LiteFold/DisProt huggingface dataset:
Protein: DP04260 (UniProt P07196)
Region: residues 40	to 63
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The values of the chemical shifts for the Hα protons, which are sensitive to the secondary structure, correspond to random coil structure. (56) Consequently, the peptide does not adopt any predominant regular secondary structure (see Figure 1). This was confirmed by the NOESY assignment.
Protein: DP04260 (UniProt P07196)
Region: residues 40	to 63
Annotation: tubulin binding (Molecular function)
Evidence: direct assay evidence used in manual assertion
Supporting statements:
The peptide (400 μM) was also studied in the presence of tubulin (60 μM), and a strong aggregation was then observed.
Protein: DP04260 (UniProt P07196)
Region: residues 40	to 63
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of the original NFL-TBS.40-63 peptide (wt NFL-TBS.40-63) in pure water indicates rather disordered conformation (black line in Figure 4A): the signal at 200 nm was negative while the ordered conformations (both α-helix and β-sheet) exhibit a positive CD signal at this UV region [31], [32].
Protein: DP04261 (UniProt P02489)
Region: residues 149	to 173
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The CTR of αA-crystallin displays significant flexibility and can be detected by solution-state NMR (residues G149–S173, Fig. 3c).
Cross-references: BMRB:27109
Protein: DP04261 (UniProt P02489)
Region: residues 1	to 60
Annotation: disorder (Structural state)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
During modeling using molecular dynamics flexible fitting, a homology-modeled structure for the NTR (residues 1-60) was used that contained three short helices connected by flexible loops (Extended Data Fig. 5a,b).
The fitting procedure resulted in an ensemble of solutions with the NTRs of both apical (Map) and equatorial (Meq) protomers adopting a variety of possible conformations (Extended Data Fig. 5c,d), consistent with their flexibility.
In agreement with previous studies49, peptides from the NTR were characterized by a moderate protection at short D2O exposure times, but became increasingly deuterated at longer exposure, consistent with the dynamic nature of this region sampling different conformations.
Extended Data Fig. 5 shows that the authors used a combination of secondary structure prediction and model building based on Cryo-EM data to determine that the NTD is highly mobile and flexible. The H/DX-MS experiment further supports this, demonstrating that the region lacks a fixed 3D structure.
Protein: DP04262 (UniProt P04792)
Region: residues 178	to 205
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
This allowed us to unambiguously assign the observed resonances to residues E178–K205 (Fig. 2b). These data therefore reveal that the final 28 residues of HSP27, including the IPV motif, are predominately disordered in solution.
Cross-references: BMRB:26994
Protein: DP04263 (UniProt P18848)
Region: residues 1	to 275
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In good agreement with the CD data collected in the same conditions, the overall small 13C chemical shift deviations (displayed here as ΔCα- ΔCβ), all within +2 ppm and -1 ppm, confirm that ATF4-275 is predominantly disordered in solution (black in Fig. 3A).
Cross-references: BMRB:51062
Protein: DP04264 (UniProt Q5SWA1)
Region: residues 414	to 613
Annotation: disorder (Structural state)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
IDPs are problematic to study for many reasons. In HDX, they exchange rapidly, as observed here for R15B with saturated deuterium uptake observed after 3 s in heavy water (Figure S3A).
Protein: DP04264 (UniProt Q5SWA1)
Region: residues 556	to 571
Annotation: eukaryotic initiation factor eIF2 binding (Molecular function)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
Addition of eIF2 resulted in increased protection throughout the sequence of R15B to various degrees (Figure 3; Table S1). The most pronounced changes localized to three short regions, 426–439, 471–495, and 556–571, with weaker changes in between (Figure 3). These HDX experiments suggest that the interaction with eIF2 occurs primarily through short and separated regions of R15B and that residues in between these regions, which exhibit weaker protection, may also contribute to the binding.
Protein: DP04264 (UniProt Q5SWA1)
Region: residues 414	to 613
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The observed narrow dispersion in the 1H dimension (Figure 4A) indicates that R15B414–613 is predominantly intrinsically disordered in solution.
