LiteFold/DisProt huggingface dataset:
Protein: DP00606 (UniProt P42759)
Region: residues 1	to 260
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectra of ERD10 and ERD14 with a minimum close to 200 nm (Fig. 3B) are also typical of disordered proteins, because regular secondary structural elements, such as the α-helix and the β-sheet, in globular proteins give characteristic spectral peaks at 208, 222, and 214 nm, whereas a large negative peak at approximately 200 nm is characteristic of the coil conformation that dominates in IDPs (Receveur-Brechot et al., 2005).
Protein: DP00606 (UniProt P42759)
Region: residues 1	to 260
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Narrow peak dispersion in the 1H dimension of the 1H-15N HSQC indicates that ERD10 is an intrinsically disordered protein (Fig. 1).
Protein: DP00606 (UniProt P42759)
Region: residues 1	to 260
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
In SDS-PAGE, they show a characteristic low mobility: the real molecular mass of ERD10 is 29 kD but it runs at 45 kD, whereas the real molecular mass of ERD14 is 20 kD but it runs at 37 kD (Fig. 2A). This high apparent molecular mass caused by a highly hydrophilic character is often diagnostic of IDPs (Tompa, 2002). In addition, both proteins are heat stable (Fig. 2B) and are very sensitive to proteases (Fig. 2A).
The polypeptide chain of IDPs is more accessible to proteases than that of globular proteins, which results in much higher protease sensitivity, and this is diagnostic for their open structures. This was tested with proteases of broad substrate specificity (subtilisin and proteinase K) and proteases of narrow substrate specificity (trypsin and chymotrypsin); the pattern of the digestion was similar for all proteases, so we show only the results of proteinase K (Fig. 2A). ERD10 and ERD14 do not show any ordered motifs, which would show resistance against proteolysis.
Protein: DP00606 (UniProt P42759)
Region: residues 1	to 260
Annotation: lipid binding (Molecular function)
Evidence: experimental evidence used in manual assertion
Supporting statements:
Liposome binding suggested a possible effect of ERD10 and ERD14 on membrane fluidity. This was analyzed by fluorescence anisotropy measurements, which showed no effect of ERD10 or ERD14 on phosphatidylcholine (PC):PS (1:1) vesicles (Fig. 9).
Our results show that these intrinsically disordered proteins have chaperone activity of rather wide substrate specificity and that they interact with phospholipid vesicles through electrostatic forces.
Another putative mechanism of the protective function of ERD10 and ERD14 is membrane binding and stabilization. We could address this cryoprotective effect by analyzing their binding of PLVs and their effects on membrane fluidity. Generally, the fluorescence anisotropy is characteristic of the movement rate of the fluorescent dye in the phospholipid layer, which showed no difference in the presence or absence of ERD10 and ERD14.
This result suggests that the interaction is electrostatic, affecting membranes only peripherally, via phospholipid head groups.
Protein: DP00606 (UniProt P42759)
Region: residues 1	to 260
Annotation: lipid binding (Molecular function)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
The interaction of ERD10 and ERD14 with phospholipid vesicles (PLVs) was analyzed with mini gel filtration columns, as described in “Materials and Methods.” The analysis and comparison with the behavior of a positive control, calpain domain III, which shows calcium-dependent phospholipid binding, and a negative control, BSA, which does not bind to vesicles either in the absence or the presence of calcium (Tompa et al., 2001), confirm that ERD10 and ERD14 bind to PLVs. The interaction was statistically significant, as suggested by Student's t test (P = 0.003 and 0.056 for ERD10 and ERD14, respectively). Under the given conditions, approximately 2 μg of ERD10 and 2.5 μg of ERD14 were bound to 25 μg of PLVs, out of 15 μg total (Fig. 8A).Liposome binding suggested a possible effect of ERD10 and ERD14 on membrane fluidity. This was analyzed by fluorescence anisotropy measurements, which showed no effect of ERD10 or ERD14 on phosphatidylcholine (PC):PS (1:1) vesicles (Fig. 9).
