Conformational characterization of a protein complex involving intrinsically disordered protein by small-angle neutron scattering using the inverse contrast matching method: a case study of interaction between α-synuclein and PbaB tetramer as a model chaperone

Cumulative genomics and proteomics data have now highlighted the presence of intrinsically disordered proteins (IDPs), which are devoid of stable secondary or tertiary structures under physiological conditions. While the flexible nature of IDPs precludes their study by crystallographic methods, IDP interactions with their cognate proteins, during which the IDPs often form their secondary structures, have been characterized by nuclear magnetic resonance (NMR) spectroscopy. In view of this, a complementary small-angle neutron scattering (SANS) technique has been developed for probing IDP conformations in larger protein complexes. As a model interaction system, α-synuclein (αSN) bound to an archaeal homotetrameric chaperone, PbaB, was analyzed. To selectively observe the SANS profile of αSN in the complex, the bacterially produced PbaB was fractionally (75%) deuterated using D₂O and deuterated glucose for contrast matching to approximately 100% D₂O solvent. By employing 75%-deuterated PbaB, the conformational changes of αSN upon capture by this tetrameric chaperone were successfully observed with minimal background scattering. Together with the present NMR data, the SANS data reveal that the PbaB tetramer grasps the N-terminal segments of αSN, disrupting the residual ordered structure in this region, while leaving the remaining regions flexible within a slightly reduced conformational space.