LiteFold/DisProt huggingface dataset:
Protein: DP01156 (UniProt P07305)
Region: residues 98	to 194
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectra of unbound ProTα and H1 reflect the low secondary structure content of the individual IDPs, except for the small helix-turn-helix domain of H113,19,20 (Fig. 1c).
Protein: DP01156 (UniProt P07305)
Region: residues 98	to 194
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Surprisingly, the CD spectrum of an equimolar mixture of the two proteins can be explained by the simple sum of the individual spectra, indicating that complex formation entails minimal changes in average secondary structure content.
Note, however, that the globular domain is dispensable for complex formation (Fig. 2b, cf. High-affinity binding in spite of disorder).
Protein: DP01156 (UniProt P07305)
Region: residues 1	to 22
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectra of unbound ProTα and H1 reflect the low secondary structure content of the individual IDPs, except for the small helix-turn-helix domain of H113,19,20 (Fig. 1c).
Protein: DP01156 (UniProt P07305)
Region: residues 1	to 22
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Surprisingly, the CD spectrum of an equimolar mixture of the two proteins can be explained by the simple sum of the individual spectra, indicating that complex formation entails minimal changes in average secondary structure content.
Note, however, that the globular domain is dispensable for complex formation (Fig. 2b, cf. High-affinity binding in spite of disorder).
Protein: DP01156 (UniProt P07305)
Region: residues 98	to 194
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
1H,15N heteronuclear single quantum coherence (HSQC) spectra of the individual proteins exhibit low dispersion of the 1H chemical shifts, as expected for IDPs14,21-23 (Fig. 1e,f). Only the globular domain of H1, which is stably folded even in isolation (Extended Data Fig. 1), shows the large dispersion of resonances characteristic of tertiary structure23,24 (Fig. 1g).
Protein: DP01156 (UniProt P07305)
Region: residues 98	to 194
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Remarkably, the overall peak dispersion remains unchanged upon complex formation, confirming that no pronounced tertiary structure is formed upon binding. Nevertheless, small but clearly detectable peak shifts observed for ProTα and H1 indicate significant changes in the average chemical environment of the corresponding residues, as expected upon interaction with the large opposite charge of the other IDP.
Note, however, that the globular domain is dispensable for complex formation (Fig. 2b, cf. High-affinity binding in spite of disorder).
Cross-references: BMRB:27216
Protein: DP01156 (UniProt P07305)
Region: residues 1	to 22
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
1H,15N heteronuclear single quantum coherence (HSQC) spectra of the individual proteins exhibit low dispersion of the 1H chemical shifts, as expected for IDPs14,21-23 (Fig. 1e,f). Only the globular domain of H1, which is stably folded even in isolation (Extended Data Fig. 1), shows the large dispersion of resonances characteristic of tertiary structure23,24 (Fig. 1g).
Protein: DP01156 (UniProt P07305)
Region: residues 1	to 22
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Remarkably, the overall peak dispersion remains unchanged upon complex formation, confirming that no pronounced tertiary structure is formed upon binding. Nevertheless, small but clearly detectable peak shifts observed for ProTα and H1 indicate significant changes in the average chemical environment of the corresponding residues, as expected upon interaction with the large opposite charge of the other IDP.
Note, however, that the globular domain is dispensable for complex formation (Fig. 2b, cf. High-affinity binding in spite of disorder).
Cross-references: BMRB:27216
Protein: DP01156 (UniProt P07305)
Region: residues 104	to 194
Annotation: protein binding (Molecular function)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
The dominant contribution to the interaction with ProTα stems from the unstructured C-terminal part of H1, which alone binds with picomolar affinity. The N-terminal half and the isolated globular domain of H1 also bind ProTα, but with much lower affinity (Fig. 2b).