Protein: DP00606 (UniProt P42759)
Region: residues 1	to 260
Annotation: protein folding chaperone (Molecular function)
Evidence: cell aggregation evidence used in manual assertion
Supporting statements:
Here, citrate synthase was incubated at an elevated temperature and aggregation was followed by an increase in absorbance. ERD10 and ERD14 at an equimolar concentration showed significant protective activity (Fig. 5), slowing the rate of aggregation to about half of its control value; this effect was significantly higher than that of BSA but fell short of that of HSP90. Upon increasing ERD10 and ERD14 concentrations further, the protective effect did not change much and did not reach the efficiency of HSP90 (Table I).
Both ERD10 and ERD14 showed significant protective effects on the thermal aggregation of firefly luciferase at a 2× molar excess (Fig. 6). Under these conditions, aggregation was almost completely inhibited, similar to the effect of HSP90 (Table I). BSA was practically ineffective in this assay.
ERD10, ERD14, and HSP90 had similar protective effects on the enzyme activity of lysozyme at substoichiometric ratios of lysozyme:chaperone (7:1; Fig. 7; Table I). Although the time course of the loss of enzyme activity was somewhat different in the presence of ERD10, ERD14, and HSP90, their protective effects, as expressed by residual enzyme activity after 25 min of incubation, were commensurate. BSA, again, had a negligible effect.
To investigate these functions of ERD10 and ERD14, we studied their protective effects on the heat-induced loss of enzyme activity and/or aggregation of four different substrates. The selected assays represent different modes and mechanisms of possible chaperone action and included thermal inactivation of ADH, thermal aggregation of firefly luciferase and citrate synthase, and the chemically induced inactivation of lysozyme. In the analyses shown here, ERD10 and ERD14 demonstrated marked effects on the prevention of aggregation/deactivation of protein substrates.
Protein: DP00606 (UniProt P42759)
Region: residues 1	to 260
Annotation: cold acclimation (Biological process)
Evidence: genetic transformation evidence used in manual assertion
Supporting statements:
 In an alternative approach to detect the function of ERD10, we analyzed the T-DNA insertion knock-out line for ERD10. The T-DNA insertion site was 300 base pairs upstream from the annotated first methionine codon of the ERD10 gene. 
As shown in Fig. 2c, about 40% of the wild-type leaves were damaged by cold treatment. In comparison, 70% of the erd10 mutant leaves showed damage, a much higher rate than that observed for wild-type plants.
Protein: DP00606 (UniProt P42759)
Region: residues 1	to 260
Annotation: response to cold (Biological process)
Evidence: reverse transcription polymerase chain reaction evidence used in manual assertion
Supporting statements:
As expected, activation of the CBF/DREB1 genes by cold stress was remarkable in wild-type plants, while basal expressions levels of these genes were barely detectable in the absence of cold. In contrast, cold inducibility of any of these genes was not distinguishable in the erd10 mutant. 
These results, combined with the result in Fig. 1c showing that the expression of ERD10 dramatically increased by cold treatment, imply that ERD10 is required to activate the CBF/DREB1 genes and their downstream target genes in response to cold stress in Arabidopsis.
Protein: DP00606 (UniProt P42759)
Region: residues 1	to 260
Annotation: drought recovery (Biological process)
Evidence: genetic transformation evidence used in manual assertion
Supporting statements:
In addition, the erd10 mutant showed reduced tolerance to drought stress relative to wild-type plants. While about 10% of wild-type plants dehydrated for 12 days turned green again after re-watering, erd10 mutants barely recovered from the same stress.
Protein: DP00606 (UniProt P42759)
Region: residues 1	to 260
Annotation: regulation of seed maturation (Biological process)
Evidence: genetic transformation evidence used in manual assertion
Supporting statements:
However, seed germination itself was affected by the lack of ERD10. The germination rate of the erd10 mutant over 5 days after imbibition was lower than that of wild-type plant (Fig. 4a). More than 80% of wild-type seeds germinated within 2 days. However, only 25 and 45% of erd10 seeds had germinated at 2 and 3 days after imbibitions, respectively.
Compared to wild-type seeds, erd10 seeds are a little smaller, and the groove that is formed between the two folded-cotyledons and the radicle is not distinct in erd10 seeds (Fig. 4c). These results suggest that the accumulation of ERD10 over time is required for seed maturation and germination in Arabidopsis.
