LiteFold/DisProt huggingface dataset:
Protein: DP00667 (UniProt P42763)
Region: residues 1	to 185
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Herein we present the backbone (1)H, (15)N and (13)C NMR assignment of the 185 amino acid long ERD14 (Early Response to Dehydration 14), which is a K(3)S-type, typical dehydrin of A. thaliana. Secondary chemical shifts as well as NMR relaxation data show that ERD14 is fully disordered under near native conditions, with short regions of somewhat restricted motion and 5-25% helical propensity.
The measured NMR data give clear evidence of the almost complete disordered state of ERD14 under native conditions. SCS values and relaxation parameters fall close to the random coil values along the entire chain (Fig. 2), which suggests that the protein is fully flexible.
Cross-references: BMRB:16876
Protein: DP00667 (UniProt P42763)
Region: residues 1	to 185
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: DP00667 (UniProt P42763)
Region: residues 1	to 185
Annotation: protein folding chaperone (Molecular function)
Evidence: temperature-induced protein unfolding evidence used in manual assertion
Supporting statements:
ERD14 on the other hand, showed no loss of chaperone capacity due to freezing.
Protein: DP00667 (UniProt P42763)
Region: residues 1	to 185
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
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: DP00667 (UniProt P42763)
Region: residues 1	to 185
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).
Protein: DP00667 (UniProt P42763)
Region: residues 1	to 185
Annotation: protein folding chaperone (Molecular function)
Evidence: temperature-induced protein unfolding 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: DP00667 (UniProt P42763)
Region: residues 1	to 185
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Cellular Chaperone Function of Intrinsically Disordered Dehydrin ERD14
Here, we explored the involvement of each conserved segment in the protective function of the intrinsically disordered stress protein (IDSP) A. thaliana’s Early Response to Dehydration (ERD14).
In phosphate buffer, all tested proteins showed a CD spectral shape characteristic of a disordered protein (Figure 4A), very similar to that of the wild-type ERD14. Because CD spectroscopy reflects the average secondary structure content, this indicates that the free ERD14 molecules are essentially disordered, and the helices shown by NMR [9] are truly only transient and might be stabilized by interacting with partner molecules.
Protein: DP00667 (UniProt P42763)
Region: residues 156	to 169
Annotation: protein folding chaperone (Molecular function)
Evidence: experimental evidence used in manual assertion
Supporting statements:
Cellular Chaperone Function of Intrinsically Disordered Dehydrin ERD14
Here, we explored the involvement of each conserved segment in the protective function of the intrinsically disordered stress protein (IDSP) A. thaliana’s Early Response to Dehydration (ERD14). We show that segments that are directly involved in partner binding, and others that are not, are equally necessary for proper function and that cellular protection emerges from the balanced interplay of 
different regions of ERD14.
These results suggest that Kc and S are the primary sites of activity, together with varying contributions of other segments. These notions were further confirmed by the in vitro chaperone activities of these mutants (Supplementary Figure S3 and Table S4). In these experiments, the ∆Kc and ∆S variants showed similarly reduced chaperone activities as the FS ERD14 variant. This is an interesting observation, especially in light of the fact that all K-segments participate in partner binding within a cell, whereas the S-segment does not [9]. Although partner binding in itself is a property of large amounts of proteins, only a small portion of them exhibit chaperone activity. Beyond the necessary partner binding regions, a chaperone is expected to have segments that contribute to or are responsible for chaperone function, such as the S-segment.
Protein: DP00667 (UniProt P42763)
Region: residues 74	to 85
Annotation: protein folding chaperone (Molecular function)
Evidence: experimental evidence used in manual assertion
Supporting statements:
Cellular Chaperone Function of Intrinsically Disordered Dehydrin ERD14
Here, we explored the involvement of each conserved segment in the protective function of the intrinsically disordered stress protein (IDSP) A. thaliana’s Early Response to Dehydration (ERD14). We show that segments that are directly involved in partner binding, and others that are not, are equally necessary for proper function and that cellular protection emerges from the balanced interplay of 
different regions of ERD14.
