LiteFold/DisProt huggingface dataset:
Protein: DP00461 (UniProt P08083)
Region: residues 1	to 90
Annotation: protein binding (Molecular function)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
The binding of full-length (ColN-(1–90)) T-domain to these TolA variants was measured using fluorescence spectroscopy and gel filtration chromatography. The T-domain contains two tryptophans that become buried upon TolA binding causing both an increase and a blue shift of their fluorescence emission (32–34). Both TolA variants with natural C termini bound to T-domain with similar affinity.
A decrease in elution volume (increase in size) was observed when T-domain was mixed with TolA-(296 – 421) and TolA-(329 – 421) but not in the presence of TolAT.
Protein: DP00461 (UniProt P08083)
Region: residues 1	to 90
Annotation: pre-molten globule (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
As expected the T-domain in solution is predicted to have more random structure (H4/S31/T23/R41), but the strand content is significant.
The disordered nature of this domain is revealed by far-UV CD spectra (Fig. 1 and previous work (19, 33, 34)), and we show here that the T-domain also lacks two further features of folded proteins. The first is cooperative folding/unfolding as revealed by heat denaturation. The far-UV CD spectra recorded at increasing temperatures show a gradual almost linear change with temperature consistent with the isolated unfolding of individual structures rather than the sigmoidal unfolding curves found with proteins folded in cooperative domains (Fig. 4). The fact that the T-domain “unfolds” with temperature is supportive of the possibility that it contains some secondary structure (premolten globule) or polyproline II helix (PII), which can at higher temperatures adopt a different conformation (46).
Protein: DP00461 (UniProt P08083)
Region: residues 1	to 90
Annotation: pre-molten globule (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
The gel filtration data here further show that the hydrodynamic radius of free T-domain is only slightly larger than a folded protein of this size.
Protein: DP00461 (UniProt P08083)
Region: residues 1	to 90
Annotation: disorder (Structural state)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
The near-UV CD spectra of T-domain is virtually featureless and consistent with its mobile and exposed aromatic residues (Fig. 3A)
Protein: DP00461 (UniProt P08083)
Region: residues 1	to 90
Annotation: disorder to order (Structural transition)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
The difference between the predicted and experimental spectra is shown in Fig. 3C (solid line). This reveals an additional positive signal in the spectrum of the complex in the region 270–290 nm with clearly resolved peaks at 272, 279, and 290 nm. The latter is unique to tryptophan and thus can be directly linked to T-domain folding upon binding.
In fact, the near-UV CD spectrum of the complex provides evidence of an additional tryptophan signal that can only come from ordering of the T-domain.
Protein: DP00461 (UniProt P08083)
Region: residues 40	to 76
Annotation: protein binding (Molecular function)
Evidence: surface plasmon resonance evidence used in manual assertion
Supporting statements:
The peptide was concentrated with a Speed-Vac (Savant, Albertville, MN) and desalted on PD-10 columns (Amersham Biosciences). Its binding to
TolA-II,III resembled the binding of the full-length T-domain since a Kd of 1.3 uM was obtained by the surface plasmon resonance (SPR) measurement.
Protein: DP00461 (UniProt P08083)
Region: residues 40	to 76
Annotation: protein binding (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
The peptide was concentrated with a Speed-Vac (Savant, Albertville, MN) and desalted on PD-10 columns (Amersham Biosciences). Its binding to
TolA-II,III resembled the binding of the full-length T-domain since a Kd of 1.3 uM was obtained by the surface plasmon resonance (SPR) measurement. In addition, the tryptophan fluorescence spectrum exhibited the same increase and blue-shift upon TolA-II,III binding.
Protein: DP00461 (UniProt P08083)
Region: residues 40	to 76
Annotation: pre-molten globule to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Adding unlabeled TolA-III to the labeled T-domain peptide immediately caused new peaks to appear with some of the original peaks reducing in intensity. The number and intensity of the new signals continued to increase with further additions of TolA-III and the intensity of the original peaks reducing further.
Thus, the NMR data clearly demonstrate that the colicin N T-domain 40 –76 peptide and TolA-III formed a complex and that the peptide adopts an organized structure in the complex.
