LiteFold/DisProt huggingface dataset:
Protein: DP03369 (UniProt O15391)
Region: residues 1	to 372
Annotation: pre-molten globule (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
The spectrum registered for YY2 is typical for a protein with a considerable content of α-helices and β-sheets, with a double minimum at 200–230 nm and a maximum around 190 nm. The spectrum of NTF2 lacks the 190 nm maximum, which comes from α-helical structures. The 205 nm minimum is blue-shifted for NTF2 and red-shifted for DBD2, suggesting differing contributions from α- and β-structures. The spectra of YY1 and YY2 variants are generally similar in shape, especially the ones of DBD1 and DBD2. The spectrum of NTF2 has a more pronounced shoulder at 222 nm than the one of NTF1. The 222 nm shoulder also differentiates the spectra of full-length YY1 and YY2, together with the maximum at 190 nm, which is greater for YY2 than for YY1. The results of the bioinformatic analysis presented in Fig. 1 correspond with the CD spectra of YY1, YY2, and their fragments (Fig. 5)
Here, we provide the first detailed structural analysis of YY2, which allows to classify it as an intrinsically disordered protein. The attribution is based on YY2's hydrodynamic properties that are characteristic for a premolten globule, its high proteolytic susceptibility, high content of irregular structures shown by both CD measurements and bioinformatic analyses, and its anomalous migration in SDS/PAGE that arises from atypical amino acid composition.
To conclude, YY2 can be classified as an intrinsically disordered protein (IDP) with a bipartite structure: the ordered DBD2, responsible for DNA binding, and the disordered, flexible NTF2.
Protein: DP03372 (UniProt P04554)
Region: residues 46	to 102
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectra of protamine is characteristic of random coil proteins with a large minima at 197 nm.
Protein: DP03372 (UniProt P04554)
Region: residues 46	to 102
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Using CD we show that human group II protamines undergo novel zinc-dependent secondary structure transitions.
We have demonstrated that human protamine II is a zinc binding protein based on the solution structure modulations induced by zinc and monitored by the CD spectra at 197 nm.
Protein: DP03372 (UniProt P04554)
Region: residues 46	to 102
Annotation: zinc ion binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We have demonstrated that human protamine II is a zinc binding protein based on the solution structure modulations induced by zinc and monitored by the CD spectra at 197 nm.
Protein: DP03374 (UniProt P02400)
Region: residues 1	to 110
Annotation: molten globule (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
In fact, the experimental data indicate that the protein resembles a “molten globule” under physiological conditions.
bis-ANS binding experiments show that the hydrophobic core is accessible to the solvent at neutral pH, and more so at low pH.
Protein: DP03374 (UniProt P02400)
Region: residues 1	to 110
Annotation: molten globule (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
In fact, the experimental data indicate that the protein resembles a “molten globule” under physiological conditions.
The differences between the 1D NMR spectra of the native (Figure 8a) and the urea-denatured YP2β protein (Figure 8c) confirm the existence of a partly structured state at pH 7 clearly different from a fully unfolded one.
The fact that all the amide protons of the protein exchange so quickly with solvent suggests that no stable tight structured region exists in the protein.
Protein: DP03374 (UniProt P02400)
Region: residues 1	to 110
Annotation: protein binding (Molecular function)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Incubation of both proteins was followed by far-UV CD and 1D-NMR measurements, and spectra were compared with those of the isolated proteins under the same conditions. The CD spectra of the protein mixture, when compared to the arithmetical addition of spectra from the individual proteins indicate that some secondary structural changes take place upon incubation of both proteins together (Figure 9A).
Protein: DP03374 (UniProt P02400)
Region: residues 1	to 110
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Incubation of both proteins was followed by far-UV CD and 1D-NMR measurements, and spectra were compared with those of the isolated proteins under the same conditions. The CD spectra of the protein mixture, when compared to the arithmetical addition of spectra from the individual proteins indicate that some secondary structural changes take place upon incubation of both proteins together (Figure 9A).
Protein interactions seems to increase the secondary structure of one or both proteins.