These results suggest that Kc and S are the primary sites of activity, together with varying contributions of other segments. These notions were further confirmed by the in vitro chaperone activities of these mutants (Supplementary Figure S3 and Table S4). In these experiments, the ∆Kc and ∆S variants showed similarly reduced chaperone activities as the FS ERD14 variant. This is an interesting observation, especially in light of the fact that all K-segments participate in partner binding within a cell, whereas the S-segment does not [9]. Although partner binding in itself is a property of large amounts of proteins, only a small portion of them exhibit chaperone activity. Beyond the necessary partner binding regions, a chaperone is expected to have segments that contribute to or are responsible for chaperone function, such as the S-segment.
Protein: DP00668 (UniProt P19250)
Region: residues 25	to 35
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
There was no electron density observed for the N-terminal region (residues 1–11), suggesting that this region is highly flexible or adopts more than one conformation.
What the authors refer to as residues 1-11 correspond to residues 25-35 in the UniProt sequence
Cross-references: PDB:3A57
Protein: DP00668 (UniProt P19250)
Region: residues 25	to 35
Annotation: disorder (Structural state)
Evidence: microscopy evidence used in manual assertion
Supporting statements:
It should also be noted that the three-dimensional TEM analysis did not produce a structure for the N-terminal region that was disordered in the crystal structure.
Protein: DP00668 (UniProt P19250)
Region: residues 25	to 35
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The averaged most populated volume envelope from the 20 SAXS models showed that the N-terminal region projected from the central pore and was found primarily on the longitudinal side of the tetramer. The structural model indicated that the missing N-terminal region was exposed to solvent and adopted a highly mobile conformation.
However, the N-terminal region (residues 1–11) was disordered in the crystal structure, and SAXS analysis revealed that this region was exposed to solvent and highly flexible. 
What the authors refer to as residues 1-11 correspond to residues 25-35 in the UniProt sequence
Protein: DP00668 (UniProt P19250)
Region: residues 25	to 35
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The N-terminal Pro-rich region (FELPSVPFPAP), however, was apparently hydrophobic, but its structure was not discernable by x-ray crystallography, three-dimensional TEM (Fig. 1), or NMR studies (supplemental Fig. 3)
Protein: DP00669 (UniProt P81019)
Region: residues 26	to 96
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The circular dichroism (CD) spectrum of His-S–N-terminal part exhibits a negative peak at 201.5 nm (Fig. 3B), which is characteristic of a protein in largely unfolded conformation. The lack of characteristic minima around 208 and 222 nm is indicative of the absence of a -helix. There is a broad but weak negative ‘shoulder’ peak between 215 and 230 nm, implying the existence of small proportion of residual secondary structure.
Protein: DP00669 (UniProt P81019)
Region: residues 26	to 96
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
The puriﬁed Trx-His-S tagged recombinant proteins, i.e. FL, N-terminal part, A, B, and AB domain showed molecular weights of 42, 34, 29, 29 and 32 kDa, respectively. These sizes are 18%, 38%, 29%, 28%, and 6% larger for FL,
N-terminal part (Fig. 2B), A, B, and AB domains, respectively (not shown). The reason for the anomalous migration of recombinant A and B domains is not clear. As depicted in Fig. 2A the His-S–N-terminal part migrated >90% higher than its theoretical molecular mass (12.8 kDa). This is probably due to the primary sequence of N-terminal part of BSP5, which includes many acidic residues and proline (Table 1). Such abnormal behavior has already been
observed in other intrinsically disordered proteins and can most
likely be ascribed to their unusual sequence and composition
Protein: DP00670 (UniProt Q29983)
Region: residues 175	to 184
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In MIC-A, no electron density is observed for ten residues (152–161) in one section of these helices (corresponding to helix 2a in the α2 domain of HLA-B27) or for the polyhistidine purification tag.
The region corresponds to region 175-184 of the protein sequence.
