LiteFold/DisProt huggingface dataset:
Protein: DP03389 (UniProt Q9UBT3)
Region: residues 19	to 38
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The N-terminal region of hDkk4 (M1–G21) and the relatively long linker between the two cysteine-rich regions (E77–Q123) appear to be unstructured and relatively mobile.
The N-terminus of the protein (M1–S21), the non-conserved linker (E77–Q123) between the two cysteine-rich regions and the C-terminal histidine-tag (E208–H222) are characterised by relatively intense and close to random coil chemical shifts for backbone amide signals, which together with predicted order parameters of 0.3–0.7 from TALOS+ for residues 2–22, 81–122 and 206–217 suggests that these regions are unstructured and relatively mobile compared to the cysteine-rich regions.
The mature form of the protein was studied UniProt (19-224), with an extra Met at the N-terminus and a tag at the C-terminus. Therefore there is a shift in the residue numbering and G21 in the construct is equivalent to G38 in the UniProt sequence.
Cross-references: BMRB:19768
Protein: DP03389 (UniProt Q9UBT3)
Region: residues 94	to 140
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The N-terminal region of hDkk4 (M1–G21) and the relatively long linker between the two cysteine-rich regions (E77–Q123) appear to be unstructured and relatively mobile.
The N-terminus of the protein (M1–S21), the non-conserved linker (E77–Q123) between the two cysteine-rich regions and the C-terminal histidine-tag (E208–H222) are characterised by relatively intense and close to random coil chemical shifts for backbone amide signals, which together with predicted order parameters of 0.3–0.7 from TALOS+ for residues 2–22, 81–122 and 206–217 suggests that these regions are unstructured and relatively mobile compared to the cysteine-rich regions.
The mature form of the protein was studied UniProt (19-224), with an extra Met at the N-terminus and a tag at the C-terminus. Therefore there is a shift in the residue numbering and E77-Q123 in the construct is equivalent to E94-Q140 in the UniProt sequence.
Cross-references: BMRB:19768
Protein: DP03389 (UniProt Q9UBT3)
Region: residues 94	to 140
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The N-terminal region of hDkk4 (M1–G21) and the relatively long linker between the two cysteine-rich regions (E77–Q123) appear to be unstructured and relatively mobile.
The N-terminus of the protein (M1–S21), the non-conserved linker (E77–Q123) between the two cysteine-rich regions and the C-terminal histidine-tag (E208–H222) are characterised by relatively intense and close to random coil chemical shifts for backbone amide signals, which together with predicted order parameters of 0.3–0.7 from TALOS+ for residues 2–22, 81–122 and 206–217 suggests that these regions are unstructured and relatively mobile compared to the cysteine-rich regions.
The mature form of the protein was studied UniProt (19-224), with an extra Met at the N-terminus and a tag at the C-terminus. Therefore there is a shift in the residue numbering and E77-Q123 in the construct is equivalent to E94-Q140 in the UniProt sequence.
Protein: DP03390 (UniProt Q2UZM9)
Region: residues 42	to 76
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The mature form of mitochondrial Tb1-C-Grx1 (residues 42–184) was analyzed by NMR.
Although the good dispersion of peaks observed in the 15N-HSQC of Tb1-C-Grx1 WT clearly indicates that the protein is well folded in aqueous buffer, resonance assignment showed that the majority of the signals generated by the residues of the N-terminal tail resonate within a relative narrow region in the proton dimension. This feature suggests that the 35-mer N-terminal region is a largely unstructured element.
The first 35 residues of the mature protein are equivalent to UniProt residues 42-76.
Cross-references: BMRB:19736
Protein: DP03391 (UniProt C9ZXG5)
Region: residues 42	to 76
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The residues belonging to the NTE show a poor dispersion of the proton chemical shifts
in the 1H-15N HSQC spectrum. Most of these peaks cluster in the region between 8 and 8.5 ppm, with significantly higher intensities than average.
