LiteFold/DisProt huggingface dataset:
Protein: DP03379 (UniProt Q14766)
Region: residues 1507	to 1521
Annotation: flexible linker (Disorder function)
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: flexible linker (Disorder function)
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 1618	to 1624
Annotation: protein binding (Molecular function)
Evidence: surface plasmon resonance evidence used in manual assertion
Supporting statements:
LTBP1 anchors itself to FBN1 using two independent epitopes. As part of this mechanism, a flexible pivot adjacent to the FBN1/LTBP1 binding site allows LTBP1 to make contacts with different ECM networks while presumably facilitating a force-induced/traction-based TGF-b activation mechanism.
We observed a specific interaction between a three-domain C-terminal LTBP1TB3cbEGF15 construct and a four-domain FBN1E2cbEGF1 construct using both surface plasmon resonance (SPR) and a plate-based binding assay (Figures 1B and 1C).
Dissociation constants (Kd) of _100 ± 20 and _300 ± 100 mM for the interaction of FBN1E2cbEGF1 with LTBP1E3cbEGF15, and LTBP1cbEGF14TB3, respectively, can be estimated from the SPR data (Figure S2). In contrast, the binding of LTBP1TB3E3 to FBN1E2cbEGF1 gives a non-linear Scatchard plot (Figure S2); this is not surprising as the multi-site mode of interaction for this LTBP1 construct may give rise to complicated binding kinetics. Nevertheless, a Kd of _0.5–1 mM can be estimated from the SPR data at the lowest analyte concentrations (which are similar to concentrations used in previous studies [Massam- Wu et al., 2010; Ono et al., 2009]). Thus, the pair of interaction sites between FBN1 and LTBP1 results in a substantial enhancement in overall binding affinity. A cartoon summarizing our proposed binding model based on our domain dissection data is shown in Figure 2C.
The necessity of the linker for the binding function is revealed by fragment-based dissection of the interacting regions. The presence of the linker allows affinity enhancement of this interaction, and the linker region is further shown to make contacts with FBN1 through NMR experiments.
Protein: DP03379 (UniProt Q14766)
Region: residues 1618	to 1624
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
LTBP1 anchors itself to FBN1 using two independent epitopes. As part of this mechanism, a flexible pivot adjacent to the FBN1/LTBP1 binding site allows LTBP1 to make contacts with different ECM networks while presumably facilitating a force-induced/traction-based TGF-b activation mechanism.
Titration of the four-domain FBN1E2cbEGF1 construct with the two-domain LTBP1 construct, LTBP1E3cbEGF15, shows specific broadening effects rather than chemical shift changes; this indicates intermediate/slow exchange behavior consistent with the stronger interaction between this pair of protein constructs seen by SPR (Figures 3C and 3D). These titrations show that residues located in the EGF3 domain of LTBP1, and some of the unstructured region that immediately precedes EGF3, interact with residues located in the Hyb1 and cbEGF1 domains of FBN1 (Figures 3C and 3D).
The boundaries of the linker region interacting with FBN1 was deduced from chemical shift and intensity changes shown in Figure 3 C and D.
Protein: DP03379 (UniProt Q14766)
Region: residues 1578	to 1624
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
LTBP1 anchors itself to FBN1 using two independent epitopes. As part of this mechanism, a flexible pivot adjacent to the FBN1/LTBP1 binding site allows LTBP1 to make contacts with different ECM networks while presumably facilitating a force-induced/traction-based TGF-b activation mechanism.
In the HADDOCK model of the FBN1/LTBP1 complex, the distance separating the last residue of LTBP1-TB3 and the first residue of LTBP1-EGF3 is small enough to be easily accommodated by the 36-residue flexible linker joining the two domains (Figure 8A). An LTBP1TB3E3 variant in which this linker was deleted showed lower binding to FBN1E2cbEGF1 in a plate-based assay (Figures 8B and 8C), consistent with only one of the two LTBP1 domains being able to interact at any given time in this construct. Replacement of the LTBP1 linker with the shorter 22-residue linker from LTBP3, which has a very different amino acid sequence, restored binding to levels comparable with the WT interaction indicating the linker plays a passive role as a connector (Figures 8B and 8C).
The boundaries of the linker region are taken from this paper and a previous publication (PMID:24489852). The structure-based prediction was performed based on experimental data from NMR chemical shifts and intensity changes.
Protein: DP03379 (UniProt Q14766)
Region: residues 1578	to 1624
Annotation: molecular adaptor activity (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
LTBP1 anchors itself to FBN1 using two independent epitopes. As part of this mechanism, a flexible pivot adjacent to the FBN1/LTBP1 binding site allows LTBP1 to make contacts with different ECM networks while presumably facilitating a force-induced/traction-based TGF-b activation mechanism.
In the HADDOCK model of the FBN1/LTBP1 complex, the distance separating the last residue of LTBP1-TB3 and the first residue of LTBP1-EGF3 is small enough to be easily accommodated by the 36-residue flexible linker joining the two domains (Figure 8A). An LTBP1TB3E3 variant in which this linker was deleted showed lower binding to FBN1E2cbEGF1 in a plate-based assay (Figures 8B and 8C), consistent with only one of the two LTBP1 domains being able to interact at any given time in this construct. Replacement of the LTBP1 linker with the shorter 22-residue linker from LTBP3, which has a very different amino acid sequence, restored binding to levels comparable with the WT interaction indicating the linker plays a passive role as a connector (Figures 8B and 8C).
