LiteFold/DisProt huggingface dataset:
Protein: DP03414 (UniProt P40949)
Region: residues 33	to 253
Annotation: disorder (Structural state)
Evidence: temperature-induced protein unfolding evidence used in manual assertion
Supporting statements:
Thermal stability was determined for partially disordered FL
TapA and its CTD and NTD. Figure 3 A–C shows the CD spectra
of the FL, NTD, and CTD, respectively, upon gradual temperature increase. These plots surprisingly showed that TapA and its two domains were not melted with increasing temperature, but rather that they gained some a-helical structure (see Table S2 and Figure S5 for secondary-structure analysis). This thermodynamic signature is often an indication that folding under heating is entropically driven, and can be explained by the release of water molecules upon partial folding events.
In contrast to the semi-sigmoidal curve measured for the FL protein and the NTD fragment, the CTD melting curve decreased monotonically, which suggested that despite the clear existence of two states, the denatured-to-folded process was not cooperative.[27] Similar melting behavior has been previously observed for a variety of disordered proteins.
Protein: DP03414 (UniProt P40949)
Region: residues 191	to 253
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We used circular dichroism and NMR spectroscopy to show that, unlike the structured TasA, TapA is disordered. In addition, TapA is composed of two weakly interacting domains: a disordered C-terminal domain and a more structured N-terminal domain. 
The structure of TapA, studied herein by using circular dichroism (CD) and solution NMR spectroscopy, showed that it was partially disordered and composed of two domains: a 63- residue C-terminal domain (CTD) and a 158-residue N-terminal domain (NTD).
The 1H,15N HSQC NMR spectrum of the 15N-enriched CTD fragment (Figure 5, left-hand
side, and the full spectrum in Figure S9) was typical for disordered proteins,[29] as indicated by the narrow chemical shift
dispersion (Dd1H =0.56 ppm), and in agreement with the CD
spectrum of the fragment (showing &70% disorder, excluding
turns).
Protein: DP03415 (UniProt A0A0M4HM24)
Region: residues 1	to 212
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
The purity of the protein was assessed by SDS-PAGE and western blotting (Fig. 1a). The protein migrated at a position in the gel corresponding to a higher molecular mass (35 kDa) than calculated from the amino acid sequence (21.9 kDa; Table 1), which has been frequently observed for LEA proteins34.
Protein: DP03415 (UniProt A0A0M4HM24)
Region: residues 1	to 212
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far UV-CD spectrum of TdLEA3 under fully hydrated conditions showed a negative ellipticity around 200 nm, indicating a largely unstructured conformation, typical for IDPs (Fig. 2a).
Protein: DP03415 (UniProt A0A0M4HM24)
Region: residues 1	to 212
Annotation: disorder (Structural state)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
The Amide I peak of the hydrated protein was centered at 1648 cm−1, indicating a mainly unstructured protein.
Protein: DP03415 (UniProt A0A0M4HM24)
Region: residues 1	to 212
Annotation: disorder to order (Structural transition)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
The Amide I peak of the hydrated protein was centered at 1648 cm−1, indicating a mainly unstructured protein. Upon drying, this maximum was shifted to 1657 cm−1 (Fig. 3), indicating a gain in α-helix conformation during drying, in agreement with the CD spectra.
Protein: DP03415 (UniProt A0A0M4HM24)
Region: residues 1	to 212
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far UV-CD spectrum of TdLEA3 under fully hydrated conditions showed a negative ellipticity around 200 nm, indicating a largely unstructured conformation, typical for IDPs (Fig. 2a). However, after drying, the spectrum changed drastically and showed two minima at 208 and 222 nm, typical of a mainly α-helical conformation. A similar spectrum was also obtained in the presence a chemical inducer of α-helicity, trifluoroethanol (TFE).
Many LEA proteins are dehydrins, so drying is physiologically relevant in their case, so the transition can be annotated.
