Using chirality to probe the conformational dynamics and assembly of intrinsically disordered amyloid proteins

Abstract

Intrinsically disordered protein (IDP) conformers occupy large regions of conformational space and display relatively flat energy surfaces. Amyloid-forming IDPs, unlike natively folded proteins, have folding trajectories that frequently involve movements up shallow energy gradients prior to the "downhill" folding leading to fibril formation. We suggest that structural perturbations caused by chiral inversions of amino acid side-chains may be especially valuable in elucidating these pathways of IDP folding. Chiral inversions are subtle in that they do not change side-chain size, flexibility, hydropathy, charge, or polarizability. They allow focus to be placed solely on the question of how changes in amino acid side-chain orientation, and the resultant alterations in peptide backbone structure, affect a peptide's conformational landscape (Ramachandran space). If specific inversions affect folding and assembly, then the sites involved likely are important in mediating these processes. We suggest here a "focused chiral mutant library" approach for the unbiased study of amyloid-forming IDPs.

Figure 1

Schematic energy landscape for protein folding and aggregation. The surface shows the multitude of conformations “funneling” towards the native state via intramolecular contact formation, or towards the formation of amyloid fibrils via intermolecular contacts. The landscape is represented by the free energy of the protein as a function of some reaction coordinate (planar slices through the 3D surface). Entropy is schematized as width within any particular sub-funnel. Unfolded conformers possess the highest free energies and the largest entropies (top of funnel). Folding occurs as conformers move within (i.e., explore) different regions of conformational space, experiencing progressive decreases in free energy and entropy until the native state is formed. Within the minimum of the native state, a multitude of substrates exist (protein “breathing”). Figure is Fig. 1.2 of Fichou, as adapted from Fig. 1 of Jahn.

Figure 2

Energy landscapes. (a) An intrinsically disordered peptide, CcdA C-terminus. Local free energy is represented spectrally, with red highest and blue lowest. (b) A natively folded protein, human nucleoside diphosphate kinase (NDPK). Figure adapted from Fig. 2 of Burger et al..