Protein: DP00606 (UniProt P42759)
Region: residues 1	to 260
Annotation: regulation of seed germination (Biological process)
Evidence: genetic transformation evidence used in manual assertion
Supporting statements:
However, seed germination itself was affected by the lack of ERD10. The germination rate of the erd10 mutant over 5 days after imbibition was lower than that of wild-type plant (Fig. 4a). More than 80% of wild-type seeds germinated within 2 days. However, only 25 and 45% of erd10 seeds had germinated at 2 and 3 days after imbibitions, respectively.
Compared to wild-type seeds, erd10 seeds are a little smaller, and the groove that is formed between the two folded-cotyledons and the radicle is not distinct in erd10 seeds (Fig. 4c). These results suggest that the accumulation of ERD10 over time is required for seed maturation and germination in Arabidopsis.
Protein: DP00607 (UniProt Q16595)
Region: residues 81	to 92
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Analysis of the secondary chemical shifts using chemical shift indices [23] supports the hypothesis of am absence of secondary structure in the region 81-92 (Fig. 3A).
Protein: DP00607 (UniProt Q16595)
Region: residues 61	to 74
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
 The second spans residues 61-210 [hfra(61-210)]. As described previously [11], unless otherwise protected, this construct degrades spontaneously to produce a fragment comprising residues 75-210 [hfra(75-210)]. However, we found that use of the Complete anti-protease cocktail (Roche) prevents proteolytic cleavage.
Protein: DP00611 (UniProt P30291)
Region: residues 436	to 455
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
All 279 residues of the kinase domain construct have been modeled except for residues 436–455 and 570–575, which had no interpretable electron density.
Cross-references: PDB:1X8B
Protein: DP00611 (UniProt P30291)
Region: residues 436	to 455
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The loop 436–455, not located in the structure, has been identified from its sequence as a potential PEST region (Watanabe et al., 1995).
Protein: DP00615 (UniProt Q9WMX2)
Region: residues 2220	to 2313
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The 1H,15N HSQC spectrum of NS5A-D2 (Con1 strain) displays a narrow 1HN chemical shift dispersion limited to 1 ppm, as expected for a mainly disordered domain (Fig. 1A).
The NS5A fragment used in this publication was derived from the Hepacivirus C UniProtKB:Q9WIK7. IDR is 100% identical to the Hepatitis C virus genotype 1b (isolate Con1) polyprotein.
Cross-references: BMRB:19055
DisProt:DP03511r002
Protein: DP00615 (UniProt Q9WMX2)
Region: residues 2280	to 2299
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
 The final set of 28 low energy structures that fulfill the experimental restraints displays a well defined small structural motif (from Met313 to Ala317) in PepD2-WT (Fig. 5 and Table 1; PDB code 2M5L), whereas the N and C termini remain highly flexible.
The NS5A fragment used in this publication was derived from the Hepacivirus C UniProtKB:Q9WIK7. IDR is 100% identical to the Hepatitis C virus genotype 1b (isolate Con1) polyprotein. PepD2-WT comprises the region 2280-2299 of the Hepatitis C virus genotype 1b (isolate Con1) genome polyprotein.
Cross-references: BMRB:19059
PDB:2m5l
DisProt:DP03511r005
Protein: DP00615 (UniProt Q9WMX2)
Region: residues 2280	to 2299
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The affinity between CypA and the PW turn containing PepD2-WT peptide (KD = 0.5 mm) is three times better than the one involving the random coil PepD2-I315G peptide (KD = 1.4 mm).
The NS5A fragment used in this publication was derived from the Hepacivirus C UniProtKB:Q9WIK7. IDR is 100% identical to the Hepatitis C virus genotype 1b (isolate Con1) polyprotein. PepD2-WT comprises the region 2280-2299 of the Hepatitis C virus genotype 1b (isolate Con1) genome polyprotein.
Cross-references: DisProt:DP03511r003
Protein: DP00615 (UniProt Q9WMX2)
Region: residues 2280	to 2299
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Region 2280-2299 is mainly unstructured, as shown by its large negative ellipticity at 200 nm and moderate ellipticity at 190 nm in the far-UV CD spectra (Figure 7).
