LiteFold/DisProt huggingface dataset:
Protein: DP03361 (UniProt Q8ZKB0)
Region: residues 238	to 250
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
missing electron density region of rsgA from Salmonella typhimurium.
Cross-references: PDB:2RCN
Protein: DP03361 (UniProt Q8ZKB0)
Region: residues 338	to 350
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
IDR corresponding to the C-terminal domain of rsgA from Salmonella typhimurium.
Cross-references: PDB:2RCN
Protein: DP03362 (UniProt B0Y813)
Region: residues 119	to 142
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The mutation K127G appears to increase the flexibility of helix a4, leading to a disordered active site pocket.
Cross-references: PDB:7NC1
Protein: DP03362 (UniProt B0Y813)
Region: residues 119	to 142
Annotation: molecular function activator activity (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The mutation K127G appears to increase the flexibility of helix a4, leading to a disordered active site pocket.
Cross-references: PDB:7NC1
Protein: DP03363 (UniProt O05574)
Region: residues 50	to 110
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To evaluate the degree of disorder in Ruc, we measured the secondary structures found in Rucred and Rucox using circular dichroism (CD) spectroscopy (reviewed in reference 37). In accordance with structural predictions, both Rucred and Rucox yielded a CD spectrum characteristic of disordered proteins (Fig. 3C) (38).
Protein: DP03363 (UniProt O05574)
Region: residues 50	to 110
Annotation: protein folding chaperone (Molecular function)
Evidence: light scattering evidence used in manual assertion
Supporting statements:
We therefore propose that Rv0991c, which we named “Ruc” (redox-regulated protein with unstructured C terminus), represents a founding member of a new chaperone family that protects M. tuberculosis and other species from proteotoxicity during oxidative stress. 
Oxidized Ruc prevents unfolded protein aggregation in vitro.
When we measured luciferase aggregation using a different method of detection, light scattering (40), we also observed the inhibition of aggregation by Rucox but not by Rucred (Fig. S1A). Furthermore, chaperone activity by Ruc was observed when Ruc was pretreated with the oxidizing agents hypochlorite or nitric oxide (Fig. S1B), further supporting a model whereby oxidized Ruc counteracts protein aggregation.
In this study, we identified Ruc as the founding member of a new family of bacterial redox-regulated chaperones.
Protein: DP03363 (UniProt O05574)
Region: residues 50	to 110
Annotation: protein folding chaperone (Molecular function)
Evidence: deletion mutation phenotypic evidence used in manual assertion
Supporting statements:
We therefore propose that Rv0991c, which we named “Ruc” (redox-regulated protein with unstructured C terminus), represents a founding member of a new chaperone family that protects M. tuberculosis and other species from proteotoxicity during oxidative stress. 
We therefore asked if the intrinsically disordered C-terminal domain of Ruc was required for its chaperone activity. We produced a truncated Ruc variant, RucNterm (amino acids 1 through 49), which harbors only the zinc-binding motif (Fig. 4B, lane 2). In contrast to the variety of multimers observed for Rucox, oxidized RucNterm (RucNterm-ox) formed a single high-molecular-weight species (Fig. 4B, compare lanes 3 and 4). When we tested the chaperone activity of oxidized RucNterm (RucNterm-ox), we found that it was unable to prevent luciferase aggregation (Fig. 4C). Thus, the disordered C terminus of Ruc is required for its chaperone activity, either by binding to client protein, by influencing the conformation or oligomerization state of Ruc, or through a combination of factors.
In this study, we identified Ruc as the founding member of a new family of bacterial redox-regulated chaperones.
Protein: DP03364 (UniProt Q15582)
Region: residues 24	to 42
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The protein consists of a 23-residue signal peptide for secretion (M1-A23), a flexible linker (G24-R42), an N-terminal
cysteine-rich domain (Q43-P102), four consecutive FAS1 domains (FAS1-1, L103-T238; FAS1-2, I239-K377; FAS1-3, T378-P500; andFAS1-4, P501-N637) with 20% sequence identity to Drosophila fasciclin-1, and a 46-residue C-terminal segment (CTS;
R638-H683), which includes a ‘‘classic’’ integrin-recognition motif (RGD, residues R642-D644; Clout and Hohenester, 2003; Skonieret al., 1992).