Cross-references: PDB:1B3J
Protein: DP00670 (UniProt Q29983)
Region: residues 175	to 184
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Preliminary results from limited proteolysis with thermolysin at pH 7.5, in which MIC-A is initially cleaved in the region of this loop, suggest that this loop is exposed and flexible at near neutral pH as well (data not shown).
The region corresponds to region 175-184 of the protein sequence.
Protein: DP00672 (UniProt Q92886)
Region: residues 90	to 150
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1D-NMR spectrum of bHLHN at 298 K did not show a chemical shift dispersion in the amide (Figure 3A) nor in the methyl regions (Figure 2 of Supporting Information). In those regions all of the resonances were clustered as expected for random-coil proteins (54), namely, between 8.0 and 8.7 ppm (for the amide signals) (Figure 3A,B) and between 0.8 and 1.0 ppm (for the methyl protons) (Figure 2 of Supporting Information).
Protein: DP00672 (UniProt Q92886)
Region: residues 90	to 150
Annotation: DNA binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
This lack of signal dispersion in the NMR spectra, even though there is an increase of structure (as reported by CD, Figure 5A,B), could be due to the different spectroscopic time scales of far-UV CD and NMR, but it could be also reflecting the presence of a “fuzzy” complex between DNA and bHLHN (20, 68), where the increased amount of secondary structure (as monitored by CD) is flickering and not hydrogen-bonded, and there are still long polypeptide patches which remain disordered.
The assayed E-boxes correspond to E3-oligo, 5′-CTCTAACTGGCGACAGATGGGCCACTTTCT-3′, and E1-oligo, 5′-GGACCGGGAAGACCATATGGCGCATGCCGG-3′, which are the boxes recognized by NGN3, when forming heterodimers with the bHLH of the E47 protein (28).
Protein: DP00672 (UniProt Q92886)
Region: residues 90	to 150
Annotation: pre-molten globule (Structural state)
Evidence: fluorescence anisotropy evidence used in manual assertion
Supporting statements:
Our calculations suggest that the size of bHLHN is halfway between that of a molten globule (16.9 Å) and that of a premolten globule (21 Å). Since we have tested that bHLHN does not bind ANS (see above), as happens in other premolten globule structures (18), we suggest that the domain acquires a slightly collapsed premolten globule conformation.
Protein: DP00673 (UniProt P06935)
Region: residues 1	to 24
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD spectroscopy of WNV peptides (1–24) and (80–105) revealed that they are both completely unfolded (Figure 7C; deconvolution data not shown), suggesting that RNA chaperone activity of WNV core protein does not require a well-defined structure.
Protein: DP00673 (UniProt P06935)
Region: residues 80	to 105
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD spectroscopy of WNV peptides (1–24) and (80–105) revealed that they are both completely unfolded (Figure 7C; deconvolution data not shown), suggesting that RNA chaperone activity of WNV core protein does not require a well-defined structure.
Protein: DP00673 (UniProt P06935)
Region: residues 1	to 24
Annotation: DNA binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
As shown in Figure 7A, WNV 1–24 exhibited only a low level of strand-annealing activity, while WNV 80–105 caused efficient DNA duplex formation.
Protein: DP00673 (UniProt P06935)
Region: residues 80	to 105
Annotation: DNA binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
As shown in Figure 7A, WNV 1–24 exhibited only a low level of strand-annealing activity, while WNV 80–105 caused efficient DNA duplex formation.
Protein: DP00673 (UniProt P06935)
Region: residues 80	to 105
Annotation: RNA folding chaperone (Molecular function)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
The RNA chaperone activity of the WNV (80–105) peptide was further confirmed with the ribozyme cleavage assay, which requires both the strand annealing and helix unwinding activities of a chaperone.
 As expected, all core proteins induced a considerable increase in the cleavage rates, with hepacivirus core proteins demonstrating a higher activity compared to WNV and BVDV cores (Figure 4C).
Protein: DP00673 (UniProt P06935)
Region: residues 80	to 105
Annotation: RNA binding (Molecular function)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
The RNA chaperone activity of the WNV (80–105) peptide was further confirmed with the ribozyme cleavage assay, which requires both the strand annealing and helix unwinding activities of a chaperone.