Protein: DP03415 (UniProt A0A0M4HM24)
Region: residues 1	to 212
Annotation: protein folding chaperone (Molecular function)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
Therefore, we tested the ability of TdLEA3 to prevent the loss of LDH activity after heating, dehydration and freezing. We compared the effects of TdLEA3 with the effects of BSA as an example of a non-specific protectant and with LDH treated in buffer without additional protein. Under all stress conditions and at all concentrations, TdLEA3 provided a higher degree of protection for LDH than BSA, indicating that the LEA protein had a protective activity that went beyond the unspecific effects of having a second protein present (Fig. 6). After heating at 48 °C for 10 min, LDH had lost about half of its activity in buffer and activity was further reduced with longer incubation times, to about 20% after 30 min. In contrast, the enzyme activity was completely preserved after 10 or 20 min of heat treatment in the presence of TdLEA3 at mass ratios (LDH: TdLEA3) of 1:20 and 1:40. At the highest mass ratio TdLEA3 preserved more than 90% of the enzyme activity after 30 min at 48 °C.
 TdLEA3 did not only protect LDH from loss of catalytic activity, but also prevented enzyme aggregation. Such a reduction of enzyme aggregation, in particular during drying, has been observed for other LEA_4 proteins before and has been explained on the basis of the “molecular shield” hypothesis.
Quite strikingly, TdLEA3 protected LDH not only during drying and freezing, activities that have been reported frequently for LEA proteins in the literature, but also under heat stress. To the best of our knowledge, such a chaperone activity has previously only been reported for two dehydrins from Arabidopsis34, while a LEA_4 protein from an anhydrobiotic nematode was not able to stabilize enzymes during heating
Protein: DP03415 (UniProt A0A0M4HM24)
Region: residues 1	to 212
Annotation: protein folding chaperone (Molecular function)
Evidence: turbidity measurement evidence used in manual assertion
Supporting statements:
We therefore investigated the ability of TdLEA3 to reduce LDH aggregation during stress treatments by measuring apparent light scattering of protein solutions as absorbance. We used two mass ratios of enzyme: protein (1:1 and 1:2). After heating for 20 min at 80 °C, LDH showed massive aggregation. The presence of TdLEA3 reduced the aggregation of LDH at both investigated mass ratios to a larger extent than BSA (Fig. 7a).
TdLEA3 did not only protect LDH from loss of catalytic activity, but also prevented enzyme aggregation. Such a reduction of enzyme aggregation, in particular during drying, has been observed for other LEA_4 proteins before and has been explained on the basis of the “molecular shield” hypothesis.
Quite strikingly, TdLEA3 protected LDH not only during drying and freezing, activities that have been reported frequently for LEA proteins in the literature, but also under heat stress. To the best of our knowledge, such a chaperone activity has previously only been reported for two dehydrins from Arabidopsis34, while a LEA_4 protein from an anhydrobiotic nematode was not able to stabilize enzymes during heating.
Protein: DP03416 (UniProt Q87GF9)
Region: residues 361	to 428
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The circular dichroism spectrum of VopVrep1 was clearly indicative of a random coil pattern, demonstrating that the recombinant VopVrep1 did not form a stable fold in solution.
Protein: DP03416 (UniProt Q87GF9)
Region: residues 361	to 428
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
To assess whether the recombinant protein bound to actin, the binding affinity of VopVrep1 to cytoskeletal actin was determined using isothermal titration calorimetry (ITC). Without a stable fold in solution, VopVrep1 bound to actin with high affinity (Kd = 54.4 nM) at a binding stoichiometry of N = 1.06, which is comparable to the well-known F-actin-binding toxin phalloidin17,18, which has a binding affinity of Kd = 36.5 nM and a binding stoichiometry of N = 1.16 in our experiment (Fig. 1(c,d) and Supplementary Table S1).
Protein: DP03416 (UniProt Q87GF9)
Region: residues 361	to 428
Annotation: protein binding (Molecular function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
Recent advances in the cryoEM method applied to F-actin25 have enabled the direct visualization of the human cytoskeletal actin/VopVrep1 complex at 9.6-Å resolution (Fig. 2(a)).
