LiteFold/DisProt huggingface dataset:
Protein: DP01432 (UniProt E1UJ20)
Region: residues 2	to 109
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Maximum intensity of bis-ANS fluorescence in the presence of apo-csPA exceeds that value for the Ca2+-loaded protein by a factor of 8, while bis-ANS emission spectrum maximum position (λmax) for apo-csPA is blue shifted by 2 nm with respect to the λmax value for the Ca2+-bound protein.
Protein: DP01433 (UniProt P04052)
Region: residues 1657	to 1739
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In summary, the
unphosphorylated state CTD2' is highly disordered, temporally
dynamic and contains nearly all trans-proline.
Protein: DP01434 (UniProt P31431)
Region: residues 171	to 198
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Two-dimensional NOESY proton spectrum shows that the intracellular regions of syndecan-4 exhibit extensive flexibility.
Protein: DP01435 (UniProt O60829)
Region: residues 1	to 102
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
1) Thus, the lack of signal dispersion is strongly indicative of a polypeptide chain with little or no defined tertiary structure
2) Taken together, the CD and NMR data show that PAGE4 does not have detectable secondary and tertiary structure, consistent with an IDP
Protein: DP01435 (UniProt O60829)
Region: residues 1	to 102
Annotation: nucleic acid binding (Molecular function)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
PAGE4 preferential binding sites when the PAGE4-FLAG protein was present (lane 3) as well as FLAG-p53, which was used as a positive control. DNA sequence analysis revealed that PAGE4 preferentially binds to a GC-rich sequence, 5'-GCCGCGGGG-3' (Fig. 4)
Protein: DP01435 (UniProt O60829)
Region: residues 1	to 102
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
1) These spectra showed that the PAGE4 polypeptide chain contains no significant alpha-helical or beta-strand secondary structural elements over this temperature range as evidenced by low ellipticity values in the 215–230 nm region
2) Taken together, the CD and NMR data show that PAGE4 does not have detectable secondary and tertiary structure, consistent with an IDP
Protein: DP01435 (UniProt O60829)
Region: residues 1	to 102
Annotation: nucleic acid binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
PAGE4 preferential binding sites when the PAGE4-FLAG protein was present (lane 3) as well as FLAG-p53, which was used as a positive control. DNA sequence analysis revealed that PAGE4 preferentially binds to a GC-rich sequence, 5'-GCCGCGGGG-3' (Fig. 4)
Protein: DP01435 (UniProt O60829)
Region: residues 1	to 102
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
These data show that WT PAGE4 is highly flexible, with average heteronuclear NOE values (∼0.1–0.2) similar to those of comparable molecular weight IDPs (53).
Cross-references: BMRB:26544
Protein: DP01435 (UniProt O60829)
Region: residues 40	to 70
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
As expected, the largest effects for 15N, HN, and CO shifts were seen at Thr-51 itself, with relatively smaller changes for the nearest neighbors. In contrast to these localized effects, significant differences were detected for Cα chemical shifts over a region extending from residues 40–70 (Fig. 4C).
Phosphorylation on Thr-51 decreases picosecond-nanosecond timescale motions in the immediate vicinity, with higher heteronuclear NOE values for Thr-51, Ile-54, and Glu-55 and smaller changes in other parts of the chain.
Therefore, phosphorylation switches the conformational ensemble to a more compact but still flexible state.
Cross-references: BMRB:26545
BMRB:26544
Protein: DP01435 (UniProt O60829)
Region: residues 49	to 53
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR assignment of phospho-PAGE4 using the above methods revealed complete phosphorylation at Thr-51 and partial (∼30–40%) phosphorylation at Ser-9.
Cross-references: BMRB:26545
Protein: DP01435 (UniProt O60829)
Region: residues 7	to 11
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR assignment of phospho-PAGE4 using the above methods revealed complete phosphorylation at Thr-51 and partial (∼30–40%) phosphorylation at Ser-9.
Cross-references: BMRB:26545
Protein: DP01435 (UniProt O60829)
Region: residues 7	to 11
Annotation: phosphorylation display site (Disorder function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
The original HIPK1 kinase study suggested single-site specificity of phosphorylation at Thr-51, but the coexpression experiments carried out here on a larger scale for NMR analysis produced an ∼2:1 mixture of singly and doubly phosphorylated PAGE4, evident from both NMR analysis (Fig. 2, B and D) and mass spectrometry (Fig. 3).
Protein: DP01435 (UniProt O60829)
Region: residues 49	to 53
Annotation: phosphorylation display site (Disorder function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
The original HIPK1 kinase study suggested single-site specificity of phosphorylation at Thr-51, but the coexpression experiments carried out here on a larger scale for NMR analysis produced an ∼2:1 mixture of singly and doubly phosphorylated PAGE4, evident from both NMR analysis (Fig. 2, B and D) and mass spectrometry (Fig. 3).
