Protein folding, protein homeostasis, and cancer

AbstractIntrinsically disordered regions (IDRs) are protein sequences lacking fixed or ordered three-dimensional structures. Many IDRs are endowed with important molecular functions such as physical interactions, posttranslational modifications or solubility enhancement. We reveal that several biologically important IDRs can act as N-terminal fusion carriers to promote target protein folding or protein quality control, thereby enhancing protein expression. This nanny function has a reasonably strong correlation with high S/T/Q/N amino acid content in IDRs and it is tunable (e.g., via phosphorylation) to regulate protein homeostasis. We propose a hypothesis that “N-terminal intrinsic disorder facilitates abundance” (NIDFA) to explain how some yeast proteins use their N-terminal IDRs (N-IDRs) to generate high levels of protein product. These N-IDRs are versatile toolkits for functional divergence in signaling and evolution.SignificanceDisorder within an otherwise well-structured protein is mostly found in intrinsically disordered regions (IDRs). IDRs can provide many advantages to proteins, including: (1) mediating protein-protein or protein-peptide interactions by adopting different conformations; (2) facilitating protein regulation via diverse posttranslational modifications; and (3) regulating the half-lives of proteins that have been targeted for proteasomal degradation. Here, we report that several biologically important IDRs in S. cerevisiae can act as N-terminal fusion carriers to promote target protein folding or protein quality control, thereby enhancing protein expression. We demonstrate by genetic and bioinformatic analyses that this nanny function is well correlated with high content of serine, threonine, glutamine and asparagine in IDRs and is tunable (e.g., via phosphorylation) to regulate protein homeostasis.

Download Full-text

Pulse labeling reveals the tail end of protein folding by proteome profiling

10.1101/2021.03.28.437442 ◽

2021 ◽

Author(s):

Mang Zhu ◽

Erich R. Kuechler ◽

Nikolay Stoynov ◽

Joerg Gsponer ◽

Thibault Mayor

Keyword(s):

Mass Spectrometry ◽

Protein Folding ◽

Heat Stress ◽

Protein Complexes ◽

Protein Sequences ◽

Protein Homeostasis ◽

Native State ◽

Binding Motifs ◽

Specific Subset ◽

Β Sheet

SummaryAccurate and efficient folding of nascent protein sequences into their native state requires support from the protein homeostasis network. Herein we probed which newly translated proteins are less thermostable to infer which polypeptides require more time to fold within the proteome. Specifically, we determined which of these proteins were more susceptible to misfolding and aggregation under heat stress using pulse SILAC coupled mass spectrometry. These proteins are abundant, short, and highly structured. Notably these proteins display a tendency to form β-sheet structures, a configuration which typically requires more time for folding, and were enriched for Hsp70/Ssb and TRiC/CCT binding motifs, suggesting a higher demand for chaperone-assisted folding. These polypeptides were also more often components of stable protein complexes in comparison to other proteins. All evidence combined suggests that a specific subset of newly translated proteins requires more time following synthesis to reach a thermostable native state in the cell.

Download Full-text

Hsp90 Chaperones Bluetongue Virus Proteins and Prevents Proteasomal Degradation

Journal of Virology ◽

10.1128/jvi.00898-19 ◽

2019 ◽

Vol 93 (20) ◽

Cited By ~ 2

Author(s):

Bjorn-Patrick Mohl ◽

Polly Roy

Keyword(s):

