LiteFold/DisProt huggingface dataset:
Protein: DP00824 (UniProt Q9NJS1)
Region: residues 54	to 83
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
...the inhibitor adopts a mostly extended conformation and binds to the proteinase in a reverse orientation (i.e., opposite to substrates) (Fig. S4).
Protein: DP00824 (UniProt Q9NJS1)
Region: residues 54	to 83
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the two independent crystal structures of the human α-thrombin·anophelin complex, only the C-terminal portion of the inhibitor (...) was fully defined by electron density.
Protein: DP00824 (UniProt Q9NJS1)
Region: residues 54	to 83
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
...the inhibitor adopts a mostly extended conformation and binds to the proteinase in a reverse orientation (i.e., opposite to substrates) (Fig. S4).
Protein: DP00824 (UniProt Q9NJS1)
Region: residues 23	to 83
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In line with their lack of cysteines and the preponderance of polar residues, anophelins are predicted to be intrinsically disordered in solution (Fig. S1A). Indeed, the circular dichroism (CD) spectrum of anophelinAa is typical of random coils, and its deconvolution with different methods suggests a mostly disordered polypeptide (Fig. S1B).
Cross-references: PDB:4E05
Protein: DP00824 (UniProt Q9NJS1)
Region: residues 23	to 53
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In line with their lack of cysteines and the preponderance of polar residues, anophelins are predicted to be intrinsically disordered in solution (Fig. S1A). Indeed, the circular dichroism (CD) spectrum of anophelinAa is typical of random coils, and its deconvolution with different methods suggests a mostly disordered polypeptide (Fig. S1B).
Protein: DP00824 (UniProt Q9NJS1)
Region: residues 54	to 83
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In line with their lack of cysteines and the preponderance of polar residues, anophelins are predicted to be intrinsically disordered in solution (Fig. S1A). Indeed, the circular dichroism (CD) spectrum of anophelinAa is typical of random coils, and its deconvolution with different methods suggests a mostly disordered polypeptide (Fig. S1B).
Protein: DP00824 (UniProt Q9NJS1)
Region: residues 23	to 53
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
...no significant density was detectable for the remaining N-terminal residues AA1 to AD31.
Cross-references: PDB:4E05
Protein: DP00824 (UniProt Q9NJS1)
Region: residues 56	to 83
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This N-terminal segment was similarly disordered in a second crystal form of the anophelin·thrombin complex solved at 3.2-Å resolution (space group H32; rmsd of 0.25 Å for 263 aligned Cα atoms) (Table 4) and also in this case, not constrained by crystal packing.
Cross-references: PDB:4E06
Protein: DP00824 (UniProt Q9NJS1)
Region: residues 56	to 83
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
...the inhibitor adopts a mostly extended conformation and binds to the proteinase in a reverse orientation (i.e., opposite to substrates) (Fig. S4).
Protein: DP00824 (UniProt Q9NJS1)
Region: residues 56	to 83
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
...the inhibitor adopts a mostly extended conformation and binds to the proteinase in a reverse orientation (i.e., opposite to substrates) (Fig. S4).
Protein: DP00824 (UniProt Q9NJS1)
Region: residues 56	to 83
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the two independent crystal structures of the human α-thrombin·anophelin complex, only the C-terminal portion of the inhibitor (...) was fully defined by electron density.
Protein: DP00824 (UniProt Q9NJS1)
Region: residues 23	to 55
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 23 to 55 are missing in PDB entry 4E06, being therefore disordered.
Cross-references: PDB:4E06
Protein: DP00833 (UniProt P22995)
Region: residues 58	to 83
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
15N longitudinal (T1 ) and transverse (T2 ) relaxation measurements and heteronuclear NOEs showed that ParD is divided into two separate domains, a well-ordered N-terminal domain and a very flexible C-terminal domain. An increase in secondary structure was observed upon addition of trifluoroethanol, suggested to result from the formation of structured stretches in the C-terminal part of the protein
Consensus chemical shifts and NOE data (Figures 3B and 3C) indicate that the C-terminal region is less well ordered or undergoing rapid conformational change on the NMR timescale. However, "13Cα chemical shifts show a tendency for the formation of further αhelices beyond the well-ordered N-terminal domain.[...] The negative NOE values for the C-terminal domain (Asp59–Ala83) indicate the presence of significant flexibility in this region. This is in excellent agreement with the "15N-T1 and 15N-T2 relaxation times, which clearly show two structurally different moieties ranging from Leu4 to Ile57 for the well-structured N-terminus and from Asp59–Ala83 for the remaining flexible C-terminal region.[,,,] Cα chemical-shift data show a down-field shift from the random-coil values for residues in the C-terminus for residues 58–64, 66, 68–72, 74–81 and 83, indicating a tendency for the formation of helical structures. The deviations are, however, smaller than in the N-terminal region, which again supports the presence of a predominantly unstructured C-terminal domain.