Protein: DP01435 (UniProt O60829)
Region: residues 69	to 73
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In contrast, addition of either unlabeled full-length c-Jun or c-Jun (1–223) perturbed a specific set of WT PAGE4 residues in a similar way, albeit weakly (Fig. 10A). The largest chemical shift changes occurred in the transient helix region of PAGE4 from residues 69–73 (Fig. 10, A and C). The binding interaction between WT PAGE4 and c-Jun was estimated at a KD of >50 μm from the NMR titration data, with precipitation of c-Jun at higher concentrations preventing a more accurate determination.
Protein: DP01436 (UniProt P54936)
Region: residues 423	to 487
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Spectra for L27 monomers (Lin-2 and Lin-7 proteins) show little ellipticity at 222 nm, indicating that the individual monomers are largely unfolded.
Protein: DP01436 (UniProt P54936)
Region: residues 423	to 487
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
There is a striking increase of ellipticity at 222 nm upon mixing of the monomers. The individual unfolded monomers become a stable, helical, folded unit upon association.
Protein: DP01436 (UniProt P54936)
Region: residues 423	to 487
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Difference CD spectra for the interacting pair of proteins (C.e. LIN-7:C.e. LIN-2C) show minima at 222 nm, indicative of a significant increase in α-helical content upon association.
Protein: DP01437 (UniProt P90976)
Region: residues 115	to 180
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Spectra for L27 monomers (Lin-2 and Lin-7 proteins) show little ellipticity at 222 nm, indicating that the individual monomers are largely unfolded.
Protein: DP01437 (UniProt P90976)
Region: residues 115	to 180
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
There is a striking increase of ellipticity at 222 nm upon mixing of the monomers. The individual unfolded monomers become a stable, helical, folded unit upon association.
Protein: DP01437 (UniProt P90976)
Region: residues 115	to 180
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Difference CD spectra for the interacting pair of proteins (C.e. LIN-7:C.e. LIN-2C) show minima at 222 nm, indicative of a significant increase in α-helical content upon association.
Cross-references: PDB:1zl8
Protein: DP01438 (UniProt O14936)
Region: residues 335	to 401
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The binding and folding events are linked for the LIN-2C:LIN-7 L27 pair; the individual monomers are largely unfolded but become a stable, helical, folded unit upon association.
Cross-references: PDB:1zl8
Protein: DP01438 (UniProt O14936)
Region: residues 394	to 460
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Spectra for L27 monomers (CASK/Lin-2) show little ellipticity at 222 nm, indicating that the individual monomers are largely unfolded.
Protein: DP01438 (UniProt O14936)
Region: residues 394	to 460
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The binding and folding events are linked for the LIN-2C:LIN-7 L27 pair; the individual monomers are largely unfolded but become a stable, helical, folded unit upon association.
Protein: DP01438 (UniProt O14936)
Region: residues 304	to 337
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB evidence shows this region lacks electron density, indicating it is disordered
Cross-references: PDB:7OAI
PDB:7OAJ
PDB:7OAK
PDB:7OAL
Protein: DP01438 (UniProt O14936)
Region: residues 307	to 337
Annotation: disorder (Structural state)
Evidence: experimental evidence used in manual assertion
Supporting statements:
The PDB evidence shows this region lacks amminoacid residues 307-337, indicating it is disordered
Cross-references: PDB:3MFU
PDB:3MFT
PDB:3MFS
PDB:3MFR
Protein: DP01438 (UniProt O14936)
Region: residues 317	to 345
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB evidence shows this region lacks electron density, indicating it is disordered
Cross-references: PDB:3TAC
Protein: DP01438 (UniProt O14936)
Region: residues 305	to 337
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Both the P1 and P212121 structures exhibited uninterrupted backbone electron densities throughout the entire domain from residues 5 to 304.
Cross-references: PDB:3C0H
PDB:3C0I
Protein: DP01439 (UniProt A5F384)
Region: residues 101	to 110
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Helix α1 and sheet β9 are linked by a disordered region between residues 101 and 110
Cross-references: PDB:3GBG
Protein: DP01439 (UniProt A5F384)
Region: residues 101	to 109
Annotation: limited proteolysis display site (Disorder function)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
The solved crystal structure of ToxT revealed an unstructured region in the N-terminal domain between residues 100 and 110. This region and the surrounding amino acids have been previously implicated in ToxT proteolysis, resistance to inhibition by negative effectors, and ToxT dimerization. To better characterize this region, site-directed mutagenesis was performed to assess the effects on ToxT proteolysis and bile sensitivity. This analysis identified specific mutations within this unstructured region that prevent ToxT proteolysis and other mutations that reduce inhibition by bile and unsaturated fatty acids.