Protein: DP01156 (UniProt P07305)
Region: residues 101	to 194
Annotation: nucleosome binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
Both H1.0ΔC and H1.0 ΔCpartial bind nucleosomes at a concentration of about 30 nM (Figure 4B,C), while full length H1.0 binds nucleosomes at about 3 nM (Figure 2A). This implies that both deletion mutants have about a 10-fold lower affinity to nucleosomes than full length H1.0.
Protein: DP01157 (UniProt P04908)
Region: residues 1	to 27
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We examined the secondary structures of the isolated H2A-H2B heterodimer by TROSY-NMR. Almost all of the main-chain signals (i.e., HN, N, Cα, Cβ and C’ signals) could be assigned (96% for H2A; 95% for H2B). As shown in the experimental chemical shift indices obtained from the Cα and Cβ chemical shift values, both H2A and H2B contain a core histone fold comprising four α-helices together with two β-strands—namely, α1–β1–α2–β2–α3–αC, much as is observed for their counterparts in the nucleosome. Outside the histone fold of H2A, however, the N-terminal αN helix and the C-terminal β3 strand and 310 helix observed in the nucleosome are entirely disordered in the isolated H2A-H2B heterodimer.
Cross-references: BMRB:11609
Protein: DP01157 (UniProt P04908)
Region: residues 1	to 27
Annotation: acetylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Histone proteins have N-terminal and/or C-terminal flexible tails, which are modified by methylation and acetylation, and influence chromatin remodeling.
Protein: DP01157 (UniProt P04908)
Region: residues 1	to 27
Annotation: methylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Histone tails play important roles in the dynamic functions of chromatin through posttranslational modifications such as acetylation, phosphorylation and methylation.
Protein: DP01157 (UniProt P04908)
Region: residues 98	to 130
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We examined the secondary structures of the isolated H2A-H2B heterodimer by TROSY-NMR. Almost all of the main-chain signals (i.e., HN, N, Cα, Cβ and C’ signals) could be assigned (96% for H2A; 95% for H2B). As shown in the experimental chemical shift indices obtained from the Cα and Cβ chemical shift values, both H2A and H2B contain a core histone fold comprising four α-helices together with two β-strands—namely, α1–β1–α2–β2–α3–αC, much as is observed for their counterparts in the nucleosome. Outside the histone fold of H2A, however, the N-terminal αN helix and the C-terminal β3 strand and 310 helix observed in the nucleosome are entirely disordered in the isolated H2A-H2B heterodimer.
Cross-references: BMRB:11609
Protein: DP01157 (UniProt P04908)
Region: residues 98	to 130
Annotation: acetylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Histone proteins have N-terminal and/or C-terminal flexible tails, which are modified by methylation and acetylation, and influence chromatin remodeling.
Protein: DP01157 (UniProt P04908)
Region: residues 98	to 130
Annotation: methylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Histone tails play important roles in the dynamic functions of chromatin through posttranslational modifications such as acetylation, phosphorylation and methylation.
Protein: DP01158 (UniProt P06899)
Region: residues 1	to 38
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
H2A and H2B each contain a histone fold, comprising four α-helices and two β-strands (α1-β1-α2-β2-α3-αC), together with the long disordered N- and C-terminal H2A tails and the long N-terminal H2B tail.
Cross-references: BMRB:11609
Protein: DP01159 (UniProt A6NF83)
Region: residues 1	to 97
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far-UV CD spectrum of NUPR1L at pH 7.5 had minima at 210 nm, and a wide shoulder around 222 nm, which suggest the presence of helix- or turn-like conformations. This spectrum is different to that observed for NUPR1, with a minimum at around 205 nm, which was characteristic of random-coil conformations. However, as NUPR1L has one Trp, five Tyr, one Phe and two His, we cannot rule out the absorbance of aromatic residues, which also occur at these wavelengths. As it happened with the thermal denaturations followed by fluorescence, the transitions followed by the ellipticity at 222 nm did not show any sigmoidal behaviour, suggesting that possible helical or turn-like conformations were not rigid. We conclude that NUPR1L was an IDP on the basis of two pieces of evidence. The absence of sigmoidal transitions in fluorescence and CD thermal and in the fluorescence chemical denaturations indicates the lack of secondary and tertiary structures. Although such absence is one of the features to assess protein disorder, it could be argued that non- sigmoidal denaturation curves are also due to non-cooperative transitions. However, it would be highly unlikely that non-cooperative transitions for the same protein were observed in chemical and thermal denaturations.
