LiteFold/DisProt huggingface dataset:
Protein: DP03505 (UniProt Q77M43)
Region: residues 486	to 505
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
As expected the P–N complex resembles a four-helix bundle, with the helix contributed by N (helix Nα1) packed on the surface created by helices α2 and α3 of the binding domain from P.
It is clear from consideration of both crystal packing and linker length that the complex observed in the crystal results from an intermolecular association with the N moiety from one protein binding to the P moiety of a separate molecule.
Crystallographic analysis of a chimeric protein in which amino acids 486–505 from N (N486–505) were fused to the carboxyl terminus of the nucleocapsid-binding domain of P (P457–507). The two binding elements were connected with a flexible linker, (GS)4, designed to be long enough to accommodate either parallel or antiparallel packing of the helix from N.
Cross-references: PDB:1T6O
Protein: DP03505 (UniProt Q77M43)
Region: residues 477	to 505
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Typical association rates for protein–protein interactions are in the order of 105 to 106 M-1·s-1 (24), hence association of the measles P-binding domain with the measles N-tail peptide proceeds relatively quickly and is approaching the diffusion-controlled limit.
Protein: DP03505 (UniProt Q77M43)
Region: residues 495	to 505
Annotation: protein binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
Deletions of 10 (MEN374-515) and 20 (MEN374-505) amino acids from the tail had no effect on the ability of the molecules to bind to P in a pulldown assay (Fig.1B). However, a third construct in which 30 amino acids were deleted (MEN374-495) lost the ability to bind the P protein (Fig. ​1B). This suggested that the region from 495 to 505 within the tail of N was critical for binding P.
Protein: DP03505 (UniProt Q77M43)
Region: residues 477	to 505
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Additionally, we have shown that the binding of MEN477-505 to MEP457-507 occurs with low affinity and is entropically disfavored at both temperatures studied.
Protein: DP03505 (UniProt Q77M43)
Region: residues 477	to 505
Annotation: molecular adaptor activity (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Typical association rates for protein–protein interactions are in the order of 105 to 106 M-1·s-1 (24), hence association of the measles P-binding domain with the measles N-tail peptide proceeds relatively quickly and is approaching the diffusion-controlled limit.
Protein: DP03505 (UniProt Q77M43)
Region: residues 486	to 505
Annotation: molecular adaptor activity (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
As expected the P–N complex resembles a four-helix bundle, with the helix contributed by N (helix Nα1) packed on the surface created by helices α2 and α3 of the binding domain from P.
It is clear from consideration of both crystal packing and linker length that the complex observed in the crystal results from an intermolecular association with the N moiety from one protein binding to the P moiety of a separate molecule.
Crystallographic analysis of a chimeric protein in which amino acids 486–505 from N (N486–505) were fused to the carboxyl terminus of the nucleocapsid-binding domain of P (P457–507). The two binding elements were connected with a flexible linker, (GS)4, designed to be long enough to accommodate either parallel or antiparallel packing of the helix from N.
Cross-references: PDB:1T6O
Protein: DP03505 (UniProt Q77M43)
Region: residues 400	to 525
Annotation: disorder (Structural state)
Evidence: combinatorial experimental and curator inference evidence used in manual assertion
Supporting statements:
IDR is 100% identical to the Measles virus (strain Edmonston B), UniProtKB:P0DXN6.
Cross-references: DisProt:DP04423
Protein: DP03506 (UniProt P33309)
Region: residues 48	to 59
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the final model, the following Dom34 regions Met1-Phe47, Thr60-Tyr170, and Asp180-Asp382 could be modeled in the electron density as well as 228 water molecules, one phosphate ion from the crystallization solution and two glycerol molecules, which was used as cryoprotectant (supplemental Fig. S1B).
24 loop residues (Thr48-Ser59, Ser171-Thr179, and Asp383-Glu386) were absent in the final model due to the lack of electron density, reflecting intrinsic flexibility.
