Hsp90 mutants with distinct defects provide novel insights into cochaperone regulation of the folding cycle

Ordered ATP hydrolysis in the Hsp90 chaperone is regulated by Aha1 and a conserved post-translational modification

Hsp90 is a dimeric molecular chaperone that is important for the folding, stabilization, activation, and maturation of hundreds of protein substrates called "clients" in cells. Dozens of co-chaperones and hundreds of post-translational modifications (PTMs) regulate the ATP-dependent client activation cycle. The Aha1 co-chaperone is the most potent stimulator of the ATPase cycle of Hsp90 and phosphorylation of threonine 22 in Hsp90 can regulate the recruitment of Aha1 in cells. We report here that phosphorylation of threonine 22 regulates specific aspects of Aha1 function after recruitment occurs. The phosphomimetic substitution, T22E, neutralizes the action of the Aha1 NxNNWHW motif. Moreover, this substitution can exert this effect from only one protomer of the Hsp90 dimer. This work sheds light on how asymmetric modifications in the Hsp90 dimer can functionalize individual protomers and fine-tune the Hsp90 cycle.

Hsp90 and cochaperones have two genetically distinct roles in regulating eEF2 function

Protein homeostasis relies on the accurate translation and folding of newly synthesized proteins. Eukaryotic elongation factor 2 (eEF2) promotes GTP-dependent translocation of the ribosome during translation. eEF2 folding was recently shown to be dependent on Hsp90 as well as the cochaperones Hgh1, Cns1, and Cpr7. We examined the requirement for Hsp90 and cochaperones more closely and found that Hsp90 and cochaperones have two distinct roles in regulating eEF2 function. Yeast expressing one group of Hsp90 mutations or one group of cochaperone mutations had reduced steady-state levels of eEF2. The growth of Hsp90 mutants that affected eEF2 accumulation was also negatively affected by deletion of the gene encoding Hgh1. Further, mutations in yeast eEF2 that mimic disease-associated mutations in human eEF2 were negatively impacted by loss of Hgh1 and growth of one mutant was partially rescued by overexpression of Hgh1. In contrast, yeast expressing different groups of Hsp90 mutations or a different cochaperone mutation had altered sensitivity to diphtheria toxin, which is dictated by a unique posttranslational modification on eEF2. Our results provide further evidence that Hsp90 contributes to proteostasis not just by assisting protein folding, but also by enabling accurate translation of newly synthesized proteins. In addition, these results provide further evidence that yeast Hsp90 mutants have distinct in vivo effects that correlate with defects in subsets of cochaperones.

Evolution of the conformational dynamics of the molecular chaperone Hsp90

Hsp90 is a molecular chaperone of central importance for protein homeostasis in the cytosol of eukaryotic cells, with key functional and structural traits conserved from yeast to man. During evolution, Hsp90 has gained additional functional importance, leading to an increased number of interacting co-chaperones and client proteins. Here, we show that the overall conformational transitions coupled to the ATPase cycle of Hsp90 are conserved from yeast to humans, but cycle timing as well as the dynamics are significantly altered. In contrast to yeast Hsp90, the human Hsp90 is characterized by broad ensembles of conformational states, irrespective of the absence or presence of ATP. The differences in the ATPase rate and conformational transitions between yeast and human Hsp90 are based on two residues in otherwise conserved structural elements that are involved in triggering structural changes in response to ATP binding. The exchange of these two mutations allows swapping of the ATPase rate and of the conformational transitions between human and yeast Hsp90. Our combined results show that Hsp90 evolved to a protein with increased conformational dynamics that populates ensembles of different states with strong preferences for the N-terminally open, client-accepting states.

Quantitative proteomic analysis reveals unique Hsp90 cycle-dependent client interactions

Hsp90 is an abundant and essential molecular chaperone that mediates the folding and activation of client proteins in a nucleotide-dependent cycle. Hsp90 inhibition directly or indirectly impacts the function of 10-15% of all proteins due to degradation of client proteins or indirect downstream effects. Due to its role in chaperoning oncogenic proteins, Hsp90 is an important drug target. However, compounds that occupy the ATP-binding pocket and broadly inhibit function have not achieved widespread use due to negative effects. More selective inhibitors are needed; however, it is unclear how to achieve selective inhibition. We conducted a quantitative proteomic analysis of soluble proteins in yeast strains expressing wild-type Hsp90 or mutants that disrupt different steps in the client folding pathway. Out of 2,482 proteins in our sample set (approximately 38% of yeast proteins), we observed statistically significant changes in abundance of 350 (14%) of those proteins (log2 fold change ≥ 1.5). Of these, 257/350 (∼73%) with the strongest differences in abundance were previously connected to Hsp90 function. Principal component analysis of the entire dataset revealed that the effects of the mutants could be separated into 3 primary clusters. As evidence that Hsp90 mutants affect different pools of clients, simultaneous co-expression of 2 mutants in different clusters restored wild-type growth. Our data suggest that the ability of Hsp90 to sample a wide range of conformations allows the chaperone to mediate folding of a broad array of clients and that disruption of conformational flexibility results in client defects dependent on those states.

Insights into Hsp90 mechanism and in vivo functions learned from studies in the yeast, Saccharomyces cerevisiae

The molecular chaperone Hsp90 (Heat shock protein, 90 kDa) is an abundant and essential cytosolic protein required for the stability and/or folding of hundreds of client proteins. Hsp90, along with helper cochaperone proteins, assists client protein folding in an ATP-dependent pathway. The laboratory of Susan Lindquist, in collaboration with other researchers, was the first to establish the yeast Saccharomyces cerevisiae as a model organism to study the functional interaction between Hsp90 and clients. Important insights from studies in her lab were that Hsp90 is essential, and that Hsp90 functions and cochaperone interactions are highly conserved between yeast and mammalian cells. Here, we describe key mechanistic insights into the Hsp90 folding cycle that were obtained using the yeast system. We highlight the early contributions of the laboratory of Susan Lindquist and extend our analysis into the broader use of the yeast system to analyze the understanding of the conformational cycle of Hsp90 and the impact of altered Hsp90 function on the proteome.

Ab initio protein structure prediction: the necessary presence of external force field as it is delivered by Hsp40 chaperone

BACKGROUND

The aqueous environment directs the protein folding process towards the generation of micelle-type structures, which results in the exposure of hydrophilic residues on the surface (polarity) and the concentration of hydrophobic residues in the center (hydrophobic core). Obtaining a structure without a hydrophobic core requires a different type of external force field than those generated by a water. The examples are membrane proteins, where the distribution of hydrophobicity is opposite to that of water-soluble proteins. Apart from these two extreme examples, the process of protein folding can be directed by chaperones, resulting in a structure devoid of a hydrophobic core.

RESULTS

The current work presents such example: DnaJ Hsp40 in complex with alkaline phosphatase PhoA-U (PDB ID-6PSI)-the client molecule. The availability of WT form of the folding protein-alkaline phosphatase (PDB ID-1EW8) enables a comparative analysis of the structures: at the stage of interaction with the chaperone and the final, folded structure of this biologically active protein. The fuzzy oil drop model in its modified FOD-M version was used in this analysis, taking into account the influence of an external force field, in this case coming from a chaperone.

CONCLUSIONS

The FOD-M model identifies the external force field introduced by chaperon influencing the folding proces. The identified specific external force field can be applied in Ab Initio protein structure prediction as the environmental conditioning the folding proces.