Cα secondary chemical shifts are highly sensitive probes for local conformation; most residues of the tail present absolute values below 0.5 ppm, which is typical of non-structured elements.
The model-free order parameters estimated with the RCI method show that most residues from the NTE present values consistently lower than the average value of 0.7 of the globular domain.
In contrast, hetNOE values below 0.4 were obtained for all residues upstream L70 providing additional evidence that the NTE is largely unstructured.
The plot of 1H-15N RDCs as a function of the residue number confirm that the NTE is largely disordered, presenting for most of the residues RDC absolute values below 3 Hz, hence significantly smaller than the average for the globular domain (7.2 Hz).
Assuming that the protein is monomeric, from the measured hydrodynamic radius it is possible to calculate for FL 1CGrx1 a compaction factor of 0.73, which is fully in agreement with the presence of a structured domain of around 100 residues, namely the Grx domain, and a disordered region of about 40 residues, the NTE.
Cross-references: PDB:2MXN
Protein: DP03391 (UniProt C9ZXG5)
Region: residues 65	to 76
Annotation: molecular function regulator (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Interestingly, the portion comprising residues 65–76 of the NTE modulates the conformational dynamics of the glutathione-binding pocket, which may play a role in iron-sulfur cluster assembly and delivery.
Comparison of the 1H-15N-HSQC spectra of Δ76 and FL 1CGrx1 revealed shifts in a significant number of peaks, which can be ascribed to structural rearrangements caused by the presence of the NTE.
Notably, the peak pattern of the 1H-15N-HSQC spectrum from Δ64 1CGrx1 is essentially identical to that observed for the full-length protein. This result clearly shows that the segment comprising amino acids L65 to M76, (i.e., the C-terminal part of the NTE), is responsible for modulating the conformational dynamics of FL 1CGrx1.
Altogether, our results support a pivotal role for residues 65-76 of the N-terminal tail of FL 1CGrx1 in modulating the structural dynamic properties of the binding pocket through a network of polar and hydrophobic interactions between residues from α1 and α3.
Cross-references: PDB:2MXN
Protein: DP03391 (UniProt C9ZXG5)
Region: residues 65	to 76
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The chemical shift perturbation (CSP) is evident not only for α1, to which the NTE is connected, but also for α3 and the downstream loop containing the conserved cis-proline. Mapping the CSP on the bundle of conformations for FL 1CGrx1 clearly shows that the regions of the protein most affected by the presence of the NTE correspond to those where the structure is less well defined because of internal mobility, as already described in the previous section.
Comparison of the 1H-15N-HSQC spectra of Δ76 and FL 1CGrx1 revealed shifts in a significant number of peaks, which can be ascribed to structural rearrangements caused by the presence of the NTE.
Notably, the peak pattern of the 1H-15N-HSQC spectrum from Δ64 1CGrx1 is essentially identical to that observed for the full-length protein. This result clearly shows that the segment comprising amino acids L65 to M76, (i.e., the C-terminal part of the NTE), is responsible for modulating the conformational dynamics of FL 1CGrx1.
Cross-references: PDB:2MXN
Protein: DP03391 (UniProt C9ZXG5)
Region: residues 42	to 75
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Based on size exclusion chromatography (SEC), we have previously proposed that the NTE may promote the formation of non-covalent dimers in apo-1CGrx. Considering the IDR nature of the NTE and its potential contribution to an anomalous behaviour of 1CGrx1 in solution, we revisited this hypothesis by applying three complementary experimental approaches.
After filtering out residues from flexible regions or involved in chemical exchange processes, we estimated τc = 9.5 ± 0.5 ns for FL 1CGrx1, which is fully compatible with a monomeric and not a dimeric state, as previously assumed. Not surprisingly, this value is significantly larger than the previously measured τc for the Δ76 mutant (7.9 ± 0.6 ns) due to the expanded size of the protein containing the unstructured NTE.