Protein: DP03416 (UniProt Q87GF9)
Region: residues 361	to 428
Annotation: molecular function regulator (Molecular function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
In the density map, VopVrep1 occupied a key position surrounded by three actin monomers that reinforced both the lateral and longitudinal interactions within the filament, suggesting the ability of VopVrep1 to stabilize F-actin. In addition to the observed binding mode, the specific, high-affinity recognition of F-actin results in F-actin stabilization19.
Protein: DP03416 (UniProt Q87GF9)
Region: residues 361	to 428
Annotation: molecular function regulator (Molecular function)
Evidence: physical interaction evidence used in manual assertion
Supporting statements:
As expected, the F-actin-stabilizing activity of VopVrep1 was demonstrated by the observation that VopVrep1 strongly protected the actin filament from depolymerization in low-salt conditions (Fig. 3) to the same extent as phalloidin.
Protein: DP03417 (UniProt P10997)
Region: residues 23	to 33
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We show that the solution NMR ensemble structure of the protein exchanges between multiple conformers, containing an unfolded Npro segment (residues 1–11) and a mostly helical IAPP region (residues 12–48).
There is a 22 residues long signal peptide in the UniProt sequence, therefore residue 1 of the propeptide corrsponds to residue 23 of the UniProt sequence.
The N‐terminal propeptide segment (T1‐R11) is unfolded in DPC micelles, with average S2 values below 0.4.
Cross-references: BMRB:50007
PDB:6UCK
PDB:6UCJ
Protein: DP03417 (UniProt P10997)
Region: residues 62	to 71
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
There is a 22 residues long signal peptide in the UniProt sequence, therefore residue 1 of the propeptide corrsponds to residue 23 of the UniProt sequence.
A disordered loop from S40‐G49 connects the C terminus of immature IAPP with the C‐terminal propeptide segment of N52‐L67, which appears fairly rigid.
The unstructured loop (S40‐K50) that tethers IAPP to Cpro is highly accessible to solvent.
Cross-references: BMRB:50007
PDB:6UCJ
PDB:6UCK
Protein: DP03417 (UniProt P10997)
Region: residues 23	to 89
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In the absence of lipid, unfolded features dominate the CD spectra for proIAPP, and the protein is intrinsically disordered.
Protein: DP03417 (UniProt P10997)
Region: residues 23	to 89
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In the absence of lipid, unfolded features dominate the CD spectra for proIAPP, and the protein is intrinsically disordered. In the presence of detergent micelles and bicelles, the protein adopts a mostly α‐helical structure at both pH values. The helical structure is indicated by the mean residue ellipticity ([θ]) minima near 208 and 222 nm (Fig. 7A,B).
In the presence of membranes at pH 4.5, the proIAPP helicity is 47 ± 4%, 46 ± 5%, 50 ± 5%, and 31 ± 5% for DPC, SDS, 3 : 1 1,2‐dimyristoyl‐sn‐glycero‐3‐phosphocholine (DMPC)/1,2‐dimyristoyl‐sn‐glycero‐3‐phospho‐l‐serine (DMPS) bicelles, and DMPC bicelles, respectively. At pH 7.0, proIAPP helicity is 42 ± 4%, 50 ± 4%, 47 ± 5%, and 34 ± 5% for DPC, SDS, DMPC/DMPS bicelles, and DMPC bicelles respectively. The helical content of the protein in the absence of lipid is 14 ± 3% and 14 ± 3% at pH 4.5 at pH 7.0, respectively, which agrees with a previous report on the transiently helical α1 in IAPP and the presence of the C2‐C7 (C13‐C18 in proIAPP) disulfide bond [57].
Protein: DP03417 (UniProt P10997)
Region: residues 23	to 89
Annotation: lipid binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In the absence of lipid, unfolded features dominate the CD spectra for proIAPP, and the protein is intrinsically disordered. In the presence of detergent micelles and bicelles, the protein adopts a mostly α‐helical structure at both pH values. The helical structure is indicated by the mean residue ellipticity ([θ]) minima near 208 and 222 nm (Fig. 7A,B).
