A Conceptual Framework for Integrating Cellular Protein Folding, Misfolding and Aggregation

Abstract

How proteins properly fold and maintain solubility at the risk of misfolding and aggregation in the cellular environments still remains largely unknown. Aggregation has been traditionally treated as a consequence of protein folding (or misfolding). Notably, however, aggregation can be generally inhibited by affecting the intermolecular interactions leading to aggregation, independently of protein folding and conformation. We here point out that rigorous distinction between protein folding and aggregation as two independent processes is necessary to reconcile and underlie all observations regarding the combined cellular protein folding and aggregation. So far, the direct attractive interactions (e.g., hydrophobic interactions) between cellular macromolecules including chaperones and interacting polypeptides have been widely believed to mainly stabilize polypeptides against aggregation. However, the intermolecular repulsions by large excluded volume and surface charges of cellular macromolecules can play a key role in stabilizing their physically connected polypeptides against aggregation, irrespective of the connection types and induced conformational changes, underlying the generic intrinsic chaperone activity of cellular macromolecules. Such rigorous distinction and intermolecular repulsive force-driven aggregation inhibition by cellular macromolecules could give new insights into understanding the complex cellular protein landscapes that remain uncharted.

Keywords: aggregation; chaperones; excluded volume; intermolecular repulsions; misfolding; protein folding; surface charges.

Figure 1

Independency between protein folding and aggregation in the chamber of GroEL/ES. A client protein in the chamber of GroEL/ES is completely protected from the self-aggregation by the encapsulation, independently of protein folding and client’s conformations. The encapsulation independently affects protein folding and aggregation. Orange and blue spheres represent unfolded and folded states, respectively.

Figure 2

A unifying model for integrating protein folding and aggregation. Protein folding and aggregation free energy landscapes are independent (see the text for detailed description). The two landscapes are overlapped with the aggregation-competent monomers (or common monomers). Due to their independency, the intrinsic and extrinsic factors independently affect them as indicated by arrows. F, U, and A represent folded, unfolded and aggregated states, respectively. This figure is adapted from [8].

Figure 3

Intermolecular repulsion-driven aggregation inhibition by cellular macromolecules. The intermolecular repulsions (red arrows) by large excluded volume and surface charges of cellular macromolecules (green spheres) inhibit the aggregation of the physically connected polypeptides (orange sphere) regardless of the physical connection type, keeping the polypeptide in a folding-competent state. This figure is adapted from [4].

Figure 4

Macromolecular tethering as a hallmark of de novo protein folding environments. (A) Newly synthesized polypeptides are tethered to relatively gigantic ribosome with supernegative surface charges. (B) Approximately 30% of proteome are anchored at membranes. (C) More than 80% of proteome are multidomain proteins in which prefolded (cotranslationally folded) domains are tethered to unfolded domains. This figure is adapted from [24].

Figure 5

Conversion of a soluble protein into a potent chaperone. To demonstrate the intrinsic chaperone activity of cellular macromolecules, an artificial chaperone is constructed harboring a solubility-enhancing module (RS) and a substrate-recognition module (mTEV) that specifically bind to a short tag of 7 residues (L tag denoted by red bar). The aggregation-prone protein (EGFP-Hbx) with the L tag is the client protein of RS-mTEV. This figure is adapted from [17].