LiteFold/DisProt huggingface dataset:
Protein: DP01078 (UniProt P40477)
Region: residues 441	to 881
Annotation: disorder (Structural state)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
Because FTIR spectroscopy is more sensitive to β-sheet structure than CD, we also generated FTIR spectra (amide I region) for each FG Nup. These spectra show broad absorbance bands near 1,655 cm−1 corresponding to disordered conformations (Table 3 and Fig. 5, which is published as supporting information on the PNAS web site). Deconvolution (Fourier self-deconvolution and second derivative) and curve fitting of the FTIR spectra permitted quantitative analyses of secondary structure content, confirming that purified FG Nups are composed mostly (≈80%) of disordered structure (Table ​3; Fig. ​3B).
Protein: DP01078 (UniProt P40477)
Region: residues 441	to 881
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
In contrast, most FG Nups in nuclei are fully proteolysed within 60 min (category III) or 15 min (category IV) (Fig. ​4A). Nups localized to the nuclear basket structure of the NPC (Nup60p, Nup1p, and Nup2p) and to cytoplasmic fibrils (Nup159p and Nup42p) (30–32) are the most sensitive to proteinase K (Fig. ​4A). Some FG Nups located at the center of the NPC (Nup57p, Nup53p, and nNup145p) (30) degrade after a lag period of 10 min (category II), suggesting that these Nups also contain highly flexible structures but are not immediately accessible to the protease (Fig. ​4A).
Protein: DP01078 (UniProt P40477)
Region: residues 441	to 881
Annotation: disorder (Structural state)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
Instead, the experimentally determined RS values for the FG Nups compare favorably to theoretical RS values predicted for monomeric proteins in natively unfolded conformations (Table 4, which is published as supporting information on the PNAS web site, www.pnas.org) (17).
Protein: DP01079 (UniProt P40517)
Region: residues 1	to 203
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
In contrast, most FG Nups in nuclei are fully proteolysed within 60 min (category III) or 15 min (category IV) (Fig. ​4A). Nups localized to the nuclear basket structure of the NPC (Nup60p, Nup1p, and Nup2p) and to cytoplasmic fibrils (Nup159p and Nup42p) (30–32) are the most sensitive to proteinase K (Fig. ​4A). Some FG Nups located at the center of the NPC (Nup57p, Nup53p, and nNup145p) (30) degrade after a lag period of 10 min (category II), suggesting that these Nups also contain highly flexible structures but are not immediately accessible to the protease (Fig. ​4A).
Protein: DP01079 (UniProt P40517)
Region: residues 1	to 203
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Far-UV CD measurements of purified FG Nups produce spectra characteristic of unfolded proteins (Fig. ​3A). Each FG Nup has an intensive minimum near 200 nm and low ellipticity at 222 nm that reflect extensive contributions of unstructured coil and a lack of α-helical structure.
Protein: DP01079 (UniProt P40517)
Region: residues 1	to 203
Annotation: disorder (Structural state)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
Because FTIR spectroscopy is more sensitive to β-sheet structure than CD, we also generated FTIR spectra (amide I region) for each FG Nup. These spectra show broad absorbance bands near 1,655 cm−1 corresponding to disordered conformations (Table 3 and Fig. 5, which is published as supporting information on the PNAS web site). Deconvolution (Fourier self-deconvolution and second derivative) and curve fitting of the FTIR spectra permitted quantitative analyses of secondary structure content, confirming that purified FG Nups are composed mostly (≈80%) of disordered structure (Table ​3; Fig. ​3B).
Protein: DP01079 (UniProt P40517)
Region: residues 1	to 203
Annotation: disorder (Structural state)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
Instead, the experimentally determined RS values for the FG Nups compare favorably to theoretical RS values predicted for monomeric proteins in natively unfolded conformations (Table 4, which is published as supporting information on the PNAS web site, www.pnas.org) (17).
