBSs) at their dimer interface [6,7]
The domain-specific rmsd values for the NBDs in the 30 ns simulation performed with POPC lipid are within the range observed in the 40 ns simulations with DPPC lipid, but those of the TMDs are lower in the POPC simulation (Table 1)
Summary
ATP-binding cassette (ABC) transporters are a large family of membrane proteins that use MgATP hydrolysis to drive the import or export of solutes to or from the cytoplasm. They undertake a number of physiological roles, for example bacterial nutrient uptake, bacterial drug resistance, tumor drug resistance, and peptide secretion [1]. Most ABC transporters consist of two transmembrane domains (TMDs) that provide a pathway across the membrane for the transported substrate, and two nucleotide-binding domains (NBDs) which form two nucleotide-binding sites (NBSs) at their dimer interface (see Figure 1) [6,7]. Bacterial exporters are typically formed by dimers of TMD-NBD halftransporters. Such motifs are the Walker-A, Walker-B, Q-loop, signature and switch motifs, as illustrated in Figure 1B [8,9]
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