Protein Folding ◽

Heat Shock ◽

Heat Shock Protein ◽

Virus Replication ◽

Heat Shock Protein 70 ◽

Bluetongue Virus ◽

Proteasomal Degradation ◽

Viral Proteins ◽

Protein Homeostasis ◽

Virus Proteins

ABSTRACT The molecular chaperone machinery is important for the maintenance of protein homeostasis within the cells. The principle activities of the chaperone machinery are to facilitate protein folding and organize conformationally dynamic client proteins. Prominent among the members of the chaperone family are heat shock protein 70 (Hsp70) and 90 (Hsp90). Like cellular proteins, viral proteins depend upon molecular chaperones to mediate their stabilization and folding. Bluetongue virus (BTV), which is a model system for the Reoviridae family, is a nonenveloped arbovirus that causes hemorrhagic disease in ruminants. This constitutes a significant burden upon animals of commercial significance, such as sheep and cattle. Here, for the first time, we examined the role of chaperone proteins in the viral lifecycle of BTV. Using a combination of molecular, biochemical, and microscopic techniques, we examined the function of Hsp90 and its relevance to BTV replication. We demonstrate that Hsp70, the chaperone that is commonly usurped by viral proteins, does not influence virus replication, while Hsp90 activity is important for virus replication by stabilizing BTV proteins and preventing their degradation via the ubiquitin-proteasome pathway. To our knowledge this is the first report showing the involvement of Hsp90 as a modulator of BTV infection. IMPORTANCE Protein chaperones are instrumental for maintaining protein homeostasis, enabling correct protein folding and organization; prominent members include heat shock proteins 70 and 90. Virus infections place a large burden on this homeostasis. Identifying and understanding the underlying mechanisms that facilitate Bluetongue virus replication and spread through the usurpation of host factors is of primary importance for the development of intervention strategies. Our data identify and show that heat shock protein 90, but not heat shock protein 70, stabilizes bluetongue virus proteins, safeguarding them from proteasomal degradation.

Download Full-text

The cryo-EM structure of the chloroplast ClpP complex reveals an interaction with the co-chaperonin complex that inhibits ClpP proteolytic activity

10.1101/2021.07.26.453741 ◽

2021 ◽

Author(s):

Ning Wang ◽

Yifan Wang ◽

Qian Zhao ◽

Xiang Zhang ◽

Chao Peng ◽

...

Keyword(s):

Quality Control ◽

Protein Folding ◽

Control System ◽

Proteolytic Activity ◽

Protease Activity ◽

Protein Quality ◽

Protein Homeostasis ◽

Clp Protease ◽

Protein Quality Control System

Protein homeostasis in plastids is strategically regulated by the protein quality control system involving multiple chaperones and proteases, among them the Clp protease. We determined the structure of the chloroplast ClpP complex from Chlamydomonas reinhardtiiby cryo-EM. ClpP contains two heptameric catalytic rings without any symmetry. The top ring contains one ClpR6, three ClpP4 and three ClpP5 subunits while the bottom ring is composed of three ClpP1C subunits and one each of the ClpR1-4 subunits. ClpR3, ClpR4 and ClpT4 subunits connect the two rings and stabilize the complex. The chloroplast Cpn11/20/23 co-chaperonin, a co-factor of Cpn60, forms a cap on the top of ClpP by protruding mobile loops into hydrophobic clefts at the surface of the top ring. The co-chaperonin repressed ClpP proteolytic activity in vitro. By regulating Cpn60 chaperone and ClpP protease activity, the co-chaperonin may play a role in coordinating protein folding and degradation in the chloroplast.

Download Full-text

The Hsp70–Hsp90 go-between Hop/Stip1/Sti1 is a proteostatic switch and may be a drug target in cancer and neurodegeneration

Cellular and Molecular Life Sciences ◽

10.1007/s00018-021-03962-z ◽

2021 ◽

Author(s):

Kaushik Bhattacharya ◽

Didier Picard

Keyword(s):

Protein Folding ◽

Human Brain ◽

Molecular Chaperone ◽

Drug Target ◽

Ternary Complex ◽

Eukaryotic Cells ◽

Small Subset ◽

Binary Complex ◽

Protein Homeostasis ◽

Chaperone Complex

AbstractThe Hsp70 and Hsp90 molecular chaperone systems are critical regulators of protein homeostasis (proteostasis) in eukaryotes under normal and stressed conditions. The Hsp70 and Hsp90 systems physically and functionally interact to ensure cellular proteostasis. Co-chaperones interact with Hsp70 and Hsp90 to regulate and to promote their molecular chaperone functions. Mammalian Hop, also called Stip1, and its budding yeast ortholog Sti1 are eukaryote-specific co-chaperones, which have been thought to be essential for substrate (“client”) transfer from Hsp70 to Hsp90. Substrate transfer is facilitated by the ability of Hop to interact simultaneously with Hsp70 and Hsp90 as part of a ternary complex. Intriguingly, in prokaryotes, which lack a Hop ortholog, the Hsp70 and Hsp90 orthologs interact directly. Recent evidence shows that eukaryotic Hsp70 and Hsp90 can also form a prokaryote-like binary chaperone complex in the absence of Hop, and that this binary complex displays enhanced protein folding and anti-aggregation activities. The canonical Hsp70-Hop-Hsp90 ternary chaperone complex is essential for optimal maturation and stability of a small subset of clients, including the glucocorticoid receptor, the tyrosine kinase v-Src, and the 26S/30S proteasome. Whereas many cancers have increased levels of Hop, the levels of Hop decrease in the aging human brain. Since Hop is not essential in all eukaryotic cells and organisms, tuning Hop levels or activity might be beneficial for the treatment of cancer and neurodegeneration.