Protein: DP03374 (UniProt P02400)
Region: residues 1	to 110
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: enzyme-linked immunoabsorbent assay evidence used in manual assertion
Supporting statements:
Protein P2α protects protein P1β from degradation.
 As shown above, transformation of S.cerevisiae W303-1b with the P1β-encoding multicopy plasmid alone causes an increase in expression of this protein. This increase was notably smaller than the increase detected when P2 protein was overexpressed, due to the higher sensitivity of P1 proteins to degradation.
Protein: DP03377 (UniProt Q7T2G3)
Region: residues 571	to 623
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The data support the conclusion that both the phosphorylated and unphosphorylated isolated TAD are primarily unstructured.
Protein: DP03377 (UniProt Q7T2G3)
Region: residues 569	to 593
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
These results in comparison with the NMR data for the NRD-TAD complex (Figure 2B–2D) suggest that the β-hairpin structure of the TAD is adopted upon binding to the NRD.
The observations that the NRD and TAD appear unstructured when alone suggest that the repressive NRD-TAD association drives the domains to fold into the inhibitory conformation, and conversely that activation of FoxM1 is marked by an order-to-disorder structural transition.
We find significant structural order within a set of residues including sequences from both the NRD and TAD. Importantly, within this ordered region, the backbone chemical shifts for 71 out of 75 non-proline residues were assigned. Notably, the SSI analysis suggests that a stretch of residues in the TAD adopts a β-hairpin conformation, which contrasts the helical TAD structures typically observed in complexes with co-activator domains
FoxM1 demonstrates a new example in which the order-to-disorder transition occurs coincident with modulation of an intramolecular association between domains. This plasticity of disordered domains and the ability to regulate the plasticity through posttranslational modifications explains why intrinsically disordered proteins are so well suited to regulate biological function.
Cross-references: PDB:6OSW
Protein: DP03377 (UniProt Q7T2G3)
Region: residues 582	to 592
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
 The NRD-TAD structure consists of a five-stranded pleated β-sheet and a single α-helix. Three of the beta strands (β1-β3) are from sequences in the NRD, and two additional strands are from sequences in the TAD (β4-β5) 
The fact that both the NRD and TAD contribute essential residues to the hydrophobic core suggests the requirement of an association for forming the observed structure of both domains. 
The structured region of the TAD consists of a 12 amino acid sequence that adopts a β-hairpin conformation and binds the NRD by extending the β-sheet
Cross-references: PDB:60SW
Protein: DP03377 (UniProt Q7T2G3)
Region: residues 582	to 592
Annotation: molecular function regulator (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
We conclude that Ser715 phosphorylation by Plk1 is necessary and sufficient for inhibiting the NRD-TAD association.
Protein: DP03378 (UniProt P20849)
Region: residues 24	to 41
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Except for residues 1–18, 25–29, and 234–245, the main chain is well defined by the electron density
The first ~30 residues, bearing the major heparin binding site (7), are unique for NC4. Unfortunately these N-terminal residues were largely unresolved both in the crystal structure and NMR chemical shift assignments
Residues 1-18 mentioned by the authors corresponds to residues 24-41 of the uniprot entry. The numbering used by the authors starts after the signal peptide.
Cross-references: PDB:2UUR
Protein: DP03378 (UniProt P20849)
Region: residues 24	to 40
Annotation: carbohydrate binding (Molecular function)
Evidence: affinity chromatography evidence used in manual assertion
Supporting statements:
NC4 Lacking the N Terminus Has Only Residual Heparin Affinity—To verify our initial mapping of the heparin binding site of NC4 to the N terminus of the domain (7), we created mutant NC4Ndel lacking the first 17 residues of the domain. Analytical heparin affinity chromatography showed that N-terminally truncated NC4 could not bind to the column at a physiological salt concentration. When bound to the column in a buffer containing no added NaCl, NC4Ndel eluted at 0.13 M salt compared with the 0.31 M salt required for elution of wild-type NC4 (Fig. 5).
