LiteFold/DisProt huggingface dataset:
Protein: DP01787 (UniProt A0A1Z3GD05)
Region: residues 1	to 138
Annotation: disorder to order (Structural transition)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
We first recorded the fluorescence emission spectra of the proteins either in the presence or absence of increasing zinc concentrations (Fig. 9). As expected for Tyr-containing proteins, both ASR1 proteins exhibit a maximum close to 303 nm. Interestingly, the intensity of the emission peak is gradually quenched with increasing zinc concentration, reflecting a decrease in the solvent exposure of Tyr residues. This behavior is indicative of a zinc-induced gain of tertiary structure.
Protein: DP01787 (UniProt A0A1Z3GD05)
Region: residues 1	to 138
Annotation: zinc ion binding (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
We first recorded the fluorescence emission spectra of the proteins either in the presence or absence of increasing zinc concentrations (Fig. 9). As expected for Tyr-containing proteins, both ASR1 proteins exhibit a maximum close to 303 nm. Interestingly, the intensity of the emission peak is gradually quenched with increasing zinc concentration, reflecting a decrease in the solvent exposure of Tyr residues. This behavior is indicative of a zinc-induced gain of tertiary structure.
Protein: DP01787 (UniProt A0A1Z3GD05)
Region: residues 1	to 138
Annotation: zinc ion sequestering activity (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
We first recorded the fluorescence emission spectra of the proteins either in the presence or absence of increasing zinc concentrations (Fig. 9). As expected for Tyr-containing proteins, both ASR1 proteins exhibit a maximum close to 303 nm. Interestingly, the intensity of the emission peak is gradually quenched with increasing zinc concentration, reflecting a decrease in the solvent exposure of Tyr residues. This behavior is indicative of a zinc-induced gain of tertiary structure.
Protein: DP01788 (UniProt P98177)
Region: residues 82	to 91
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The residues outside the structured DNA binding domain (residues 100−180) all showed random coil chemical shifts and very narrow resonance lines resulting in severe resonance overlap in some spectral regions. Nevertheless, complete backbone resonance assignments were obtained for nearly all residues, and side chain resonance assignments were more than 96% complete for residues 95−181.
Cross-references: PDB:1E17
Protein: DP01788 (UniProt P98177)
Region: residues 82	to 91
Annotation: nucleic acid binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Non-specific contacts involving this segment are important for DNA binding affinity of FOXO4 (ref.  PubMed ID: 17244620).
Protein: DP01788 (UniProt P98177)
Region: residues 86	to 96
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing electron density.
Cross-references: PDB:3L2C
Protein: DP01788 (UniProt P98177)
Region: residues 182	to 204
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The residues outside the structured DNA binding domain (residues 100−180) all showed random coil chemical shifts and very narrow resonance lines resulting in severe resonance overlap in some spectral regions. Nevertheless, complete backbone resonance assignments were obtained for nearly all residues, and side chain resonance assignments were more than 96% complete for residues 95−181.
Cross-references: PDB:1E17
Protein: DP01788 (UniProt P98177)
Region: residues 182	to 204
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The PKB phosphorylation/14-3-3 protein-binding motif is RRAAS (residues 189-193, ref. PubMedID:    17244620).
Protein: DP01788 (UniProt P98177)
Region: residues 182	to 204
Annotation: nucleic acid binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Non-specific contacts involving this segment are important for DNA binding affinity and specificity of FOXO4 (refs. PubMed ID:  24121535 and PubMed ID: 17244620).
Protein: DP01789 (UniProt A0A1Z3GD08)
Region: residues 1	to 136
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
By comparing the experimentally determined Stokes radius (RS obs) of HvASR1 and TtASR1 with the Stokes radii expected for various conformational states (native, molten globule, pre-molten globule, and denaturant-unfolded), the two proteins were found to have an RS higher than the value expected for a monomeric, natively folded form (~20 Å) (Table 2).
Protein: DP01789 (UniProt A0A1Z3GD08)
Region: residues 1	to 136
Annotation: disorder (Structural state)
Evidence: temperature-induced protein unfolding evidence used in manual assertion
Supporting statements:
As shown in Supplementary Fig. S4, the experimentally observed profiles for HvASR1 and TtASR1 are consistent with lack of a stable 3D structure, as judged from their rather high basal fluorescence at 20 °C and from the flatness of their profile.
Protein: DP01789 (UniProt A0A1Z3GD08)
Region: residues 1	to 136
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Both HvASR1 and TtASR1 exhibit an abnormally slow migration in SDS-PAGE, with an apparent molecular mass (MM) comprised between 20 and 25 kDa (expected MM ~16 kDa) (Fig. 2).
The aberrant electrophoretic migration of HvASR1 and TtASR1 proteins constitutes the first experimental hint of their disordered nature.