Download Full-text

Widespread remodeling of proteome solubility in response to different protein homeostasis stresses

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1912897117 ◽

2020 ◽

Vol 117 (5) ◽

pp. 2422-2431 ◽

Cited By ~ 5

Author(s):

Xiaojing Sui ◽

Douglas E. V. Pires ◽

Angelique R. Ormsby ◽

Dezerae Cox ◽

Shuai Nie ◽

...

Keyword(s):

Oxidative Stress ◽

Endoplasmic Reticulum ◽

Protein Folding ◽

Protein Complexes ◽

Specific Pattern ◽

Protein Homeostasis ◽

Cellular Mechanisms ◽

Neuro2a Cell ◽

Protein Deposits ◽

Almost All

The accumulation of protein deposits in neurodegenerative diseases has been hypothesized to depend on a metastable subproteome vulnerable to aggregation. To investigate this phenomenon and the mechanisms that regulate it, we measured the solubility of the proteome in the mouse Neuro2a cell line under six different protein homeostasis stresses: 1) Huntington’s disease proteotoxicity, 2) Hsp70, 3) Hsp90, 4) proteasome, 5) endoplasmic reticulum (ER)-mediated folding inhibition, and 6) oxidative stress. Overall, we found that about one-fifth of the proteome changed solubility with almost all of the increases in insolubility were counteracted by increases in solubility of other proteins. Each stress directed a highly specific pattern of change, which reflected the remodeling of protein complexes involved in adaptation to perturbation, most notably, stress granule (SG) proteins, which responded differently to different stresses. These results indicate that the protein homeostasis system is organized in a modular manner and aggregation patterns were not correlated with protein folding stability (ΔG). Instead, distinct cellular mechanisms regulate assembly patterns of multiple classes of protein complexes under different stress conditions.

Download Full-text

Programmed trade-offs in protein folding networks

10.1101/2020.04.07.030056 ◽

2020 ◽

Author(s):

Sebastian Pechmann

Keyword(s):

Quality Control ◽

Protein Folding ◽

Protein Quality ◽

De Novo ◽

Protein Quality Control ◽

Cellular Protein ◽

Amino Acid Sequences ◽

Integrated Analysis ◽

Protein Homeostasis ◽

Trade Offs

Maintaining protein homeostasis, i.e. a folded and functional proteome, depends on the efficient allocation of cellular protein quality control resources. Decline and dysregulation of protein homeostasis are directly associated to conditions of aging and neurodegeneration. Molecular chaperones as specialized protein quality control enzymes form the core of protein homeostasis. However, how chaperones selectively interact with their substrate proteins thus allocate their overall limited capacity remains poorly understood. Here, I present an integrated analysis of sequence and structural determinants that define interactions of the Saccharomyces cerevisiae Hsp70 Ssb. Structural homologues that differentially interact with Ssb for de novo folding were found to systematically differ in complexity of their folding landscapes, selective use of nonoptimal codons, and presence of short discriminative sequences. All analyzed characteristics contributed to the prediction of Ssb interactions in highly complementary manner, highlighting pervasive trade-offs in chaperone-assisted protein folding landscapes. However, short discriminative sequences were found to contribute by far the strongest signal towards explaining Ssb interactions. This observation suggested that some chaperone interactions may be directly programmed in the amino acid sequences rather than responding to folding challenges, possibly for regulatory advantages.

Download Full-text

ATP emerged to induce protein folding, inhibit aggregation and increase stability

10.1101/739581 ◽

2019 ◽

Author(s):

Jian Kang ◽

Liangzhong Lim ◽

Jianxing Song

Keyword(s):

Protein Folding ◽

Small Molecules ◽

Origin Of Life ◽

Protein Homeostasis ◽

Nmr Characterization ◽

General Capacity ◽

The Origin Of Life ◽

First Time ◽

Control Protein

AbstractBy NMR characterization of effects of ATP and related molecules on the folding and dynamics of the ALS-causing C71G-PFN1 and nascent hSOD1, we reveal for the first time that ATP has a general capacity in inducing protein folding with the highest efficiency known so far. This capacity was further identified to result from triphosphate, a key intermediate in prebiotic chemistry, which, however, can severely trigger protein aggregation. Remarkably, by joining adenosine and triphosphate together, ATP integrates three abilities to simultaneously induce protein folding, inhibit aggregation and increase thermodynamic stability. Our study implies that the emergence of ATP might represent an irreplaceable step essential for the Origin of Life, and decrypts a principle for engineering small molecules with three functions to treat aggregation-associated ageing and diseases.One sentence summaryBy joining adenosine and triphosphate, ATP integrates three abilities to control protein homeostasis for the Origin of Life.