The NS5A fragment used in this publication was derived from the Hepacivirus C UniProtKB:Q9WIK7. IDR is 100% identical to the Hepatitis C virus genotype 1b (isolate Con1) polyprotein.
Cross-references: DisProt:DP03511r001
Protein: DP00615 (UniProt Q9WMX2)
Region: residues 2212	to 2307
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The chemical shifts of the backbone amide proton resonances are clustered in a narrow 1.3 ppm window from 7.2 to 8.5 ppm, and the dispersion of the 15N chemical shifts is narrowed in 19.2 ppm, as typical signs of an unfolded protein (23).
 As shown in Figure 2a, multinuclear (CA, CB, HA, and CO) chemical shift indexing, consensus CSI (30) values are zeros, suggesting that NS5A-D2 largely exists in a random coil conformation.
The steady-state heteronuclear 1H−15N NOE for the backbone amide of NS5A-D2 exhibited a relatively featureless and flattened variation with the amino acid sequences (Figure 3a), as seen in unfolded proteins (33).
The high T2 values measured for NS5A-D2 indicate large amplitude motions on the nanosecond to picosecond time scale, which is characteristic of a random coil conformation.
Protein: DP00615 (UniProt Q9WMX2)
Region: residues 2212	to 2307
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
As shown in Figure 5a, the CD spectrum of NS5A-D2 without TFE exhibits a minimum near 201 nm, with a slight negative ellipticity at about 222 nm, suggesting that it is mainly unfolded.
Protein: DP00615 (UniProt Q9WMX2)
Region: residues 2212	to 2307
Annotation: protein binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Our NMR results showed that perturbations in the chemical shifts were observed in 1H−15N HSQC spectrum of 15N-labeled NS5A-D2 in the presence of 5 mM of the MK-17 peptide (Figure 7a), whereas the titration with the peptide SP-24 caused a heavy precipitate upon its addition (data not shown).
NS5A-D2 interacts with NS5B MK-17 peptide. 
NS5A-D2 comprises the region 2212-2307 of the Hepatitis C virus genotype 1b (isolate Con1) genome polyprotein. The MK-17 peptide consist on the 139−155 residues of NS5B, which corresponds to 2558-2574 region of the Hepatitis C virus genotype 1b (isolate Con1) genome polyprotein.
Protein: DP00615 (UniProt Q9WMX2)
Region: residues 2280	to 2299
Annotation: viral genome replication (Biological process)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The affinity between CypA and the PW turn containing PepD2-WT peptide (KD = 0.5 mm) is three times better than the one involving the random coil PepD2-I315G peptide (KD = 1.4 mm).
The NS5A fragment used in this publication was derived from the Hepacivirus C UniProtKB:Q9WIK7. IDR is 100% identical to the Hepatitis C virus genotype 1b (isolate Con1) polyprotein. PepD2-WT comprises the region 2280-2299 of the Hepatitis C virus genotype 1b (isolate Con1) genome polyprotein.
Cross-references: DisProt:DP03511r006
Protein: DP00615 (UniProt Q9WMX2)
Region: residues 2331	to 2417
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of NS5A-D3 is typical for a poorly folded protein with a large negative peak centered at 198 nm.
Protein: DP00615 (UniProt Q9WMX2)
Region: residues 2331	to 2417
Annotation: protein binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
By comparison with the NS5A-D3 spectra recorded alone, we identified the residues involved in interaction with CypA based on chemical shift perturbations and/or peak broadening.
Protein: DP00615 (UniProt Q9WMX2)
Region: residues 2331	to 2417
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
The purified protein exhibited the expected mass (9925 Da) as determined by mass spectroscopy (not shown). By SDS–PAGE, NS5A-D3 has an apparent molecular weight (MW) of ∼20 kDa (Fig. 2A). This discrepancy is probably due to the primary sequence of NS5A-D3, which includes many acidic residues and prolines.
The anomalous electrophoretic mobility is frequently observed in intrinsically disordered proteins.
