LiteFold/DisProt huggingface dataset:
Protein: DP00265 (UniProt P04925)
Region: residues 23	to 51
Annotation: protein binding (Molecular function)
Evidence: enzyme-linked immunoabsorbent assay evidence used in manual assertion
Supporting statements:
Authors test whether AB soluble aggregates (SBAs), alpha-synuclein soluble aggregates (SAAs) and TAU soluble aggregates (STAs) are able to bind PrP in the absence and in the presence of competing antibodies, analyzed by ELISA. Being, MI-0131 a specific antibody of the 23-51 region and ICSM35 a specific antibody of the region 93-105. Both regions comprised in the N-terminus intrinsically disordered region of PrP. To confirm the hypothesis, the authors analyzed the interaction of PrP truncations lacking one or both of the hypothesized interacting regions.
AB-->SBAs bound to PrP23–231 with an average EC50 of 38.9 nM, whereas neither Aβ monomers nor fibrils showed appreciable affinity for PrP (Fig. 2a). We tested whether mAbs directed to Site I (MI-0131) and Site II (ICSM35) (Supplementary Table 2) could prevent SPA binding. Both mAbs bound similarly well to PrP (Supplementary Figure 1e) and displaced SBAs to a comparable extent, with ICSM35 always slightly more effective (Fig. 2d).
Alpha-synuclein and TAU --> SAAs (Fig. 2b) and STAs (Fig. 2c) also bound to PrP in a saturable manner with average EC50s of 34.3 nM and 9.5 nM, respectively. Monomeric and fibrillar forms of αSyn and tau exhibited weak or no affinity for PrP23–231. we tested whether mAbs directed to Site I (MI-0131) and Site II (ICSM35) (Supplementary Table 2) could prevent SPA binding. Both mAbs bound similarly well to PrP (Supplementary Figure 1e) and displaced SBAs to a comparable extent, with ICSM35 always slightly more effective (Fig. 2d). Interestingly, comparable IC50 trends were observed for SAAs (Fig. 2e; ICSM35 = 5.2 nM and MI-0131 = 11.9 nM) and STAs (Fig. 2f; ICSM35 = 2.0 nM and MI-0131 = 5.0 nM). Similarly, SAAs and STAs showed little affinity for PrP119–231 and greatly diminished binding to PrP91–231 (Fig. 2h, i).
Protein: DP00265 (UniProt P04925)
Region: residues 93	to 105
Annotation: protein binding (Molecular function)
Evidence: enzyme-linked immunoabsorbent assay evidence used in manual assertion
Supporting statements:
Authors test whether AB soluble aggregates (SBAs), alpha-synuclein soluble aggregates (SAAs) and TAU soluble aggregates (STAs) are able to bind PrP in the absence and in the presence of competing antibodies, analyzed by ELISA. Being, MI-0131 a specific antibody of the 23-51 region and ICSM35 a specific antibody of the region 93-105. Both regions comprised in the N-terminus intrinsically disordered region of PrP. To confirm the hypothesis, the authors analyzed the interaction of PrP truncations lacking one or both of the hypothesized interacting regions.
AB-->SBAs bound to PrP23–231 with an average EC50 of 38.9 nM, whereas neither Aβ monomers nor fibrils showed appreciable affinity for PrP (Fig. 2a). We tested whether mAbs directed to Site I (MI-0131) and Site II (ICSM35) (Supplementary Table 2) could prevent SPA binding. Both mAbs bound similarly well to PrP (Supplementary Figure 1e) and displaced SBAs to a comparable extent, with ICSM35 always slightly more effective (Fig. 2d).
Alpha-synuclein and TAU --> SAAs (Fig. 2b) and STAs (Fig. 2c) also bound to PrP in a saturable manner with average EC50s of 34.3 nM and 9.5 nM, respectively. Monomeric and fibrillar forms of αSyn and tau exhibited weak or no affinity for PrP23–231. we tested whether mAbs directed to Site I (MI-0131) and Site II (ICSM35) (Supplementary Table 2) could prevent SPA binding. Both mAbs bound similarly well to PrP (Supplementary Figure 1e) and displaced SBAs to a comparable extent, with ICSM35 always slightly more effective (Fig. 2d). Interestingly, comparable IC50 trends were observed for SAAs (Fig. 2e; ICSM35 = 5.2 nM and MI-0131 = 11.9 nM) and STAs (Fig. 2f; ICSM35 = 2.0 nM and MI-0131 = 5.0 nM). Similarly, SAAs and STAs showed little affinity for PrP119–231 and greatly diminished binding to PrP91–231 (Fig. 2h, i).
