Under-folded proteins: Conformational ensembles and their roles in protein folding, function, and pathogenesis

Abstract

For decades, protein function was intimately linked to the presence of a unique, aperiodic crystal-like structure in a functional protein. The two only places for conformational ensembles of under-folded (or partially folded) protein forms in this picture were either the end points of the protein denaturation processes or transiently populated folding intermediates. Recent years witnessed dramatic change in this perception and conformational ensembles, which the under-folded proteins are, have moved from the shadow. Accumulated to date data suggest that a protein can exist in at least three global forms-functional and folded, functional and intrinsically disordered (nonfolded), and nonfunctional and misfolded/aggregated. Under-folded protein states are crucial for each of these forms, serving as important folding intermediates of ordered proteins, or as functional states of intrinsically disordered proteins (IDPs) and IDP regions (IDPRs), or as pathology triggers of misfolded proteins. Based on these observations, conformational ensembles of under-folded proteins can be classified as transient (folding and misfolding intermediates) and permanent (IDPs and stable misfolded proteins). Permanently under-folded proteins can further be split into intentionally designed (IDPs and IDPRs) and unintentionally designed (misfolded proteins). Although intrinsic flexibility, dynamics, and pliability are crucial for all under-folded proteins, the different categories of under-foldedness are differently encoded in protein amino acid sequences.

Keywords: conformational ensemble; intrinsically disordered protein; protein folding; protein misfolding.

Figure 1

Fate of a newly synthesized polypeptide chain in a cell.

Figure 2

Diversity of conformational ensembles of under‐folded proteins.

Figure 3

An oversimplified representation of a protein folding landscape.

Figure 4

Fuzziness of protein structures and complexes. A: Fuzzy structure of a hybrid protein (p53 tetramer) that contains structured DNA‐binding and tetramerization domains (gray space‐filling models) and a disordered transactivator domain (shown as an ensemble of 20 conformations in different colors for each molecule in the tetramer). Figure is modified from Ref. 253 with permission. B: The NMR structure of a fuzzy complex between the cyclin‐dependent kinase inhibitor Sic1 [depicted as a ribbon with color‐coding from cyan (N‐terminus) to magenta (C‐terminus)] and the ubiquitin ligase Cdc4 (depicted as space‐filling gray model). At any given moment, only one out of the nine phosphorylated sites of Sic1 interacts with a single binding site in Cdc4, generating a highly dynamic conformational ensemble of a complex described within the frames of the “polyelectrostatic” model.254, 255 C. Fuzzy complex of the negative regulatory domain (NRD) of p53 with dimeric S100B(ββ). According to the extensive all‐atom explicit solvent simulations, NRD of p53 remains highly dynamic in the S100B(ββ)‐bound state.256

Figure 5

An oversimplified schematic representation of protein self‐association process. Formation of multiple association‐prone monomeric forms generates multiple aggregation pathways. There are three major products of the aggregation reaction–amorphous aggregates (bottom pathway), morphologically different soluble oligomers (second and third from the top pathways), and morphologically different amyloid fibrils (two bottom pathways). Two types of soluble oligomers (spheroidal and annular) and two morphologically different amyloid fibrils are shown. Changes in color reflect potential structural changes within a monomer taking place at each elementary step. In reality, the picture is much more complex and much more species can be observed. Interconversions between various species at different pathways are also possible. Figure is adopted, with permission, from Ref. 246.