Cross-references: PDB:2VGM
PDB:2VGN
Protein: DP03507 (UniProt Q9ERC1)
Region: residues 1146	to 1912
Annotation: molten globule (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In addition, the Myo16Tail possesses high structural flexibility and a solvent-exposed hydrophobic core, indicating the largely unstructured, intrinsically disordered nature of this protein region. Some secondary structure elements were also observed, indicating that the Myo16Tail likely adopts a molten globule-like structure.
The CD spectrum of Myo16Tail in the far-UV region revealed the minimum at 205 nm, the positive maximum at 190 nm, and a significant signal in a wide, 215 to 225 nm region (Fig. 9A). This suggests that the protein contains both α-helical and β-structured elements. On the other hand, the large minimum at 205 nm and the relatively weak positive maximum around 190 nm indicate the presence of a significant amount of disordered structure as well.
The thermal behavior of Myo16Tail showing low cooperativity detected by CD measurements supports the idea of lacking a stable globular fold and is characteristic of a molten globule–like state (90). In conclusion, CD spectroscopy analysis indicates the presence of both disordered and structured regions in Myo16Tail, supporting our conclusions from fluorescence spectroscopic measurements according to which the tail of Myo16 might be in a molten globule–like conformation.
Protein: DP03507 (UniProt Q9ERC1)
Region: residues 1146	to 1912
Annotation: molten globule (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
In addition, the Myo16Tail possesses high structural flexibility and a solvent-exposed hydrophobic core, indicating the largely unstructured, intrinsically disordered nature of this protein region. Some secondary structure elements were also observed, indicating that the Myo16Tail likely adopts a molten globule-like structure.
The expression and purification results were analyzed and confirmed by SDS-PAGE and Anti-His Western blot (Fig. 4, B and C). We noted that Myo16Tail showed an anomalous electrophoretic migration (Fig. 4, B and C). The apparent molecular weight of Myo16Tail seemed to be ∼120 kDa in SDS-PAGE, which is higher than that calculated based on its amino acid sequence (86.47 kDa, ProtParam) (56). This abnormal electrophoretic mobility is a characteristic feature of IDPs, which could result from poor interaction with SDS molecules because of their irregular amino acid composition (28, 39).
The first experimental indication of the disordered structural characteristics of Myo16Tail is its anomalous migration showing higher apparent molecular mass as revealed by SDS-PAGE, which was confirmed by anti-His Western blot (Fig. 4, B and C). The unusual SDS-PAGE mobility as a characteristic feature of IDPs (28, 39) supports that Myo16Tail or parts of it are intrinsically disordered.
Protein: DP03507 (UniProt Q9ERC1)
Region: residues 1146	to 1912
Annotation: protein binding (Molecular function)
Evidence: fluorescence anisotropy evidence used in manual assertion
Supporting statements:
The C-terminal tail extension of myosin 16 acts as a molten globule, including intrinsically disordered regions, and interacts with the N-terminal ankyrin
Our results revealed that the Myo16Tail is functionally active and interacts with the N-terminal ankyrin domain of myosin 16, suggesting an intramolecular binding between the C and N termini of Myo16 as an autoregulatory mechanism involving backfolding of the motor domain.
The steady-state anisotropy of fluorescently labeled Alexa568–Myo16Ank (1.2 μM) increased by the addition of an increasing concentration of Myo16Tail as expected for binding interaction. The analysis revealed that the affinity (KD) of Myo16Tail to Myo16Ank is ∼2.5 μM according to Equation 1 (Fig. 5A).
Altogether, on the one hand, our results can confirm the functional activity of the recombinantly produced Myo16Tail and Myo16Tail (−IQ). On the other hand, our anisotropy findings revealed that the tail of Myo16 is dominant in the binding of Myo16Ank; however, the presence of Myo16IQ seems to influence the strength of this interaction. This moderate strength of the interaction of Myo16Tail is relatively common in regulatory functions and consistent with its possible role as a multiple interaction site for PI3K, WRC (17), and Myo16Ank.