Download Full-text

Senescence inhibits the chaperone response to thermal stress

10.1101/2021.06.15.448532 ◽

2021 ◽

Author(s):

Jack Llewellyn ◽

Venkatesh Mallikarjun ◽

Ellen Appleton ◽

Maria Osipova ◽

Hamish TJ Gilbert ◽

...

Keyword(s):

Protein Folding ◽

Stress Response ◽

Heat Shock ◽

Protein Misfolding ◽

Replicative Senescence ◽

Protein A ◽

Human Mesenchymal Stem Cells ◽

Protein Homeostasis ◽

Time Resolved

Cells respond to stress by synthesising chaperone proteins that correct protein misfolding to maintain function. However, protein homeostasis is lost in ageing, leading to aggregates characteristic of protein- folding diseases. Whilst much is known about how these diseases progress, discovering what causes protein- folding to deteriorate could be key to their prevention. Here, we examined primary human mesenchymal stem cells (hMSCs), cultured to a point of replicative senescence and subjected to heat shock, as an in vitro model of the ageing stress response. We found through proteomic analysis that the maintenance of homeostasis deteriorated in senescent cells. Time-resolved analysis of factors regulating heat shock protein 70 kDa (HSPA1A) revealed a lack of capacities for protein turnover and translation to be key factors in limiting the stress response during senescence. A kinetic model predicted a consequence of these reduced capacities to be the accumulation of misfolded protein, a hypothesis supported by evidence of systematic changes to protein fold state. These results thus further our understanding of the underlying mechanistic links between ageing and loss of protein homeostasis.

Download Full-text

ATP induces protein folding, inhibits aggregation and antagonizes destabilization by effectively mediating water-protein-ion interactions, the heart of protein folding and aggregation

10.1101/2020.06.21.163758 ◽

2020 ◽

Author(s):

Jian Kang ◽

Liangzhong Lim ◽

Jianxing Song

Keyword(s):

Protein Folding ◽

Prebiotic Chemistry ◽

Specific Binding ◽

Protein Homeostasis ◽

Molar Ratios ◽

Ion Interactions ◽

Regulate Protein ◽

First Time ◽

Control Protein ◽

Liquid Liquid Phase Separation

AbstractMany, particularly β-dominant proteins, are prone to misfolding/aggregation in the crowded cells, a hallmark of ageing and neurodegenerative diseases including ALS. ATP provides energy to drive supramolecular machineries to control protein hemostasis in modern cells. Recently ATP was decoded to hydrotropically inhibit/dissolve liquid-liquid phase separation (LLPS) and aggregation/fibrillation at millimolar concentrations. We also found that by specific binding, ATP induces and subsequently dissolves LLPS, as well as inhibits fibrillation. Nevertheless, no report shows that ATP can directly induce protein folding. Here, by selecting two aggregation-prone ALS-causing proteins with the unfolded states, we successfully visualized the effects of ATP and 11 molecules with NMR directly on their folding and aggregation. The study reveals for the first time that ATP can induce folding at molar ratios of 2-8, the highest efficiency known so far. Intriguingly, this inducing-capacity comes from triphosphate, a key intermediate in prebiotic chemistry, which, however, also triggers aggregation. Most unexpectedly, upon joining with adenosine, the ability of triphosphate to trigger aggregation is shielded. Marvelously, ATP emerged to manifest three integrated abilities: to induce folding, inhibit aggregation and increase stability, that are absent in ATPP, AMP-PCP and AMP-PNP. Our study sheds the first light on previously-unknown roles of ATP in energy-independently controlling protein folding and aggregation by effectively mediating water-protein-ion interactions. Therefore, ATP might be not just irreplaceable for solving protein folding and aggregation problems simultaneously in primitive cells for Origin of Life, but also energy-independently operating in modern cells to regulate protein homeostasis fundamentally critical for physiology and pathology.

Download Full-text