id: P31539
gene_symbol: HSP104
product_type: PROTEIN
status: IN_PROGRESS
taxon:
  id: NCBITaxon:559292
  label: Saccharomyces cerevisiae
description: >-
  HSP104 encodes a hexameric AAA+ ATPase disaggregase that is the founding
  member of the Hsp100/ClpB family. Its core molecular function is
  ATP-dependent protein disaggregation: it threads aggregated/misfolded
  polypeptides through its central pore in an ATP-driven process, solubilizing
  protein aggregates and enabling downstream refolding by the Hsp70/Hsp40
  (Ssa1/Ydj1) chaperone system. HSP104 is essential for induced
  thermotolerance and is required for the propagation of yeast prions
  ([PSI+], [URE3], [PIN+]) by fragmenting prion fibrils into transmissible
  seeds. It also functions in stress granule disassembly during recovery from
  heat stress. HSP104 forms a homohexameric ring with two AAA ATPase domains
  (NBD1 and NBD2) per monomer, and substrate binding is regulated by
  nucleotide occupancy at NBD1. There is no direct mammalian ortholog;
  disaggregation in metazoans is performed by the Hsp70/Hsp40/Hsp110 system.
existing_annotations:
# ============================================================
# IBA annotations (phylogenetic inference via PANTHER/GO_Central)
# ============================================================
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      HSP104 is well-established to localize to the cytoplasm, confirmed by
      immunoelectron microscopy (PMID:10467108) and high-throughput GFP-tagging
      (PMID:14562095 via UniProt). The IBA annotation is consistent with
      multiple lines of direct experimental evidence.
    action: ACCEPT
    reason: >-
      HSP104 cytoplasmic localization is its primary site of action for protein
      disaggregation. Confirmed by IDA (PMID:10467108): "a small amount of
      Hsp104 was located in the cytoplasm and nucleus" and by HDA
      (PMID:22842922).
    supported_by:
      - reference_id: PMID:10467108
        supporting_text: >-
          At normal temperature (25 degrees C), a small amount of Hsp104 was
          located in the cytoplasm and nucleus.

- term:
    id: GO:0016887
    label: ATP hydrolysis activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      HSP104 is a well-characterized ATPase with two AAA-type nucleotide-binding
      domains per monomer. ATP hydrolysis is central to its disaggregase function.
      Extensive biochemical characterization (PMID:9624144, PMID:11782421,
      PMID:16135516) demonstrates robust ATPase activity.
    action: ACCEPT
    reason: >-
      ATP hydrolysis is a core enzymatic activity of HSP104, required for its
      protein disaggregation mechanism. Supported by multiple IDA and IMP
      annotations. PMID:16135516 directly demonstrates ATPase activity and its
      regulation by substrate binding.
    supported_by:
      - reference_id: PMID:16135516
        supporting_text: >-
          upon association with a polypeptide, a conformational change occurs
          within Hsp104 that strongly reduces the dynamics of nucleotide
          exchange and commits the bound polypeptide to ATP hydrolysis.

- term:
    id: GO:0042026
    label: protein refolding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      HSP104 participates in protein refolding, though it does so indirectly
      -- it solubilizes aggregated proteins and hands them off to Hsp70/Hsp40
      for actual refolding (PMID:9674429). The IBA annotation is reasonable
      as HSP104 is required for the overall refolding process.
    action: ACCEPT
    reason: >-
      While HSP104 itself does not refold proteins (that is done by Hsp70/40),
      it is an essential component of the refolding pathway by extracting
      substrates from aggregates. PMID:9674429 demonstrates that "in concert
      with Hsp40 and Hsp70, Hsp104 can reactivate proteins that have been
      denatured and allowed to aggregate." The annotation to the BP "protein
      refolding" is appropriate.
    supported_by:
      - reference_id: PMID:9674429
        supporting_text: >-
          in concert with Hsp40 and Hsp70, Hsp104 can reactivate proteins
          that have been denatured and allowed to aggregate, substrates
          refractory to the action of other chaperones.

- term:
    id: GO:0043335
    label: protein unfolding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      HSP104 unfolds/threads aggregated proteins through its central pore as
      part of its disaggregation mechanism (PMID:15128736, PMID:18312264).
      This is a core aspect of the disaggregation mechanism.
    action: ACCEPT
    reason: >-
      Protein unfolding is mechanistically integral to HSP104 disaggregase
      function. The threading mechanism requires unfolding substrates to pass
      through the narrow central pore of the hexamer. Supported by
      PMID:18312264 "Substrate threading through the central pore of the
      Hsp104 chaperone as a common mechanism for protein disaggregation."
    supported_by:
      - reference_id: PMID:7984243
        supporting_text: >-
          Hsp104 functions in a manner not previously described for other
          heat-shock proteins: it mediates the resolubilization of
          heat-inactivated luciferase from insoluble aggregates.

- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      HSP104 is active in the cytosol, consistent with its role in
      disaggregating cytosolic protein aggregates. Confirmed by multiple
      localization studies.
    action: ACCEPT
    reason: >-
      The cytosol is the primary compartment where HSP104 performs its
      disaggregation function. Consistent with IDA evidence at PMID:10467108
      and NAS at PMID:20850366.

- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      While HSP104 does bind unfolded/aggregated polypeptides in an
      ATP-dependent manner (PMID:16135516), this annotation understates its
      core molecular function. HSP104 is the canonical protein disaggregase;
      its binding of unfolded substrates is in service of the disaggregation
      mechanism, not passive chaperone holdase activity. GO:0140545
      "ATP-dependent protein disaggregase activity" is the more appropriate
      and specific term.
    action: MODIFY
    reason: >-
      GO:0051082 "unfolded protein binding" is too general for HSP104. The
      protein does not merely bind unfolded proteins; it actively threads
      them through its central pore in an ATP-dependent disaggregation
      reaction. GO:0140545 "ATP-dependent protein disaggregase activity"
      precisely describes HSP104's core molecular function. PMID:16135516
      shows ATP-regulated substrate binding, and PMID:7984243 established
      the disaggregation function. PMID:18312264 demonstrated the threading
      mechanism.
    proposed_replacement_terms:
      - id: GO:0140545
        label: ATP-dependent protein disaggregase activity
    supported_by:
      - reference_id: PMID:7984243
        supporting_text: >-
          Hsp104 functions in a manner not previously described for other
          heat-shock proteins: it mediates the resolubilization of
          heat-inactivated luciferase from insoluble aggregates.
      - reference_id: PMID:16135516
        supporting_text: >-
          the affinity of Hsp104 toward polypeptides is regulated by
          nucleotides. In the presence of ATP or
          adenosine-5' -O-(3-thiotriphosphate), the chaperone formed complexes
          with RCMLa, whereas no binding was observed in the presence of ADP.