Protein: DP03507 (UniProt Q9ERC1)
Region: residues 1146	to 1912
Annotation: self-assembly (Disorder function)
Evidence: fluorescence anisotropy evidence used in manual assertion
Supporting statements:
The C-terminal tail extension of myosin 16 acts as a molten globule, including intrinsically disordered regions, and interacts with the N-terminal ankyrin
Our results revealed that the Myo16Tail is functionally active and interacts with the N-terminal ankyrin domain of myosin 16, suggesting an intramolecular binding between the C and N termini of Myo16 as an autoregulatory mechanism involving backfolding of the motor domain.
The steady-state anisotropy of fluorescently labeled Alexa568–Myo16Ank (1.2 μM) increased by the addition of an increasing concentration of Myo16Tail as expected for binding interaction. The analysis revealed that the affinity (KD) of Myo16Tail to Myo16Ank is ∼2.5 μM according to Equation 1 (Fig. 5A).
Altogether, on the one hand, our results can confirm the functional activity of the recombinantly produced Myo16Tail and Myo16Tail (−IQ). On the other hand, our anisotropy findings revealed that the tail of Myo16 is dominant in the binding of Myo16Ank; however, the presence of Myo16IQ seems to influence the strength of this interaction. This moderate strength of the interaction of Myo16Tail is relatively common in regulatory functions and consistent with its possible role as a multiple interaction site for PI3K, WRC (17), and Myo16Ank.
Protein: DP03507 (UniProt Q9ERC1)
Region: residues 1146	to 1912
Annotation: disorder (Structural state)
Evidence: fluorescence anisotropy evidence used in manual assertion
Supporting statements:
Importantly, the highest intensity and wavelength maximum of ANS fluorescence of Myo16Tail at low GuHCl (∼480 nm) is in accordance with the maximum values of G-actin in the range of 1 to 2 M GuHCl (∼480 nm), when the latter one is in molten globule conformation (Fig. 7C). Our ANS fluorescence results corroborate that Myo16Tail might have molten globule conformation under native conditions.
Protein: DP03508 (UniProt P26662)
Region: residues 2	to 169
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The isolated N-terminal domain of HCV core [core(2–117)], as well as the FL HCV and GBV-B core proteins are mostly unstructured in solution, showing an ellipticity minimum at ∼198 nm, characteristically of random-coil like peptides [(36) and Figure 5].
FL HCV core protein comprises the 2-169 region of the Hepatitis C virus genotype 1b (isolate Japanese) polyprotein.
Protein: DP03508 (UniProt P26662)
Region: residues 2	to 117
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The isolated N-terminal domain of HCV core [core(2–117)], as well as the FL HCV and GBV-B core proteins are mostly unstructured in solution, showing an ellipticity minimum at ∼198 nm, characteristically of random-coil like peptides [(36) and Figure 5].
Protein: DP03508 (UniProt P26662)
Region: residues 2	to 117
Annotation: DNA binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The ability of purified proteins to stably bind RNA and DNA was verified by means of mobility shift assays. All four proteins bound both to RNA and DNA without a strict sequence specificity, and they caused complete retention of the nucleic acids at the top of the gel (indicative of the formation of large nucleoprotein complexes) at a protein-to-nucleotide molar ratio of ∼1:20 (data not shown).
Protein: DP03508 (UniProt P26662)
Region: residues 2	to 117
Annotation: RNA binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The ability of purified proteins to stably bind RNA and DNA was verified by means of mobility shift assays. All four proteins bound both to RNA and DNA without a strict sequence specificity, and they caused complete retention of the nucleic acids at the top of the gel (indicative of the formation of large nucleoprotein complexes) at a protein-to-nucleotide molar ratio of ∼1:20 (data not shown).
Protein: DP03508 (UniProt P26662)
Region: residues 2	to 169
Annotation: RNA folding chaperone (Molecular function)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
By means of classical in vitro RNA chaperone assays (e.g. strand annealing, strand exchange and ribozyme assays; Figures 2 and ​and3,3, and data not shown), we showed that nucleic acid chaperone activity is also conserved between the two hepacivirus core proteins, and that GBV-B core also efficiently facilitates the formation of the most stable nucleic acid structure. 