Protein: DP00461 (UniProt P08083)
Region: residues 40	to 76
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Adding unlabeled TolA-III to the labeled T-domain peptide immediately caused new peaks to appear with some of the original peaks reducing in intensity. The number and intensity of the new signals continued to increase with further additions of TolA-III and the intensity of the original peaks reducing further. This trend continued until a 1:2 molar ratio was obtained. Increasing the ratio to 1:4 gave no further changes, indicating that the proteins were already fully bound.
Protein: DP00461 (UniProt P08083)
Region: residues 1	to 90
Annotation: protein binding (Molecular function)
Evidence: surface plasmon resonance evidence used in manual assertion
Supporting statements:
Complex formation was also checked in the temperature range 20–40 °C by SPR (BIACORE) (Fig. 7). TolA-(296–421) was immobilized, and increasing concentra- tions of T-domain were injected over it. The amount of stably bound T-domain at each temperature was determined by allowing the binding to reach equilibrium. The binding decreased with increasing temperature.
Kd values for the binding of TolA constructs to T-domain of colicin N
The averages of two to three independent experiments +/- S.D. are presented.
SPR: TolA-(296–421), 20 °C – Kd: 0.35 +/- 0.02 uM; 30 °C – Kd: 2.72 +/- 1.51 uM
Protein: DP00463 (UniProt Q9Z0U4)
Region: residues 17	to 98
Annotation: molten globule (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The 1H-15N HSQC spectrum of CCP1 is characterized by a mixture of sharp and broad resonances. Many of these signals have poor 1H dispersion, implying that there is a substantial part of CCP1 that is not compactly structured. On the other hand, the presence of a number of dispersed non-glycine resonances in its 1H-15N HSQC spectrum indicates some structure within CCP1.
Taken together, the biophysical data suggest that CCP1 contains a mixture of ordered and molten globular parts.
Protein: DP00463 (UniProt Q9Z0U4)
Region: residues 17	to 98
Annotation: molten globule (Structural state)
Evidence: differential scanning calorimetry evidence used in manual assertion
Supporting statements:
In contrast, the CCP1 DSC profile (Fig. 4b) has no heat absorption peak over the temperature range employed (22–100 °C), although a weak negative transition can be observed at ∼52 °C prior to a substantial decline in heat capacity above 60 °C.
This result strongly suggests that recombinant CCP1 has little rigid tertiary structure, in contrast to CCP2.
Taken together, the biophysical data suggest that CCP1 contains a mixture of ordered and molten globular parts.
Protein: DP00463 (UniProt Q9Z0U4)
Region: residues 17	to 98
Annotation: molten globule (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CCP1 showed a well defined positive ellipticity in the far-UV region centered at 228 nm (Fig. 5a), which was noteworthy in view of the low extent of folding implied by NMR spectroscopy and the lack of thermal stability inferred from the DSC studies.
Taken together, the biophysical data suggest that CCP1 contains a mixture of ordered and molten globular parts.
Protein: DP00463 (UniProt Q9Z0U4)
Region: residues 17	to 98
Annotation: molten globule (Structural state)
Evidence: fluorescence anisotropy evidence used in manual assertion
Supporting statements:
By contrast, ANS bound strongly to CCP1 (Fig. 6b). This is evidence of the presence of a substantial number of solvent-accessible non-polar groups in CCP1 and implies strongly that CCP1 is not compactly folded.
Taken together, the biophysical data suggest that CCP1 contains a mixture of ordered and molten globular parts.
Protein: DP00463 (UniProt Q9Z0U4)
Region: residues 17	to 98
Annotation: protein binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
As shown in Fig. 2d (lower panel), CCP1 (but not CCP2) pulled down full-length fibulin-2.
Protein: DP00466 (UniProt P04156)
Region: residues 23	to 124
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The NMR structure of the intact recombinant human prion protein, hPrP(23–230), contains a globular domain that extends approximately from residues 125–228, a flexibly extended N-terminal tail of residues 23–124, and a short flexible chain end of residues 229–230 ​(Fig. 1a), which is similar to the previously described structure of mPrP(23–231) (14, 15) and the characterization of shPrP(29–231) (16). These global features are qualitatively manifested in the small dispersion of the 1H chemical shifts and negative values of the 15N{1H}-NOEs for the residues 23–124, as described in detail for mPrP(23–231) (14), which contrasts with the fact that the corresponding parameters for the residues 125–228 have typical values for a globular protein of the size of hPrP(23–230).