- term:
    id: GO:0051087
    label: protein-folding chaperone binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      HSP104 interacts directly with Hsp70 (Ssa1) and Hsp40 (Ydj1)
      chaperones as part of its disaggregation system. Also interacts with
      co-chaperones CNS1, CPR7, and STI1 (PMID:11604493). The
      species-specific interaction with the Hsp70 middle domain is essential
      for disaggregation (PMID:21474779).
    action: ACCEPT
    reason: >-
      Chaperone binding is essential for HSP104 function. It requires
      cooperation with Hsp70/Hsp40 to disaggregate and refold substrates.
      PMID:9674429 directly demonstrates the physical and functional
      interaction.
    supported_by:
      - reference_id: PMID:9674429
        supporting_text: >-
          Hsp104 has a protein remodeling activity that acts on trapped,
          aggregated proteins and requires specific interactions with
          conventional chaperones to promote refolding of the intermediates
          it produces.
      - reference_id: PMID:21474779
        supporting_text: >-
          the interaction between Hsp70/DnaK and helix 2 of the middle
          domain of Hsp104/ClpB determines the specificity required for
          protein disaggregation both in vivo and in vitro, as well as for
          cellular thermotolerance.

- term:
    id: GO:0070370
    label: cellular heat acclimation
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      HSP104 is the defining gene for induced thermotolerance in yeast.
      Deletion mutants fail to acquire thermotolerance after mild heat
      pretreatment (PMID:2188365). This is the original and best-established
      phenotype.
    action: ACCEPT
    reason: >-
      Cellular heat acclimation (induced thermotolerance) is the core
      biological process for which HSP104 was originally identified.
      PMID:2188365: "when given a mild pre-heat treatment, the mutant cells
      did not acquire tolerance to heat, as did wild-type cells."
    supported_by:
      - reference_id: PMID:2188365
        supporting_text: >-
          when given a mild pre-heat treatment, the mutant cells did not
          acquire tolerance to heat, as did wild-type cells.

# ============================================================
# IEA annotations (electronic/automated)
# ============================================================
- term:
    id: GO:0000166
    label: nucleotide binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      HSP104 has two AAA ATPase domains (NBD1 and NBD2) that bind ATP and
      ADP. This IEA annotation from UniProt keyword mapping is correct but
      very general. More specific terms (ATP binding, ADP binding) are
      already annotated with experimental evidence.
    action: ACCEPT
    reason: >-
      While overly general, this is a valid parent term for the more specific
      ATP binding and ADP binding annotations. IEA annotations at broader
      levels that are consistent with experimental data are acceptable.

- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      HSP104 binds ATP at both NBD1 and NBD2. This is supported by extensive
      experimental evidence (PMID:11867765, PMID:16135516) and confirmed by
      IMP annotation. The IEA is consistent.
    action: ACCEPT
    reason: >-
      ATP binding is a core biochemical property of HSP104, confirmed by
      IMP evidence at PMID:11867765 and detailed kinetic analysis.

- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      HSP104 shuttles between cytoplasm and nucleus. Nuclear localization
      is confirmed by immunoelectron microscopy (PMID:10467108) and is
      enhanced under heat stress. IEA is consistent with IDA evidence.
    action: ACCEPT
    reason: >-
      Confirmed by IDA at PMID:10467108. UniProt subcellular location
      mapping is accurate here.

- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      Duplicate of IBA and IDA annotations for cytoplasm. The IEA from
      UniProt subcellular location is consistent with experimental evidence.
    action: ACCEPT
    reason: >-
      Consistent with IBA (GO_REF:0000033), IDA (PMID:10467108), and HDA
      (PMID:22842922) evidence for cytoplasmic localization.

- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      Cytosol annotation by ARBA machine learning. Consistent with IBA and
      NAS annotations for the same term.
    action: ACCEPT
    reason: >-
      Consistent with experimental and phylogenetic evidence.

- term:
    id: GO:0006457
    label: protein folding
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      ARBA annotation for protein folding. HSP104 participates in the
      refolding of aggregated proteins in cooperation with Hsp70/Hsp40.
      More precisely, HSP104 participates in protein refolding
      (GO:0042026) rather than de novo protein folding.
    action: MODIFY
    reason: >-
      HSP104 does not participate in de novo protein folding. It
      specifically disaggregates and enables refolding of already-aggregated
      proteins. GO:0042026 "protein refolding" is the more precise term,
      consistent with the IDA annotation at PMID:9674429.
    proposed_replacement_terms:
      - id: GO:0042026
        label: protein refolding

- term:
    id: GO:0016887
    label: ATP hydrolysis activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      IEA annotation for ATP hydrolysis activity from InterPro domain
      mapping. Fully consistent with IBA and IDA/IMP experimental evidence.
    action: ACCEPT
    reason: >-
      Consistent with IBA (GO_REF:0000033), IDA (PMID:16135516), and IMP
      (PMID:16135516, PMID:9674429) evidence.

- term:
    id: GO:0034605
    label: cellular response to heat
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      ARBA annotation for cellular response to heat. HSP104 is massively
      induced by heat shock and plays a critical role in thermotolerance.
      Consistent with IDA at PMID:24291094.
    action: ACCEPT
    reason: >-
      Consistent with direct experimental evidence (IDA at PMID:24291094)
      and the well-established role of HSP104 in heat stress response.