Together, our NMR data define R15B414–613 as a largely disordered protein with discrete regions with helical propensity.
Cross-references: BMRB:52233
Protein: DP04264 (UniProt Q5SWA1)
Region: residues 557	to 561
Annotation: eukaryotic initiation factor eIF2 binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Together, these NMR analyses revealed 3 sites in R15B that undergo binding-induced dynamic changes: those were most significant for residues 421–431, followed by residues 474–480 and, to a lesser extent, 558–560 (Figure 4D) and coincided with elements of R15B that adopt an α-helical conformation (Figure 4B). Less pronounced, but also significant, changes were observed between the first 2 helical binding elements (Figure 4D), suggesting that this extended region might contribute to the binding.
Protein: DP04264 (UniProt Q5SWA1)
Region: residues 425	to 430
Annotation: eukaryotic initiation factor eIF2 binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
R15B411–613 with the H1A mutation was immunoprecipitated at levels similar to the WT proteins, but the capture of eIF2α was dramatically reduced (Figure 5B). H2A was slightly compromised, whereas H3A seemed more efficient at capturing the substrate when compared to WT (Figure 5B).
Thus, we propose that H1 serves to anchor R15B to eIF2 and H2 contributes an additional binding site.
Protein: DP04264 (UniProt Q5SWA1)
Region: residues 420	to 425
Annotation: eukaryotic initiation factor eIF2 binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
A genetic variant in the substrate recognition module of R15B reduces its function and causes microcephaly, developmental delay, and intellectual disability
 Whole exome sequencing identified a homozygous missense variant in the PPP1R15B gene, c.1267A>G resulting in a N423D mutation in the protein (Figure 6B).
When overexpressed in HEK293T cells, both H1A and N423D mutants captured significantly less eIF2α than the WT R15B411–613 fragment or full-length protein (Figures 6D and 6E).
Protein: DP04264 (UniProt Q5SWA1)
Region: residues 420	to 425
Annotation: protein phosphatase regulator activity (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
This reduced eIF2α binding in the N423D and H1A mutants resulted in decreased, but not abolished, dephosphorylation activity to-ward P-eIF2α in cell lysates when compared with the WT R15B (Figures 6F and 6G). Thus, this identifies a disease-associated variant in R15B substrate recognition module that reduced its ability to recruit and dephosphorylate the substrate eIF2α.
Protein: DP04264 (UniProt Q5SWA1)
Region: residues 1	to 713
Annotation: disorder (Structural state)
Evidence: in vitro cleavage assay evidence used in manual assertion
Supporting statements:
As expected for natively unstructured proteins41, R15A and R15B were sensitive to a limited trypsin proteolysis (Fig. 4c).
Protein: DP04264 (UniProt Q5SWA1)
Region: residues 414	to 639
Annotation: eukaryotic initiation factor eIF2 binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Full-length R15B as well as R15B414–713 immunoprecipitated with both eIF2α and PP1, whereas R15B414–639 only immunoprecipitated eIF2α and R15B639–713 captured PP1, but not eIF2α (Figure 1B).
Protein: DP04264 (UniProt Q5SWA1)
Region: residues 639	to 713
Annotation: protein phosphatase 1 binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Full-length R15B as well as R15B414–713 immunoprecipitated with both eIF2α and PP1, whereas R15B414–639 only immunoprecipitated eIF2α and R15B639–713 captured PP1, but not eIF2α (Figure 1B).
Protein: DP04264 (UniProt Q5SWA1)
Region: residues 1	to 713
Annotation: protein phosphatase type 1 complex (Cellular component)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Full-length R15B as well as R15B414–713 immunoprecipitated with both eIF2α and PP1, whereas R15B414–639 only immunoprecipitated eIF2α and R15B639–713 captured PP1, but not eIF2α (Figure 1B).