Cross-references: PDB:1QLX
PDB:1QLZ
Protein: DP00466 (UniProt P04156)
Region: residues 23	to 124
Annotation: flexible N-terminal tail (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The NMR structure of the intact recombinant human prion protein, hPrP(23–230), contains a globular domain that extends approximately from residues 125–228, a flexibly extended N-terminal tail of residues 23–124, and a short flexible chain end of residues 229–230 ​(Fig. 1a), which is similar to the previously described structure of mPrP(23–231) (14, 15) and the characterization of shPrP(29–231) (16). These global features are qualitatively manifested in the small dispersion of the 1H chemical shifts and negative values of the 15N{1H}-NOEs for the residues 23–124, as described in detail for mPrP(23–231) (14), which contrasts with the fact that the corresponding parameters for the residues 125–228 have typical values for a globular protein of the size of hPrP(23–230).
The region 1-22 corresponds to a signal peptide, absent in the mature form of the protein. Therefore this region corresponds to the N-terminal flexible tail of the mature protein. 
Cross-references: PDB:1QLZ
PDB:1QLX
Protein: DP00466 (UniProt P04156)
Region: residues 23	to 124
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Upon Aβo binding and hydrogel formation (Fig. 4B, 4D, 4F), both Gly and Ala spectral regions shift from random coil to α-helical secondary chemical shifts. For Ala, the Cα-Cβ peaks (Fig. 4E, 4F) shift entirely from random coil to α-helical, indicating that a domain including AA113–120 forms an α-helix upon Aßo binding. A similar shift is observed for most Gly resonances. This implies that the octapeptide-repeat region adopts a helical conformation upon Aßo binding.
Protein: DP00466 (UniProt P04156)
Region: residues 23	to 124
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: fluorescence recovery after photobleaching evidence used in manual assertion
Supporting statements:
FRAP demonstrated rapid recovery of PrP-Alexa568 fluorescence due to facile translational diffusion of PrPC (Fig. 1E).
Protein: DP00466 (UniProt P04156)
Region: residues 23	to 124
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: confocal microscopy evidence used in manual assertion
Supporting statements:
Time lapse imaging reveals that as PrPC droplets settle, they spread and relax within seconds, accumulating as flat pools. The PrPC layer grows thicker as PrPC droplets settle (Fig. 1F, Fig. S1E, Movie M1). 
Confocal imaging of PrPC liquid droplet spreading on surface. 
PrPC droplets are dense, settling to form a viscous PrPC liquid layer (Fig. 1B–D). 
3D reconstructions of confocal imaging of LLPS in solutions of increasing PrPC 1 h after PBS addition (120*120*50 µm, x*y*z). Liquid layer thickness is proportional to the pre-LLPS PrPC levle allowing estimation of liquid concentration at 20 mM PrPC.
Protein: DP00466 (UniProt P04156)
Region: residues 23	to 124
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: fluorescence microscopy evidence used in manual assertion
Supporting statements:
Microscopy of opaque PrPC suspensions by DIC and fluorescence of Alexa 568-tagged PrPC reveals phase transition with demixed spherical droplets (Fig. 1A, Fig. S1A), which dissolve upon dilution.
Protein: DP00466 (UniProt P04156)
Region: residues 23	to 124
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: differential interference contrast microscopy evidence used in manual assertion
Supporting statements:
Microscopy of opaque PrPC suspensions by DIC and fluorescence of Alexa 568-tagged PrPC reveals phase transition with demixed spherical droplets (Fig. 1A, Fig. S1A), which dissolve upon dilution.
Protein: DP00466 (UniProt P04156)
Region: residues 23	to 124
Annotation: molecular adaptor activity (Molecular function)
Evidence: fluorescence recovery after photobleaching evidence used in manual assertion
Supporting statements:
The mobility of PrPC and mGluR5 were studied by FRAP of CLIP-Surface 547-PrP and SNAP-Alexa 647-mGluR5. Following Aβo, there is parallel reduction of PrPC and mGluR5 mobility (Fig. 5A). Both PrPC and Aβo are necessary to slow mGluR5 mobility, as Aβo-treated cells expressing SNAP-mGluR5 alone or vehicle-treated cells expressing both SNAP-mGluR5 and CLIP-PrP do not repond (Fig. 5B, Fig. S5A). Moreover, mGluR5 recruitment is specific, since Aβo-treatment of cells co-expressing CLIP-PrP and GPI-anchored SNAP tag has no effect on SNAP-GPI mobility (Fig. 5C, 5D, Fig. S5B).
