Dynamics and Structural Changes Induced by ATP Binding in SAV1866, a Bacterial ABC Exporter

Abstract

Multidrug transporters of the ATP-binding cassette family export a wide variety of compounds across membranes in both prokaryotes and eukaryotes, using ATP hydrolysis as energy source. Several of these membrane proteins are of clinical importance. Although biochemical and structural studies have provided insights into the mechanism underlying substrate transport, many key questions subsist regarding the molecular and structural nature of this mechanism. In particular, the detailed conformational changes occurring during the catalytic cycle are still elusive. We explored the conformational changes occurring upon ATP/Mg 2+ binding using molecular dynamics simulations starting from the nucleotide-bound structure of SAV1866 embedded in an explicit lipid bilayer. The removal of nucleotide revealed a major rearrangement in the outer membrane leaflet portion of the transmembrane domain (TMD) resulting in the closure of the central cavity at the extracellular side. This closure is similar to that observed in the crystal nucleotide-free structures. The interface of the nucleotide-binding domain dimer (NDB) is significantly more hydrated in the nucleotide-free trajectory though it is not disrupted. This finding suggests that the TMD closure could occur as a first step preceding the dissociation of the dimer. The transmission pathway of the signal triggered by the removal of ATP/Mg 2+ mainly involves the conserved Q-loop and X-loop as well as TM6.

Structural basis for antibacterial peptide self‐immunity by the bacterial ABC transporter McjD

“…We acknowledge, however, that longer MD simulations might be required to explore the possibility that the larger L53–L53 distances detected in two simulations, together with the larger A122–A122 distances mainly sampled in some of the ADP‐bound simulations, might trigger a conformational change towards an outward‐facing state. Interestingly, an occluded state of the cavity was also sampled in previous MD simulations studies carried out starting from the outward‐facing structure of Sav1866 in the presence of ADP (St‐Pierre et al , 2012), or in the absence of nucleotide (Becker et al , 2010). Combined, our experimental and theoretical work provides strong evidence that McjD exists mostly in an occluded state within the membrane in the absence of the substrate MccJ25.…”

“…Our cross‐linking data show that the NBDs are in very close proximity to each other within the membrane; binding of ATP would be sufficient to allow dimerization of the NBDs without the need of large conformational changes. Previous MD studies carried out on the outward‐facing state of Sav1866, where the NBDs are engaged in a tight dimer as in the outward‐occluded state of McjD, showed different results, highlighting (i) partial NBD dissociation in the presence of ADP and inorganic phosphate (Oliveira et al , 2011); (ii) how the pattern of interactions between domains changes after hydrolysis of just one ATP molecule (Gyimesi et al , 2011) or after ATP removal (Becker et al , 2010); and (iii) the stability of this particular conformation even in the presence of ADP (St‐Pierre et al , 2012). Here, our MD simulations, carried out at much larger timescales, reveal no dissociation at the NBD interface, independently by the presence of ADP or ATP.…”

Structure and mechanism of ATP-dependent phospholipid transporters

“…In this conformation, a 2-fold pseudo-symmetry can be observed for TM1-3 with respect to TM4-6 for each individual TMD [38][39][40]. During catalysis, the TMDs suffer extensive structural rearrangement establishing a new interaction surface that changes the orientation of the exposed cavity in the membrane [38,39,[41][42][43]. This reorganization results in the "open-outwards" conformation in which TM1 and TM2 in one monomer now interact with TM3 and TM6 of the other [44].…”

The transporter associated with antigen processing: a key player in adaptive immunity

“…CH1 is coupled in cis and trans to the Q-loops of both NBDs, whereas CH2 solely contacts the opposite NBD in trans (Dalmas et al, 2005;Dawson and Locher, 2006;He et al, 2008;Serohijos et al, 2008;Oancea et al, 2009) ( Figure 2B). In TAP and other ABC exporters, the X-loop also contributes to the inter-domain crosstalk by interacting with CHs of TAP1 and TAP2 (Oancea et al, 2009;Becker et al, 2010;Damas et al, 2011).…”