Protein: DP00615 (UniProt Q9WMX2)
Region: residues 2331	to 2417
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The circular dichroism (CD) spectrum of NS5A-D3 exhibits a single negative peak centered at 198 nm (Fig. 2C) that is typical of unfolded polypeptide. The lack of characteristic minima around 208 and 222 nm indicative of α-helix, or the minimum around 215 nm that points to β-sheet elements, confirms the absence of regular secondary structure in NS5A-D3.
Protein: DP00615 (UniProt Q9WMX2)
Region: residues 2331	to 2417
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The 1H,15N HSQC spectrum of NS5A-D3 (Fig. 3A) exhibits a rather narrow 1H chemical shift dispersion limited to 0.75 ppm. NS5A-D3 resonances are clustered in three regions of the NMR spectrum corresponding to, respectively, the glycines, the serine and threonine and finally the other residues. This clustering and the limited dispersion in proton dimension are typical of non-structured polypeptides. 
The resulting CSI consensus values are zero (Fig 3B, bottom), confirming the absence in NS5A-D3 of stable secondary structure elements even at the local level.
Cross-references: BMRB:16166
Protein: DP00615 (UniProt Q9WMX2)
Region: residues 2222	to 2314
Annotation: RNA binding (Molecular function)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
Increases in EFRET,apparent with increasing concentrations of RNA provide evidence for binding (Figure 1A). A plateau in the EFRET,apparent indicates that the binding of cy3NS5ADII to cy5rU20 was saturated and reached its equilibrium after the addition of 50 nM RNA substrate.
Protein: DP00615 (UniProt Q9WMX2)
Region: residues 2222	to 2314
Annotation: protein binding (Molecular function)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
The increase in EFRET,apparent is again indicative of binding. A higher maximum EFRET,apparent of 0.4 was reached with CypA, suggesting that NS5ADII bound more efficiently to CypA than RNA.
Protein: DP00615 (UniProt Q9WMX2)
Region: residues 2222	to 2314
Annotation: protein binding (Molecular function)
Evidence: fluorescence anisotropy evidence used in manual assertion
Supporting statements:
With increasing concentrations of NS5B, a significant change in anisotropy was observed, which confirms the formation of a protein–protein complex with NS5B (Figure 1C).
NS5B peptide used corresponds to the 2442-3011 region of the Hepatitis C virus genotype 1b (isolate Con1) genome polyprotein.
Protein: DP00615 (UniProt Q9WMX2)
Region: residues 2289	to 2293
Annotation: viral genome replication (Biological process)
Evidence: luciferase reporter gene assay evidence used in manual assertion
Supporting statements:
As illustrated in Fig. 8, the sole mutation I315G in NS5A almost completely abolished viral replication that was close to the background as determined with the replicon encoding an inactive NS5B RNA-polymerase (GND mutant). The replication levels corresponding to the I315G and P314A mutations, respectively, were similar.
Hence, the short PW turn structural motif in the mainly disordered NS5A-D2 domain plays an essential role for HCV RNA replication.
The NS5A fragment used in this publication was derived from the Hepacivirus C UniProtKB:Q9WIK7. IDR is 100% identical to the Hepatitis C virus genotype 1b (isolate Con1) polyprotein. PepD2-WT comprises the region 2280-2299 of 
PW turn corresponds to the 2290-2292 region of the Hepatitis C virus genotype 1b (isolate Con1) genome polyprotein (P316 -W318 of the Ns5B protein). Although the authors describes this region as a small structural motif, the region is to short to form any secondary structure so is interpreted as disordered here.
Cross-references: DisProt:DP03511r007
Protein: DP00617 (UniProt P60896)
Region: residues 26	to 36
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density, indicating it is disordered.
Cross-references: PDB:1MIU
Protein: DP00617 (UniProt P60896)
Region: residues 1	to 51
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
For both proteins, the assigned 1H-15N HSQC spectra (Figure 2b) demonstrated low dispersion in the proton dimension characteristic of disordered proteins, in full accordance with the CD spectra.
Cross-references: BMRB:50906
Protein: DP00617 (UniProt P60896)
Region: residues 38	to 46
Annotation: ubiquitin binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The region binding ubiquitin with the highest affinity, UBS1, was identified from a set of disappearing peaks originating from residues V38‐D46, combined with large CSPs from residues D35‐H37 (Figure 3b).