To further characterize this region in regard to these roles, we performed site-directed alanine mutagenesis of ToxT amino acids 100 to 109, shown in Fig. 1.
The previously described degradation intermediate of ToxT (24) was present in cell extracts from strains carrying each of the mutations in the unstructured region between amino acids 100 and 109 except for the G100A and M103A mutant strains (Fig. 2A). Densitometry was performed using ImageJ software (Fig. 2B) and revealed that the L107A and S109A mutants also had decreased levels of degradation compared to the results for the WT. Mutations I104A and R105A resulted in increased degradation of ToxT, possibly due to decreased ToxT stability. The identification of mutations in this region affecting ToxT proteolysis both confirms previous work demonstrating the importance of amino acids 100 to 109 and pinpoints amino acids 100 and 103 as crucial for ToxT proteolysis.
Protein: DP01439 (UniProt A5F384)
Region: residues 101	to 110
Annotation: molecular function regulator (Molecular function)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
The solved crystal structure of ToxT revealed an unstructured region in the N-terminal domain between residues 100 and 110. This region and the surrounding amino acids have been previously implicated in ToxT proteolysis, resistance to inhibition by negative effectors, and ToxT dimerization. To better characterize this region, site-directed mutagenesis was performed to assess the effects on ToxT proteolysis and bile sensitivity. This analysis identified specific mutations within this unstructured region that prevent ToxT proteolysis and other mutations that reduce inhibition by bile and unsaturated fatty acids.
As was observed in the bile experiments, mutation of residues 100 to 104, 107, and 108 caused decreased overall transcriptional activity with and without added effector. Also, the D101A, I104A, and Y108A mutants had increased sensitivity to linoleic acid, as we had observed with bile. 
This analysis revealed ToxT mutations (G100A, D101A, I104A, Y108A, and E110A) that caused greater sensitivity to the negative effect of bile.
ToxT alanine substitutions at amino acids 100 to 104, 107, and 108 caused decreased overall ToxT activity, as we observed in the bile/UFA experiments described above. Additionally, mutation of S109 and E110 caused slight decreases in overall activity compared to that of the WT. The L107A mutant was completely inactive, and bicarbonate had no activating effect on this variant of ToxT. Bicarbonate increased the activity of WT MBP-ToxT 2.6-fold in these experiments (Fig. 5). ToxT G100A, D101A, M103A, I104A, and Y108A mutants all had an increased response to the activating effect of bicarbonate. 
These results suggest that the same ToxT residues within the unstructured region from amino acid 100 to 109 may be involved in the response to both positive and negative effectors.
Protein: DP01440 (UniProt P44228)
Region: residues 12	to 28
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
"Residues at the N terminus (residues 1–7) and at the C terminus (residues 121–131) are unstructured, as evidenced by a low number of inter-residue NOEs."
Cross-references: PDB:2OUT
Protein: DP01440 (UniProt P44228)
Region: residues 12	to 28
Annotation: DNA binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
"In conclusion, the structure of HI1506 reveals a novel two-domain conformation, in which each domain contains a significant contiguous area of positively charged surface. For both the N- and C-domains, some of the more closely related structures are associated with an RNA binding function."
Protein: DP01440 (UniProt P44228)
Region: residues 54	to 84
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
"The solution structure of HI1506 consists of two structured domains connected by an unstructured 30 amino acid loop"
Cross-references: PDB:2OUT
Protein: DP01440 (UniProt P44228)
Region: residues 54	to 84
Annotation: DNA binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
"In conclusion, the structure of HI1506 reveals a novel two-domain conformation, in which each domain contains a significant contiguous area of positively charged surface. For both the N- and C-domains, some of the more closely related structures are associated with an RNA binding function."
Protein: DP01441 (UniProt P14921)
Region: residues 276	to 318
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The conformation of the inhibitory module of Ets1 in (Ets1)2–DNA and Ets1–Pax5–DNA complexes, which do not contain Runx1, resembled that of free Ets1, although HI-1 was disordered
Cross-references: PDB:3WTS
Protein: DP01441 (UniProt P14921)
Region: residues 276	to 318
Annotation: nucleic acid binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
CaMKII-catalyzed phosphorylation of Ets1 in a
serine-rich region of the N-terminal extension of HI-1
is known to stabilize the inhibitory hydrophobic core
(Fig. 1b, f, and j), resulting in a 50- to 1000-fold
reduction in its affinity for DNA
Protein: DP01442 (UniProt Q2Q4X9)
Region: residues 1	to 260
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Inspection of the spectrum (Fig. 1a) shows a negative peak at 200 nm, which is indicative of a highly unfolded protein in a random coil structure.