Protein: DP00265 (UniProt P04925)
Region: residues 23	to 114
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: confocal laser scanning microscopy evidence used in manual assertion
Supporting statements:
Authors study LLPS of the full-length protein and truncated versions corresponding to the disordered N-term, occurring in vivo. N1 harbors both interacting regions of the IDR of PrP, while N2 only harbors one interacting region. C1 and C2 correspond to the C-terminus PrP resulting from each cleavage, respectively. Finally, they mutate key charged residues (recognition motifs) and hydrophobic residues (central region of N1) to demonstrate that LLPS of Prp is driven by cation-pi interaction. 
Full-length PrP rapidly formed droplets upon TEV protease cleavage, indicative of LLPS (Fig. 1C, TEV+). N1 underwent phase separation similarly to full-length PrP, indicating that the structural elements in the C-terminal domain are not required for the formation of biomolecular condensates. In contrast, N2 formed irregular assemblies instead of liquid-like droplets. Consequently, we analyzed C1 and C2, the C-terminal fragments generated after α- or β-cleavage, in parallel to N1 or N2 (Fig. 1A). Both before and after TEV cleavage, GFP fluorescence was evenly distributed, indicating that neither C1 nor C2 formed biomolecular condensates under these conditions, corroborating recent results (41).
Full-length PrPs as well as N1 molecules in the droplets were highly dynamic, characteristic of a liquid-like state. In contrast, fluorescence recovery of the irregular N2 structures was greatly delayed, indicating formation of a gel-like or aggregated state (Fig. 2A, lower panels). 
Results: We analyzed the conformation of phase-separated N1 after purifying recombinant N1 lacking both the MBP and GFP tag. The CD spectrum of N1 is characterized by a negative CD band below 210 nm, indicating that the protein displays a fully disordered secondary structure at this condition (46).
On the molecular level, phase separation is governed primarily by basic residues within the Aβ-binding domain, most likely through intermolecular cation–π interactions of the lysines with neighboring aromatic side chains (Fig. 4).
Protein: DP00265 (UniProt P04925)
Region: residues 23	to 114
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
Authors study LLPS of the full-length protein and truncated versions corresponding to the disordered N-term, occurring in vivo. N1 harbors both interacting regions of the IDR of PrP.
Dynamic light scattering (DLS) experiments were carried out to determine the size of the N1 droplets (Fig. 2E). Based on the intensity distribution functions of the hydrodynamic radius, the N1 samples exhibited a largely polydisperse size distribution pattern, indicative of droplet formation of sizes ranging from 40 to several 1000 nm.
Protein: DP00265 (UniProt P04925)
Region: residues 23	to 114
Annotation: molecular adaptor activity (Molecular function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
n total we identified 233 N-PrP-binding partners in the AD brain (Fig 2, S1 Table) and 212 in the non-AD brain (Fig 2, S2 Table). Among those 104 were overlapping interactors found in both brain homogenates (Fig 2, S3 Table), while 129 proteins were exclusively found in AD brain (Fig 2, S4 Table) and 107 in non-AD brain (Fig 2, S5 Table).
These findings support the concept that the intrinsically disordered N-terminal domain is a major mediator of PrP-protein interactions.
Protein: DP00269 (UniProt Q24298)
Region: residues 1350	to 1507
Annotation: disorder (Structural state)
Evidence: experimental evidence used in manual assertion
Supporting statements:
DEcyto has two tryptophans that are near the N and C termini, the latter in a position distinct from the tryptophan in Ecyto. In a folded protein, the tryptophan indole ring is frequently buried within a hydrophobic core or is otherwise shielded from solvent, resulting in a blue shift of the fluorescence maximum relative to free tryptophan (36). The tryptophan emission maximum for β76, a thrombin-generated fragment of β-catenin (see “Experimental Procedures”), is significantly blue-shifted relative to tryptophan alone, whereas the maxima for Ecyto and DEcyto are not (Table I). Thus, the single Ecyto tryptophan and two DEcyto tryptophans appear to be solvent exposed.