In the crystal structure (seeTable 1), the protein was defined for residues Q43-N637, was monomeric, and had an elongated banana shape maximally spanning 120 A˚ (Figure 1A), which is in accordance with low-resolution small-angle X-ray scattering studies (Basaiawmoit et al., 2011).
Cross-references: PDB:5NV6
Protein: DP03364 (UniProt Q15582)
Region: residues 636	to 657
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Finally, based on the relaxation experiment described below, we have determined the C-terminal part (residues A636-Ala657) of the full-length WT FAS1-4 domain (Met502–Ala657) to be unstructured (data not shown).
Protein: DP03364 (UniProt Q15582)
Region: residues 638	to 683
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The protein consists of a 23-residue signal peptide for secretion (M1-A23), a flexible linker (G24-R42), an N-terminal cysteine-rich domain (Q43-P102), four consecutive FAS1 domains (FAS1-1, L103-T238; FAS1-2, I239-K377; FAS1-3, T378-P500; andFAS1-4, P501-N637) with 20% sequence identity to Drosophila fasciclin-1, and a 46-residue C-terminal segment (CTS; R638-H683), which includes a ‘‘classic’’ integrin-recognition motif (RGD, residues R642-D644; Clout and Hohenester, 2003; Skonieret al., 1992).
In the crystal structure (seeTable 1), the protein was defined for residues Q43-N637, was monomeric, and had an elongated banana shape maximally spanning 120 A˚ (Figure 1A), which is in accordance with low-resolution small-angle X-ray scattering studies (Basaiawmoit et al., 2011).
Cross-references: PDB:5NV6
Protein: DP03364 (UniProt Q15582)
Region: residues 641	to 645
Annotation: protein binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Co-immunoprecipitation revealed that TGFBIp interacted with integrin αVβ3.
Previous studies demonstrated that TGFBIp interacts directly with several integrins, including αVβ3, through mechanisms dependent and independent of the RGD binding motif [56,57]. These data suggest that the RGD motif mediates the internalization of TGFBIp through interaction with integrins.
TGFBIp interacts with integrin αVβ3 and αV.
We also examined the potential association of TGFBIp with αVβ3 integrin by co-immunoprecipitation. Cell lysates from corneal fibroblasts were subjected to immunoprecipitation with specific antibodies against integrin αV or αVβ3, and the resulting immunoprecipitates were analyzed for the presence of TGFBIp by western blot. Our data demonstrate that TGFBIp was coimmunoprecipitated by both integrin αV and αVβ3 antibodies (Fig 6B), suggesting the association between integrin αVβ3 and TGFBIp.
Taken together, these data demonstrate that TGFBIp is internalized via the interaction of αVβ3 or/and αVβ5 integrins with an RGD-motif in TGFBIp.
TGFBIp is internalized via a caveolin-dependent endocytic pathway and transported to the lysosomes for degradation. This internalization is mediated by RGD motif-dependent binding of TGFBIp to integrin αVβ3 or αVβ5.
Moreover, we showed that TGFBIp interacted with αV integrin, and that RGD peptide inhibited TGFBIp internalization in a dose-dependent manner. These data suggest that the RGD motif could mediate interaction with integrins, even though TGFBIp is also able to interact with integrins in the absence of this motif [71].
RGD motif (642-644) with flanking residues.
Protein: DP03364 (UniProt Q15582)
Region: residues 641	to 645
Annotation: protein binding (Molecular function)
Evidence: confocal microscopy evidence used in manual assertion
Supporting statements:
Previous studies demonstrated that TGFBIp interacts directly with several integrins, including αVβ3, through mechanisms dependent and independent of the RGD binding motif [56,57]. These data suggest that the RGD motif mediates the internalization of TGFBIp through interaction with integrins.
Consistent with these results, confocal microscopy analysis showed the co-localization of internalized TGFBIp and integrin αV in corneal fibroblasts (Fig 6C). Taken together, these data demonstrate that TGFBIp is internalized via the interaction of αVβ3 or/and αVβ5 integrins with an RGD-motif in TGFBIp.