Protein: DP03417 (UniProt P10997)
Region: residues 74	to 89
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We used CD to conduct a secondary structure analysis of the Cpro peptide at pH 4.5 and 6.1, in the presence and absence of DPC micelles (Fig. 10A). In the absence of lipid, Cpro displays unfolded or coil characteristics at both pH values.
Protein: DP03417 (UniProt P10997)
Region: residues 74	to 89
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We used CD to conduct a secondary structure analysis of the Cpro peptide at pH 4.5 and 6.1, in the presence and absence of DPC micelles (Fig. 10A). In the absence of lipid, Cpro displays unfolded or coil characteristics at both pH values. At pH 4.5 in DPC micelles, Cpro appears predominantly helical.
Protein: DP03417 (UniProt P10997)
Region: residues 74	to 89
Annotation: lipid binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We used CD to conduct a secondary structure analysis of the Cpro peptide at pH 4.5 and 6.1, in the presence and absence of DPC micelles (Fig. 10A). In the absence of lipid, Cpro displays unfolded or coil characteristics at both pH values. At pH 4.5 in DPC micelles, Cpro appears predominantly helical.
Protein: DP03417 (UniProt P10997)
Region: residues 23	to 89
Annotation: lipid binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The entire proIAPP structure appears to wrap around the DPC micelle.
Protein: DP03418 (UniProt Q96PU8-9)
Region: residues 205	to 319
Annotation: disorder (Structural state)
Evidence: synchrotron radiation circular dichroism evidence used in manual assertion
Supporting statements:
SRCD measurements of QKI6 produced a spectrum typical for a folded protein, but the minimum at 205 nm suggested the presence of disorder (Fig. 2a).
The SRCD measurement itself could not indicate the position of the disordered residues, however, for the folded part there is available structure, so it is most likely the C-terminal tail that was responsible for the presence of disoder.
Protein: DP03418 (UniProt Q96PU8-9)
Region: residues 205	to 319
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The dimeric QKI6 was highly flexible, as evident from the Kratky plot (Fig. 2c), and elongated, based on its radius of gyration (Rg, 5.24 nm) and maximum dimension (Dmax, 21 nm). Ab initio models based on the SAXS data appear elongated with a compact core (Fig. 2e).
In all three modelling sets, the 115 C-terminal residues were extended, in agreement with secondary structure predictions. To conclude, in the absence of an mRNA binding partner, the subdomains of dimeric QKI6 present a great degree of flexibility with respect to each other and most likely collapse to a more ordered arrangement upon binding to a 3′-UTR. The STAR domain is followed by an intrinsically disordered C terminus of currently unknown function.
Protein: DP03419 (UniProt A1B602)
Region: residues 1	to 14
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
As a first approach to identify the inhibitory domain of the ζ subunit, the recombinant protein was subjected to limited proteolysis with trypsin, which removed 14 and 25 residues from the N- and C-terminal extremes, respectively, as found by tandem mass spectrometry analyses.
The proteolytic accessibility of the N and C termini indicates that both extremes of the protein are exposed and most likely highly mobile, whereas the central Pd-ζ15–79 domain seems resistant to the protease treatment, suggesting that it should have a rigid folded structure that competes with Pd-ζWT for binding to the PdF1-ATPase.
Protein: DP03419 (UniProt A1B602)
Region: residues 80	to 104
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
As a first approach to identify the inhibitory domain of the ζ subunit, the recombinant protein was subjected to limited proteolysis with trypsin, which removed 14 and 25 residues from the N- and C-terminal extremes, respectively, as found by tandem mass spectrometry analyses.
The proteolytic accessibility of the N and C termini indicates that both extremes of the protein are exposed and most likely highly mobile, whereas the central Pd-ζ15–79 domain seems resistant to the protease treatment, suggesting that it should have a rigid folded structure that competes with Pd-ζWT for binding to the PdF1-ATPase.