Protein: DP00673 (UniProt P06935)
Region: residues 1672	to 1688
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:2FP7
Protein: DP00674 (UniProt Q69422)
Region: residues 2	to 155
Annotation: disorder (Structural state)
Evidence: temperature-induced protein unfolding evidence used in manual assertion
Supporting statements:
FL HCV and GBV-B core proteins retained most of their chaperone activity after boiling for 5 min (∼75%, based on PhosporImager quantification, see lanes 4–6 versus 7–9 in Figure 4A and lanes 29–31 versus 32–34 in Figure 4B).
Protein: DP00674 (UniProt Q69422)
Region: residues 2	to 155
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The isolated N-terminal domain of HCV core [core(2–117)], as well as the FL HCV and GBV-B core proteins are mostly unstructured in solution, showing an ellipticity minimum at ∼198 nm, characteristically of random-coil like peptides [(36) and Figure 5].
Protein: DP00674 (UniProt Q69422)
Region: residues 2	to 155
Annotation: DNA binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
The ability of purified proteins to stably bind RNA and DNA was verified by means of mobility shift assays. All four proteins bound both to RNA and DNA without a strict sequence specificity, and they caused complete retention of the nucleic acids at the top of the gel (indicative of the formation of large nucleoprotein complexes) at a protein-to-nucleotide molar ratio of ∼1:20 (data not shown).
Protein: DP00674 (UniProt Q69422)
Region: residues 2	to 155
Annotation: DNA binding, bending (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
The ability of purified proteins to stably bind RNA and DNA was verified by means of mobility shift assays. All four proteins bound both to RNA and DNA without a strict sequence specificity, and they caused complete retention of the nucleic acids at the top of the gel (indicative of the formation of large nucleoprotein complexes) at a protein-to-nucleotide molar ratio of ∼1:20 (data not shown).
Protein: DP00674 (UniProt Q69422)
Region: residues 2	to 155
Annotation: RNA folding chaperone (Molecular function)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
By means of classical in vitro RNA chaperone assays (e.g. strand annealing, strand exchange and ribozyme assays; Figures 2 and ​and3,3, and data not shown), we showed that nucleic acid chaperone activity is also conserved between the two hepacivirus core proteins, and that GBV-B core also efficiently facilitates the formation of the most stable nucleic acid structure. 
 As expected, all core proteins induced a considerable increase in the cleavage rates, with hepacivirus core proteins demonstrating a higher activity compared to WNV and BVDV cores (Figure 4C).
Protein: DP00675 (UniProt P19711)
Region: residues 169	to 270
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Natively unstructured proteins have a large proportion of solvent-exposed residues and are therefore highly susceptible to trace amounts of protease. Treatment of C87 or C90 with endoprotease GluC resulted in almost complete digestion within 1 minute when the core protein was present in a 10-fold excess (Fig. 2B). Similar results were seen with trypsin and chymotrypsin, and, for all three enzymes, proteolysis of C87 was complete within 1 hour even when core protein was in a 300-fold excess (data not shown). These results suggested that the majority of core residues are accessible to proteases.
Protein: DP00675 (UniProt P19711)
Region: residues 169	to 270
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
We next used intrinsic fluorescence spectroscopy to determine the environment of tyrosine residues within the core protein. The peak emission of C90 was observed at approximately 360 nm. Since an emission maximum at a wavelength greater than 340 nm indicates a high degree of solvent exposure, this again suggested that the core protein lacked significant globular structure (Fig. 2C).
Protein: DP00675 (UniProt P19711)
Region: residues 169	to 270
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The core protein was further analyzed for the presence of secondary structural elements by far-UV CD (reviewed in reference 19). The CD spectrum of C87 indicated a minimum at approximately 195 nm, consistent with a protein that lacks secondary structure ​(Fig. 2D). A minimum at 208 nm or 222 nm, indicative of α-helical or β-sheet secondary structures, was not observed.