- term:
    id: GO:0042802
    label: identical protein binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      HSP104 forms a homohexamer, so identical protein binding is expected.
      Confirmed by cryoEM structure (PMID:20404203) and IPI evidence
      (PMID:20404203, PMID:21474779).
    action: ACCEPT
    reason: >-
      HSP104 homohexamerization is well established. Consistent with IPI
      evidence.

- term:
    id: GO:0043335
    label: protein unfolding
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      IEA annotation for protein unfolding by ARBA. Consistent with IBA
      and IMP (PMID:7984243) evidence.
    action: ACCEPT
    reason: >-
      Consistent with IBA and IMP experimental evidence for protein
      unfolding as part of the disaggregation mechanism.

- term:
    id: GO:0070013
    label: intracellular organelle lumen
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      ARBA annotation placing HSP104 in intracellular organelle lumen.
      HSP104 is primarily cytosolic/nuclear but has been implicated in ER
      protein folding (PMID:10931304). However, HSP104 itself is not known
      to reside within organelle lumens; the ER role is indirect, likely
      mediated from the cytosolic side.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      HSP104 is a cytosolic/nuclear protein. While it has been implicated
      in ER protein folding (PMID:10931304), this is likely an indirect
      effect from the cytosolic side. There is no evidence that HSP104
      resides within organelle lumens. This ARBA annotation appears to be
      an over-interpretation.

# ============================================================
# IPI annotations (physical interaction evidence)
# ============================================================
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16554755
  review:
    summary: >-
      High-throughput TAP-tag study identifying global protein complexes in
      yeast. HSP104 was found to interact with multiple proteins including
      BLM10, COG6, CPR6, ECM2, EGH1, FCY1, HRD1, LAM6, LYS4, SGF73,
      SRB5, VPS4. Many of these are likely nonspecific interactions from
      the high-throughput screen.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      "Protein binding" (GO:0005515) is uninformative per GO curation
      guidelines. The underlying interactions from this high-throughput
      TAP-tag study likely include both genuine and spurious interactions.
      More specific binding terms should be used where warranted.
    supported_by:
      - reference_id: PMID:16554755
        supporting_text: >-
          We used tandem affinity purification to process 4,562 different
          tagged proteins of the yeast Saccharomyces cerevisiae.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19536198
  review:
    summary: >-
      Another high-throughput chaperone interaction study (TAP-tag based)
      mapping all 63 yeast chaperones' interaction networks. Again yields
      many interaction partners for HSP104.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Same issue as above: "protein binding" is uninformative. While HSP104
      clearly binds many proteins as a chaperone/disaggregase, the generic
      GO:0005515 term does not capture the mechanistic nature of these
      interactions. More informative terms like "protein-folding chaperone
      binding" (GO:0051087) or "misfolded protein binding" (GO:0051787)
      would better capture the biology.
    supported_by:
      - reference_id: PMID:19536198
        supporting_text: >-
          Systematic analysis of physical TAP-tag based protein-protein
          interactions of all known 63 chaperones in Saccharomyces
          cerevisiae has been carried out.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:20850366
  review:
    summary: >-
      This study identified HSP104 as part of a chaperone cascade for
      tail-anchored (TA) protein targeting to the ER. The protein binding
      annotation with MDY2/Q12285 reflects the TRC complex interaction.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      While the interaction with the TRC complex is real and interesting,
      "protein binding" is uninformative. The specific biology (TRC complex
      membership) is already captured by GO:0072380.
    supported_by:
      - reference_id: PMID:20850366
        supporting_text: >-
          we reveal the composition of a conserved multiprotein TMD
          recognition complex (TRC) and show that distinct TRC subunits
          recognize the two types of TMD signals.

- term:
    id: GO:0042802
    label: identical protein binding
  evidence_type: IPI
  original_reference_id: PMID:20404203
  review:
    summary: >-
      CryoEM structure of the HSP104 hexamer confirms self-association.
      The hexameric ring structure is fundamental to HSP104 function.
    action: ACCEPT
    reason: >-
      HSP104 homohexamerization is a core structural property essential
      for its disaggregase function. The cryoEM structure (PMID:20404203)
      provides direct structural evidence for self-association. This is
      more informative than generic "protein binding."
    supported_by:
      - reference_id: PMID:20404203
        supporting_text: >-
          Hsp104 is a ring-forming AAA+ machine that recognizes both
          aggregated proteins and prion-fibrils as substrates and, together
          with the Hsp70 system, remodels substrates in an ATP-dependent
          manner.

- term:
    id: GO:0042802
    label: identical protein binding
  evidence_type: IPI
  original_reference_id: PMID:21474779
  review:
    summary: >-
      Species-specificity study using Hsp104/ClpB chimeras confirms
      self-interaction properties. HSP104 hexamerization is well supported.
    action: ACCEPT
    reason: >-
      Confirms HSP104 self-association. The study explicitly tests
      chimeric proteins in the context of disaggregation, showing that
      the middle domain determines specificity of interaction with Hsp70.

# ============================================================
# NAS annotations (non-traceable author statement)
# ============================================================
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: NAS
  original_reference_id: PMID:20850366
  review:
    summary: >-
      ComplexPortal annotation placing HSP104 in cytosol based on the TRC
      complex study. HSP104 cytosolic localization is well supported.
    action: ACCEPT
    reason: >-
      Consistent with IBA and IDA evidence. Cytosol is the primary
      functional compartment.

- term:
    id: GO:0006620
    label: post-translational protein targeting to endoplasmic reticulum membrane
  evidence_type: NAS
  original_reference_id: PMID:20850366
  review:
    summary: >-
      ComplexPortal annotation based on HSP104's role in the TRC complex
      for tail-anchored protein targeting. This is a secondary/moonlighting
      function, not the core disaggregase activity.
    action: KEEP_AS_NON_CORE
    reason: >-
      PMID:20850366 shows HSP104 is part of a chaperone cascade for TA
      protein targeting to the ER membrane. This is a legitimate but
      non-core function. The primary function of HSP104 is protein
      disaggregation during heat stress, not TA protein targeting.
    supported_by:
      - reference_id: PMID:20850366
        supporting_text: >-
          ER-bound TA proteins are sorted at the top of a TMD chaperone
          cascade that culminates with the formation of Get3-TA protein
          complexes, which are recruited to the ER membrane for insertion.