In vitro mutagenesis (Stratagene) was used to create a mutant form of NC4, termed NC4Ndel, lacking the first 17 residues of the mature polypeptide
The mutant used by the authors lacks residues 24-40 of the uniprot entry of this protein
Protein: DP03378 (UniProt P20849)
Region: residues 24	to 42
Annotation: carbohydrate binding (Molecular function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
In an attempt to characterize the NC4 domain in more detail, we set up a prokaryotic expression system to produce the domain. The purified 27.5-kDa product was analyzed for its glycosaminoglycan-binding potential by surface plasmon resonance and solid-state assays. The results show that the NC4 domain of collagen IX specifically binds heparin with a Kd of 0.6 µM, and the full-length recombinant collagen IX has an even stronger interaction with heparin, with an apparent Kd of 3.6 nM. The heparin-binding site of the NC4 domain was located in the extreme N terminus, containing a heparin-binding consensus sequence.
Identification of the Heparin-binding Region of the NC4 Domain—Alkylated rNC4 was digested with V8 protease and the resulting mixture of peptides subjected to heparin affinity chromatography. Analysis of the peptide mixture by MALDI-TOF mass spectrometry along with unbound and bound material from the affinity chromatography revealed that the extreme N-terminal peptide (amino acids 1–19, monoisotopic mass 2098.078) was able to bind to heparin, whereas other fragments were not. 
Our results show that the NC4 domain can now be added to the growing list of extracellular matrix proteins that interact with heparin or heparan sulfate
The peptide identified by the authors corresponds to residues 24-42 of the uniprot entry of this protein
Protein: DP03378 (UniProt P20849)
Region: residues 24	to 42
Annotation: carbohydrate binding (Molecular function)
Evidence: affinity chromatography evidence used in manual assertion
Supporting statements:
In an attempt to characterize the NC4 domain in more detail, we set up a prokaryotic expression system to produce the domain. The purified 27.5-kDa product was analyzed for its glycosaminoglycan-binding potential by surface plasmon resonance and solid-state assays. The results show that the NC4 domain of collagen IX specifically binds heparin with a Kd of 0.6 µM, and the full-length recombinant collagen IX has an even stronger interaction with heparin, with an apparent Kd of 3.6 nM. The heparin-binding site of the NC4 domain was located in the extreme N terminus, containing a heparin-binding consensus sequence.
The N-terminal 19-amino acid fragment was subsequently prepared as a synthetic peptide (peptide 1–19), which was shown to bind to heparin-Sepharose and elute upon introduction of about a 0.15 M concentration of NaCl (i.e. a 40% smaller concentration than was required for the elution of native rNC4). CD analysis of peptide 1–19 indicated that it was largely devoid of secondary structure (data not shown).
Our results show that the NC4 domain can now be added to the growing list of extracellular matrix proteins that interact with heparin or heparan sulfate.
The peptide identified by the authors corresponds to residues 24-42 of the uniprot entry of this protein
Protein: DP03378 (UniProt P20849)
Region: residues 26	to 31
Annotation: carbohydrate binding (Molecular function)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
The results show that the NC4 domain of collagen IX specifically binds heparin with a Kd of 0.6 µM, and the full-length recombinant collagen IX has an even stronger interaction with heparin, with an apparent Kd of 3.6 nM. The heparin-binding site of the NC4 domain was located in the extreme N terminus, containing a heparin-binding consensus sequence.
A mutant form of rNC4, carrying a sequence NGL in place of the basic amino acid sequence KRR of the suspected heparin binding site, was created. Using heparin affinity chromatography, it was demonstrated that this mutant rNC4 was unable to interact with heparin at physiological conditions. Comparison of the mutant rNC4 with wild-type rNC4 by far-UV CD analysis (data not shown) and by FTIR spectroscopy (Fig. 6) showed that the mutation did not affect the secondary structure of the NC4 domain
Collagen XI, for example, possesses several heparin-binding sequences, two of which comply with the heparin-binding consensus sequence XBBXBX, where B denotes a basic amino acid and X is any other amino acid (25). A sequence KRRPRF matching this consensus is present in the extreme N-terminal region of the NC4 domain of collagen IX and is indeed shown here to be the site of interaction of the domain with heparin. This sequence motif is also present in the N terminus of the mouse collagen a1(IX) chain (26). Comparison of this sequence of NC4 with a reported distribution of residues in known heparin-binding proteins (27) further implicates the sequence as a potential heparin-binding site.