Protein: DP03419 (UniProt A1B602)
Region: residues 1	to 14
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: deletion mutation phenotypic evidence used in manual assertion
Supporting statements:
The recombinant Pd-ζΔNT construct was overexpressed in E. coli and purified as described for the Pd-ζWT to ~93% purity. The Pd-ζΔNT was reconstituted into the PdF1-ATPase, and the inhibitory activity was measured. As shown in Fig. 3, removal of the first 14 N-terminal residues of Pd-ζ in the Pd-ζΔNT construct completely abolished the inhibitory capacity of the protein at concentrations as high as 9 μM, i.e., concentrations that result in saturation of the Pd-ζWT and completely block PdF1-ATPase activity. These data indicate that the N-terminal side of the Pd-ζ subunit contains the inhibitory domain of the protein.
Protein: DP03419 (UniProt A1B602)
Region: residues 1	to 19
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The inhibitor is bound to the F1 domain via residues 1–19 of the N-terminal α-helix, which occupy a cleft in the lower region of the αDPβDP-catalytic interface, with the rest of the α-helix (residues 20–32) extending from the surface of the enzyme. 
In solution, residues 1–18 of the 107-aa chain of the ζ-inhibitor are unstructured, with the rest of the chain folded into a four-helix bundle (residues 19–42, 46–53, 66–77, and 81–103).
Cross-references: PDB:5DN6
Protein: DP03419 (UniProt A1B602)
Region: residues 1	to 19
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The inhibitor is bound to the F1 domain via residues 1–19 of the N-terminal α-helix, which occupy a cleft in the lower region of the αDPβDP-catalytic interface (Fig. 2 A and B), with the rest of the α-helix (residues 20–32) extending from the surface of the enzyme.
Cross-references: PDB:5DN6
Protein: DP03419 (UniProt A1B602)
Region: residues 1	to 19
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The flexibly disordered N-terminal 19-residue segment of Pd-ζ is not shown.
Cross-references: BMRB:18018
PDB:2LL0
Protein: DP03420 (UniProt Q7TMK9)
Region: residues 108	to 140
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Investigations with constructs expanding up to residue 140 revealed that AcD24–107 forms a globular domain and that the segment 108–140 is flexibly disordered in solution (Supporting Information, Fig. S1).
Protein: DP03421 (UniProt P12464)
Region: residues 84	to 173
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here, we investigate the conformational behavior of the δ subunit of RNA polymerase from Bacillus subtilis whose unfolded domain is highly charged, with 7 positively charged amino acids followed by 51 acidic amino acids. Using a specifically designed analytical strategy, we identify transient contacts between the two regions using a combination of NMR paramagnetic relaxation enhancements, residual dipolar couplings (RDCs), chemical shifts, and small-angle scattering.
The unstructured C-terminal domain is 90 aa long and highly charged. The charge distribution of this domain is distinct, with a conserved stretch of 9 residues (96–104) containing 7 positive charges followed by the rest of the domain with 51 acidic residues (K-D/E motif).
Here, the ASTEROIDS approach(11−13) is used to describe the conformational behavior of the CTD of δ subunit in solution using a combination of NMR chemical shifts (CSs), paramagnetic relaxation enhancements (PREs), and residual dipolar couplings (RDCs) as well as small-angle scattering (SAXS).
All the RDC-s, PRE-s and all depicted values in Figure 1 clearly support that the C-terminal segment is and IDR.
The most striking local feature was the deviation of Cα and C′ chemical shifts with respect to random coil values. Both shifts display negative average values as compared to secondary shifts, which translates into a tendency of the whole C-teminal domain toward an extended structure of the polyproline II type (PPII) and depletion of α helical conformations. This may be related to the high density of negative charges; indeed higher PPII conformation is detected in the acidic C-terminal part of the unfolded domain due to local electrostatic repulsion.
Cross-references: BMRB:27963