# ============================================================
# IDA annotations (direct assay)
# ============================================================
- term:
    id: GO:0034605
    label: cellular response to heat
  evidence_type: IDA
  original_reference_id: PMID:24291094
  review:
    summary: >-
      Study demonstrating HSP104/Hsp70-dependent protein disaggregation
      drives disassembly of heat stress granules and restoration of
      translation during recovery. Direct evidence for HSP104's role in
      the cellular heat response.
    action: ACCEPT
    reason: >-
      HSP104's role in heat stress response is its best-established
      biological function. PMID:24291094 provides direct evidence for
      HSP104 function in coordinating protein homeostasis and
      translational control during severe heat stress.
    supported_by:
      - reference_id: PMID:24291094
        supporting_text: >-
          heat-SG disassembly and restoration of translation activity
          during heat stress recovery is intimately linked to
          disaggregation of damaged proteins present in the mixed
          assemblies and requires Hsp104 and Hsp70 activity.

- term:
    id: GO:0016887
    label: ATP hydrolysis activity
  evidence_type: IDA
  original_reference_id: PMID:16135516
  review:
    summary: >-
      Direct biochemical demonstration of HSP104 ATPase activity and its
      regulation by substrate binding and nucleotide occupancy.
    action: ACCEPT
    reason: >-
      PMID:16135516 provides direct in vitro assay evidence for ATP
      hydrolysis by HSP104, including characterization of how substrate
      binding commits the protein to ATP hydrolysis.
    supported_by:
      - reference_id: PMID:16135516
        supporting_text: >-
          upon association with a polypeptide, a conformational change
          occurs within Hsp104 that strongly reduces the dynamics of
          nucleotide exchange and commits the bound polypeptide to ATP
          hydrolysis.

- term:
    id: GO:0016887
    label: ATP hydrolysis activity
  evidence_type: IMP
  original_reference_id: PMID:16135516
  review:
    summary: >-
      Mutant phenotype evidence for ATP hydrolysis. Walker A (K218T) and
      Walker B (E285Q, E687Q) mutations abolish or dramatically reduce
      ATPase activity and impair substrate binding and disaggregation.
    action: ACCEPT
    reason: >-
      Mutagenesis of key ATPase residues (K218T at NBD1, K620T at NBD2)
      demonstrates that ATP hydrolysis is required for HSP104 function.
      PMID:16135516 shows "When ATP binding to this domain was impaired
      by mutation, Hsp104 lost its ability to interact with RCMLa."
    supported_by:
      - reference_id: PMID:16135516
        supporting_text: >-
          When ATP binding to this domain was impaired by mutation, Hsp104
          lost its ability to interact with RCMLa.

- term:
    id: GO:0016887
    label: ATP hydrolysis activity
  evidence_type: IMP
  original_reference_id: PMID:9674429
  review:
    summary: >-
      Mutant phenotype evidence from the landmark Glover & Lindquist (1998)
      paper establishing the Hsp104/Hsp70/Hsp40 disaggregation system.
      ATP hydrolysis is required for disaggregation activity.
    action: ACCEPT
    reason: >-
      PMID:9674429 demonstrates that HSP104's protein remodeling activity
      is ATP-dependent and requires cooperation with Hsp70/Hsp40.
    supported_by:
      - reference_id: PMID:9674429
        supporting_text: >-
          Hsp104 has a protein remodeling activity that acts on trapped,
          aggregated proteins and requires specific interactions with
          conventional chaperones to promote refolding of the intermediates
          it produces.

- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: HDA
  original_reference_id: PMID:22842922
  review:
    summary: >-
      High-throughput microscopy study of GFP-tagged proteins under DNA
      replication stress. HSP104 localization to cytoplasm confirmed.
    action: ACCEPT
    reason: >-
      Consistent with all other cytoplasm annotations. High-throughput
      direct assay evidence supports cytoplasmic localization.
    supported_by:
      - reference_id: PMID:22842922
        supporting_text: >-
          Relocalization of proteins is a hallmark of the DNA damage
          response. We use high-throughput microscopic screening of the
          yeast GFP fusion collection

- term:
    id: GO:0006457
    label: protein folding
  evidence_type: IDA
  original_reference_id: PMID:9674429
  review:
    summary: >-
      PMID:9674429 demonstrates that HSP104 in concert with Hsp70/Hsp40
      can reactivate aggregated proteins. This is more precisely "protein
      refolding" (GO:0042026) rather than general protein folding, since
      HSP104 acts on previously aggregated substrates, not nascent chains.
    action: MODIFY
    reason: >-
      HSP104 does not participate in de novo protein folding. It
      specifically disaggregates and enables refolding of already-aggregated
      proteins. GO:0042026 "protein refolding" is the more precise term.
      PMID:9674429: "Hsp104 can reactivate proteins that have been denatured
      and allowed to aggregate, substrates refractory to the action of
      other chaperones."
    proposed_replacement_terms:
      - id: GO:0042026
        label: protein refolding
    supported_by:
      - reference_id: PMID:9674429
        supporting_text: >-
          Hsp104 can reactivate proteins that have been denatured and
          allowed to aggregate, substrates refractory to the action of
          other chaperones.

- term:
    id: GO:0034399
    label: nuclear periphery
  evidence_type: IDA
  original_reference_id: PMID:25817432
  review:
    summary: >-
      PMID:25817432 identifies the intranuclear quality control compartment
      (INQ) where HSP104 colocalizes with Cmr1 and misfolded proteins at
      the nuclear periphery in response to genotoxic stress.
    action: ACCEPT
    reason: >-
      PMID:25817432 provides direct evidence for HSP104 localization at
      the nuclear periphery as part of the INQ compartment, which
      sequesters misfolded proteins. This is consistent with HSP104's
      protein quality control function.
    supported_by:
      - reference_id: PMID:25817432
        supporting_text: >-
          Cmr1--together with Mrc1/Claspin, Pph3, the chaperonin
          containing TCP1 (CCT) and 25 other proteins--define a novel
          intranuclear quality control compartment (INQ) that sequesters
          misfolded, ubiquitylated and sumoylated proteins in response to
          genotoxic stress.

