LiteFold/DisProt huggingface dataset:
Protein: DP03988 (UniProt Q86WX3)
Region: residues 1	to 136
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Native PAGE experiments showed a single band corresponding to the molecular mass of an AROS monomer (Figure 1D), showing that the protein is monomeric in solution and thus apparently non-globular due to partly unfolded regions.
Protein: DP03988 (UniProt Q86WX3)
Region: residues 1	to 136
Annotation: negative regulation of deacetylase activity (Biological process)
Evidence: in vitro deacetylation assay evidence used in manual assertion
Supporting statements:
To analyze the functional effect of AROS on Sirt1, we performed Sirt1 activity assays using the p53-derived, fluorogenic Fluor-de-Lys (FdL) 1 substrate peptide [27]. Titrating in AROS protein caused a concentration-dependent, potent inhibition of full-length Sirt1 with an IC50 of 11 ± 2 µM (Figure 3B). The inhibition was confirmed in an absorption-based coupled enzymatic assay (Supplementary Figure S2C) employing a p53-derived substrate peptide devoid of FdL’s non-physiological fluorophore modification, which can artificially influence Sirtuin/ligand interactions [27]. We then analyzed the mechanism of AROS-dependent Sirt1 inhibition through competition experiments with the Sirt1 substrates, acetylated peptide, and NAD+. Adding 40 µM AROS caused only moderate changes in vmax in titrations of either substrate (Figure 3C,D). It increased KM only slightly in the NAD+ titration, but more significantly (~3-fold) in the peptide titration, suggesting a mixed-type inhibition involving competition with the acyl substrate but not with the nucleotide cosubstrate.
Analyzing the FdL deacetylation activity of Sirt1, Sirt2, Sirt3, respective desuccinylation activity of Sirt5, in the absence and presence of 100 μM AROS, revealed that the protein inhibits all isoforms, albeit with varying potency (Figure 4C). It potently inhibits Sirt1, only weakly Sirt2 and Sirt5, and it shows a medium potency against Sirt3.
The AROS effects on Sirt3 and Sirt5 are unlikely to be physiologically relevant due to the mitochondrial localization of these isoforms.
Protein: DP03988 (UniProt Q86WX3)
Region: residues 62	to 71
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Partial assignment of AROS in the complex indicated that the very N- and C-terminal parts of AROS and the middle region from 57 to 89 are involved in binding to Sirt1 (Figure 4A; Supplementary Figure S3).
The center of AROS (62–71) appears to be key to the interaction, apparently at least in part through contacts to the Sirt1-SBD, but outside regions in AROS and Sirt1 seem to contribute to their affinity (Table 2).
Protein: DP03988 (UniProt Q86WX3)
Region: residues 1	to 136
Annotation: protein binding (Molecular function)
Evidence: microscale thermophoresis evidence used in manual assertion
Supporting statements:
Full-length AROS bound to mini-Sirt1ex687 with a Kd of 1.3 ± 0.2 μM, which is one order of magnitude below the IC50 and thus consistent with competition between AROS and substrate peptide.
These results indicate that N- and C-terminus of AROS contribute to binding, as well as the Sirt1 N-terminus/SBD and the catalytic core.
Protein: DP03988 (UniProt Q86WX3)
Region: residues 1	to 136
Annotation: protein binding (Molecular function)
Evidence: cross-linking evidence used in manual assertion
Supporting statements:
DSSO treatment of a mixture of Sirtuin and AROS, but not of either protein alone, led to the formation of a potential complex band (MW of the complex: 58 kDa; Figure 4B).
We thus conclude that both halves of AROS contribute to binding to Sirt1, which employs its catalytic core for this interaction, supported by the SBD.
Consistently, CL experiments with Sirt3 and Sirt5 resulted in clear bands for linked complexes with AROS (Figure 4D,E).