Protein: DP01083 (UniProt Q7TP21)
Region: residues 91	to 167
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Dynamic Behavior of an Intrinsically Unstructured Linker Domain Is Conserved in the Face of Negligible Amino Acid Sequence Conservation
The IULD functions to tether two high affinity single stranded DNA binding domains (DBD A and B) to an N-terminal single stranded DNA (ssDNA) binding and protein interaction domain (DBD F; see Fig. 1 for domain structure of RPA70) (Daughdrill et al. 2001).
Plot showing the values for the reduced spectral density function at 0 frequency, J(0). J(0) values are plotted on the vertical axis and residue number is plotted on the horizontal axis.
Unstructured linker domain (IULD) connecting two compact globular regions - the N-terminal DBD F domain and the ss-DNA binding DBD A domain - in the 70 kDa subunit of replication protein A (RPA70).
Protein: DP01083 (UniProt Q7TP21)
Region: residues 91	to 167
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Dynamic Behavior of an Intrinsically Unstructured Linker Domain Is Conserved in the Face of Negligible Amino Acid Sequence Conservation
The IULD functions to tether two high affinity single stranded DNA binding domains (DBD A and B) to an N-terminal single stranded DNA (ssDNA) binding and protein interaction domain (DBD F; see Fig. 1 for domain structure of RPA70) (Daughdrill et al. 2001).
Plot showing the values for the reduced spectral density function at 0 frequency, J(0). J(0) values are plotted on the vertical axis and residue number is plotted on the horizontal axis.
Unstructured linker domain (IULD) connecting two compact globular regions - the N-terminal DBD F domain and the ss-DNA binding DBD A domain - in the 70 kDa subunit of replication protein A (RPA70).
Protein: DP01084 (UniProt Q1K7R9)
Region: residues 111	to 173
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Dynamic Behavior of an Intrinsically Unstructured Linker Domain Is Conserved in the Face of Negligible Amino Acid Sequence Conservation
The IULD functions to tether two high affinity single stranded DNA binding domains (DBD A and B) to an N-terminal single stranded DNA (ssDNA) binding and protein interaction domain (DBD F; see Fig. 1 for domain structure of RPA70) (Daughdrill et al. 2001).
Plot showing the values for the reduced spectral density function at 0 frequency, J(0). J(0) values are plotted on the vertical axis and residue number is plotted on the horizontal axis.
Unstructured linker domain (IULD) connecting two compact globular regions - the N-terminal DBD F domain and the ss-DNA binding DBD A domain - in the 70 kDa subunit of replication protein A (RPA70).
Protein: DP01084 (UniProt Q1K7R9)
Region: residues 111	to 173
Annotation: flexible linker (Disorder function)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Dynamic Behavior of an Intrinsically Unstructured Linker Domain Is Conserved in the Face of Negligible Amino Acid Sequence Conservation
The IULD functions to tether two high affinity single stranded DNA binding domains (DBD A and B) to an N-terminal single stranded DNA (ssDNA) binding and protein interaction domain (DBD F; see Fig. 1 for domain structure of RPA70) (Daughdrill et al. 2001).
Plot showing the values for the reduced spectral density function at 0 frequency, J(0). J(0) values are plotted on the vertical axis and residue number is plotted on the horizontal axis.
Unstructured linker domain (IULD) connecting two compact globular regions - the N-terminal DBD F domain and the ss-DNA binding DBD A domain - in the 70 kDa subunit of replication protein A (RPA70).
Protein: DP01085 (UniProt Q9SKI4)
Region: residues 106	to 193
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Dynamic Behavior of an Intrinsically Unstructured Linker Domain Is Conserved in the Face of Negligible Amino Acid Sequence Conservation
The IULD functions to tether two high affinity single stranded DNA binding domains (DBD A and B) to an N-terminal single stranded DNA (ssDNA) binding and protein interaction domain (DBD F; see Fig. 1 for domain structure of RPA70) (Daughdrill et al. 2001).
Plot showing the values for the reduced spectral density function at 0 frequency, J(0). J(0) values are plotted on the vertical axis and residue number is plotted on the horizontal axis.
Unstructured linker domain (IULD) connecting two compact globular regions - the N-terminal DBD F domain and the ss-DNA binding DBD A domain - in the 70 kDa subunit of replication protein A (RPA70).