- term:
    id: GO:0035617
    label: stress granule disassembly
  evidence_type: IDA
  original_reference_id: PMID:24291094
  review:
    summary: >-
      PMID:24291094 demonstrates that HSP104 is required for stress granule
      disassembly during recovery from severe heat stress. Heat-SGs
      coassemble with protein aggregates, and their disassembly is coupled
      to Hsp104-dependent protein disaggregation.
    action: ACCEPT
    reason: >-
      This is a well-supported secondary function of HSP104. Stress granule
      disassembly is mechanistically linked to its core disaggregase
      activity. PMID:24291094 shows "heat-SG disassembly... requires
      Hsp104 and Hsp70 activity."
    supported_by:
      - reference_id: PMID:24291094
        supporting_text: >-
          heat-SG disassembly and restoration of translation activity
          during heat stress recovery is intimately linked to
          disaggregation of damaged proteins present in the mixed
          assemblies and requires Hsp104 and Hsp70 activity.

- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: IMP
  original_reference_id: PMID:11867765
  review:
    summary: >-
      Mutagenesis study of the AAA sensor-2 motif in NBD2. R826M mutation
      decreases ATP and ADP affinity at NBD2, confirming nucleotide binding
      properties. Fluorescence probe (Y819W) directly measures ATP/ADP
      binding at NBD2.
    action: ACCEPT
    reason: >-
      PMID:11867765 provides direct evidence for ATP binding through
      mutagenesis of the sensor-2 motif, confirming the importance of
      NBD2 nucleotide binding for HSP104 function.
    supported_by:
      - reference_id: PMID:11867765
        supporting_text: >-
          The fluorescence of this tryptophan changes in response to ATP
          and ADP binding, allowing the K(d) and Hill coefficient to be
          determined for each nucleotide.

- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IDA
  original_reference_id: PMID:10467108
  review:
    summary: >-
      Immunoelectron microscopy demonstrating HSP104 presence in the
      nucleus. Nuclear accumulation is enhanced by heat shock.
    action: ACCEPT
    reason: >-
      Direct immunoEM evidence for nuclear localization. PMID:10467108:
      "a small amount of Hsp104 was located in the cytoplasm and nucleus."
      This is consistent with HSP104's role in nuclear protein quality
      control (INQ compartment).
    supported_by:
      - reference_id: PMID:10467108
        supporting_text: >-
          At normal temperature (25 degrees C), a small amount of Hsp104
          was located in the cytoplasm and nucleus.

- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IDA
  original_reference_id: PMID:10467108
  review:
    summary: >-
      Same immunoelectron microscopy study confirming cytoplasmic
      localization. HSP104 concentrates around protein aggregates in the
      cytoplasm during heat shock.
    action: ACCEPT
    reason: >-
      Direct evidence. PMID:10467108: "Hsp104 increased around the
      aggregates with increasing time of the mild heat-shock treatment."
    supported_by:
      - reference_id: PMID:10467108
        supporting_text: >-
          On exposure to mild heat-shock at 40 degrees C, protein
          aggregates appeared in the cytoplasm and nucleus, and Hsp104
          increased around the aggregates with increasing time of the
          mild heat-shock treatment.

- term:
    id: GO:0005991
    label: trehalose metabolic process
  evidence_type: IMP
  original_reference_id: PMID:9797333
  review:
    summary: >-
      PMID:9797333 shows that HSP104 disruption affects trehalose
      metabolism: activities of trehalose-synthesizing and -hydrolyzing
      enzymes are reduced in hsp104 mutants during heat shock. However,
      this is likely an indirect effect of impaired protein quality
      control, not a direct role in trehalose metabolism.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The effect on trehalose metabolism is likely indirect. HSP104's
      disaggregase activity may be needed to maintain the functional
      integrity of trehalose metabolic enzymes during heat stress, rather
      than HSP104 directly participating in trehalose metabolism.
      PMID:9797333: "The activities of trehalose-synthesizing and
      -hydrolyzing enzymes are low in the HSP104 disruption mutant
      during heat shock." This is consistent with a general protein
      quality control defect rather than a direct metabolic role.
    supported_by:
      - reference_id: PMID:9797333
        supporting_text: >-
          The activities of trehalose-synthesizing and -hydrolyzing
          enzymes are low in the HSP104 disruption mutant during heat
          shock.

- term:
    id: GO:0034975
    label: protein folding in endoplasmic reticulum
  evidence_type: IMP
  original_reference_id: PMID:10931304
  review:
    summary: >-
      PMID:10931304 shows that HSP104 is required for conformational repair
      of heat-denatured proteins in the ER. However, HSP104 is a cytosolic
      protein and likely acts indirectly on ER protein folding, possibly
      through effects on the cytosolic face of the ER or through indirect
      signaling.
    action: KEEP_AS_NON_CORE
    reason: >-
      While the genetic evidence is clear that HSP104 affects ER protein
      folding after heat stress, the mechanism is indirect since HSP104
      is cytosolic. PMID:10931304: "not only ER chaperones but also the
      cytosolic Hsp104 chaperone is required for conformational repair
      events in the ER lumen." This is a non-core function and the
      mechanism may involve maintaining cytosolic factors needed for ER
      homeostasis.
    supported_by:
      - reference_id: PMID:10931304
        supporting_text: >-
          not only ER chaperones but also the cytosolic Hsp104 chaperone
          is required for conformational repair events in the ER lumen.