TGFBIp is internalized via a caveolin-dependent endocytic pathway and transported to the lysosomes for degradation. This internalization is mediated by RGD motif-dependent binding of TGFBIp to integrin αVβ3 or αVβ5.
Moreover, we showed that TGFBIp interacted with αV integrin, and that RGD peptide inhibited TGFBIp internalization in a dose-dependent manner. These data suggest that the RGD motif could mediate interaction with integrins, even though TGFBIp is also able to interact with integrins in the absence of this motif [71].
RGD motif (642-644) with flanking residues.
Protein: DP03364 (UniProt Q15582)
Region: residues 641	to 645
Annotation: localization (Biological process)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
Moreover, treatment with arginine-glycine-aspartic acid (RGD) tripeptide suppressed the internalization of TGFBIp.
These data suggest that the RGD motif mediates the internalization of TGFBIp through interaction with integrins. Therefore, we evaluated whether RGD-mediated interactions of TGFBIp with integrins are involved in its internalization. Exogenous human TGFBIp was incubated with corneal fibroblasts in the presence of either RGD peptide or control RAD peptide for 2 h. In the presence of the RGD peptide, the amount of internalized TGFBIp was reduced in a dose-dependent manner (Fig 6A, left panel). However, intracellular TGFBIp levels did not change in cells incubated with the control RAD peptide (Fig 6A, right panel). These results suggest that RGD peptides disrupt TGFBIp internalization by preventing its endocytosis from the ECM.
TGFBIp is internalized via a caveolin-dependent endocytic pathway and transported to the lysosomes for degradation. This internalization is mediated by RGD motif-dependent binding of TGFBIp to integrin αVβ3 or αVβ5.
Moreover, we showed that TGFBIp interacted with αV integrin, and that RGD peptide inhibited TGFBIp internalization in a dose-dependent manner. These data suggest that the RGD motif could mediate interaction with integrins, even though TGFBIp is also able to interact with integrins in the absence of this motif [71].
RGD motif (642-644) with flanking residues.
Protein: DP03365 (UniProt P27469)
Region: residues 1	to 103
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
In analytical SEC experiments, human G0S2 eluted as a single peak (Figure ​Figure2A) with a retention volume corresponding to a Stokes radius (RS) of 18.8 Å. This value is 1.1 times larger than the theoretical value of 17.5 Å that can be calculated assuming that human G0S2 has a globular structure and a molecular weight of 11.3 kDa (Figure ​Figure2B).20 This difference resulted in being significant by means of a t-test of one sample (P = 0.0003). The experimental volume was 28.0 Å3, which was higher than the theoretical volume (22.4 Å3), while the experimental density of 0.4 kDa/Å3 was lower than the theoretical value (0.5 kDa/Å3, Table 1).
The extended conformation in human G0S2 could be explained in at least two possible ways. It may be due to a partially swelled tertiary structure, which would generate a globular conformation with larger dimensions, as in the case of a molten globule (MG). In this regard, the observed RS value (18.8 Å) is smaller compared to the expected RS value for an MG (19.9 Å).20 Alternatively, the extended conformation could also be attained by the presence of a disordered and extended region exposed to the solvent; in this case, the protein would have a globular domain with an extended segment that would generate an elongated conformation with the observed Rs.
Our SEC and DLS results suggest that the human G0S2 protein has an elongated shape with a globular domain of approximately 8 kDa.
Protein: DP03365 (UniProt P27469)
Region: residues 1	to 103
Annotation: disorder (Structural state)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
To gain further insights into the molecular shape of human and mouse G0S2 proteins, DLS measurements were subsequently carried out to calculate the hydrodynamic radius (Rh) for each protein. The size distribution of protein samples showed the presence of a single species with an apparent Rh of 1.4 ± 0.03 and 1.7 ± 0.02 nm, human and mouse G0S2, respectively (Figure3A).
Interestingly, the Rh obtained for the human G0S2 protein was smaller than the calculated RS value of 1.9 nm determined by SEC, indicating that this protein diffuses like a smaller protein in solution with an apparent size of 8 kDa.