Protein: DP01159 (UniProt A6NF83)
Region: residues 1	to 97
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Thermal denaturations of NUPR1L at several pH values (3.0, 5.5, 7.0, 8.4 and 13.0) were carried out by following the changes in the intrinsic fluorescence. At all pH values explored, we did not observe any sigmoidal transition, and protein precipitation was observed at acidic pH. Thermal denaturations of isolated NUPR1 do not show any sigmoidal transition. We also tried to follow the denaturation of NUPR1L in the presence of urea by excitation either at 280 or 295 nm. However, as it happened with the thermal denaturations, no sigmoidal curves were observed at any of the two excitation wavelengths. A similar behaviour has been reported in the chemical denaturations of isolated NUPR.
Protein: DP01159 (UniProt A6NF83)
Region: residues 1	to 97
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We acquired a 1D 1H NMR spectrum at very low NUPR1L concentration (9 μM, in protomer units) at pH 8.0, in the presence of 500 mM NaCl and 1 mM β-ME. In the up-field region of the spectrum, all the methyl protons appeared clustered around 0.9 ppm, as they are expected in a polypeptide chain devoid of rigid secondary and tertiary structures. On the other hand, in the amide region a very low signal intensity was observed and very broad peaks were detected (the sharp peaks are due to the aromatic protons of the His-tail (around 8.5 ppm) and the presence of protons of the bases of deoxy-oligonucleotides); furthermore, no signal, around 10.20 ppm, was observed for the indole moiety of Trp62, where it should be observed for a disordered polypeptide chain [61]. These results can be explained as due to: (i) the presence of slow-to-intermediate conformational exchange in NUPR1L involving such aromatic ring, which broadens the signal; or alternatively, (ii) signal broadening due to presence of large molecular weight species. The latter explanation agrees with the experimental observation that Trp62 was involved in the self-association equilibrium of NUPR1L as shown by the quenching results. Then, the NMR indicates that NUPR1L was a disordered protein.
Protein: DP01159 (UniProt A6NF83)
Region: residues 1	to 97
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We have shown that NUPR1L was capable of interacting with the same partners of NUPR1, namely, prothymosin α and C-RING1B. However, while the affinity for prothymosin α was the same, within the uncertainty, for both protein isoforms, in the case of C-RING1B the apparent affinity of NUPR1L was smaller (i.e., larger Kd) compared to that of NUPR1: 60 μM versus 10 μM. This difference is due to the self-association of NUPR1L, since the reported constants should include the dissociation of both C-RING1B and NUPR1L, unless the complex involves the formation of a higher-order state between the oligomeric species of both proteins, in which case the real affinity between the two proteins must be lower.
Protein: DP01160 (UniProt P9WPI9)
Region: residues 1	to 81
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The sequence-based analysis of PtkA (30.6 kDa, 291 amino acids) predicts a high disorder tendency for the N-terminal part comprising 80 amino acids (Fig. S1). Our NMR data confirm the prediction, showing that PtkA consists of a well-folded KCD and an unstructured IDD. The 2D 1H,15N TROSY spectrum of the full-length PtkA shows in total 231 of 270 expected amide resonances (Fig. 1A). Two subsets of signals can be clearly observed: (i) a set of well-dispersed peaks, typical for a well-folded structure, and (ii) another set of signals with high intensity, which are clustered in the center of the spectrum (1H: 7.6–8.6 ppm), indicative of unstructured regions within the full-length PtkA. The 2D 1H,15N HSQC spectrum of PtkA shows only minor changes of the chemical shift in the presence of ATP (Fig. S8).