Protein: DP03391 (UniProt C9ZXG5)
Region: residues 42	to 75
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
After optimization of the cleavage conditions, trypsin treatment of FL 1CGrx1 yielded protein cleaved between K64 and L65, as confirmed by mass spectrometry, and therefore named Δ64 1CGrx1.
Protein: DP03392 (UniProt A0A2U8QNT7)
Region: residues 1	to 257
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Assessment of secondary structure in aqueous and dried states with circular dichroism (CD) reveals 89% random coil in the aqueous state, thus supporting classification of AfrLEA6 as an IDP.
AfrLEA6 exists as an intrinsically disordered protein in solution with a minimum ellipticity of 200 nm that is characteristic of disordered, random coil proteins.
Our CD studies indicate that AfrLEA6 is clearly intrinsically disordered in solution based on an estimated 89% content of random coil.
Protein: DP03392 (UniProt A0A2U8QNT7)
Region: residues 1	to 257
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Removal of water from the protein by drying or exposure to trifluoroethanol (a chemical de-solvating agent) promotes a large gain in secondary structure of AfrLEA6, predominated by α-helix and exhibiting minimal β-sheet structure.
When interactions with water are decreased by drying or by the addition of 70% trifluoroethanol (TFE; a chemical de-solvating agent), AfrLEA6 gains significant secondary structure (α-helix, β-sheet, turns). A similar outcome was promoted by adding 2% SDS. A substantial increase in the proportion of α-helix was indicated in the CD spectra by double minima at 208 and 222 nm and a maximum at 191 nm.
Since AfrLEA6 is a LEA protein and many of those are dehydrins, the structural transition observed upon drying is likely to be physiologically relevant.
Protein: DP03393 (UniProt J2EKT7)
Region: residues 54	to 82
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here we present the first NMR solution structure of a Pseudomonas MT, PflQ2 MT, using the strain P. fluorescens Q2-87. It consists of a metal binding domain and an intrinsically disordered C-terminal tail, that was not observed in other MTs so far.
To experimentally confirm this prediction but also to investigate the influence of the tail on the metal binding abilities and on the structure, the full-length protein PflQ2 MT and its shortened version, lacking the tail, (sh_PflQ2 MT) were compared using NMR and optical spectroscopy.
MT refers to Metallothionein. In the methods the authors state that "The shortened version of the protein lacking the C-terminal tail, sh_PflQ2 MT (residues 1-52)", these residues are equivalent to UniProt residues 2-53, therefore the C-terminal tail must span UniProt residues 54-82
Backbone dynamics studies show a gradual decrease of 15N{1H}-NOE values from residue R51 on, which, however, only level off to -0.5 after residue 76. This indicates that there is still some, albeit rather loose, interaction of the tail with the folded part of the protein, and that it resembles a molten globule.
The disordered C-terminal tail has never been observed in other MTs so far. We
could demonstrate that this tail has no influence on the metal binding properties of the Pseudomonas MT and does not change the overall protein fold.
Cross-references: BMRB:34282
PDB:6GRV
Protein: DP03394 (UniProt O60493)
Region: residues 2	to 28
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The secondary structure of SNX3 was predicted from Hα, Cα, Cβ, C′ chemical shifts using Ccpnmr analysis suite and the corresponding chemical shift index. Three β-strands (29–39, 46–55, 64–69) followed by three α-helices (71–84, 112–130, 133–145) were predicted, consistent with the structural characteristics of PX domains and SNX12-PX in particular. The third helix may contain an irregularity midway based on an interrupted CSI pattern, while both termini exhibit random coil resonances and are intrinsically disordered.
Cross-references: BMRB:25402
Protein: DP03394 (UniProt O60493)
Region: residues 146	to 162
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The secondary structure of SNX3 was predicted from Hα, Cα, Cβ, C′ chemical shifts using Ccpnmr analysis suite and the corresponding chemical shift index. Three β-strands (29–39, 46–55, 64–69) followed by three α-helices (71–84, 112–130, 133–145) were predicted, consistent with the structural characteristics of PX domains and SNX12-PX in particular. The third helix may contain an irregularity midway based on an interrupted CSI pattern, while both termini exhibit random coil resonances and are intrinsically disordered.