Protein: DP03989 (UniProt Q2YLR6)
Region: residues 22	to 85
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Analysis of the backbone secondary chemical shifts along the U-Omp19 sequence confirmed that the first 65 residues are disordered, while the rest of the protein adopts mostly b-sheet folding (Fig. 3B).
Protein: DP03989 (UniProt Q2YLR6)
Region: residues 22	to 61
Annotation: negative regulation of peptidase activity (Biological process)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
The isolated N-terminal fragment U-Omp19(1–60) presented anomalous electrophoretic mobility in SDS-PAGE. Although anomalous migration in SDS-PAGE can be attributed to the high content of acidic residues and thus low binding of SDS [63], other parameters such as expansion in solution [64] and a high proline content [65] can contribute to anomalous migration. This is probably
the case for U-Omp19(1–60), since its acidic content does not differ significantly from that of globular proteins and its expansion inferred from SEC experiments is compatible with a random coil conformation [55]. This intrinsically disordered and highly expanded U-Omp19(1–60) N-terminal fragment has demonstrated
to be necessary and sufficient to encode the full inhibitory activity of U-Omp19 towards pancreatic elastase (serine-protease), papain (cysteine-protease) and pepsin (aspartic-protease).
Surprisingly, U-Omp19(1–60) retained the full inhibitory activity of full-length U-Omp19 against pancreatic elastase, papain (Fig. 9E) and pepsin (Fig. S6), indicating that this region is not only required, but is also sufficient for the protease inhibitor activity of U-Omp19.
Protein: DP03989 (UniProt Q2YLR6)
Region: residues 22	to 81
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The Far-UV CD spectrum of U-Omp19(1–60) was compatible with that of an IDP with a minimum near 200 nm and low ellipticity at 222 nm (Fig. 9D). However, the small negative signal at 222 nm suggests some residual secondary structure content. Analysis of the ellipticity at 222 vs 200 nm allowed to classify U-Omp19(1–60) within the random coil subclass of IDPs [55].
Protein: DP03989 (UniProt Q2YLR6)
Region: residues 22	to 81
Annotation: positive regulation of immune response (Biological process)
Evidence: in vivo assay evidence used in manual assertion
Supporting statements:
The adjuvant activity of U-Omp19 was evidenced by the significant increase in the proliferation of OVA-specific CD8+ T cells in OVA + U-Omp19 compared to OVA alone-immunized mice. U-Omp19(1–60) fully conserved this adjuvanticity since the increase in proliferation was similar when OVA was co-delivered either with U-Omp19 or U-Omp19(1–60). In contrast, U-Omp19(60-159) was not able to increase the assessed proliferation (Fig. 10).
Protein: DP03989 (UniProt Q2YLR6)
Region: residues 22	to 81
Annotation: disorder (Structural state)
Evidence: gel electrophoresis evidence used in manual assertion
Supporting statements:
Also, U-Omp19(1–60) showed an-omalous electrophoretic mobility as revealed by Western blot (Fig. 9A). Although U-Omp19(1–60) presented the electrophoretic migration of a globular protein of ∼15 kDa (Fig. 9A), mass spectrometry studies indicated a MW of 6836.4 Da (data not shown), compatible with its theoretical MWTHEO of 6835.6 Da.
Protein: DP03989 (UniProt Q2YLR6)
Region: residues 22	to 81
Annotation: disorder (Structural state)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
SEC analysis showed a single and symmetric peak that eluted as a globular protein of higher MW (Fig. 9B) with a high MWSEC/MWTHEO ratio of 3.36 ± 0.05 (Fig. 9C) that is consistent with the IDP character of U-Omp19(1–60).
Protein: DP03990 (UniProt Q92597)
Region: residues 312	to 394
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of hNDRG1*C is typical of an intrinsically disordered protein, with a pronounced negative peak around 198 nm and a quantitative analysis of the spectrum confirming the low amount of secondary structure, with 6.6% α-helices, 26.3% β-strands and 67% unordered (Figure 3).
