Protein–Protein Interactions in the Molecular Chaperone Network

Abstract

Molecular chaperones play a central role in protein homeostasis (a.k.a. proteostasis) by balancing protein folding, quality control, and turnover. To perform these diverse tasks, chaperones need the malleability to bind nearly any "client" protein and the fidelity to detect when it is misfolded. Remarkably, these activities are carried out by only ∼180 dedicated chaperones in humans. How do a relatively small number of chaperones maintain cellular and organismal proteostasis for an entire proteome? Furthermore, once a chaperone binds a client, how does it "decide" what to do with it? One clue comes from observations that individual chaperones engage in protein-protein interactions (PPIs)-both with each other and with their clients. These physical links coordinate multiple chaperones into organized, functional complexes and facilitate the "handoff" of clients between them. PPIs also link chaperones and their clients to other cellular pathways, such as those that mediate trafficking (e.g., cytoskeleton) and degradation (e.g., proteasome). The PPIs of the chaperone network have a wide range of affinity values (nanomolar to micromolar) and involve many distinct types of domain modules, such as J domains, zinc fingers, and tetratricopeptide repeats. Many of these motifs have the same binding surfaces on shared partners, such that members of one chaperone class often compete for the same interactions. Somehow, this collection of PPIs draws together chaperone families and creates multiprotein subnetworks that are able to make the "decisions" of protein quality control. The key to understanding chaperone-mediated proteostasis might be to understand how PPIs are regulated. This Account will discuss the efforts of our group and others to map, measure, and chemically perturb the PPIs within the molecular chaperone network. Structural biology methods, including X-ray crystallography, NMR spectroscopy, and electron microscopy, have all played important roles in visualizing the chaperone PPIs. Guided by these efforts and -omics approaches to measure PPIs, new advances in high-throughput chemical screening that are specially designed to account for the challenges of this system have emerged. Indeed, chemical biology has played a particularly important role in this effort, as molecules that either promote or inhibit specific PPIs have proven to be invaluable research probes in cells and animals. In addition, these molecules have provided leads for the potential treatment of protein misfolding diseases. One of the major products of this research field has been the identification of putative PPI drug targets within the chaperone network, which might be used to change chaperone "decisions" and rebalance proteostasis.

Multiple functionalities of molecular chaperones revealed through systematic mapping of their interaction networks

“…For example, it is estimated that CCos mediate the folding of about 62% of the total yeast proteins (31). These client-CCo interactions have a broad range of affinities and typically involve protein complexes of varying protomer number with diverse contact surface sizes (32). Given the varied biochemical nature of chaperone interactions, it is critical to choose the optimal experimental method to decipher these transient spatiotemporal events.…”

Co-expressing GroEL–GroES, Ssa1–Sis1 and Bip–PDI chaperones for enhanced intracellular production and partial-wall breaking improved stability of porcine growth hormone

“…Proteins must be strictly checked before transported to ensure their correct folding [7]. The molecular chaperone is a class of molecules that play an important role in protein translation, transport, folding and modification [8]. Pichia pastoris Hsp40 family members have many ways to identify and delivery misfolded proteins [9].…”

Differentiation drives widespread rewiring of the neural stem cell chaperone network

“…The complex proteostasis network (PN) maintaining the proteome consists of different molecular chaperones and clearance pathways. These contribute distinctly to cellular proteostasis (Freilich et al, 2018) but together determine polypeptide fate throughout the life of a protein (Jayaraj et al, 2019; Sala et al, 2017). How the distinct PN components recognize a misfolded protein and decide whether to refold, degrade or sequester it into an inclusion is poorly understood; particularly in stem cells and other highly specialized cell types.…”