- term:
    id: GO:0043335
    label: protein unfolding
  evidence_type: IMP
  original_reference_id: PMID:7984243
  review:
    summary: >-
      The landmark Parsell et al. (1994) paper demonstrating that HSP104
      mediates resolubilization of heat-inactivated protein aggregates.
      The "protein unfolding" annotation captures the mechanical unfolding
      of aggregated polypeptides during the threading/disaggregation process.
    action: ACCEPT
    reason: >-
      PMID:7984243 establishes HSP104's unique protein disaggregation
      function, which mechanistically involves unfolding aggregated proteins.
      This is a core aspect of HSP104 function.
    supported_by:
      - reference_id: PMID:7984243
        supporting_text: >-
          Hsp104 functions in a manner not previously described for other
          heat-shock proteins: it mediates the resolubilization of
          heat-inactivated luciferase from insoluble aggregates.

- term:
    id: GO:0043531
    label: ADP binding
  evidence_type: IMP
  original_reference_id: PMID:11867765
  review:
    summary: >-
      PMID:11867765 uses a site-specific fluorescent probe (Y819W) to
      measure both ATP and ADP binding at NBD2, confirming ADP binding
      with defined affinity.
    action: ACCEPT
    reason: >-
      ADP binding at NBD2 is important for HSP104 hexamer stabilization
      and allosteric regulation. PMID:11867765 directly measures ADP
      binding affinity using fluorescence changes.
    supported_by:
      - reference_id: PMID:11867765
        supporting_text: >-
          The fluorescence of this tryptophan changes in response to ATP
          and ADP binding, allowing the K(d) and Hill coefficient to be
          determined for each nucleotide.

- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IDA
  original_reference_id: PMID:16135516
  review:
    summary: >-
      PMID:16135516 directly demonstrates ATP-dependent binding of HSP104
      to the permanently unfolded substrate RCMLa. While the substrate
      binding data is correct, the GO term "unfolded protein binding"
      understates the mechanistic specificity of HSP104. The core function
      is ATP-dependent protein disaggregation (GO:0140545), not passive
      unfolded protein binding.
    action: MODIFY
    reason: >-
      Same reasoning as for the IBA annotation of this term. HSP104 does
      not merely bind unfolded proteins; it uses ATP hydrolysis to actively
      thread and solubilize aggregated substrates. GO:0140545 "ATP-dependent
      protein disaggregase activity" is the correct and specific term.
      PMID:16135516: "the affinity of Hsp104 toward polypeptides is
      regulated by nucleotides... the occupation of the N-terminally
      located nucleotide-binding domain with ATP seems to be crucial for
      substrate interaction."
    proposed_replacement_terms:
      - id: GO:0140545
        label: ATP-dependent protein disaggregase activity
    supported_by:
      - reference_id: PMID:16135516
        supporting_text: >-
          the affinity of Hsp104 toward polypeptides is regulated by
          nucleotides. In the presence of ATP or
          adenosine-5' -O-(3-thiotriphosphate), the chaperone formed
          complexes with RCMLa, whereas no binding was observed in the
          presence of ADP.
      - reference_id: PMID:7984243
        supporting_text: >-
          Hsp104 functions in a manner not previously described for other
          heat-shock proteins: it mediates the resolubilization of
          heat-inactivated luciferase from insoluble aggregates.

- term:
    id: GO:0051087
    label: protein-folding chaperone binding
  evidence_type: IDA
  original_reference_id: PMID:9674429
  review:
    summary: >-
      PMID:9674429 demonstrates direct functional cooperation between
      HSP104 and Hsp70/Hsp40 chaperones. HSP104 requires these partner
      chaperones for effective disaggregation and refolding.
    action: ACCEPT
    reason: >-
      Physical and functional interaction with Hsp70 (Ssa1) and Hsp40
      (Ydj1) is essential for HSP104 disaggregase function. PMID:9674429
      is the definitive study establishing the Hsp104/Hsp70/Hsp40
      chaperone system.
    supported_by:
      - reference_id: PMID:9674429
        supporting_text: >-
          Hsp104 has a protein remodeling activity that acts on trapped,
          aggregated proteins and requires specific interactions with
          conventional chaperones to promote refolding of the intermediates
          it produces.

- term:
    id: GO:0070370
    label: cellular heat acclimation
  evidence_type: IMP
  original_reference_id: PMID:2188365
  review:
    summary: >-
      The foundational paper showing HSP104 is required for induced
      thermotolerance. hsp104 deletion mutants fail to acquire heat
      tolerance after mild preconditioning.
    action: ACCEPT
    reason: >-
      This is the original and defining functional study for HSP104.
      PMID:2188365: "when given a mild pre-heat treatment, the mutant
      cells did not acquire tolerance to heat, as did wild-type cells."
    supported_by:
      - reference_id: PMID:2188365
        supporting_text: >-
          when given a mild pre-heat treatment, the mutant cells did not
          acquire tolerance to heat, as did wild-type cells. Transformation
          with the wild-type gene rescued the defect of mutant cells.

- term:
    id: GO:0072380
    label: TRC complex
  evidence_type: IDA
  original_reference_id: PMID:20850366
  review:
    summary: >-
      PMID:20850366 identifies HSP104 as a component of the TMD recognition
      complex (TRC), involved in sorting tail-anchored proteins for ER
      membrane insertion. This is a secondary/moonlighting function for
      HSP104.
    action: KEEP_AS_NON_CORE
    reason: >-
      The TRC complex role is a legitimate but non-core function of HSP104.
      Its primary role is as a protein disaggregase. The TRC complex
      function represents a specialized use of HSP104's chaperone
      capabilities in TA protein biogenesis.
    supported_by:
      - reference_id: PMID:20850366
        supporting_text: >-
          we reveal the composition of a conserved multiprotein TMD
          recognition complex (TRC) and show that distinct TRC subunits
          recognize the two types of TMD signals.