 As expected, all core proteins induced a considerable increase in the cleavage rates, with hepacivirus core proteins demonstrating a higher activity compared to WNV and BVDV cores (Figure 4C).
Protein: DP03508 (UniProt P26662)
Region: residues 2	to 117
Annotation: RNA folding chaperone (Molecular function)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
By means of classical in vitro RNA chaperone assays (e.g. strand annealing, strand exchange and ribozyme assays; Figures 2 and ​and3,3, and data not shown), we showed that nucleic acid chaperone activity is also conserved between the two hepacivirus core proteins, and that GBV-B core also efficiently facilitates the formation of the most stable nucleic acid structure.
Protein: DP03508 (UniProt P26662)
Region: residues 2	to 169
Annotation: disorder (Structural state)
Evidence: temperature-induced protein unfolding evidence used in manual assertion
Supporting statements:
FL HCV and GBV-B core proteins retained most of their chaperone activity after boiling for 5 min (∼75%, based on PhosporImager quantification, see lanes 4–6 versus 7–9 in Figure 4A and lanes 29–31 versus 32–34 in Figure 4B).
Protein: DP03508 (UniProt P26662)
Region: residues 1202	to 1213
Annotation: disorder (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The PDB shows the disordered region 1202-1213 of the Serine protease/helicase NS3.
Cross-references: PDB:1DY9
PDB:1DY8
PDB:1DXP
Protein: DP03508 (UniProt P26662)
Region: residues 1202	to 1213
Annotation: disorder (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The PDB shows the disordered region 1202-1213 of the Serine protease/helicase NS3.
Cross-references: PDB:3OYP
Protein: DP03509 (UniProt K9MZ21)
Region: residues 267	to 328
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The Linker Sequence Can Be Modeled as A Worm-like Chain and Exhibits Only Weak Local Conformational Preferences RES
In contrast, the Kratky plot for the isolated linker (L) increases monotonically with the scattering angle, which is characteristic of unfolded proteins [76].
From the pair distance distribution function P(r) (Figure 4), the radius of gyration (Rg) of the linker is estimated as 26.4 Å by numerical integration. For comparison, the radius of gyration of an intrinsically disordered protein of this chain length (62 residues) is predicted to be 22.7 Å, using a power law expression developed for chemically denatured proteins [77]. Hence, the linker is globally disordered.
Cross-references: SASBDB:SASDLJ9
SASBDB:SASDLH9
Protein: DP03509 (UniProt K9MZ21)
Region: residues 267	to 328
Annotation: pre-molten globule (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
As expected, backbone amide resonances associated with the linker (L) showed very limited chemical shift dispersion in the proton dimension, consistent with global disorder, while those associated with the binding domain (BD) were widely dispersed, consistent with overwhelming population of the folded state [61]. The propensity for structure formation in the linker was assessed using the ncSPC algorithm (Figure S4B), based on the weighted deviation of the chemical shifts of five backbone nuclei (1Hα, 13CO, 13Cα, 13Cβ, 15N) from reference values specific for intrinsically disordered proteins [83]. The results are fairly concordant with secondary structure prediction (Figure S4A) and suggest that very weak local structural preferences for extended beta-conformation or alpha-helical conformation do exist, with these preferences alternating along the length of the linker.
Overall, the NMR analysis confirmed that the linker is not uniformly disordered. It contains localized segments with very weak conformational preferences, and there is evidence for conformational exchange occurring in some regions.
Cross-references: BMRB:27634
Protein: DP03510 (UniProt P49753)
Region: residues 46	to 56
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The current model contains residues 58-435 and 443-472 for the first ACOT2 molecule, residues 57-436 and 442-472 for the second ACOT2 molecule, and 442 waters.
