Molecular chaperones are nanomachines that catalytically unfold misfolded and alternatively folded proteins

Abstract

By virtue of their general ability to bind (hold) translocating or unfolding polypeptides otherwise doomed to aggregate, molecular chaperones are commonly dubbed "holdases". Yet, chaperones also carry physiological functions that do not necessitate prevention of aggregation, such as altering the native states of proteins, as in the disassembly of SNARE complexes and clathrin coats. To carry such physiological functions, major members of the Hsp70, Hsp110, Hsp100, and Hsp60/CCT chaperone families act as catalytic unfolding enzymes or unfoldases that drive iterative cycles of protein binding, unfolding/pulling, and release. One unfoldase chaperone may thus successively convert many misfolded or alternatively folded polypeptide substrates into transiently unfolded intermediates, which, once released, can spontaneously refold into low-affinity native products. Whereas during stress, a large excess of non-catalytic chaperones in holding mode may optimally prevent protein aggregation, after the stress, catalytic disaggregases and unfoldases may act as nanomachines that use the energy of ATP hydrolysis to repair proteins with compromised conformations. Thus, holding and catalytic unfolding chaperones can act as primary cellular defenses against the formation of early misfolded and aggregated proteotoxic conformers in order to avert or retard the onset of degenerative protein conformational diseases.

Fig. 1

Folding of nascent and misfolded polypeptides by the cytosolic chaperone network. A newly synthesized polypeptide emerging from the eukaryotic ribosome (PDB:3O2Z) tunnel (red circle) encounters in a typical eukaryotic cell such as yeast, ribosome-associated chaperones that can apply an entropic pulling force to unfold misfolded secondary structures in the growing nascent polypeptide chain. Upon exposure of the nascent polypeptide to the crowded environment of cytosol it may expose hydrophobic residues leading to misfolding. The misfolded conformers may then become a substrate of Hsp70 (PDB:1KHO) system (Hsp70–Hsp40 and nucleotide exchange factor, PDB:1DKG), which by reiterative cycles of binding, ATP-fueled unfolding and spontaneous refolding, converts the misfolded polypeptide into a native protein (cycle I). In case of failure, the misfolded substrate can bind instead to holding chaperones such as Hsp90 or sHsps that may keep the substrate in a non-aggregated, folding competent state, which may be subsequently passed on to the unfolding machinery of Hsp70 system for refolding to the native state. Possible unfolding of misfolded substrate by sHsps, structure adapted from [157], is unclear and is shown as a question mark. The aggregated protein in the cytosol of metazoans can be reverted to the native state by the Hsp110–Hsp70 system (PDB:3C7N) and also by the Hsp100s (structure adapted from [158]) and Hsp70 system in yeasts and plants (cycle II). In case of failure, the misfolded polypeptide can bind instead the CCT chaperonin (PDB:4A13), where it will undergo cycles of binding, unfolding, and ATP-fueled release, leading to the native state (cycle III). The structures are from highly homologous chaperone orthologs from various organisms, because they are not all available from yeast

Fig. 2

Disaggregating and unfolding chaperones transiently increase the free energy of misfolded or alternatively folded substrates but not of natively folded products. The 3D mesh-plot shows a typical unfolded polypeptide with the highest free energy, which can spontaneously reach to lower free energy states, either by folding to the native conformation (right) or by misfolding to the aggregated state (left). When conditions are not favorable for native folding, the unfolded polypeptide may prefer undertaking the misfolding pathway to aggregation (green arrows). Native proteins under stress gaining free energy may partially unfold to a state from which it can readily seek a more stable misfolded state [3] and further aggregate (brown arrow) [2]. ATP-fueled unfoldase chaperones drive the substrate uphill the free energy barrier (red arrows) by converting stable aggregates and misfolded species into unfolded products with a higher free energy. From there, if conditions are favorable to the end product, the unfolded species can collapse to the stable native state