# ============================================================
# NEW annotations (proposed additions)
# ============================================================
- term:
    id: GO:0140545
    label: ATP-dependent protein disaggregase activity
  evidence_type: IDA
  original_reference_id: PMID:7984243
  review:
    summary: >-
      HSP104 is the founding member of the ATP-dependent protein disaggregase
      class. PMID:7984243 first demonstrated that HSP104 resolubilizes
      heat-inactivated luciferase from insoluble aggregates. PMID:9674429
      showed this requires cooperation with Hsp70/Hsp40. PMID:18312264
      confirmed the substrate-threading mechanism. PMID:16135516 demonstrated
      ATP-dependent substrate binding. This is the single most important
      molecular function annotation for HSP104 and is currently missing
      from the GO annotation set.
    action: NEW
    reason: >-
      GO:0140545 "ATP-dependent protein disaggregase activity" is the
      definitive molecular function of HSP104. It is the canonical protein
      disaggregase and the term was essentially created to describe this
      class of enzyme activity. The current annotations include
      GO:0051082 (unfolded protein binding) which is too general, and
      GO:0016887 (ATP hydrolysis activity) which is a component activity,
      but the specific disaggregase term is conspicuously absent.
    additional_reference_ids:
      - PMID:9674429
      - PMID:18312264
      - PMID:16135516
    supported_by:
      - reference_id: PMID:7984243
        supporting_text: >-
          Hsp104 functions in a manner not previously described for other
          heat-shock proteins: it mediates the resolubilization of
          heat-inactivated luciferase from insoluble aggregates.
      - reference_id: PMID:9674429
        supporting_text: >-
          in concert with Hsp40 and Hsp70, Hsp104 can reactivate proteins
          that have been denatured and allowed to aggregate, substrates
          refractory to the action of other chaperones.
      - reference_id: PMID:16135516
        supporting_text: >-
          the affinity of Hsp104 toward polypeptides is regulated by
          nucleotides. In the presence of ATP or
          adenosine-5' -O-(3-thiotriphosphate), the chaperone formed
          complexes with RCMLa, whereas no binding was observed in the
          presence of ADP.

references:
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  findings: []
- id: GO_REF:0000044
  title: >-
    Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular
    Location vocabulary mapping, accompanied by conservative changes to GO
    terms applied by UniProt
  findings: []
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:2188365
  title: HSP104 required for induced thermotolerance.
  findings:
    - statement: HSP104 deletion mutants cannot acquire thermotolerance after mild heat pretreatment, establishing HSP104 as essential for induced thermotolerance.
      supporting_text: when given a mild pre-heat treatment, the mutant cells did not acquire tolerance to heat, as did wild-type cells.
- id: PMID:7984243
  title: Protein disaggregation mediated by heat-shock protein Hsp104.
  findings:
    - statement: >-
        HSP104 mediates resolubilization of heat-inactivated protein from
        insoluble aggregates, establishing the disaggregation function.
      supporting_text: >-
        Hsp104 functions in a manner not previously described for other
        heat-shock proteins: it mediates the resolubilization of
        heat-inactivated luciferase from insoluble aggregates.
- id: PMID:9674429
  title: >-
    Hsp104, Hsp70, and Hsp40: a novel chaperone system that rescues
    previously aggregated proteins.
  findings:
    - statement: HSP104 in concert with Hsp70 and Hsp40 can reactivate aggregated proteins via a protein remodeling activity requiring specific chaperone interactions.
      supporting_text: in concert with Hsp40 and Hsp70, Hsp104 can reactivate proteins that have been denatured and allowed to aggregate, substrates refractory to the action of other chaperones.
- id: PMID:9797333
  title: Evidence for the interplay between trehalose metabolism and Hsp104 in yeast.
  findings:
    - statement: HSP104 disruption affects trehalose metabolism during heat shock, likely through indirect effects on enzyme integrity.
      supporting_text: The activities of trehalose-synthesizing and -hydrolyzing enzymes are low in the HSP104 disruption mutant during heat shock.
- id: PMID:10467108
  title: >-
    Direct evidence for the intracellular localization of Hsp104 in
    Saccharomyces cerevisiae by immunoelectron microscopy.
  findings:
    - statement: ImmunoEM shows HSP104 in cytoplasm and nucleus, concentrating around protein aggregates during heat shock.
      supporting_text: At normal temperature (25 degrees C), a small amount of Hsp104 was located in the cytoplasm and nucleus.
- id: PMID:10931304
  title: >-
    Trehalose is required for conformational repair of heat-denatured proteins
    in the yeast endoplasmic reticulum but not for maintenance of membrane
    traffic functions after severe heat stress.
  findings:
    - statement: Cytosolic HSP104 is required for conformational repair of heat-denatured proteins in the ER, suggesting indirect role in ER protein quality control.
      supporting_text: not only ER chaperones but also the cytosolic Hsp104 chaperone is required for conformational repair events in the ER lumen.
- id: PMID:11867765
  title: >-
    Analysis of the AAA sensor-2 motif in the C-terminal ATPase domain of
    Hsp104 with a site-specific fluorescent probe of nucleotide binding.
  findings:
    - statement: Fluorescent probe (Y819W) directly measures ATP and ADP binding at NBD2; R826M sensor-2 mutation decreases nucleotide affinity and reveals interdomain communication.
      supporting_text: The fluorescence of this tryptophan changes in response to ATP and ADP binding, allowing the K(d) and Hill coefficient to be determined for each nucleotide.
- id: PMID:16135516
  title: >-
    Substrate binding to the molecular chaperone Hsp104 and its regulation
    by nucleotides.
  findings:
    - statement: ATP-dependent substrate binding demonstrated; ATP at NBD1 is crucial for polypeptide interaction, and substrate binding triggers conformational change committing to ATP hydrolysis.
      supporting_text: the affinity of Hsp104 toward polypeptides is regulated by nucleotides. In the presence of ATP or adenosine-5' -O-(3-thiotriphosphate), the chaperone formed complexes with RCMLa, whereas no binding was observed in the presence of ADP.
- id: PMID:16554755
  title: >-
    Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
  findings:
    - statement: >-
        High-throughput TAP-tag/MS study identifying HSP104 interactions
        with multiple yeast proteins.
      supporting_text: >-
        We used tandem affinity purification to process 4,562 different
        tagged proteins of the yeast Saccharomyces cerevisiae.
- id: PMID:19536198
  title: >-
    An atlas of chaperone-protein interactions in Saccharomyces cerevisiae:
    implications to protein folding pathways in the cell.
  findings:
    - statement: >-
        Systematic TAP-tag analysis of all 63 yeast chaperones, mapping
        HSP104 interaction network.
      supporting_text: >-
        Systematic analysis of physical TAP-tag based protein-protein
        interactions of all known 63 chaperones in Saccharomyces cerevisiae
        has been carried out.
- id: PMID:20404203
  title: >-
    CryoEM structure of Hsp104 and its mechanistic implication for protein
    disaggregation.
  findings:
    - statement: CryoEM structure confirms hexameric ring architecture with M-domain on the exterior, where it can interact with aggregated proteins.
      supporting_text: Hsp104 is a ring-forming AAA+ machine that recognizes both aggregated proteins and prion-fibrils as substrates and, together with the Hsp70 system, remodels substrates in an ATP-dependent manner.
- id: PMID:20850366
  title: >-
    A chaperone cascade sorts proteins for posttranslational membrane
    insertion into the endoplasmic reticulum.
  findings:
    - statement: HSP104 identified as part of the TRC complex for tail-anchored protein targeting to ER.
      supporting_text: we reveal the composition of a conserved multiprotein TMD recognition complex (TRC) and show that distinct TRC subunits recognize the two types of TMD signals.
- id: PMID:21474779
  title: >-
    Species-specific collaboration of heat shock proteins (Hsp) 70 and 100
    in thermotolerance and protein disaggregation.
  findings:
    - statement: Middle domain of HSP104 determines species-specific interaction with Hsp70, required for disaggregation and thermotolerance.
      supporting_text: the interaction between Hsp70/DnaK and helix 2 of the middle domain of Hsp104/ClpB determines the specificity required for protein disaggregation both in vivo and in vitro, as well as for cellular thermotolerance.
- id: PMID:22842922
  title: >-
    Dissecting DNA damage response pathways by analysing protein localization
    and abundance changes during DNA replication stress.
  findings:
    - statement: >-
        High-throughput microscopy confirms HSP104 cytoplasmic localization.
      supporting_text: >-
        Relocalization of proteins is a hallmark of the DNA damage
        response. We use high-throughput microscopic screening of the
        yeast GFP fusion collection
- id: PMID:24291094
  title: >-
    Coordination of translational control and protein homeostasis during
    severe heat stress.
  findings:
    - statement: HSP104 and Hsp70 are required for stress granule disassembly and restoration of translation during heat stress recovery.
      supporting_text: heat-SG disassembly and restoration of translation activity during heat stress recovery is intimately linked to disaggregation of damaged proteins present in the mixed assemblies and requires Hsp104 and Hsp70 activity.
- id: PMID:25817432
  title: >-
    Cmr1/WDR76 defines a nuclear genotoxic stress body linking genome
    integrity and protein quality control.
  findings:
    - statement: >-
        HSP104 localizes at the intranuclear quality control compartment
        (INQ) at the nuclear periphery.
      supporting_text: >-
        Cmr1--together with Mrc1/Claspin, Pph3, the chaperonin containing
        TCP1 (CCT) and 25 other proteins--define a novel intranuclear
        quality control compartment (INQ) that sequesters misfolded,
        ubiquitylated and sumoylated proteins in response to genotoxic
        stress.
- id: PMID:18312264
  title: >-
    Substrate threading through the central pore of the Hsp104 chaperone as
    a common mechanism for protein disaggregation and prion propagation.
  findings:
    - statement: >-
        Substrate threading through HSP104's central pore is the mechanism
        for both protein disaggregation and prion propagation.
      supporting_text: >-
        HAP variants that harbour a reduced threading activity were
        affected in both protein disaggregation and prion propagation,
        demonstrating that substrate threading represents the common
        mechanism for the processing of both substrate classes.