Cross-references: PDB:3HLK
Protein: DP03510 (UniProt P49753)
Region: residues 473	to 483
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The current model contains residues 58-435 and 443-472 for the first ACOT2 molecule, residues 57-436 and 442-472 for the second ACOT2 molecule, and 442 waters.
Cross-references: PDB:3HLK
Protein: DP03511 (UniProt Q9WIK7)
Region: residues 2282	to 2301
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Region 2280-2299 is mainly unstructured, as shown by its large negative ellipticity at 200 nm and moderate ellipticity at 190 nm in the far-UV CD spectra (Figure 7).
Protein: DP03511 (UniProt Q9WIK7)
Region: residues 2282	to 2315
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The 1H,15N HSQC spectrum of NS5A-D2 (Con1 strain) displays a narrow 1HN chemical shift dispersion limited to 1 ppm, as expected for a mainly disordered domain (Fig. 1A).
The NS5A fragment used in this publication was derived from the Hepacivirus C. IDR is 100% identical to the Hepatitis C virus genotype 1b (isolate Con1) polyprotein UniProtKB:Q9WMX2.
Protein: DP03511 (UniProt Q9WIK7)
Region: residues 2282	to 2301
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The affinity between CypA and the PW turn containing PepD2-WT peptide (KD = 0.5 mm) is three times better than the one involving the random coil PepD2-I315G peptide (KD = 1.4 mm).
PepD2-WT comprises the region 2282-2301 of the Hepatitis C virus genome polyprotein.
Protein: DP03511 (UniProt Q9WIK7)
Region: residues 2282	to 2301
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The final set of 28 low energy structures that fulfill the experimental restraints displays a well defined small structural motif (from Met313 to Ala317) in PepD2-WT (Fig. 5 and Table 1; PDB code 2M5L), whereas the N and C termini remain highly flexible.
PepD2-WT comprises the region 2282-2301 of the Hepatitis C virus genome polyprotein.
Cross-references: BMRB:19059
PDB:2M5L
Protein: DP03511 (UniProt Q9WIK7)
Region: residues 2282	to 2301
Annotation: viral genome replication (Biological process)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The affinity between CypA and the PW turn containing PepD2-WT peptide (KD = 0.5 mm) is three times better than the one involving the random coil PepD2-I315G peptide (KD = 1.4 mm).
PepD2-WT comprises the region 2282-2301 of the Hepatitis C virus genome polyprotein.
Protein: DP03511 (UniProt Q9WIK7)
Region: residues 2287	to 2291
Annotation: viral genome replication (Biological process)
Evidence: luciferase reporter gene assay evidence used in manual assertion
Supporting statements:
 As illustrated in Fig. 8, the sole mutation I315G in NS5A almost completely abolished viral replication that was close to the background as determined with the replicon encoding an inactive NS5B RNA-polymerase (GND mutant). The replication levels corresponding to the I315G and P314A mutations, respectively, were similar. 
Hence, the short PW turn structural motif in the mainly disordered NS5A-D2 domain plays an essential role for HCV RNA replication.
PW turn corresponds to the 2288-2290 region of the core polyprotein (P314 -W316 of the Ns5B protein). Although the authors describes this region as a small structural motif, the region is to short to form any secondary structure so is interpreted as disordered here.
Protein: DP03512 (UniProt P18827)
Region: residues 23	to 254
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
The molecular weight of the syndecan EDs were higher than the theoretical values when calculated by SDS-PAGE and size-exclusion chromatography but consistent with them and with the existence of a dimer of ED-4 when determined by ESI-MS and SEC-MALLS (Supplementary Table S2 and Supplementary Fig. S1).
Protein: DP03512 (UniProt P18827)
Region: residues 23	to 254
Annotation: disorder (Structural state)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
The molecular weight of the syndecan EDs were higher than the theoretical values when calculated by SDS-PAGE and size-exclusion chromatography but consistent with them and with the existence of a dimer of ED-4 when determined by ESI-MS and SEC-MALLS (Supplementary Table S2 and Supplementary Fig. S1).