The fluoresence anisotropy data suggest that the Ecyto and DEcyto domains are unfolded under native conditions.
Fluorescence, circular dichroism, and proton NMR were used to characterize the folded state of recombinant E-cadherin and DE-cadherin cytoplasmic domains (rEcyto and rDEcyto respectively).
Protein: DP00269 (UniProt Q24298)
Region: residues 1350	to 1507
Annotation: disorder to order (Structural transition)
Evidence: experimental evidence used in manual assertion
Supporting statements:
Fluorescence, circular dichroism, and proton NMR were used to characterize the folded state of recombinant E-cadherin and DE-cadherin cytoplasmic domains (rEcyto and rDEcyto respectively).
DEcyto has two tryptophans that are near the N and C termini, the latter in a position distinct from the tryptophan in Ecyto. In a folded protein, the tryptophan indole ring is frequently buried within a hydrophobic core or is otherwise shielded from solvent, resulting in a blue shift of the fluorescence maximum relative to free tryptophan (36). The tryptophan emission maximum for β76, a thrombin-generated fragment of β-catenin (see “Experimental Procedures”), is significantly blue-shifted relative to tryptophan alone, whereas the maxima for Ecyto and DEcyto are not (Table I). Thus, the single Ecyto tryptophan and two DEcyto tryptophans appear to be solvent exposed.
Protein: DP00269 (UniProt Q24298)
Region: residues 1350	to 1507
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Fluorescence, circular dichroism, and proton NMR were used to characterize the folded state of recombinant E-cadherin and DE-cadherin cytoplasmic domains (rEcyto and rDEcyto respectively).
The spectra measured for rEcyto and rDEcyto at 0 °C are essentially identical and feature a single minimum in mean residue ellipticity at ∼202 nm (Fig. 1). This spectrum indicates a lack of secondary structure, which would be expected of an unstructured polypeptide.
Protein: DP00269 (UniProt Q24298)
Region: residues 1350	to 1507
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Fluorescence, circular dichroism, and proton NMR were used to characterize the folded state of recombinant E-cadherin and DE-cadherin cytoplasmic domains (rEcyto and rDEcyto respectively).
Protein: DP00269 (UniProt Q24298)
Region: residues 1350	to 1507
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
rDEcyto-β-catenin complex was also digested with subtilisin as described for rEcyto.
However, in the presence of β-catenin, what appears to be full-length rEcyto remains at subtilisin (Fig.5) and endoproteinase Glu-C (data not shown) concentrations that completely degrade rEcyto alone (Fig. 5, lanes 5 and 7 or lanes 12 and14). Similar protection results were obtained with the DEcyto-β-catenin complex and subtilisin (data not shown).
Protein: DP00269 (UniProt Q24298)
Region: residues 1350	to 1507
Annotation: protein binding (Molecular function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
rDEcyto-β-catenin complex was also digested with subtilisin as described for rEcyto.
However, in the presence of β-catenin, what appears to be full-length rEcyto remains at subtilisin (Fig.5) and endoproteinase Glu-C (data not shown) concentrations that completely degrade rEcyto alone (Fig. 5, lanes 5 and 7 or lanes 12 and14). Similar protection results were obtained with the DEcyto-β-catenin complex and subtilisin (data not shown).
Protein: DP00269 (UniProt Q24298)
Region: residues 1350	to 1507
Annotation: protein binding (Molecular function)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Mixtures of rEcyto or rDEcyto and various β-catenin constructs were incubated for more than 1 h at 4 °C and injected onto an Amersham Pharmacia Biotech HR 10/30 Superdex 200 size exclusion column equilibrated with 50 mm Tris-HCl, pH 8, 200 mm NaCl, 20 mm EDTA, and 1 mmDTT.
Protein: DP00269 (UniProt Q24298)
Region: residues 1350	to 1507
Annotation: molecular function regulator (Molecular function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
It is proposed that binding of cadherins to beta-catenin prevents recognition of degradation signals that are exposed in the unstructured cadherin cytoplasmic domain, favoring a cell surface population of catenin-bound cadherins capable of participating in cell adhesion.