Protein: DP03990 (UniProt Q92597)
Region: residues 312	to 394
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The BEST-TROSY 1H-15N HSQC spectrum of hNDRG1*C at pH 6.5 (Figure 4A) features a narrow 1H chemical shift dispersion (8.0–8.6 ppm) typically seen for intrinsically disordered proteins (IDPs). 
The 1H 15N HSQC spectra of hNDRG1*C are characteristic of an intrinsically disordered protein, with low signal dispersion in the 1H dimension. This observation is maintained from pH 6.5 to 7.5 and confirms that this region is dominated by random coil conformations, lacking a well-defined structure, as predicted by the in silico disorder prediction analysis.
Protein: DP03990 (UniProt Q92597)
Region: residues 338	to 394
Annotation: nickel cation binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Overall, the picture that can be drawn from the NMR spectra analysis indicates the involvement of the side chains of Asp338, His345, Glu348, His355, Glu358, His365, Glu368, His371, Asp373, Asn377 and Cys394 in the uptake of Ni(II) by hNDRG1*C.
Protein: DP03990 (UniProt Q92597)
Region: residues 312	to 394
Annotation: nickel cation binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
The binding parameters, obtained from the fit of four binding isotherms (Figure 2B) and by averaging the results of the fits, indicate that the protein presents a single binding event (n = 1.4 ± 0.5) with affinity in the micromolar range (KA = 1.4 ± 0.3 × 104; KD = 70 ± 1 µM) and enthalpically driven (ΔH = −9 ± 6 kcal mol−1 and ΔS = −19 ± 13 cal mol−1 K−1).
Protein: DP03991 (UniProt Q9UN86)
Region: residues 45	to 54
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The asymmetric unit of the space group, H32, contains a single G3BP2 NTF2 polypeptide chain that could be traced from residue 1 to 139 except for a disordered loop region, residues 45-54.
Cross-references: PDB:5DRV
Protein: DP03992 (UniProt P0A7I7)
Region: residues 175	to 196
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Indeed, automated model building with Arp/warp resulted in the fitting of 167 of 173 ordered residues, there being no density visible for the C-terminal region.
Residues 175-196 are disordered in both structures.
Cross-references: PDB:2BZ1
PDB:2BZ0
Protein: DP03993 (UniProt Q12395)
Region: residues 1	to 11
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 1–11 and the interdomain linker corresponding to residues 56–65 in the final ScDcn1 model were not modeled due to disorder.
Cross-references: PDB:3BQ3
Protein: DP03993 (UniProt Q12395)
Region: residues 56	to 65
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 1–11 and the interdomain linker corresponding to residues 56–65 in the final ScDcn1 model were not modeled due to disorder.
Cross-references: PDB:3BQ3
Protein: DP03994 (UniProt P42641)
Region: residues 361	to 382
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Intrinsically disordered regions often fold upon binding to partner proteins (72). To verify whether the intrinsically disordered C-terminus of ObgE folds upon binding to YbiB, far-UV CDspectra were recorded for peptide1, YbiB and the YbiB-peptide1 complex (1:1 molar ratio) (Figure 3D). As expected, the CD spectrum of peptide1 shows a minimum around 200 nm, which is characteristic for a disordered peptide. On the other hand, the CD spectrum of YbiB displays the characteristics of a helical fold (minima around 208 and 222 nm), corresponding to its high -helix content as shown by the crystal structure (41).
Protein: DP03994 (UniProt P42641)
Region: residues 361	to 382
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Intrinsically disordered regions often fold upon binding to partner proteins (72). To verify whether the intrinsically disordered C-terminus of ObgE folds upon binding to YbiB, far-UV CDspectra were recorded for peptide1, YbiB and the YbiB-peptide1 complex (1:1 molar ratio) (Figure 3D). As expected, the CD spectrum of peptide1 shows a minimum around 200 nm, which is characteristic for a disordered peptide. On the other hand, the CD spectrum of YbiB displays the characteristics of a helical fold (minima around 208 and 222 nm), corresponding to its high -helix content as shown by the crystal structure (41).