Protein: DP01160 (UniProt P9WPI9)
Region: residues 1	to 81
Annotation: self-inhibition (Disorder function)
Evidence: in vitro protein kinase assay evidence used in manual assertion
Supporting statements:
The results thus obtained suggest that the KCDPtkA is 5 times more active than the full-length PtkA. Activity of the KCDPtkA measured together with isolated IDD (IDDPtkA) shows a decrease compared with the KCDPtkA alone, suggesting that the IDD has an inhibitory effect on the kinase activity.
 The decrease of the PtkA activity in the presence of IDD suggests an inhibitory effect of the disordered domain during the autophosphorylation. Spin label studies indicated the existence of residual long-range transient interactions of the IDD with the KCD.
These results strongly suggest that the IDD transiently binds to the KCD and masks the substrate-binding site and inhibits the kinase activity.
Protein: DP01161 (UniProt Q9UMS4)
Region: residues 169	to 194
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure covering the WD40 domain part of human PRFP19 (residues 169–504 ) has been solved. Residues 169-194 was invisible in the structure.
Cross-references: PDB:4LG8
Protein: DP01163 (UniProt O14974)
Region: residues 1	to 40
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
MYPT1 residues 1-40 form the disordered region, while MYPT1 residues 41-98 form the folded ankyrin-repeat region.
Furthermore, while i,i+1 1HN-1HN NOE cross-peaks, typical for α-helical secondary structure elements, can be detected in the well-folded ankyrin-repeat region (residues 41-98) of MYPT11-98, no significant i,i+1 1HN-1HN NOE cross-peaks are identified in the disordered region (residues 1-40).
Protein: DP01164 (UniProt Q13625)
Region: residues 331	to 692
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Using size exclusion chromatography, we observed a low level of compactness for ASPP2331–692, indicative of an extended conformation of this domain, typical of intrinsically disordered proteins.
Protein: DP01164 (UniProt Q13625)
Region: residues 331	to 692
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We also analyzed ASPP2331–692 by far-UV CD and observed a spectrum that consisted mainly of a minimum at 200 nm, indicative of a high content of unstructured protein (Figure 2C). We calculated the secondary structure content (47, 48) of ASPP2331–692 to be 56% disordered, 2% helix, 28% strand, and 14% turn conformations.
Protein: DP01164 (UniProt Q13625)
Region: residues 331	to 692
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The HSQC-TROSY spectrum of 15N-labeled ASPP2331–692 exhibited a pattern typical for disordered proteins (Figure 2E), in which the observed resonances of the amide protons are dispersed in a narrow cluster ranged from δ1H 7.7 to 8.5 ppm (Δ = 0.8 ppm), unlike wider distributions typical for structured proteins.
Protein: DP01164 (UniProt Q13625)
Region: residues 693	to 918
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
The ASPP2 Pro domain eluted earlier than predicted from its molecular mass, and its apparent molecular mass estimated from the calibration curve was ∼130,000 Da (Fig. 2A), a value five times higher than the theoretical value of 24,500 Da. This early elution in the gel filtration may be attributed to an extended or unfolded native structure of the protein (39) or to putative oligomerization.
Protein: DP01164 (UniProt Q13625)
Region: residues 693	to 918
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far-UV CD spectrum of the recombinant purified protein exhibited a minimum at only ∼200 nm (Fig. 3A), suggesting a highly unstructured conformation.
Protein: DP01164 (UniProt Q13625)
Region: residues 484	to 692
Annotation: protein binding (Molecular function)
Evidence: surface plasmon resonance evidence used in manual assertion
Supporting statements:
By further dissecting ASPP2331–692 into two nonoverlapping parts, we observed that this interaction is mediated solely through residues 484–692, as ASPP2484–692 bound CagA with a KD of 13 μM (Figure 4B), with no contribution to binding from the N-terminal part, ASPP2331–484 (Figure 4C).