The elongated conformation of the human G0S2 could be explained by the presence of a disordered C-terminal region, as suggested by the bioinformatic analysis. Indeed, a theoretical molecular weight of 7.5 kDa can be calculated for human G0S2 by omitting the C-terminal region, which is in accordance with the observed Rh value.
Our SEC and DLS results suggest that the human G0S2 protein has an elongated shape with a globular domain of approximately 8 kDa.
Protein: DP03365 (UniProt P27469)
Region: residues 1	to 103
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Secondary Structure Content Analysis Reveals That G0S2 Is Largely Unstructured.
To gain more insight into the structural content of G0S2, we used circular dichroism (CD) spectroscopy in the far UV region.31 The human and mouse G0S2 CD spectra exhibit properties previously observed for IDPs. They show a strong minimum signal close to 200 nm (−11.67 × 10–3 and −12.05 × 10–3 deg·cm2·dmol–1, human and mouse G0S2, respectively) and a small negative contribution close to 222 nm (−2.55 × 10–3 and −1.48 × 10–3 deg·cm2·dmol–1, human and mouse G0S2, respectively) (​Figure 5A).
Protein: DP03366 (UniProt P53778)
Region: residues 354	to 367
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
 No electron density was observed for amino acids 1–7, 34–39, 316–321, 330–334, and 354–end, therefore these residues were not included in the model.
Cross-references: PDB:1CM8
Protein: DP03367 (UniProt Q61585)
Region: residues 1	to 103
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To gain more insight into the structural content of G0S2, we used circular dichroism (CD) spectroscopy in the far UV region.31 The human and mouse G0S2 CD spectra exhibit properties previously observed for IDPs. They show a strong minimum signal close to 200 nm (−11.67 × 10–3 and −12.05 × 10–3 deg·cm2·dmol–1, human and mouse G0S2, respectively) and a small negative contribution close to 222 nm (−2.55 × 10–3 and −1.48 × 10–3 deg·cm2·dmol–1, human and mouse G0S2, respectively) (​Figure5A).
Protein: DP03368 (UniProt P38532-2)
Region: residues 213	to 503
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD spectroscopy was performed to determine the secondary- and tertiary-structure components of CT. Similar to several papers showing that intrinsically unstructured proteins display a very low abundance of secondary and tertiary structure (19−21, 23, 25), the CD spectra revealed that CT possesses an extended structure with little secondary or tertiary structure. The far-UV CD spectrum at pH 7 (Figure 2a and Table 1) revealed that the random coil is the major component (45). In the near-UV CD spectra, the weak signal at pH 7 also indicated no tertiary structure in CT (Figure 2b).
Protein: DP03368 (UniProt P38532-2)
Region: residues 213	to 503
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Determination of CT Hydrophobic Domain Formation. One characteristic of a natively unfolded protein is a lack of hydrophobic clusters. The hydrophobic probe TNS was used to monitor the hydrophobicity of CT. This probe has a low fluorescence quantum yield in a polar environment, such as water, and the quantum yield significantly increases when the probe is in a nonpolar environment. TNS fluorescence was nearly 0 when CT was incubated at neutral pH (pH 7.4), in the presence of 1 M TMAO, or in 30% TFE, indicating that CT lacks hydrophobic clusters under these conditions (Figure 4).
Protein: DP03368 (UniProt P38532-2)
Region: residues 213	to 503
Annotation: disorder (Structural state)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD spectroscopy was performed to determine the secondary- and tertiary-structure components of CT. Similar to several papers showing that intrinsically unstructured proteins display a very low abundance of secondary and tertiary structure (19−21, 23, 25), the CD spectra revealed that CT possesses an extended structure with little secondary or tertiary structure. The far-UV CD spectrum at pH 7 (Figure 2a and Table 1) revealed that the random coil is the major component (45). In the near-UV CD spectra, the weak signal at pH 7 also indicated no tertiary structure in CT (Figure 2b)
Protein: DP03368 (UniProt P38532-2)
Region: residues 213	to 503
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
The degree of compactness of CT was used as an indicator of the collapse to a globular structure. When CT migrated in a size-exclusion column, it eluted fastest at pH 7.4 and slowest at pH 4 (Figure 5). When CT both at pH 7.4 and in the presence of 1 M TMAO was compared to the molecular-weight markers that were run under the same conditions, it eluted with a molecular weight of 165 kDa, about 5 times greater than its calculated molecular weight of 31 kDa. At pH 4 or in the presence of 1 mM DTA, on the other hand, CT eluted at the volume corresponding to a molecular weight of 12.5−30 kDa.