Cross-references: BMRB:25402
Protein: DP03395 (UniProt C8CGS7)
Region: residues 1630	to 1756
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H–15N HSQC spectrum of R1 TraIC126 and the apparent limited peak dispersion along the hydrogen dimension, all the backbone amide peaks between 7.6 and 8.7 ppm, shows that R1 TraIC126 is at least partially disordered.
Secondary structure information was obtained from the backbone chemical shifts processed using Talos-N. The prediction shows major disordered regions, as expected from the 1H–15N HSQC spectrum’s poor peak dispersion along the hydrogen dimension. Talos prediction shows that two stretches of helices, spanning from residues 16 to 41 and 102 to 111 are connected through a loop region. The residues 3 to 15, 42 to 101 and 112 to 127 are predicted to be loop / disordered regions.
Cross-references: BMRB:27596
Protein: DP03396 (UniProt Q716H0)
Region: residues 320	to 332
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In lieu of the D-loop, the Sf6 I-domain appears to have a new disordered loop between strands 5 and 6 of the β-barrel that is not observed in P22 or CUS-3.
For each protein the following are shown: amino acid sequence, residues protected from hydrogen exchange (indicated by filled circles), secondary structure prediction from sequence calculated with the JPred program, chemical-shift based secondary structure prediction calculated with TALOS-N (except for P22 where the schematic is based on the NMR structure) and prediction of backbone dynamics from TALOS-N where the green symbols “x” indicate flexible regions with small predicted S2 order parameters (except for P22 where the dynamics information is based on 15N-relaxation measurements).
Cross-references: BMRB:26844
Protein: DP03397 (UniProt P13051-1)
Region: residues 1	to 92
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Human uracil N-glycosylase isoform 2—UNG2 consists of an N-terminal intrinsically disordered regulatory domain (UNG2 residues 1–92, 9.3 kDa) and a C-terminal structured catalytic domain (UNG2 residues 93–313, 25.1 kDa).
In Figure 1 the N-HSQC spectrum of N-UNG2 (residues 1-92) shows very narrow peak dispersion that is typical for IDPs.
Lack of any significant chemical shift changes indicates no interaction between the disorder N-UNG2 region and structured catalytic domain C-UNG2. 
The chemical shifts of HN, N, C′, Hα, Cα and Cβ were used to calculate secondary structure elements by TALOS+ (Shen et al. 2009) and SSP (Marsh et al. 2006). TALOS+ was developed to predict stable secondary structure elements while SSP was made for disordered proteins and therefore allows a more detailed view of the disordered regions. Both programs show similar predictions of N-UNG2 and C-UNG2. Both programs predict that the first 60 amino acids of N-UNG2 are intrinsically disordered followed by a long helical part from Ser67-Ala86.
Cross-references: BMRB:27133
Protein: DP03398 (UniProt Q1HRL7)
Region: residues 127	to 138
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
These assignments reveal that the protein consists of seven α-helices, and that the arachidonic acid is bound tightly to the protein. Comparison with the chemical shift assignments of the apo-form of the protein reveals that binding of the fatty acid is accompanied by a large conformational change in the C-terminal helix, which appears disordered in the absence of lipid.
There are large chemical shift differences between the apo and bound states of AeOBP22 in multiple locations in the protein, with the largest differences localized to the C-terminal residues 104–123. A comparison of the calculated secondary structure propensities for the apo and bound states reveals that the overall secondary structure of the protein is maintained throughout most of the protein between the apo and bound states. In contrast, the C-terminal residues are significantly less ordered in the apo state.
The location of the predicted alpha-helical regions in the bound state is shown in the panel above as blue bars. For the apo-protein there is a clear break in the predicted secondary structure at residue 111.