Cross-references: BMRB:4792
Protein: DP00833 (UniProt P22995)
Region: residues 58	to 83
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Cα chemical-shift data show a down-field shift from the random-coil values for residues in the C-terminus for residues 58–64, 66, 68–72, 74–81 and 83, indicating a tendency for the formation of helical structures. The deviations are, however, smaller than in the N-terminal region, which again supports the presence of a predominantly unstructured C-terminal domain.

As can be seen from the combined chemical shift changes (Figure 7), addition of TFE influenced mainly the residues starting from Gly38), resulting in major chemical-shift differences. This indicates a transition from the more flexible and random-coil C-terminal moiety to an α-helical domain consistent with the CD experiment

The structural changes of ParD, which are induced by TFE addition as observed in the near-UV CD spectrum, indicate the formation of additional helical structure. As monitored by NMR spectroscopy, C-terminal residues appear to be involved mainly in these changes. 

Cross-references: BMRB:4792
Protein: DP00833 (UniProt P22995)
Region: residues 58	to 83
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:

TFE was added to a ParD solution and changes in the secondary structure were monitored by CD spectroscopy. Upon an increase in the TFE concentration (from 0 to 5, 10, 20, 30, 40, 50, 60, 70 and 80%) the α-helical content rose gradually (from 37 to 44, 50, 53, 55, 62, 65, 68, 70 and 72%) with an isodichroic point at 200.4 nm (Figure 6).
The structural changes of ParD, which are induced by TFE addition as observed in the near-UV CD spectrum, indicate the formation of additional helical structure. As monitored by NMR spectroscopy, C-terminal residues appear to be involved mainly in these changes. 
Experimental 13Cα chemical-shift data, however, only indicate a propensity for α-helical regions in the C-terminus. We tried to induce this ‘missing’ helicity by the addition of TFE […] The structural changes of ParD, which are induced by TFE addition as observed in the near-UV CD spectrum, indicate the formation of additional helical structure
Near-UV CD is wrongly written by the authors, the spectrum shown in Figure 6 is a Far-UV CD spectrum
Protein: DP00833 (UniProt P22995)
Region: residues 50	to 83
Annotation: toxin sequestering activity (Molecular function)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
The mutations changed codons corresponding to Q51 and S53 of kis into the Ochre stop codon UAA. As this stop codon is not suppressed in the CSH16 (supE) background, the mutations should remove 35 and 33 residues, respectively, from the carboxyl terminus of the protein [...] Compared to the missense mutants, the nonsense mutants lose the antitoxin activity of the protein (Fig. 2). This suggests either that the deletions affect the region of Kis needed to inactivate Kid and to form with this protein an efficient repressor, or that these mutations severely affect the overall three-dimensional fold of Kis. However, since circular dichroism spectroscopy indicates that isolated Kis protein mainly has a flexible coil structure (our unpublished results), the latter hypothesis seems unlikely
Protein: DP00833 (UniProt P22995)
Region: residues 38	to 83
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In this study, we show that the well-ordered N-terminal domain adopts the RHH fold whereas the C-terminal region is highly flexible in solution.
The lower number of NOEs found for the C-terminal portion of ParD is in agreement with the dynamic behavior already described for this protein, indicating an unstructured domain. Mainly intraresidual NOEs could be identified for the flexible C-terminal part of ParD.
The authors do not provide region boundaries. The region with high flexibility was determined based on the NMR structure PDB:2an7 using CYRANGE to include the bit that shows high RMSD between various models. This region however contains secondary structural elements and therefore isn't fully flexible.
Cross-references: PDB:2AN7
Protein: DP00834 (UniProt P69428)
Region: residues 21	to 89
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
An expressed construct without the transmembrane segment is largely unstructured in aqueous solution but is able to insert into phospholipid monolayers and interacts with membrane bilayers.
Secondary structure analysis suggests that 80% of the polypeptide is in an “other” conformation which is usually indicative of an unfolded protein.
CD spectroscopy indicates that membrane association of the ΔTMS-TatA fragment induces some α-helix formation in this otherwise unstructured protein (Figure 5B).
Protein: DP00834 (UniProt P69428)
Region: residues 21	to 89
Annotation: lipid binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
An expressed construct without the transmembrane segment is largely unstructured in aqueous solution but is able to insert into phospholipid monolayers and interacts with membrane bilayers.