Protein: DP01085 (UniProt Q9SKI4)
Region: residues 106	to 193
Annotation: flexible linker (Disorder function)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Dynamic Behavior of an Intrinsically Unstructured Linker Domain Is Conserved in the Face of Negligible Amino Acid Sequence Conservation
The IULD functions to tether two high affinity single stranded DNA binding domains (DBD A and B) to an N-terminal single stranded DNA (ssDNA) binding and protein interaction domain (DBD F; see Fig. 1 for domain structure of RPA70) (Daughdrill et al. 2001).
Plot showing the values for the reduced spectral density function at 0 frequency, J(0). J(0) values are plotted on the vertical axis and residue number is plotted on the horizontal axis.
Unstructured linker domain (IULD) connecting two compact globular regions - the N-terminal DBD F domain and the ss-DNA binding DBD A domain - in the 70 kDa subunit of replication protein A (RPA70).
Protein: DP01086 (UniProt Q10Q08)
Region: residues 105	to 180
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Dynamic Behavior of an Intrinsically Unstructured Linker Domain Is Conserved in the Face of Negligible Amino Acid Sequence Conservation
The IULD functions to tether two high affinity single stranded DNA binding domains (DBD A and B) to an N-terminal single stranded DNA (ssDNA) binding and protein interaction domain (DBD F; see Fig. 1 for domain structure of RPA70) (Daughdrill et al. 2001). 
Plot showing the values for the reduced spectral density function at 0 frequency, J(0). J(0) values are plotted on the vertical axis and residue number is plotted on the horizontal axis.
Unstructured linker domain (IULD) connecting two compact globular regions - the N-terminal DBD F domain and the ss-DNA binding DBD A domain - in the 70 kDa subunit of replication protein A (RPA70).
Protein: DP01086 (UniProt Q10Q08)
Region: residues 105	to 180
Annotation: flexible linker (Disorder function)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Dynamic Behavior of an Intrinsically Unstructured Linker Domain Is Conserved in the Face of Negligible Amino Acid Sequence Conservation
The IULD functions to tether two high affinity single stranded DNA binding domains (DBD A and B) to an N-terminal single stranded DNA (ssDNA) binding and protein interaction domain (DBD F; see Fig. 1 for domain structure of RPA70) (Daughdrill et al. 2001).
Plot showing the values for the reduced spectral density function at 0 frequency, J(0). J(0) values are plotted on the vertical axis and residue number is plotted on the horizontal axis.
Unstructured linker domain (IULD) connecting two compact globular regions - the N-terminal DBD F domain and the ss-DNA binding DBD A domain - in the 70 kDa subunit of replication protein A (RPA70).
Protein: DP01087 (UniProt Q1PAB4)
Region: residues 1	to 101
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In line with data in the literature concerning other Tat variants, the CD spectra demonstrated the absence of any significant ordered secondary structure for these proteins, as seen from the intensive minimum at 198 nm and an ellipticity close to zero in the vicinity of 185 and 222 nm (see Fig. 2).
Protein: DP01087 (UniProt Q1PAB4)
Region: residues 1	to 101
Annotation: disorder (Structural state)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
 As expected, the CD spectrum of wt-Tat133 alone or in the presence of 6M urea was characteristic of a fully unfolded protein.
Protein: DP01087 (UniProt Q1PAB4)
Region: residues 1	to 101
Annotation: disorder (Structural state)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
Thus, the Stokes radii measured by DLS and gel filtration for Tat proteins are not compatible with a globular protein, but with a disordered state.
The hydrodynamic radii measured for wt-Tat133 and STLA-Tat133 by DLS analysis at a concentration of 1 mg/mL were RS = 30 ± 3 Å (data not shown), which is coherent with a fully unfolded protein.
Protein: DP01087 (UniProt Q1PAB4)
Region: residues 1	to 101
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
For wt-Tat133, this ratio Rg/Rs is between 1.1 and 1.4 depending if we use the Rs value measured by DLS or gel filtration, respectively, and is thus coherent with a fully unfolded protein.
In the case of wt-Tat133, the Kratky plot is typical of a fully unfolded protein without significant residual structure [Fig. 4(B)].