Protein: DP01789 (UniProt A0A1Z3GD08)
Region: residues 1	to 136
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The experimental Rg values are therefore in very good agreement with the expected Rg values using parameters inferred from IDPs, while they are three times smaller that those expected for fully unfolded forms.
The Rg value obtained for the ASR1 proteins (~35 Å) is 2.25 times higher than that expected for globular, fully unfolded proteins and IDPs of the same size (~15.5 Å) (see Eq. 10 in Methods)45
Protein: DP01789 (UniProt A0A1Z3GD08)
Region: residues 1	to 136
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Under native conditions and neutral pH, both proteins present spectra typical of proteins lacking any stable organized secondary structure, as judged from their large negative ellipticity at 200 nm, low amplitude in the 210–230 nm region, and low ellipticity at 190 nm (Fig. 5A). Spectral deconvolution revealed a high content (>60%) of unordered structure in both ASR1 proteins (see insets in Fig. 5A).
Protein: DP01789 (UniProt A0A1Z3GD08)
Region: residues 1	to 136
Annotation: zinc ion binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We then recorded the far-UV CD spectra in the presence of zinc (Fig. 10). The addition of 2.5 mM ZnSO4 does not trigger a gain in α-helical structure, but rather, leads to a decrease in the amplitude of the negative peak at 200 nm, consistent with a decrease in disorder content. By combining 10% TFE and 2 mM ZnSO4, a much more pronounced gain of structure is observed (Fig. 10), resulting in an increase in α-helical content, as judged from the appearance of the characteristic double minima at 208 and 222 nm (Fig. 10). While the addition of Zn2+ and 10% TFE does not promote an additional gain in α-helicity in HvASR1 (Fig. 10A), the reverse is observed for TtASR1, where the effects appear cumulative (Fig. 10B).
Protein: DP01789 (UniProt A0A1Z3GD08)
Region: residues 1	to 136
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
In the absence of TFE, the two proteins are readily degraded after an incubation as short as one hour, and entirely digested after 6 hours (Fig. 8), a behavior that is consistent with an overall high solvent accessibility and disordered nature.
Protein: DP01789 (UniProt A0A1Z3GD08)
Region: residues 1	to 136
Annotation: disorder to order (Structural transition)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
We first recorded the fluorescence emission spectra of the proteins either in the presence or absence of increasing zinc concentrations (Fig. 9). As expected for Tyr-containing proteins, both ASR1 proteins exhibit a maximum close to 303 nm. Interestingly, the intensity of the emission peak is gradually quenched with increasing zinc concentration, reflecting a decrease in the solvent exposure of Tyr residues. This behavior is indicative of a zinc-induced gain of tertiary structure.
Protein: DP01789 (UniProt A0A1Z3GD08)
Region: residues 1	to 136
Annotation: zinc ion binding (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
We first recorded the fluorescence emission spectra of the proteins either in the presence or absence of increasing zinc concentrations (Fig. 9). As expected for Tyr-containing proteins, both ASR1 proteins exhibit a maximum close to 303 nm. Interestingly, the intensity of the emission peak is gradually quenched with increasing zinc concentration, reflecting a decrease in the solvent exposure of Tyr residues. This behavior is indicative of a zinc-induced gain of tertiary structure.
Protein: DP01789 (UniProt A0A1Z3GD08)
Region: residues 1	to 136
Annotation: zinc ion sequestering activity (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
We first recorded the fluorescence emission spectra of the proteins either in the presence or absence of increasing zinc concentrations (Fig. 9). As expected for Tyr-containing proteins, both ASR1 proteins exhibit a maximum close to 303 nm. Interestingly, the intensity of the emission peak is gradually quenched with increasing zinc concentration, reflecting a decrease in the solvent exposure of Tyr residues. This behavior is indicative of a zinc-induced gain of tertiary structure.
Protein: DP01789 (UniProt A0A1Z3GD08)
Region: residues 1	to 136
Annotation: zinc ion sequestering activity (Molecular function)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
Near-UV CD studies further support this conclusion (Supplementary Text 5). For both proteins, the addition of 2 mM ZnSO4 results in a spectral modification, consistent with the gain of some tertiary structure (Fig. 5D). In particular, a peak between 275 and 282 nm, which corresponds to Tyr residues60, becomes discernible, reflecting a conformational change in the environment of Tyr residues (Fig. 5D).
Protein: DP01789 (UniProt A0A1Z3GD08)
Region: residues 1	to 136
Annotation: disorder to order (Structural transition)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
Near-UV CD studies further support this conclusion (Supplementary Text 5). For both proteins, the addition of 2 mM ZnSO4 results in a spectral modification, consistent with the gain of some tertiary structure (Fig. 5D). In particular, a peak between 275 and 282 nm, which corresponds to Tyr residues60, becomes discernible, reflecting a conformational change in the environment of Tyr residues (Fig. 5D).