The CD spectrum of ΔTMS-TatA in the presence of liposomes is clearly significantly changed from that of the protein alone, with the appearance of a peak at approximately 224 nm indicating helix formation (Figure 5B). This experiment demonstrates that ΔTMS-TatA interacts with membrane bilayers as well as monolayers. Secondary structure analysis shows that the liposomes increase the proportion of ΔTMS-TatA that is in an α-helical conformation and correspondingly reduce the number of “unfolded” residues (Table 1).
CD spectroscopy indicates that membrane association of the ΔTMS-TatA fragment induces some α-helix formation in this otherwise unstructured protein (Figure 5B).
Protein: DP00834 (UniProt P69428)
Region: residues 22	to 44
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
A far-UV CD spectrum of TatAH2 showed that the peptide is relatively unstructured in aqueous buffer and with a low concentration (0.25 mM lipid) of small unilamellar vesicles (SUVs) made of E. coli polar lipids.
These observations suggest that the peptide is mostly unstructured in aqueous solution, but that it adopts a helical structure when placed in a membrane mimetic environment such as stable SUVs or detergent micelles.
Protein: DP00834 (UniProt P69428)
Region: residues 22	to 44
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
A far-UV CD spectrum of TatAH2 showed that the peptide is relatively unstructured in aqueous buffer and with a low concentration (0.25 mM lipid) of small unilamellar vesicles (SUVs) made of E. coli polar lipids. However, the shape of the CD spectra in the presence of SUVs is not identical to that of the peptide in buffer, suggesting a slight difference in its secondary structure. In the presence of higher concentration E. coli SUVs, DPC and SDS micelles, and 50% trifluoroethanol, the CD spectra change to what is highly indicative of α-helical structure (Fig. 2). The vesicles generated at the low 0.25 mM lipid concentration are likely unstable and may contribute to the lack of secondary structure observed for TatAH2. These observations suggest that the peptide is mostly unstructured in aqueous solution, but that it adopts a helical structure when placed in a membrane mimetic environment such as stable SUVs or detergent micelles.
Protein: DP00834 (UniProt P69428)
Region: residues 22	to 44
Annotation: lipid binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
A far-UV CD spectrum of TatAH2 showed that the peptide is relatively unstructured in aqueous buffer and with a low concentration (0.25 mM lipid) of small unilamellar vesicles (SUVs) made of E. coli polar lipids. However, the shape of the CD spectra in the presence of SUVs is not identical to that of the peptide in buffer, suggesting a slight difference in its secondary structure. In the presence of higher concentration E. coli SUVs, DPC and SDS micelles, and 50% trifluoroethanol, the CD spectra change to what is highly indicative of α-helical structure (Fig. 2). The vesicles generated at the low 0.25 mM lipid concentration are likely unstable and may contribute to the lack of secondary structure observed for TatAH2. These observations suggest that the peptide is mostly unstructured in aqueous solution, but that it adopts a helical structure when placed in a membrane mimetic environment such as stable SUVs or detergent micelles.
Protein: DP00834 (UniProt P69428)
Region: residues 44	to 89
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In contrast, a synthetic peptide representing the C-terminal region (residues 44 to 89 of TatA), displayed a lack of secondary structure with all these membrane mimetics except in the presence of SDS, which showed induction of some helical structure (Supplementary Fig. 1).
Protein: DP00834 (UniProt P69428)
Region: residues 47	to 89
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Secondary structural analysis by consensus chemical shifts
index (CSI) demonstrates that the protein comprises two helices in
the N-terminal region and an unstructured C-terminus (Figure S2
in File S1) [27,28], which is in accordance with previously
reported TatA structures [10,12].
As shown in Figure 4A, the structure of the monomeric E. coli
TatA consists of a 15-residue TMH (residues Ile6-Phe20), a 21-
residue APH (residues Lys24-Met43) and a mostly unstructured C-
terminal region.
Cross-references: PDB:2MN6
PDB:2MN7
Protein: DP00834 (UniProt P69428)
Region: residues 22	to 44
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The two-dimensional NOESY spectrum of TatAH2 in aqueous
solution did not indicate the presence of a well defined peptide
structure due to the lack of observable inter-residue nOe cross peaks,
poor peak dispersion, and a low number of peaks in general (not
shown). This demonstrates that TatAH2 is essentially unstructured in
water, consistent with the results from the CD experiments in
aqueous buffer.