Protein: DP01087 (UniProt Q1PAB4)
Region: residues 1	to 101
Annotation: disorder (Structural state)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
Thus, the Stokes radii measured by DLS and gel filtration for Tat proteins are not compatible with a globular protein, but with a disordered state.
Protein: DP01087 (UniProt Q1PAB4)
Region: residues 1	to 101
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
An α-helix transition was observed for the wt-Tat133/14C12B5 Fab′ complexes, as indicated by the more pronounced minimum between 210 and 220 nm and by the shifting of the maximum toward 195 nm of the experimentally observed spectrum compared with the corresponding theoretical average curve [Fig. 7(A)].
Protein: DP01087 (UniProt Q1PAB4)
Region: residues 1	to 101
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
As shown in Figure 6(B), the emission spectra of WT-Tat in water or in 6M urea are identical, with a maximal emission wavelength at ∼347 nm characteristic of a tryptophan in an aqueous environment,63 confirming that the region around Trp11 is natively unfolded.
Our fluorescence emission experiments showed that the peak of fluorescence of Tat alone at ∼347 nm is close to the location of the peak of a fully accessible tryptophan.63 Moreover, the fluorescence did not display any shift when Tat was placed in a denaturing environment (6M urea). This confirms that Tat is natively unfolded and suggests that, in the native conformation of Tat, the only tryptophan of Tat (Trp11) is not involved in a putative hydrophobic pocket contrarily to what has been suggested by others studies.
Protein: DP01087 (UniProt Q1PAB4)
Region: residues 48	to 52
Annotation: transcription regulator activator activity (Molecular function)
Evidence: combinatorial experimental and curator inference evidence used in manual assertion
Supporting statements:
The results of such an experiment are shown in Fig. 5A, where upon electroporation of K50A or K51A with reporter HIV-LTR CAT, we observed a slight drop in transcriptional activity (less than 50%, compare lanes 3±6).
However, a more pronounced drop in transactivation was observed with the double-mutant 50 and 51 (~5-fold, lanes 7 and 8).
The results in Fig. 5C indicate that only lysine residues and not alanine or
arginine substitutions at positions 50 and 51 are critical for the observed acetylation effect. Taken together, the transient transfection results indicate that neither K50 nor K51 mutations alone are sufficient to completely lose the Tat transactivation on HIV-1 LTR.
The authors describe an HIV-1 subtype B Tat protein that is 101 residues long (UniProtKB:P20879; DisProt:DP03560). However, since the residues Lys50 and Lys51 is in the identical IDR (100%), it is considered to be involved in the same function.
Protein: DP01087 (UniProt Q1PAB4)
Region: residues 41	to 54
Annotation: trans-activation response element binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
The results of such an experiment are shown in Fig. 3A, where wild-type peptide 41-54 was capable of binding to TAR RNA (lane 3).
While the authors describe a different HIV-1 Tat protein (subtype B), this region is considered to be involved in the same function, since the region sequence is identical.
Protein: DP01087 (UniProt Q1PAB4)
Region: residues 41	to 54
Annotation: acetylation display site (Disorder function)
Evidence: radioisotope assay evidence used in manual assertion
Supporting statements:
The results of such an experiment are shown in Fig. 1C, where Tat 41-54
peptide, but not 41-50 peptide (lanes 7±10), was acetylated with GST-HAT.
While the authors describe a different HIV-1 Tat protein (subtype B), this region is considered to be involved in the same function, since the region sequence is identical.
Protein: DP01087 (UniProt Q1PAB4)
Region: residues 41	to 54
Annotation: negative regulation of RNA binding (Biological process)
Evidence: radioligand binding assay evidence used in manual assertion
Supporting statements:
The results of such an experiment are shown in Fig. 3A, where wild-type peptide 41-54 was capable of binding to TAR RNA (lane 3). The TAR RNA binding is completely abolished when lysines 50 and 51 are acetylated (lanes 6 and 7). We observed no binding of double-acetylated 50 and 51 peptide to TAR RNA at any peptide concentration (data not shown). Similar results were also observed when Tat protein was acetylated with GST-HAT prior to TAR RNA binding (Fig. 3B, lanes 4 and 5).