Protein: DP00466 (UniProt P04156)
Region: residues 23	to 124
Annotation: molecular adaptor activity (Molecular function)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
In parallel, we sought biochemical evidence for mGluR5 recruitment to Aβo/PrP hydrogels by a centrifugation-based condensation assay. To facilitate mGluR5 expression, we utilized a truncated form (mGluR5-∆ICD). We detected the assembly of Aβo/PrP hydrogels as a shift of PrPC and Aβo from supernatants into pellets (Fig. 5E, 5F). A substantial fraction of mGluR5-∆ICD segregates to hydrogel pellets together with PrPC and Aβo. Neither Aβo nor PrPC alone cause a shift for mGluR5. Moreover, the amount of mGluR5 in the hydrogel decreases with Aβo excess.
Protein: DP00472 (UniProt P50542)
Region: residues 1	to 324
Annotation: disorder (Structural state)
Evidence: differential scanning calorimetry evidence used in manual assertion
Supporting statements:
The DSC analysis of DC1-Pex5p is also presented in Figure 1. Remarkably, the thermogram of this protein corresponds basically to the baseline of the calorimeter. This observation indicates that the N-terminal half of Pex5p lacks any stable tertiary structure.
Protein: DP00472 (UniProt P50542)
Region: residues 1	to 324
Annotation: disorder (Structural state)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
On the other hand, DC1-Pex5p is the most enriched in random coil structure.
Protein: DP00472 (UniProt P50542)
Region: residues 1	to 324
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Plotting the molecular mass and the Stokes radius of this protein into the graphic presented in Figure 4(c), reveals that DC1-Pex5p falls in a region between the two straight lines corresponding to natively unfolded intrinsic coils and natively unfolded pre-molten globules.
Protein: DP00472 (UniProt P50542)
Region: residues 1	to 324
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
This protein displays a maximum of negative ellipticity at 203 nm. Intense negative ellipticity in the vicinity of 200 nm is a property of unfolded polypeptides.
Protein: DP00472 (UniProt P50542)
Region: residues 1	to 110
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR fingerprint spectra of 15N-labeled Pex5-(1–110) show very little dispersion, characteristic of an unstructured protein.
Protein: DP00472 (UniProt P50542)
Region: residues 57	to 71
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
However, upon addition of unlabeled Pex14-NTD, the spectrum changes significantly, indicating a strong interaction between Pex5-(1–110) and Pex14-NTD (Fig. 2A).
The binding site of the LVXEF motif on the structure of Pex14-NTD was mapped based on chemical shift perturbations seen upon addition of a 16-mer Pex5 peptide containing the LVAEF sequence to 15N-labeled Pex14-NTD (Fig. 3A). The chemical shift perturbations (data not shown) involve the same set of residues that have been previously shown to bind to a WXXX(F/Y) motif of Pex5, indicating that the new motif interacts with the same surface of Pex14-NTD (16).
The Pex5 LVXEF motif binds in an α-helical conformation to the hydrophobic surface of Pex14-NTD (Fig. 3B). Three conserved residues (Leu-62, Val-63, and Phe-66) of the LVXEF motif are involved in hydrophobic interactions with Pex14-NTD.
Cross-references: PDB:4BXU
ELM:LIG_Pex14_3
Protein: DP00472 (UniProt P50542)
Region: residues 59	to 70
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
However, upon addition of unlabeled Pex14-NTD, the spectrum changes significantly, indicating a strong interaction between Pex5-(1–110) and Pex14-NTD (Fig. 2A). Analysis of 13Cα/β secondary chemical shifts revealed that the region including residues Glu-59 to Gln-70 of human Pex5 (59EDELVAEFLQDQ70) forms an α-helix upon interacting with Pex14-NTD (Fig. 2B).