Protein: DP03369 (UniProt O15391)
Region: residues 1	to 253
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
The SDS/PAGE profile of the purified proteins (Fig. 2A) shows an anomalous migration of YY2 and NTF2, in agreement with the observations of Nguyen et al. [1] and similar to what we had found for YY1 and NTF1 [11]. The apparent masses calculated from SDS/PAGE are higher than the formula molecular masses for YY2 and NTF2 (Table 1). The discrepancy is typical for intrinsically disordered proteins, as they bind less SDS due to the decreased content of hydrophobic residues [23].
Here, we provide the first detailed structural analysis of YY2, which allows to classify it as an intrinsically disordered protein. The attribution is based on YY2's hydrodynamic properties that are characteristic for a premolten globule, its high proteolytic susceptibility, high content of irregular structures shown by both CD measurements and bioinformatic analyses, and its anomalous migration in SDS/PAGE that arises from atypical amino acid composition.
To conclude, YY2 can be classified as an intrinsically disordered protein (IDP) with a bipartite structure: the ordered DBD2, responsible for DNA binding, and the disordered, flexible NTF2.
Protein: DP03369 (UniProt O15391)
Region: residues 1	to 253
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Interestingly, the hydrodynamic radius of full-length YY2 was nearly the same as for its fragment NTF2 (42.2 Å vs 43.3 Å). The calculated Stokes radii can be compared to formula molecular masses to determine the compactness of the protein conformation (Fig. 4). The analysis of the Stokes radii vs the molecular masses predicts a premolten globule structure for YY2, a molten globule for DBD2 and a natively unfolded state for NTF2. Stokes radii of all three proteins increase in the presence of urea as compared to their respective values in native conditions (Table 3). Therefore, NTF2 also contains some residual stable structures in native conditions.
Here, we provide the first detailed structural analysis of YY2, which allows to classify it as an intrinsically disordered protein. The attribution is based on YY2's hydrodynamic properties that are characteristic for a premolten globule, its high proteolytic susceptibility, high content of irregular structures shown by both CD measurements and bioinformatic analyses, and its anomalous migration in SDS/PAGE that arises from atypical amino acid composition.
To conclude, YY2 can be classified as an intrinsically disordered protein (IDP) with a bipartite structure: the ordered DBD2, responsible for DNA binding, and the disordered, flexible NTF2.
Protein: DP03369 (UniProt O15391)
Region: residues 1	to 253
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The spectrum registered for YY2 is typical for a protein with a considerable content of α-helices and β-sheets, with a double minimum at 200–230 nm and a maximum around 190 nm. The spectrum of NTF2 lacks the 190 nm maximum, which comes from α-helical structures. The 205 nm minimum is blue-shifted for NTF2 and red-shifted for DBD2, suggesting differing contributions from α- and β-structures. The spectra of YY1 and YY2 variants are generally similar in shape, especially the ones of DBD1 and DBD2. The spectrum of NTF2 has a more pronounced shoulder at 222 nm than the one of NTF1. The 222 nm shoulder also differentiates the spectra of full-length YY1 and YY2, together with the maximum at 190 nm, which is greater for YY2 than for YY1. The results of the bioinformatic analysis presented in Fig. 1 correspond with the CD spectra of YY1, YY2, and their fragments (Fig. 5)
Here, we provide the first detailed structural analysis of YY2, which allows to classify it as an intrinsically disordered protein. The attribution is based on YY2's hydrodynamic properties that are characteristic for a premolten globule, its high proteolytic susceptibility, high content of irregular structures shown by both CD measurements and bioinformatic analyses, and its anomalous migration in SDS/PAGE that arises from atypical amino acid composition.
To conclude, YY2 can be classified as an intrinsically disordered protein (IDP) with a bipartite structure: the ordered DBD2, responsible for DNA binding, and the disordered, flexible NTF2.