Cross-references: PDB:8BFT
Protein: DP03994 (UniProt P42641)
Region: residues 338	to 390
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
However, we did not find extra densities that could be attributed to the CTD of ObgE, indicating that this domain is highly flexible.
The obtained Cryo-EM structure corresponds to ObgE bound to the 50S ribosome subunit.
Cross-references: PDB:4CSU
Protein: DP03995 (UniProt P40484)
Region: residues 114	to 125
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The linker between the Mob1 core and helix H0 (residues 140–142), and the linker between helix H0 and strand S0 (residues 113–125) are disordered and hence could not be modeled in the crystal structure. 
Cross-references: PDB:2HJN
Protein: DP03995 (UniProt P40484)
Region: residues 86	to 97
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The linker joining strands S-1 and S0 (residues 86–97) was disordered and could not be modeled.
Cross-references: PDB:2HJN
Protein: DP03995 (UniProt P40484)
Region: residues 114	to 125
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The linker between the Mob1 core and helix H0 (residues 140–142), and the linker between helix H0 and strand S0 (residues 113–125) are disordered and hence could not be modeled in the crystal structure. 
Cross-references: PDB:2HJN
Protein: DP03995 (UniProt P40484)
Region: residues 86	to 97
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The linker between the Mob1 core and helix H0 (residues 140–142), and the linker between helix H0 and strand S0 (residues 113–125) are disordered and hence could not be modeled in the crystal structure. 
Cross-references: PDB:2HJN
Protein: DP03996 (UniProt C0IR59)
Region: residues 173	to 193
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model of BdAMA1 incorporates residue 93 through 510, with two apical surface loops and a portion of the DII loop disordered. 
Cross-references: PDB:4APM
Protein: DP03996 (UniProt C0IR59)
Region: residues 258	to 271
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model of BdAMA1 incorporates residue 93 through 510, with two apical surface loops and a portion of the DII loop disordered. 
Cross-references: PDB:4APM
Protein: DP03996 (UniProt C0IR59)
Region: residues 353	to 391
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model of BdAMA1 incorporates residue 93 through 510, with two apical surface loops and a portion of the DII loop disordered. 
The tip of the BdAMA1 DII loop is disordered [Fig. 2(B top)], which is not surprising given that the corresponding region is completely disordered in PvAMA1,45 only partially modeled in PfAMA1,43 and displaced from the apical groove in Tg/PfAMA1 upon Tg/PfRON2 binding.
Cross-references: PDB:4APM
Protein: DP03997 (UniProt A0A3Q7EK40)
Region: residues 275	to 287
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The initial autobuilding placed 171 residues in 15 fragments. Iterative manual rebuilding and refinement resulted in a final structure consisting of 252 of a total 346 residues present in the expressed protein construct. Several regions of the protein could not be modelled due to discontinuous electron density, including much of the ARC1 subdomain, and the solvent-exposed ɑ-helices of the NB domain.
Cross-references: PDB:6S2P
Protein: DP03997 (UniProt A0A3Q7EK40)
Region: residues 374	to 391
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The initial autobuilding placed 171 residues in 15 fragments. Iterative manual rebuilding and refinement resulted in a final structure consisting of 252 of a total 346 residues present in the expressed protein construct. Several regions of the protein could not be modelled due to discontinuous electron density, including much of the ARC1 subdomain, and the solvent-exposed ɑ-helices of the NB domain.
Cross-references: PDB:6S2P
Protein: DP03997 (UniProt A0A3Q7EK40)
Region: residues 416	to 435
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The initial autobuilding placed 171 residues in 15 fragments. Iterative manual rebuilding and refinement resulted in a final structure consisting of 252 of a total 346 residues present in the expressed protein construct. Several regions of the protein could not be modelled due to discontinuous electron density, including much of the ARC1 subdomain, and the solvent-exposed ɑ-helices of the NB domain.