Protein: DP00834 (UniProt P69428)
Region: residues 22	to 44
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Spectra for the peptide in the presence of SDS micelles were
acquired at 25, 30, and 37 °C on a 600 and 700 MHz spectrometer to
obtain fully resolved cross-peaks. The final conditions yielding well
resolved spectra were 1.43 mM peptide in 200 mM SDS, 100 mM NaCl
at 37 °C (Fig. 5 and Supplementary Fig. 3). The solution structure of
TatAH2 bound to SDS micelles at 37 °C is shown in Fig. 6. The peptide
adopts a predominantly helical conformation consistent with the
structural motif suggested by CD spectroscopy.
Protein: DP00834 (UniProt P69428)
Region: residues 22	to 44
Annotation: lipid binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Spectra for the peptide in the presence of SDS micelles were
acquired at 25, 30, and 37 °C on a 600 and 700 MHz spectrometer to
obtain fully resolved cross-peaks. The final conditions yielding well
resolved spectra were 1.43 mM peptide in 200 mM SDS, 100 mM NaCl
at 37 °C (Fig. 5 and Supplementary Fig. 3). The solution structure of
TatAH2 bound to SDS micelles at 37 °C is shown in Fig. 6. The peptide
adopts a predominantly helical conformation consistent with the
structural motif suggested by CD spectroscopy.
Protein: DP00841 (UniProt O14733)
Region: residues 30	to 100
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 13Cα secondary chemical shifts reveal that MKK7 contains helical propensity at its N terminus (residues 5–30), whereas the remaining residues have secondary chemical shifts close to zero indicating a near random coil state (Fig. 1C).
Protein: DP00841 (UniProt O14733)
Region: residues 70	to 82
Annotation: mitogen-activated protein kinase binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The intensity profile of MKK7 shows a decrease in signal intensities localized at the three JNK1 docking sites with D2 and D3 showing the clearest binding signatures (Fig. 4B).
The analysis gives an exchange rate of 707 ± 34 s−1 and a population of bound MKK7 of 0.8%. Clear dispersion profiles are observed for the residues T80, L81, and F82 that are located outside the canonical D3 docking site (R70-L77), confirming their involvement in the binding of JNK1.
Protein: DP00841 (UniProt O14733)
Region: residues 25	to 34
Annotation: mitogen-activated protein kinase binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
NMR experiments carried out by using a shorter construct of the regulatory domain containing only the D1 docking site demonstrate that D1 binds JNK1 under these conditions (Fig. S7).
Protein: DP00841 (UniProt O14733)
Region: residues 36	to 47
Annotation: mitogen-activated protein kinase binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
The ITC measurements reveal that all docking sites bind with similar affinity in the low micromolar range with D2 (Kd = 7.9 μM) as the strongest binder followed by D3 (Kd = 11 μM) and D1 (Kd = 12 μM) (Fig. 3 A–C).
Protein: DP00841 (UniProt O14733)
Region: residues 69	to 78
Annotation: mitogen-activated protein kinase binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
The ITC measurements reveal that all docking sites bind with similar affinity in the low micromolar range with D2 (Kd = 7.9 μM) as the strongest binder followed by D3 (Kd = 11 μM) and D1 (Kd = 12 μM) (Fig. 3 A–C).
Protein: DP00841 (UniProt O14733)
Region: residues 38	to 47
Annotation: mitogen-activated protein kinase binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The intensity profile of MKK7 shows a decrease in signal intensities localized at the three JNK1 docking sites with D2 and D3 showing the clearest binding signatures (Fig. 4B).
These observations suggest that the residues L43, L45, and L47 function as anchors of the docking site, whereas the charged residues R38 and R40 establish less well-defined contacts with the surface of JNK1.
Protein: DP00841 (UniProt O14733)
Region: residues 37	to 48
Annotation: mitogen-activated protein kinase binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Interestingly, an alternative binding mode is observed in subunit D, where R40 contacts D326 and E329 on the surface of JNK1 and P41, L45, and L47 occupy the three pockets, resulting in increased flexibility at the level of T42 and L43 and consequently missing electron density for these two residues (Fig. 5 G and H).
Cross-references: PDB:4UX9
Protein: DP00842 (UniProt P12506)
Region: residues 1	to 86
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In aqueous buffer (Fig. 4 A), it can be deduced from the intensity of the negative 200 nm band that nonorganized structures are predominant (29). TableI reveals that there is no α helix in aqueous buffer excepted for Tat Mal and Tat Z2, which could have a short helix of eight to nine residues.
Protein: DP00842 (UniProt P12506)
Region: residues 1	to 86
Annotation: regulatory region RNA binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
The six synthetic Tat proteins can bind to TAR RNA (Fig.3) and can inhibit PKR (data not shown).