Cross-references: PDB:4BXU
Protein: DP00472 (UniProt P50542)
Region: residues 61	to 67
Annotation: protein binding (Molecular function)
Evidence: peptide array evidence used in manual assertion
Supporting statements:
The overlapping region of the new binding site represents 7 amino acids with the sequence ELVAEFL. The core sequence LVAEF resembles the Pex5 WXXX(F/Y) motifs with the major difference that tryptophan is replaced by the hydrophobic amino acid leucine (Fig. 1A).
Cross-references: ELM:LIG_Pex14_3
Protein: DP00472 (UniProt P50542)
Region: residues 1	to 110
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
The ITC data show that Pex5-(1–110) binds to Pex14-NTD with a dissociation constant (KD) of 157 ± 9 nm (Fig. 5A), demonstrating high affinity binding, similar to the WXXX(F/Y) motifs (12, 16). The stoichiometry of binding was 1:1, confirming that the identified binding sequence represents the only accessible interacting site within the N-terminal 110 residues of Pex5.
Cross-references: ELM:LIG_Pex14_3
Protein: DP00472 (UniProt P50542)
Region: residues 62	to 66
Annotation: protein binding (Molecular function)
Evidence: site-directed spin-labelling electron paramagnetic resonance evidence used in manual assertion
Supporting statements:
Analysis of the PRE data for both peptides shows that experimentally observed line broadening effects are in agreement with the theoretically calculated ones based on our NMR structure (Fig. 4). Thus, the PRE data independently confirm that the Pex5 LVXEF motif binds to Pex14 in the same orientation as the Pex5 WXXX(F/Y) peptide.
Cross-references: ELM:LIG_Pex14_3
Protein: DP00472 (UniProt P50542)
Region: residues 62	to 66
Annotation: protein binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
To study the kinetics of W1-containing Pex5-(1–131), the newly identified LVXEF motif was replaced by penta-alanine. As shown by in vitro binding assays, this mutation abolishes the monovalent interaction between N-terminal fragments of Pex5 and Pex14 (Fig. 6).
A, surface plasmon resonance spectroscopy shows that Pex5-(1–113) binds to immobilized GST-tagged N-terminal domain of Pex14 (GST-Pex14-NTD), although Pex5-(1–113)(LVAEF > AAAAA) lacking the LVXEF motif does not.
Cross-references: ELM:LIG_Pex14_3
Protein: DP00472 (UniProt P50542)
Region: residues 62	to 66
Annotation: protein import into peroxisome matrix (Biological process)
Evidence: immunofluorescence wide-field microscopy evidence used in manual assertion
Supporting statements:
Wild-type Pex5 rescued the PTS1 import defect of most of the transfected cells (82%), whereas the LVAEF → AAAAA mutant restored peroxisomal protein import in only 43% of the cells. Thus, most cells exhibited no punctate staining, indicative of a complete mislocalization of the peroxisomal marker protein to the cytosol and thus a severe import defect. Moreover, almost all cells that still exhibited a punctate staining upon expression of the LVAEF → AAAAA mutant displayed a partial import defect with strong cytosolic background (Fig. 7A, lower panel). The data indicate that inactivation of the novel Pex14-binding motif strongly affects the efficiency of peroxisomal protein.
Protein: DP00472 (UniProt P50542)
Region: residues 1	to 100
Annotation: disorder (Structural state)
Evidence: immunofluorescence wide-field microscopy evidence used in manual assertion
Supporting statements:
As shown in Figure 4, the Stokes radii of polypeptides comprising amino acid residues 1–110, 1–197 or 1–268 of Pex5p are compatible with the existence of a natively unfolded conformation in these regions of the protein.
Protein: DP00472 (UniProt P50542)
Region: residues 1	to 197
Annotation: disorder (Structural state)
Evidence: immunofluorescence wide-field microscopy evidence used in manual assertion
Supporting statements:
As shown in Figure 4, the Stokes radii of polypeptides comprising amino acid residues 1–110, 1–197 or 1–268 of Pex5p are compatible with the existence of a natively unfolded conformation in these regions of the protein.
Protein: DP00472 (UniProt P50542)
Region: residues 1	to 268
Annotation: disorder (Structural state)
Evidence: immunofluorescence wide-field microscopy evidence used in manual assertion
Supporting statements:
As shown in Figure 4, the Stokes radii of polypeptides comprising amino acid residues 1–110, 1–197 or 1–268 of Pex5p are compatible with the existence of a natively unfolded conformation in these regions of the protein.