Protein: DP01442 (UniProt Q2Q4X9)
Region: residues 1	to 260
Annotation: disorder (Structural state)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
Superficial inspection of the IR spectrum in the amide-I region (Fig. 9) revealed that in D2O the proteins displayed a broadened band at a wavenumber position (1,460 cm−1) that was lower than in the case of the fast-dried proteins (1,550 cm−1). This behavior in D2O may be partly due to 2H exchange with protons in the protein backbone, which is particularly likely in unordered structures (Raussens et al., 1997).
Apparently, the amide protons (N-H) were, to a considerable extent, open for 2H exchange from D2O, which is interpreted to mean that both proteins have a fairly unordered structure in water (Haris et al., 1989).
Protein: DP01442 (UniProt Q2Q4X9)
Region: residues 1	to 260
Annotation: disorder to order (Structural transition)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
 In contrast to MtEm6, MtPM25 tended to form extended β sheets upon slow drying, which appeared to be reversible upon rehydration. When indicated as percentages of α helix, β sheet, and unordered structures, MtEm6 consisted of 57%, 12%, and 31%, and 60%, 8%, and 32%, after fast and slow drying, respectively. Data for MtPM25 were 54%, 17%, and 29%, and 56%, 25%, and 19%, respectively.
The removal of the water induced a transition from a fairly disordered conformation to the formation of a considerable amount of ordered structures (Table IV).
Protein: DP01442 (UniProt Q2Q4X9)
Region: residues 1	to 260
Annotation: protein stabilization (Biological process)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
Figure 3a shows that PM25 is a potent stabilizer of LDH during three cycles of freezing/thawing in a concentration dependent fashion. The enzyme activity is completely recovered at a mass ratio (PM25 : enzyme) of 6:1. In contrast, EM6 was mildly efficient regardless as to whether data were expressed on mass ratio (Fig. 3a) or molar ratio (EM6 being ca. half the weight of PM25) whereas lyzozyme is almost ineffective.
PM25 stabilizes proteins in aggregation assays more efficiently than EM6
Figure 3e shows that both PM25 and EM6 could offer a partial protection to CS against drying in a concentration dependent manner, as previously described for other LEA proteins (Goyal et al. 2005; Gilles et al. 2007). Again, PM25 was more efficient at protecting CS from drying than EM6.
Protein: DP01442 (UniProt Q2Q4X9)
Region: residues 1	to 260
Annotation: stress granule disassembly (Biological process)
Evidence: turbidity measurement evidence used in manual assertion
Supporting statements:
Figure 5a shows that the addition of PM25 to the water SP after thawing leads to a significant decrease in turbidity compared with water controls, suggesting that PM25 is able to dissolve aggregates formed after two successive freeze–thawing cycles.
Protein: DP01442 (UniProt Q2Q4X9)
Region: residues 1	to 260
Annotation: stress granule disassembly (Biological process)
Evidence: protein separation evidence used in manual assertion
Supporting statements:
Figure 5a shows that the addition of PM25 to the water SP after thawing leads to a significant decrease in turbidity compared with water controls, suggesting that PM25 is able to dissolve aggregates formed after two successive freeze–thawing cycles.
PM25 dissolves stress-induced aggregates of water-soluble proteins upon thawing and rehydration
Protein: DP01442 (UniProt Q2Q4X9)
Region: residues 1	to 260
Annotation: protein stabilization (Biological process)
Evidence: temperature-induced protein unfolding evidence used in manual assertion
Supporting statements:
Next, we assessed whether PM25 behaved like a chaperone using a standard thermally-induced unfolding assay with CS. The inactivation kinetics experiment shows that during heating at 43 °C, CS lost virtually all activity within 20 min, whereas the presence of PM25 significantly retarded the loss of the activity early during heating (Fig. 3b).
This suggests that PM25 stabilizes CS against heating by acting on certain intermediates that are transiently formed during heating, but not on the denatured enzyme.
Protein: DP01442 (UniProt Q2Q4X9)
Region: residues 1	to 260
Annotation: stress granule disassembly (Biological process)
Evidence: microscopy evidence used in manual assertion
Supporting statements:
 Adding PM25 upon thawing resulted in the disappearance of the aggregates, with those remaining being much smaller and of different morphology (Fig. 6d). Also, no coacervate was observed in the thawed solution in the presence of PM25. We assayed the effect of PM25 on the size distribution of the aggregates using light microscopy because they were too large to be analysed by light scattering. Figure 6e confirms that PM25 is able to reduce both the average surface area and the size distribution by one and seven orders of magnitude, respectively.
Protein: DP01443 (UniProt Q9UJX4)
Region: residues 1	to 26
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The regions are detailed in the Extended Data Table 2.
Cross-references: PDB:4UI9