Conversely, we observed no binding between ASPP2484–692 and CagA256–885 by both ITC (Figure 4H and Table 1) and SPR (Figure 4I). These data indicate that ASPP2484–692 interacts with the extreme N-terminal domain of CagA, inclusive of residues 1–256, which also contains the binding site for ASPP2746–765.
Protein: DP01164 (UniProt Q13625)
Region: residues 331	to 692
Annotation: protein binding (Molecular function)
Evidence: peptide array evidence used in manual assertion
Supporting statements:
Although CagA1–885 bound several peptides (I24-ASPP2386–400, J1-ASPP2397–411, and J6-ASPP2440–454) within the ASPP2331–484 region that did not bind as a contiguous protein fragment in our SPR experiments, peptides derived from the ASPP2484–692 region that confers CagA binding were both more numerous and prominent (Figure 4F). In particular, peptides centered within a set of binding peptides (J12-ASPP2494–508 and J17-ASPP2541–555) and peptides of the highest intensity (J21-ASPP2577–591 and K6-ASPP2656–670) are likely to comprise the noncontiguous binding determinants of the ASPP2484–692 protein fragment.
Protein: DP01164 (UniProt Q13625)
Region: residues 484	to 692
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
When we measured the thermodynamic parameters of binding between ASPP2484–692 and CagA1–885 (Figure 4G and Table 1), we observed binding with similar affinity (KD = 4.9 ± 0.5 μM) to that from the analogous experiment carried out by SPR. Conversely, we observed no binding between ASPP2484–692 and CagA256–885 by both ITC (Figure 4H and Table 1) and SPR (Figure 4I). These data indicate that ASPP2484–692 interacts with the extreme N-terminal domain of CagA, inclusive of residues 1–256, which also contains the binding site for ASPP2746–765.
Protein: DP01164 (UniProt Q13625)
Region: residues 693	to 918
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
To quantify and analyze the thermodynamic profile of the CagA interactions with the Pro-rich and Ank-SH3 domains of ASPP2, we performed isothermal titration calorimetry using CagA1–885 and the ASPP2 Pro-rich and Ank-SH3 domains either alone (ASPP2693–918 and ASPP2893–1128, respectively) or together (as a single fused fragment, ASPP2693–1128). We found that CagA1–885 bound ASPP2693–1128, inclusive of both Pro-rich and Ank-SH3 domains, as a 1:1 complex with an affinity of 62 nM (Figure 5A). This interaction is entirely dependent on the presence of the Pro-rich domain, as we detected no binding between CagA and the ASPP2 Ank-SH3 domain (Figure 5B).
Protein: DP01164 (UniProt Q13625)
Region: residues 710	to 904
Annotation: protein binding (Molecular function)
Evidence: peptide array evidence used in manual assertion
Supporting statements:
In the ASPP2 Pro-rich domain, three sets of binding peptides included (i) K12-ASPP2710–724/K13-ASPP2721–735, (ii) K15-ASPP2739–753/K16-ASPP2746–760, and (iii) L8-ASPP2890–904/L9-ASPP2901–915/L10-ASPP2908–922.
Protein: DP01164 (UniProt Q13625)
Region: residues 693	to 918
Annotation: self-assembly (Disorder function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
We performed a nickel-affinity pulldown experiment to test whether the two domains interact with each other. ASPP2 Ank-SH3 was retrieved by nickel beads following its incubation with His-tagged ASPP2 Pro but not when incubated with the nickel beads alone (Fig. 4A).
Protein: DP01164 (UniProt Q13625)
Region: residues 693	to 918
Annotation: protein homodimerization activity (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
We performed a nickel-affinity pulldown experiment to test whether the two domains interact with each other. ASPP2 Ank-SH3 was retrieved by nickel beads following its incubation with His-tagged ASPP2 Pro but not when incubated with the nickel beads alone (Fig. 4A).