Protein: DP00271 (UniProt P02699)
Region: residues 226	to 242
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Thus, although our model demonstrates a highly flexible nature of this region and still lacks the tetrapeptide from Gln236 to Glu239, it is obvious that C-III does not fold over the helical region at all.
Cross-references: PDB:1F88
Protein: DP00271 (UniProt P02699)
Region: residues 327	to 348
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The extreme COOH-terminal residues are themost exposed part of rhodopsin molecule and could be involved in vectorial transport of rhodopsin to rod outer segment.
The helical structure appears to be terminated by Gly324 and the following COOH-terminal tail changes the direction. Although current model lacks residues from 328 to 333, the positions of 327 and 334 suggest that this missing part runs covering the short H-VIII helix from the solvent region. As a whole, COOH-terminal tail of rhodopsin occupies the space over only a part of the helical bundle, H-I and H-VII.
Cross-references: PDB:1F88
Protein: DP00271 (UniProt P02699)
Region: residues 327	to 348
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In molecule B, more residues are missing, including the C-terminus beyond residue Asn326 (Figure 2). Almost certainly, the C-terminal residues of rhodopsin are flexible and mobile in the physiological milieu, lacking a definite single conformation (58, 59).
Cross-references: PDB:1HZX
Protein: DP00271 (UniProt P02699)
Region: residues 334	to 348
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-terminal tail in the P31 form is located in the solvent channel and disordered, while in the P41 form it is partially resolved only in molecule A, where it is stabilised through contacts with the extracellular domain of a neighbouring molecule. Finding significant NCS differences in the same surface segments indicates an intrinsic conformational variability or flexibility of those segments, and the high B-factors of the segments support this.
Cross-references: PDB:1GZM
Protein: DP00278 (UniProt P08050)
Region: residues 255	to 314
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The overall structure of the Cx43CT was mainly random coiled; however, two regions of helical structure were present (Fig. 1, A and B). These helical regions were superimposed on the basis of backbone coordinates from Ala-315–Thr-326 and Asp-340–Ala-348 (Fig. 1C). The total root mean square deviations for these alignments were 0.27 and 0.34 Å, respectively. Structural statistics are presented in Table I. The predominately random coil structure for the Cx43CT is consistent with the narrow chemical shift dispersions in the 15N HSQC (Fig. 1D).
Cross-references: PDB:1R5S
Protein: DP00278 (UniProt P08050)
Region: residues 264	to 372
Annotation: SH3 domain binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The addition of the SH3 domain affected the resonance peaks of amino acids Lys-264–Lys-287, Ser-306–Glu-316, His-331–Phe-337, Leu-356–Val-359, and Ala-367–Ser-372 (Fig. 3). Only the region Lys-264–Lys-287 contains the amino acids previously reported to act as an SH3 binding domain (43, 44, 45).
The peptide competition experiments indicated that the Cx43CT-SH3 complex was inhibited by peptides 271–287, 312–336, and 346–360 (Fig. 3B and Supplemental Data 2), as indicated by the re-emergence of all resonance peaks affected in Fig. 3A.
Protein: DP00278 (UniProt P08050)
Region: residues 327	to 382
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The overall structure of the Cx43CT was mainly random coiled; however, two regions of helical structure were present (Fig. 1, A and B). These helical regions were superimposed on the basis of backbone coordinates from Ala-315–Thr-326 and Asp-340–Ala-348 (Fig. 1C). The total root mean square deviations for these alignments were 0.27 and 0.34 Å, respectively. Structural statistics are presented in Table I. The predominately random coil structure for the Cx43CT is consistent with the narrow chemical shift dispersions in the 15N HSQC (Fig. 1D).
The helical region Asp-340–Ala-348 is too short to be considered as structured.
Cross-references: PDB:1R5S
Protein: DP00278 (UniProt P08050)
Region: residues 327	to 382
Annotation: flexible C-terminal tail (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The overall structure of the Cx43CT was mainly random coiled; however, two regions of helical structure were present (Fig. 1, A and B). These helical regions were superimposed on the basis of backbone coordinates from Ala-315–Thr-326 and Asp-340–Ala-348 (Fig. 1C). The total root mean square deviations for these alignments were 0.27 and 0.34 Å, respectively. Structural statistics are presented in Table I. The predominately random coil structure for the Cx43CT is consistent with the narrow chemical shift dispersions in the 15N HSQC (Fig. 1D).