Protein: DP01789 (UniProt A0A1Z3GD08)
Region: residues 1	to 136
Annotation: zinc ion binding (Molecular function)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
Near-UV CD studies further support this conclusion (Supplementary Text 5). For both proteins, the addition of 2 mM ZnSO4 results in a spectral modification, consistent with the gain of some tertiary structure (Fig. 5D). In particular, a peak between 275 and 282 nm, which corresponds to Tyr residues60, becomes discernible, reflecting a conformational change in the environment of Tyr residues (Fig. 5D).
Protein: DP01789 (UniProt A0A1Z3GD08)
Region: residues 1	to 136
Annotation: zinc ion sequestering activity (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We then recorded the far-UV CD spectra in the presence of zinc (Fig. 10). The addition of 2.5 mM ZnSO4 does not trigger a gain in α-helical structure, but rather, leads to a decrease in the amplitude of the negative peak at 200 nm, consistent with a decrease in disorder content. By combining 10% TFE and 2 mM ZnSO4, a much more pronounced gain of structure is observed (Fig. 10), resulting in an increase in α-helical content, as judged from the appearance of the characteristic double minima at 208 and 222 nm (Fig. 10). While the addition of Zn2+ and 10% TFE does not promote an additional gain in α-helicity in HvASR1 (Fig. 10A), the reverse is observed for TtASR1, where the effects appear cumulative (Fig. 10B).
Protein: DP01789 (UniProt A0A1Z3GD08)
Region: residues 1	to 136
Annotation: disorder (Structural state)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
Both proteins reached their maximum exchange after 10 sec of labeling, indicating that HvASR1 and TtASR1 are predominantly unfolded in their native state.
Protein: DP01789 (UniProt A0A1Z3GD08)
Region: residues 1	to 136
Annotation: zinc ion sequestering activity (Molecular function)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
The addition of 2 mM ZnSO4 induced a weak dynamic HDX-MS behavior, indicative of structure formation, throughout the entire polypeptide chain of both proteins (Panels C, Fig. 11). Notably, the addition of both 10% TFE and 2 mM ZnSO4 in a combined fashion resulted in an more pronounced change in magnitude of HDX dynamics (Panels D, Fig. 11).
Protein: DP01789 (UniProt A0A1Z3GD08)
Region: residues 1	to 136
Annotation: disorder to order (Structural transition)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
The addition of 2 mM ZnSO4 induced a weak dynamic HDX-MS behavior, indicative of structure formation, throughout the entire polypeptide chain of both proteins (Panels C, Fig. 11). Notably, the addition of both 10% TFE and 2 mM ZnSO4 in a combined fashion resulted in an more pronounced change in magnitude of HDX dynamics (Panels D, Fig. 11).
Protein: DP01789 (UniProt A0A1Z3GD08)
Region: residues 1	to 136
Annotation: zinc ion binding (Molecular function)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
The addition of 2 mM ZnSO4 induced a weak dynamic HDX-MS behavior, indicative of structure formation, throughout the entire polypeptide chain of both proteins (Panels C, Fig. 11). Notably, the addition of both 10% TFE and 2 mM ZnSO4 in a combined fashion resulted in an more pronounced change in magnitude of HDX dynamics (Panels D, Fig. 11).
Protein: DP01790 (UniProt P15941)
Region: residues 1184	to 1198
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In addition, NMR analysis of MUC1-CD confirmed the absence of a detectable secondary structure (Fig 1B–1D), as shown by the presence of the peaks between 7.5 and 8.5 ppm, consistent with MUC1-CD being an unstructured protein.
Protein: DP01790 (UniProt P15941)
Region: residues 1183	to 1187
Annotation: localization (Biological process)
Evidence: immunodetection assay evidence used in manual assertion
Supporting statements:
The double mutant chimera AQA+Y20N had reduced endocytosis and recycling rates and accumulated in EGFP-Rab11-positive endosomes, indicating that palmitoylation is the dominant feature modulating MUC1 recycling from endosomes back to the plasma membrane.
Protein: DP01790 (UniProt P15941)
Region: residues 1183	to 1187
Annotation: palmitoylation display site (Disorder function)
Evidence: immunodetection assay evidence used in manual assertion
Supporting statements:
Palmitoylation of transmembrane proteins can affect their membrane trafficking, and the MUC1 sequence CQC3RRK at the boundary of the transmembrane and cytoplasmic domains mimics reported site(s) of S-palmitoylation.
Palmitoylation of transmembrane proteins can affect their membrane trafficking, and the MUC1 sequence CQC3RRK at the boundary of the transmembrane and cytoplasmic domains mimics reported site(s) of S-palmitoylation.