Protein: DP04264 (UniProt Q5SWA1)
Region: residues 1	to 713
Annotation: protein phosphatase type 1 complex (Cellular component)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
These experiments reveal that the binding of eIF2 and PP1 on R15B is not overlapping: R15B340–639 binds eIF2α while the carboxy-terminal region R15B639–713 binds PP1 (figure 1b; electronic supplementary material, figure S3).
Protein: DP04264 (UniProt Q5SWA1)
Region: residues 340	to 639
Annotation: eukaryotic initiation factor eIF2 binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
These experiments reveal that the binding of eIF2 and PP1 on R15B is not overlapping: R15B340–639 binds eIF2α while the carboxy-terminal region R15B639–713 binds PP1 (figure 1b; electronic supplementary material, figure S3).
Protein: DP04264 (UniProt Q5SWA1)
Region: residues 639	to 713
Annotation: protein phosphatase 1 binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
These experiments reveal that the binding of eIF2 and PP1 on R15B is not overlapping: R15B340–639 binds eIF2α while the carboxy-terminal region R15B639–713 binds PP1 (figure 1b; electronic supplementary material, figure S3).
Protein: DP04264 (UniProt Q5SWA1)
Region: residues 639	to 713
Annotation: protein phosphatase regulator activity (Molecular function)
Evidence: quantitative western immunoblotting evidence used in manual assertion
Supporting statements:
Similarly, full-length R15B1–713 as well as R15B340–713 were highly active (figure 3b). The amino-terminal regions of R15s, which do not bind the substrate nor PP1, as well as R15A325–554 and R15B340–639, which bind the substrate but not PP1, did not decrease phosphorylation of eIF2α (figure 3a,b).
Protein: DP04264 (UniProt Q5SWA1)
Region: residues 426	to 439
Annotation: eukaryotic initiation factor eIF2 binding (Molecular function)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
Addition of eIF2 resulted in increased protection throughout the sequence of R15B to various degrees (Figure 3; Table S1). The most pronounced changes localized to three short regions, 426–439, 471–495, and 556–571, with weaker changes in between (Figure 3). These HDX experiments suggest that the interaction with eIF2 occurs primarily through short and separated regions of R15B and that residues in between these regions, which exhibit weaker protection, may also contribute to the binding
Protein: DP04264 (UniProt Q5SWA1)
Region: residues 471	to 495
Annotation: eukaryotic initiation factor eIF2 binding (Molecular function)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
Addition of eIF2 resulted in increased protection throughout the sequence of R15B to various degrees (Figure 3; Table S1). The most pronounced changes localized to three short regions, 426–439, 471–495, and 556–571, with weaker changes in between (Figure 3). These HDX experiments suggest that the interaction with eIF2 occurs primarily through short and separated regions of R15B and that residues in between these regions, which exhibit weaker protection, may also contribute to the binding
Protein: DP04264 (UniProt Q5SWA1)
Region: residues 421	to 431
Annotation: eukaryotic initiation factor eIF2 binding (Molecular function)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
Addition of eIF2 resulted in increased protection throughout the sequence of R15B to various degrees (Figure 3; Table S1). The most pronounced changes localized to three short regions, 426–439, 471–495, and 556–571, with weaker changes in between (Figure 3). These HDX experiments suggest that the interaction with eIF2 occurs primarily through short and separated regions of R15B and that residues in between these regions, which exhibit weaker protection, may also contribute to the binding
Protein: DP04264 (UniProt Q5SWA1)
Region: residues 474	to 480
Annotation: eukaryotic initiation factor eIF2 binding (Molecular function)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
Addition of eIF2 resulted in increased protection throughout the sequence of R15B to various degrees (Figure 3; Table S1). The most pronounced changes localized to three short regions, 426–439, 471–495, and 556–571, with weaker changes in between (Figure 3). These HDX experiments suggest that the interaction with eIF2 occurs primarily through short and separated regions of R15B and that residues in between these regions, which exhibit weaker protection, may also contribute to the binding
Protein: DP04267 (UniProt Q9NPD8)
Region: residues 157	to 197
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The 1H-15N-HSQC spectra of both constructs were obtained and the cross-peaks corresponding to the C-terminal region appeared in the range of 7.5–8.5 ppm in the amide proton dimension (Fig. 1A). The narrow dispersion of the chemical shifts and high intensities of those cross-peaks suggest that the residues from the C-terminal region of UBE2T are not structured.