Protein: DP03378 (UniProt P20849)
Region: residues 24	to 42
Annotation: protein binding (Molecular function)
Evidence: surface plasmon resonance evidence used in manual assertion
Supporting statements:
To analyze the interaction of COMP in a more reliable one-to-one situation, we used a biotinylated recombinant 57-kDa C-terminal fragment of the COMP monomer (COMP T3 TC) to coat a hydrophobic sensor chip. Soluble rNC4 was injected over the surface at various concentrations, and a Kd of 0.23 ± 0.11 M
The same sensor chip was also used to analyze the effect of excess heparin on the interaction of COMP T3+TC with rNC4 and rcIX. Heparin was found to inhibit both interactions at low micromolar concentrations. Preincubation of 20 nM rcIX with 4 M heparin (molecular mass 6 kDa) prior to injection over the coated surface resulted in more than 99% inhibition of the interaction with COMP T3+TC, and 50% inhibition was achieved with a heparin concentration lower than 0.1 M.
Somewhat surprisingly, our results show that COMP and heparin compete for the same binding site or overlapping ones in the NC4 domain. Similarly, we were able to block the interaction of full-length rcIX with the C-terminal domain of COMP using relatively low heparin levels.
Protein: DP03379 (UniProt Q14766)
Region: residues 1507	to 1522
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
15N relaxation studies further demonstrate that the three interdomain regions act as flexible linkers, allowing a wide range of motion between the well-structured domains. This work is consistent with the LTBP1 C-terminus adopting a flexible ‘‘knotted rope’’ structure, which may facilitate cell matrix interactions, and the accessibility to proteases or other factors that could contribute to TGFb activation.
LTBP sequences all contain linker regions of 17 or more amino acids between the cbEGF14 and TB3 domains, and 34 or many more residues between the TB3 and EGF3 domains. These long linker regions have no clear homology to previously identified domains and are not seen between homologous TB/EGF/cbEGF domains in fibrillin.These sequences are poorly conserved between LTBP variants, suggesting that these regions may be unstructured and potentially flexible.
For residues in the linkers connecting cbEGF14 to TB3 and TB3 to EGF3 and for the 13 C-terminal residues following cbEGF15, NOE ratios below 0.3 are observed, indicating significant amplitude backbone dynamics on a sub-nanosecond timescale. This high degree of flexibility and lack of well-defined structure is consistent with the poor sequence conservation of these regions (Figure 2).
The numerous flexible linkers identified would make many regions of the LTBP1 C-terminus unsuitable for crystallographic
studies, or other structural investigations that rely on rigid body modelling. The data presented here demonstrate that the Cterminus of LTBP1 behaves like a ‘‘knotted rope’’ in solution, where the linkers either side of the TB3 domain act as the highly
flexible ‘‘rope’’ allowing the TB3 domain and EGF3-cbEGF15 domain pair, (the ‘‘knots’’ in this analogy), to move freely relative to each other and the rest of LTBP1. The presence of flexible linkers mean that long-range interdomain interactions, such as EGF3 interacting with cbEGF14 or other parts of the LTBP1 molecule, cannot be excluded by these studies.

Numbering needs to be shifted by one to correspond to the UNIPROT numbering, i.e. the C-terminal residue 1722 mentioned in the paper corresponds to residue 1721 in the uniprot sequence
Cross-references: BMRB:19322
Protein: DP03379 (UniProt Q14766)
Region: residues 1582	to 1623
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
15N relaxation studies further demonstrate that the three interdomain regions act as flexible linkers, allowing a wide range of motion between the well-structured domains. This work is consistent with the LTBP1 C-terminus adopting a flexible ‘‘knotted rope’’ structure, which may facilitate cell matrix interactions, and the accessibility to proteases or other factors that could contribute to TGFb activation.