Cross-references: PDB:6S2P
Protein: DP03998 (UniProt O25119)
Region: residues 86	to 117
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 86–117 of the N-terminal domain, residues 197–203 of LoopC, residues 336–343 of the C terminus of HpFliGMC1, and residues 337–343 of HpFliGMC2 were disordered and thus were excluded from the structural models. 
Cross-references: PDB:3USW
Protein: DP03999 (UniProt Q8IL97)
Region: residues 126	to 174
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Interestingly, the long insertion is structurally not defined and is not represented in the X-ray structure (see Figure S2).
Cross-references: PDB:5CS2
Protein: DP04000 (UniProt Q9U7C3)
Region: residues 453	to 473
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
All helices of the seven TPR motifs, with the exception of helix 4A of the “linker TPR4,” are well defined in our structures.
The five structures described in PMID: 18598704 are mapped to two different Uniprot entries, Q57W55 (3CV0, 3CVP, 3CVQ) and Q9U7C3 (3CVL, 3CVN), although the publication does refer to one protein. The differences between the two sequences are in amino acids 143 [T (Q57W55), A (Q9U7C3)], 158 [N (Q57W55), S (Q9U7C3)] and 163 [S (Q57W55), N (Q9U7C3)].
Cross-references: PDB:3CVL
PDB:3CVP
Protein: DP04000 (UniProt Q9U7C3)
Region: residues 459	to 473
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
All helices of the seven TPR motifs, with the exception of helix 4A of the “linker TPR4,” are well defined in our structures. 
The five structures described in PMID: 18598704 are mapped to two different Uniprot entries, Q57W55 (3CV0, 3CVP, 3CVQ) and Q9U7C3 (3CVL, 3CVN), although the publication does refer to one protein. The differences between the two sequences are in amino acids 143 [T (Q57W55), A (Q9U7C3)], 158 [N (Q57W55), S (Q9U7C3)] and 163 [S (Q57W55), N (Q9U7C3)].
Cross-references: PDB:3CVN
PDB:3CV0
PDB:3CVQ
Protein: DP04000 (UniProt Q9U7C3)
Region: residues 600	to 611
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No observable electron density for this region in the structures.
Cross-references: PDB:3CVP
PDB:3CVQ
Protein: DP04002 (UniProt Q71RI2)
Region: residues 201	to 300
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Figure 1 shows an interesting fact, namely that P4-201 is intrinsically disordered except for the p53 rescue motif forming segment.
Figure 1A shows the HSQC spectrum of the free state of P4-201 (residues 201-300 of SUSP4).
Cross-references: BMRB:26961
Protein: DP04002 (UniProt Q71RI2)
Region: residues 263	to 291
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The SSP scores and chemical shift perturbation data (Figure 3) indicate that the
full p53 rescue motif peptide has a binding pattern and affinity for mdm2 similar to the long-turn peptide of p53 TAD identified previously.[6] The shorter 19-residue peptide without the N-terminal affinity enhancer exhibits a much weaker binding.
Results indicate that the NMR resonances of several hydrophobic residues in P4-201 are affected upon addition of mdm2(3–109) (Figure 1).
Protein: DP04003 (UniProt P0C746)
Region: residues 3	to 77
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Far-UV circular dichroism (CD) and NMR 1H-15N heteronuclear single quantum coherence (HSQC) spectra show that the full-length and truncated HBZ AD constructs are almost entirely disordered in their free forms (SI Appendix, Fig. S1)
Protein: DP04003 (UniProt P0C746)
Region: residues 3	to 77
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Far-UV circular dichroism (CD) and NMR 1H-15N heteronuclear single quantum coherence (HSQC) spectra show that the full-length and truncated HBZ AD constructs are almost entirely disordered in their free forms (SI Appendix, Fig. S1).