 It contains an N-terminal UBC domain critical for its activity and a C-terminal short region formed by approximately 40 residues which are not structured.
Protein: DP04267 (UniProt Q9NPD8)
Region: residues 157	to 197
Annotation: flexible C-terminal tail (Disorder function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The 1H-15N-HSQC spectra of both constructs were obtained and the cross-peaks corresponding to the C-terminal region appeared in the range of 7.5–8.5 ppm in the amide proton dimension (Fig. 1A). The narrow dispersion of the chemical shifts and high intensities of those cross-peaks suggest that the residues from the C-terminal region of UBE2T are not structured.
 It contains an N-terminal UBC domain critical for its activity and a C-terminal short region formed by approximately 40 residues which are not structured.
Protein: DP04268 (UniProt P93830)
Region: residues 1	to 101
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The NMR data show an extensive region of intrinsic disorder encompassing the majority of the N-terminal domain (Fig. 1). The 1H–15N heteronuclear single quantum correlation (HSQC) spectrum for AXR31-101 is characterized by signals occurring in a narrow 1H chemical shift region (7.9 to 8.6 ppm), indicative of an IDP (Fig. 1 and SI Appendix, Table S1).
Cross-references: BMRB:52109
Protein: DP04268 (UniProt P93830)
Region: residues 1	to 101
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Here, we combine NMR and CD (circular dichroism) analysis with molecular dynamics (MD) simulations to study the disordered amino-terminal of the Aux/IAA protein AXR3 and to estimate its interactions with TIR1.
CD spectrum shows this peptide is intrinsically unstructured by its large negative ellipticity at 200 nm.
Protein: DP04268 (UniProt P93830)
Region: residues 150	to 172
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Superposition of the backbone atoms for the ensemble of the final 20 simulated annealing structures of IAA17M2 demonstrates that the secondary structures are well ordered except for the α1′ and α3 helices (Fig. 1A).
To investigate if the dynamic α1′ helix affects folding or oligomerization of IAA17M2, we prepared IAA17M2(Δ159−169) that removed the α1′ helix.
Cross-references: BMRB:25217
PDB:2MUK
Protein: DP04268 (UniProt P93830)
Region: residues 150	to 172
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Superposition of the backbone atoms for the ensemble of the final 20 simulated annealing structures of IAA17M2 demonstrates that the secondary structures are well ordered except for the α1′ and α3 helices (Fig. 1A).
To investigate if the dynamic α1′ helix affects folding or oligomerization of IAA17M2, we prepared IAA17M2(Δ159−169) that removed the α1′ helix.
The insert region forms the α1′ helix connecting α1 of domain III and β3 of domain IV (Fig. 1B).
Cross-references: BMRB:25217
PDB:2MUK
Protein: DP04270 (UniProt Q8WXC6)
Region: residues 1	to 40
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
For both proteins, the assigned 1H-15N HSQC spectra (Figure 2b) demonstrated low dispersion in the proton dimension characteristic of disordered proteins, in full accordance with the CD spectra.
Cross-references: BMRB:50908
Protein: DP04270 (UniProt Q8WXC6)
Region: residues 1	to 57
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Both showed an intense negative ellipticity with a global minimum just under 200 nm, characteristic of highly unstructured proteins (Figure 2a). Negative ellipticity was also visible as a broad minimum around 220 nm suggesting the presence of transient structures, likely from α‐helices or poly‐proline II (PPII)/extended structures.