LTBP sequences all contain linker regions of 17 or more amino acids between the cbEGF14 and TB3 domains, and 34 or many more residues between the TB3 and EGF3 domains. These long linker regions have no clear homology to previously identified domains and are not seen between homologous TB/EGF/cbEGF domains in fibrillin.These sequences are poorly conserved between LTBP variants, suggesting that these regions may be unstructured and potentially flexible.
For residues in the linkers connecting cbEGF14 to TB3 and TB3 to EGF3 and for the 13 C-terminal residues following cbEGF15, NOE ratios below 0.3 are observed, indicating significant amplitude backbone dynamics on a sub-nanosecond timescale. This high degree of flexibility and lack of well-defined structure is consistent with the poor sequence conservation of these regions (Figure 2).
The numerous flexible linkers identified would make many regions of the LTBP1 C-terminus unsuitable for crystallographic
studies, or other structural investigations that rely on rigid body modelling. The data presented here demonstrate that the Cterminus of LTBP1 behaves like a ‘‘knotted rope’’ in solution, where the linkers either side of the TB3 domain act as the highly
flexible ‘‘rope’’ allowing the TB3 domain and EGF3-cbEGF15 domain pair, (the ‘‘knots’’ in this analogy), to move freely relative to each other and the rest of LTBP1. The presence of flexible linkers mean that long-range interdomain interactions, such as EGF3 interacting with cbEGF14 or other parts of the LTBP1 molecule, cannot be excluded by these studies.

Numbering needs to be shifted by one to correspond to the UNIPROT numbering, i.e. the C-terminal residue 1722 mentioned in the paper corresponds to residue 1721 in the uniprot sequence
Cross-references: BMRB:19322
Protein: DP03379 (UniProt Q14766)
Region: residues 1709	to 1721
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
15N relaxation studies further demonstrate that the three interdomain regions act as flexible linkers, allowing a wide range of motion between the well-structured domains. This work is consistent with the LTBP1 C-terminus adopting a flexible ‘‘knotted rope’’ structure, which may facilitate cell matrix interactions, and the accessibility to proteases or other factors that could contribute to TGFb activation.
LTBP sequences all contain linker regions of 17 or more amino acids between the cbEGF14 and TB3 domains, and 34 or many more residues between the TB3 and EGF3 domains. These long linker regions have no clear homology to previously identified domains and are not seen between homologous TB/EGF/cbEGF domains in fibrillin.These sequences are poorly conserved between LTBP variants, suggesting that these regions may be unstructured and potentially flexible.
For residues in the linkers connecting cbEGF14 to TB3 and TB3 to EGF3 and for the 13 C-terminal residues following cbEGF15, NOE ratios below 0.3 are observed, indicating significant amplitude backbone dynamics on a sub-nanosecond timescale. This high degree of flexibility and lack of well-defined structure is consistent with the poor sequence conservation of these regions (Figure 2).
The numerous flexible linkers identified would make many regions of the LTBP1 C-terminus unsuitable for crystallographic
studies, or other structural investigations that rely on rigid body modelling. The data presented here demonstrate that the Cterminus of LTBP1 behaves like a ‘‘knotted rope’’ in solution, where the linkers either side of the TB3 domain act as the highly
flexible ‘‘rope’’ allowing the TB3 domain and EGF3-cbEGF15 domain pair, (the ‘‘knots’’ in this analogy), to move freely relative to each other and the rest of LTBP1. The presence of flexible linkers mean that long-range interdomain interactions, such as EGF3 interacting with cbEGF14 or other parts of the LTBP1 molecule, cannot be excluded by these studies.

Numbering needs to be shifted by one to correspond to the UNIPROT numbering, i.e. the C-terminal residue 1722 mentioned in the paper corresponds to residue 1721 in the uniprot sequence
Cross-references: BMRB:19322