In the UniProt sequence there is a signal peptide of 16 residues that was not included in the experiment, so there is a shift of 16 residues in the numbering. Residue 111 is equivalent to UniProt residue 127.
Cross-references: BMRB:27724
Protein: DP03398 (UniProt Q1HRL7)
Region: residues 127	to 138
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
These assignments reveal that the protein consists of seven α-helices, and that the arachidonic acid is bound tightly to the protein. Comparison with the chemical shift assignments of the apo-form of the protein reveals that binding of the fatty acid is accompanied by a large conformational change in the C-terminal helix, which appears disordered in the absence of lipid.
There are large chemical shift differences between the apo and bound states of AeOBP22 in multiple locations in the protein, with the largest differences localized to the C-terminal residues 104–123. A comparison of the calculated secondary structure propensities for the apo and bound states reveals that the overall secondary structure of the protein is maintained throughout most of the protein between the apo and bound states. In contrast, the C-terminal residues are significantly less ordered in the apo state.
The location of the predicted alpha-helical regions in the bound state is shown in the panel above as blue bars. For the apo-protein there is a clear break in the predicted secondary structure at residue 111.
In the UniProt sequence there is a signal peptide of 16 residues that was not included in the experiment, so there is a shift of 16 residues in the numbering. Residue 111 is equivalent to UniProt residue 127.
Cross-references: BMRB:27724
Protein: DP03398 (UniProt Q1HRL7)
Region: residues 127	to 138
Annotation: lipid binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
These assignments reveal that the protein consists of seven α-helices, and that the arachidonic acid is bound tightly to the protein. Comparison with the chemical shift assignments of the apo-form of the protein reveals that binding of the fatty acid is accompanied by a large conformational change in the C-terminal helix, which appears disordered in the absence of lipid.
There are large chemical shift differences between the apo and bound states of AeOBP22 in multiple locations in the protein, with the largest differences localized to the C-terminal residues 104–123.
In the UniProt sequence there is a signal peptide of 16 residues that was not included in the experiment, so there is a shift of 16 residues in the numbering. Residue 111 is equivalent to UniProt residue 127.
The location of the predicted alpha-helical regions in the bound state is shown in the panel above as blue bars. For the apo-protein there is a clear break in the predicted secondary structure at residue 111.
Cross-references: BMRB:27724
Protein: DP03399 (UniProt P60484-2)
Region: residues 1	to 145
Annotation: disorder (Structural state)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
HDX–MS analysis of PTEN-L-6A (Supplementary Figure S9A) indicated that the first 145 residues of PTEN-L were intrinsically disordered as previously predicted [31], exhibiting very high levels of HDX–MS (>50% exchange at 3 s of exchange at 0°C). However, one region of the N-terminal extension of PTEN-L, residues 145–176, was below this threshold, suggesting that this region may be folded and forming an α-helix, as suggested by secondary structure prediction programs.
Protein: DP03399 (UniProt P60484-2)
Region: residues 47	to 52
Annotation: localization (Biological process)
Evidence: fluorescence microscopy evidence used in manual assertion
Supporting statements:
To determine whether this sequence conferred similar properties to PTEN-Long, we constructed a PTEN-LongΔR6 construct in which these six arginines were deleted (Fig. S18). After treating cells with 100 nM purified Red Fluorescent Protein (RFP)-V5/His, PTEN-Long-RFP-V5/His, or PTEN-LongΔR6-RFP-V5/His, we detected PTEN-Long-RFP but not RFP nor PTEN-LongΔR6-RFP in the cells by fluorescence microscopy (Fig. 3A, Fig. S19).
Protein: DP03399 (UniProt P60484-2)
Region: residues 47	to 52
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: deletion mutation phenotypic evidence used in manual assertion
Supporting statements:
Inhibition of PI3K signaling appeared to be dependent upon the poly-arginine sequence of PTEN-Long because the PTEN-LongΔR6 mutant did not block Insulin or EGF-induced phosphorylation of AKT (Fig. S24).