core_functions:
  - molecular_function:
      id: GO:0140545
      label: ATP-dependent protein disaggregase activity
    directly_involved_in:
      - id: GO:0042026
        label: protein refolding
      - id: GO:0043335
        label: protein unfolding
      - id: GO:0070370
        label: cellular heat acclimation
    locations:
      - id: GO:0005829
        label: cytosol
    description: >-
      The defining molecular function of HSP104. It threads aggregated
      polypeptides through its central hexameric pore in an ATP-driven
      process, solubilizing protein aggregates for subsequent refolding by
      Hsp70/Hsp40. HSP104 is essential for induced thermotolerance and
      mechanically unfolds aggregated polypeptides as part of disaggregation.
  - molecular_function:
      id: GO:0016887
      label: ATP hydrolysis activity
    description: >-
      ATP hydrolysis by two AAA ATPase domains (NBD1 and NBD2) per monomer
      powers the disaggregation mechanism. NBD1 has low affinity/high turnover;
      NBD2 has high affinity/slow hydrolysis.
  - molecular_function:
      id: GO:0051087
      label: protein-folding chaperone binding
    description: >-
      HSP104 physically and functionally cooperates with Hsp70/Hsp40
      chaperones, which are required for substrate delivery and downstream
      refolding.

proposed_new_terms: []

suggested_questions:
  - question: >-
      Should GO:0140545 "ATP-dependent protein disaggregase activity" be the
      primary MF annotation for all ClpB/Hsp104 family members, or should
      some retain GO:0051082?
  - question: >-
      Does HSP104's role in prion propagation warrant a specific annotation?
      There is no GO term for "prion fibril fragmentation" or similar.
  - question: >-
      Is the TRC complex (GO:0072380) membership a true moonlighting function
      or a misidentification in the high-throughput study?

suggested_experiments:
  - description: >-
      In vitro reconstitution assay measuring protein disaggregation rates
      with purified HSP104/Ssa1/Ydj1 to confirm GO:0140545 annotation
      directly.
  - description: >-
      Determine whether HSP104's role in ER protein folding (PMID:10931304)
      is truly indirect or if there is a direct mechanism, such as
      translocation through the ER membrane.