The helical region Asp-340–Ala-348 is too short to be considered as structured.
Cross-references: PDB:1R5S
Protein: DP00278 (UniProt P08050)
Region: residues 364	to 382
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The addition of the PDZ-2 domain affected the resonance peaks of the last 19 amino acids of the Cx43CT, a region larger than what was expected from the putative “PDZ binding domain” of Cx43 (the final 4 amino acids in the carboxyl terminus (42)). Indeed, as seen in Fig. 2A, the signal from residues Ser-372–Ile-382 completely disappeared (i.e. broadened beyond detection), whereas the amplitude of the peaks corresponding to residues Ser-364–Ala-371 decreased in intensity. These changes can be explained by decreased tumbling rates caused by an increase in molecular weight and/or intermediate chemical exchange rates, both indicative of a structural modification caused by the association of the two molecules.
Protein: DP00278 (UniProt P08050)
Region: residues 255	to 382
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
As expected from the NMR data, Cx40CT and Cx43CT at pH 6.0 present a high proportion of random-coiled structure (major absorption at 200 nm for Cx40CT and 201 nm for Cx43CT) (Fig. 3A).
Protein: DP00282 (UniProt Q04656)
Region: residues 1125	to 1176
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The region 1125–1176, which constitutes a long loop between strands
β3 and β4, is disordered in both structures consistently with the lack of long range NOEs involving these residues and with its afore mentioned dynamics.
A protein loop of 50 amino acids located between β3 and β4 is disordered
and mobile on the subnanosecond time scale. 
The unstructured loop was omitted for simplicity. Bottom panel, the backbone traces for the twenty lowest energy conformers are superimposed.
Notably, the CopA N-domain lacks the long unstructured loop involving
residues 1125–1176 of N-MNK.
Cross-references: BMRB:16441
PDB:2KMX
PDB:2KMV
BMRB:16440
Protein: DP00284 (UniProt P16009)
Region: residues 346	to 361
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing residues reported at positions 346-361
Cross-references: PDB:5IV5
Protein: DP00284 (UniProt P16009)
Region: residues 346	to 361
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing residues reported at positions 346-361
Cross-references: PDB:1PDL
Protein: DP00284 (UniProt P16009)
Region: residues 346	to 361
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with high relative B-factor values used in manual assertion
Supporting statements:
Seven residues upstream and nine residues downstream of the cleavage site are
disordered in the crystal structure.
Cross-references: PDB:1K28
Protein: DP00284 (UniProt P16009)
Region: residues 346	to 361
Annotation: flexible linker (Disorder function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
The gp5 lysozyme domain, located on the periphery of the central
b-helix, is connected to the N-terminal domain by linker 1 and to
the C-terminal b-helical domain by linker 2, which contains the
cleavage site between gp5* and gp5C (Fig. 1a). Seven residues
upstream and nine residues downstream of the cleavage site are
disordered in the crystal structure.
Cross-references: PDB:1K28
Protein: DP00284 (UniProt P16009)
Region: residues 350	to 354
Annotation: limited proteolysis display site (Disorder function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
The gp5 lysozyme domain, located on the periphery of the central
b-helix, is connected to the N-terminal domain by linker 1 and to
the C-terminal b-helical domain by linker 2, which contains the
cleavage site between gp5* and gp5C (Fig. 1a). Seven residues
upstream and nine residues downstream of the cleavage site are
disordered in the crystal structure.
Cross-references: PDB:1K28
Protein: DP00284 (UniProt P16009)
Region: residues 346	to 361
Annotation: limited proteolysis display site (Disorder function)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
The N-terminal sequences of these three bands as determined by Edman degradation were MEMISNN-, MEMISNN-, and AMAATVA-, respectively, indicating that the last two bands were the cleavage products of the first and that the two fragments were held together after cleavage
Protein: DP00285 (UniProt P10388)
Region: residues 168	to 461
Annotation: disorder (Structural state)
Evidence: Raman spectroscopy evidence used in manual assertion
Supporting statements:
Similar ROA bands have been reported for a number of proteins with irregular, natively unfolded, and non-native folds (26−28, 53)     and have also been assigned to residues with the PPII-helical conformation in loop regions of a viral coat protein ( 54).