2.2 | Ligand-induced conformational changes, T1158 v0-v4
ABC transporters import and export small molecules across cell
boundaries, through an ATP-driven process involving a series of
conformational changes (16). A CASP15 challenge, provided by Sergei
Pourmal, was to compute the structures of a multi-drug resistant (MRP4)
Type IV ABC transporter for the apo-form (no ATP-Mg or other ligand) and
in the presence of four different ligands (three different prostanoids:
prostaglandin E1, prostaglandin E2 and dehydroepiandrosterone sulfate;
and ATP-Mg) (11). The ligand-bound structures all have a single mutation
to prevent ATP hydrolysis. Each of these five states was released as a
separate target: T1158 (apo), and T1158v1-v4 (holo). Comparison of the
experimental conformations shows three distinct inter-domain
‘clam-shell’ angles in addition to other differences: an open form for
the apo structure, with the two intra-membrane domains maximally splayed
apart; similar, partially closed (about a 20 degree closure) structures
for each of the prostanoid complexes; and a closed structure with almost
parallel helix bundles in the presence of ATP-Mg. Figure 2 shows a
superposition of the experimental structures for three of these. The
correct conformational state was submitted by more than one group for
each of the five targets. One group submitted correct conformations for
four, but no group provided correct conformations for all five targets,
and no group ranked the correct conformation highest among the five
submitted. The successful groups are not specialists in ligand binding,
and all used enhanced sampling AF2 methods. In CASP14, a number of
ligand-containing targets were also correctly modeled by DeepMind’s AF2
group in the absence of the ligands. Multiple studies have shown that
enhanced sampling and MSA selection with AF2 (17-20) can generate a
broad range of conformational models, consistent with this result.
Overall, the CASP15 models for this ensemble are of not very high
accuracy (GDT-TS values in the 70s, one of 84), but these are still
impressive and intriguing results for such a difficult
multi-conformational target.