Protein: DP01791 (UniProt A0ZWU1)
Region: residues 158	to 251
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Addition of increasing concentration of TFE showed progressive folding and increase in regularity by stimulating formation of α-helical secondary structure. Disordered region in SpEAF(158–251aa) decreased from 99% in absence of TFE to 31% in presence of 0.5% TFE
Protein: DP01794 (UniProt Q99ML1)
Region: residues 128	to 161
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Fluorescence spectra of Mcl-1 and PUMA peptide show Mcl-1 is folded,
PUMA is unfolded and binding occurs.
Protein: DP01794 (UniProt Q99ML1)
Region: residues 128	to 161
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
From the CD spectrum, it can be calculated that the PUMA peptide has ∼20% residual helicity in the unbound state (in 50 mM PO4, pH 7.0, 25 °C),24 consistent with the high predicted helicity of the BH3 region in the context of the full-length PUMA protein (Figure ​(Figure1B).
Protein: DP01794 (UniProt Q99ML1)
Region: residues 128	to 161
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Interaction with Induced myeloid leukemia cell differentiation protein Mcl-1 homolog.
Protein: DP01795 (UniProt Q9BUH6)
Region: residues 143	to 204
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Due to their being disordered, PAXX residues after 145 were not observed in the crystal structures.
Cross-references: PDB:3WTF
Protein: DP01795 (UniProt Q9BUH6)
Region: residues 143	to 204
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Homodimer. Direct interaction with the DNA-bound XRCC5/Ku80 and XRCC6/Ku70 heterodimer as part of the non-homologous end joining (NHEJ) complex for DNA repair. Mass-spectrometry, western-blotting, mutation analysis, inhibition assays and surface plasmon resonance confirmed interaction between PAXX residues 177-204 and Ku complex.
Cross-references: IntAct:ebi:EBI-16137950
 imex:IM-24329-5
 dip:DIP-198956E
Protein: DP01795 (UniProt Q9BUH6)
Region: residues 143	to 166
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Due to their being disordered, PAXX residues after 145 were not observed in the crystal structures.
Cross-references: PDB:3WTD
Protein: DP01797 (UniProt O96017)
Region: residues 64	to 90
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
These maps were readily interpretable, allowing a model consisting of residues 91–207, together with 8 residues of the phosphopeptide, to be built using “O” (Jones et al. 1991).
Cross-references: PDB:1GXC
Protein: DP01797 (UniProt O96017)
Region: residues 1	to 70
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Limited proteolysis of full-length CHK2K249R indicated that the ∼70 N-terminal residues containing the SCD and the ∼30 C-terminal residues are highly susceptible to digestion, suggesting that they are unstructured or loosely folded (data not shown).
Protein: DP01797 (UniProt O96017)
Region: residues 70	to 91
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The P1 form contains four dimers in the asymmetric unit. The refined model of four dimers encompasses residues 92–501 of each CHK2, with residues 228–232, 254–267, 383–387, and 398–401 disordered.
Cross-references: PDB:3I6W
Protein: DP01797 (UniProt O96017)
Region: residues 254	to 267
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The P1 form contains four dimers in the asymmetric unit. The refined model of four dimers encompasses residues 92–501 of each CHK2, with residues 228–232, 254–267, 383–387, and 398–401 disordered.
Cross-references: PDB:3I6W
Protein: DP01797 (UniProt O96017)
Region: residues 377	to 387
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The P212121 crystals contain one dimer in the asymmetric unit. In the refined model, both protomers encompass residues 89–501, with residues 260–267 (αB-αC loop), 377–387 (C-terminal portion of activation loop), and 398–401 (αEF-αF loop) disordered.
Cross-references: PDB:3I6U
Protein: DP01797 (UniProt O96017)
Region: residues 255	to 268
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Clear interpretable electron density is seen for residues 210–504 of the molecule, except for the loop comprised of residues 255–268 (connecting strand β3 to helix αC), which appears to be poorly ordered in these crystals. Similarly, at the C-terminus residues 505–531 have no discernable electron density and are also considered to be disordered.
Cross-references: PDB:2CN5
Protein: DP01797 (UniProt O96017)
Region: residues 505	to 531
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Clear interpretable electron density is seen for residues 210–504 of the molecule, except for the loop comprised of residues 255–268 (connecting strand β3 to helix αC), which appears to be poorly ordered in these crystals. Similarly, at the C-terminus residues 505–531 have no discernable electron density and are also considered to be disordered.
Cross-references: PDB:2CN5
Protein: DP01797 (UniProt O96017)
Region: residues 513	to 543
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Limited proteolysis of full-length CHK2K249R indicated that the ∼70 N-terminal residues containing the SCD and the ∼30 C-terminal residues are highly susceptible to digestion, suggesting that they are unstructured or loosely folded (data not shown).