Protein: DP04271 (UniProt P02647)
Region: residues 210	to 267
Annotation: disorder (Structural state)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
The total of 116 ± 8 helical residues in the 243-residue apoA-I polypeptide indicates a helix content of 48 ± 3%, consistent with CD data for wild-type apoA-I and the deletion mutant 190–243 (9, 11) at low concentration. All helices are located in the N-terminal domain between residues 1 and 178. The C-terminal
residues 186–243 are disordered (Table 1)
Protein: DP04271 (UniProt P02647)
Region: residues 140	to 170
Annotation: disorder (Structural state)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
The placement of helical structure in the N-terminal domain of apoA-I and disordered chain in the C-terminal domain (Table 1, Fig. 3) agrees with previous
mutational analyses and modeling studies (11, 13, 29, 30, 31). Also, the detection by HX of the disordered region spanning residues 116–146 between helices 4 and 5 (Table 1) is consistent with studies of apoA-I (Δ121–142) mutants (36).
Protein: DP04271 (UniProt P02647)
Region: residues 25	to 267
Annotation: amyloid-beta formation (Biological process)
Evidence: synchrotron radiation circular dichroism evidence used in manual assertion
Supporting statements:
At pH 4, although a considerable amount of protein precipitation occurred, the remaining diluted solution of the protein retained a significant amount of α-helical structure even after 2 h (insoluble material was removed by centrifugation before analysis) (Figure 2B). Fitting of the spectrum suggests a partial loss of helical content and a gain of β-sheet and disordered elements (Table 1).
Protein: DP04271 (UniProt P02647)
Region: residues 70	to 83
Annotation: disorder to order (Structural transition)
Evidence: synchrotron radiation circular dichroism evidence used in manual assertion
Supporting statements:
Here, synthetic apoA-I(46–59) readily formed amyloid-like fibrils (∼10 nm width) in the absence of heparin (Figure 5A), and SRCD revealed a concomitant structural rearrangement from mainly unordered to β-sheet after incubation at 25 °C for 4 h (Figure 5B). The minimum-to-maximum intensity transition around 194 nm after peptide aggregation is consistent with a conformational switch from an initial unfolded state to a predominantly β-sheet structure.
Protein: DP04271 (UniProt P02647)
Region: residues 70	to 83
Annotation: amyloid-beta formation (Biological process)
Evidence: transmission electron microscopy evidence used in manual assertion
Supporting statements:
Here, synthetic apoA-I(46−59) readily formed amyloid-like fibrils (∼10 nm width) in the absence of heparin (Figure 5A), and SRCD revealed a concomitant structural rearrangement from mainly unordered to β-sheet after incubation at 25 °C for 4 h (Figure 5B). The minimum to maximum intensity transition around 194 nm after peptide aggregation is consistent with a conformational switch from an initial unfolded state to a predominantly β-sheet structure.
Protein: DP04271 (UniProt P02647)
Region: residues 25	to 267
Annotation: molten globule (Structural state)
Evidence: heat capacity-based evidence used in manual assertion
Supporting statements:
The low cooperativity (ΔHv/ΔH - 0.16) of the thermal unfolding of lipid-free apoA-1 and the temperature dependence of the far- and near-UV CD spectra indicate that the a-helixes of apoA-1 are only weakly stabilized by tertiary interactions. These features suggest a molten globular-like state for apoA-1 in low-salt solution at 37°C and pH 7.
Protein: DP04271 (UniProt P02647)
Region: residues 44	to 54
Annotation: disorder (Structural state)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
A number of fragments (refer to Fig. S3 A and B) show an unstructured length following helix 1 with no apparent protection (peptides 46–50, 46–59, 47–56, 48–59, 50–57, and 51–57). 
Cylinders along the length of the parent apoA-I molecule (243 residues) place α-helix; lines represent disordered segments.
Figure 3 represents the region 44-54 as disordered
Protein: DP04273 (UniProt P33609)
Region: residues 1	to 330
Annotation: disorder (Structural state)
Evidence: gel electrophoresis evidence used in manual assertion
Supporting statements:
Notably, during purification of p180 (1–330; Figure 2a), the sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) band corresponding to p180 (1–330), with an expected molecular weight of 37.2211 kDa, migrated almost the same distance as a 50 kDa protein (Figure 1d).