While the authors describe a different HIV-1 Tat protein (subtype B), this region is considered to be involved in the same function, since the region sequence is identical.
Protein: DP01087 (UniProt Q1PAB4)
Region: residues 42	to 54
Annotation: transcription coactivator binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
While the authors describe a different HIV-1 Tat protein (subtype B), this region is considered to be involved in the same function, since the region sequence is identical.
The results of such an experiment are shown in Fig. 7A, where 35Slabeled TBP, CBP, and cyclin T could efficiently bind to wild-type but not acetylated 42-50 peptide.
Protein: DP01087 (UniProt Q1PAB4)
Region: residues 42	to 54
Annotation: protein binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
The results of such an experiment are shown in Fig. 7A, where 35Slabeled TBP, CBP, and cyclin T could efficiently bind to wild-type but not acetylated 42-50 peptide.
While the authors describe a different HIV-1 Tat protein (subtype B), this region is considered to be involved in the same function, since the region sequence is identical.
Protein: DP01087 (UniProt Q1PAB4)
Region: residues 42	to 54
Annotation: cyclin binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
The results of such an experiment are shown in Fig. 7A, where 35Slabeled TBP, CBP, and cyclin T could efficiently bind to wild-type but not acetylated 42-50 peptide.
While the authors describe a different HIV-1 Tat protein (subtype B), this region is considered to be involved in the same function, since the region sequence is identical.
Protein: DP01087 (UniProt Q1PAB4)
Region: residues 42	to 54
Annotation: RNA polymerase core enzyme binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
Results from Western blots indicated that wild-type and not acetylated peptide was capable of binding to core-Pol II.
While the authors describe a different HIV-1 Tat protein (subtype B), this region is considered to be involved in the same function, since the region sequence is identical.
Protein: DP01087 (UniProt Q1PAB4)
Region: residues 42	to 54
Annotation: nucleosome binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
The results of such an experiment are shown in Fig. 7B, where acetylated Tat peptide was able to bind to core histones. It is interesting to note that core histones in the absence of DNA did not bind to acetylated Tat, indicating that a fixed conformation of nucleosome is required for Tat to bind to core histones.
While the authors describe a different HIV-1 Tat protein (subtype B), this region is considered to be involved in the same function, since the region sequence is identical.
Experiments show that the wild-type not acetylated peptide also binds nucleosomes but in a lesser degree.
Protein: DP01087 (UniProt Q1PAB4)
Region: residues 1	to 101
Annotation: histone acetyltransferase binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Immunoprecipitation with an anti-CBP or an anti-p300 antibody resulted in the coimmunoprecipitation of CBP or p300 as well as Tat in Tat- but not GST-treated cells. Accordingly, immunoprecipitation with an anti-Tat antibody recovered Tat as well as CBP and p300.
Protein: DP01087 (UniProt Q1PAB4)
Region: residues 1	to 101
Annotation: transcription coactivator binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Immunoprecipitation with an anti-CBP or an anti-p300 antibody resulted in the coimmunoprecipitation of CBP or p300 as well as Tat in Tat- but not GST-treated cells. Accordingly, immunoprecipitation with an anti-Tat antibody recovered Tat as well as CBP and p300.
Protein: DP01087 (UniProt Q1PAB4)
Region: residues 1	to 101
Annotation: histone acetyltransferase binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
As shown in Fig. ​1c, wild-type 101 and 86 Tat proteins bound the HAT activity present in the nuclear extract with similar efficiencies.
Protein: DP01092 (UniProt O66683)
Region: residues 1	to 88
Annotation: molten globule (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD spectra were measured at 20 °C for both the S. typhimurium and A. aeolicus FlgM proteins in 10 mM sodium phosphate (pH 7.4). While the S. typhimurium FlgM protein exhibits disordered character, the A. aeolicus FlgM protein exhibits minima at 220 and 207 (Fig. 3A), consistent with significant α-helical character. 
The results presented thus far demonstrate that the A. aeolicus FlgM protein forms a molten-globule like structure with significant α-helical character at room temperature.