The presence of a flexible linker between the two FBN1- interacting sites within LTBP1 suggests a mechanism by which proteases can regulate the affinity of this interaction. Protease cleavage of the TB3–EGF3 linker in LTBP1 may release the large latent complex from the 10–12 nm microfibril network, as the affinity of the TB3 binding site alone for FBN1 is very much weaker than the bipartite interaction.
We have further demonstrated an unusual bipartite interaction of LTBP1 with FBN1, adjacent to the LAP/TGF-b binding site, which facilitates complex formation in dynamic connective tissues. We propose that this contributes to integrin mediated activation of TGF-b in FBN1-rich tissues.
The boundaries of the linker region are taken from this paper and a previous publication (PMID:24489852). The structure-based prediction was performed based on experimental data from NMR chemical shifts and intensity changes.
Protein: DP03380 (UniProt P83110)
Region: residues 279	to 289
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Chain A is the only molecule visible in full length in the ΔN-HtrA3 structure. It encompasses residues 135–459 with the exclusion of residues 163–168 and 277–289 of the loops LA and L3, respectively.
The fact that parts of the LA and L3 loops (Fig 3) were not visible in the ΔN-HtrA3 structure suggests their mobility and thus the possibility that they change conformation upon substrate binding. Similarly, the L3 loop is not visible in the HtrA1 and the E. coli HtrA(DegP) inactive structures, but is present in the active conformations [9] [56].
Residues 279-289 are missing in all chains and are presumably disordered.
Cross-references: PDB:4RI0
Protein: DP03381 (UniProt P63277-2)
Region: residues 17	to 75
Annotation: disorder (Structural state)
Evidence: small-angle neutron scattering evidence used in manual assertion
Supporting statements:
The distribution of SASSIE structures indicates that LRAP(+P) can adopt a range of conformations dominated by extended structures with Rg of 1.5 – 2.5 nm.
(+P) means that a phosphorylated form was studied, where there is a single phosphorylation on residue S16 (equivalent to UniProt residue S32 due to the presence of a 16 residues long signal peptide in the UniProt sequence).
Protein: DP03381 (UniProt P63277-2)
Region: residues 17	to 75
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The solution NMR data for LRAP(−P), therefore, is consistent with random coil structures in the C-terminal and N-terminal regions.
The NMR data suggests a largely disordered structure for LRAP (−P), similar to the disordered, extended conformation reported for full-length porcine amelogenin at pH 3.8 in solution.
Protein: DP03381 (UniProt P63277-2)
Region: residues 17	to 75
Annotation: molecular function regulator (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
In vivo studies have shown that LRAP is localized within the extracellular matrix of growing enamel and in vitro studies have shown that LRAP can control HAP crystal formation suggesting that LRAP, like amelogenin, may have an extracellular matrix function in controlling enamel crystal growth.
Protein: DP03381 (UniProt P63277-2)
Region: residues 17	to 75
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Circular dichroism (CD) spectra obtained for the phosphorylated LRAP (+P) in SCP at pH 7.4 and in solutions with 3 mM CaCl2 show that LRAP (+P) also has a largely disordered secondary structure.
CD studies show that LRAP(+P) is also predominantly unstructured.
(+P) means that a phosphorylated form was studied, where there is a single phosphorylation on residue S16 (equivalent to UniProt residue S32 due to the presence of a 16 residues long signal peptide in the UniProt sequence).
Protein: DP03381 (UniProt P63277-2)
Region: residues 30	to 34
Annotation: phosphorylation display site (Disorder function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
Both full-length amelogenin and LRAP are post-translationally modified by side chain phosphorylation of S16.
Residue S16 is equivalent to UniProt residue S32 due to the presence of a 16 residues long signal peptide in the UniProt sequence.
Protein: DP03382 (UniProt P98066)
Region: residues 250	to 277
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Only the CUB module (residues 128–249) was visible in the crystal structure with no electron density seen for the last 28 amino acid residues, although this region was verified as present in the crystals by SDS-PAGE (not shown). The last residue observed in the electron density is Pro-249, which protrudes into a large solvent channel; this might allow the C-terminal region to adopt a range of conformations, thus rendering it essentially invisible to crystallography.
Cross-references: PDB:2WNO
Protein: DP03383 (UniProt Q8WVM7)
Region: residues 1	to 85
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the SMC1 and SMC3 coiled coils (CCs), large segments of the flexible region of RAD21, and the N- and C-terminal unstructured parts of STAG1 and NIPBLC were completely unresolved.
Cross-references: PDB:6WG3
Protein: DP03383 (UniProt Q8WVM7)
Region: residues 1053	to 1258
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the SMC1 and SMC3 coiled coils (CCs), large segments of the flexible region of RAD21, and the N- and C-terminal unstructured parts of STAG1 and NIPBLC were completely unresolved.
Cross-references: PDB:6WG3
Protein: DP03383 (UniProt Q8WVM7)
Region: residues 442	to 457
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
unstructured region inside STAG1.
Cross-references: PDB:6WG3
Protein: DP03383 (UniProt Q8WVM7)
Region: residues 843	to 853
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
unstructured region inside STAG1.
Cross-references: PDB:6WG3
Protein: DP03383 (UniProt Q8WVM7)
Region: residues 34	to 52
Annotation: localization (Biological process)
Evidence: deletion mutation phenotypic evidence used in manual assertion
Supporting statements:
Since the SA1 protein was also nuclear in yeast, we asked whether the putative 19-amino acid-long bipartite NLS present in the N-terminal non-conserved part of this protein was responsible. The sequence 34KRKRGRPGRPPSTNKKPRK53 is specific to SA1 and is not homologous to the identified functional NLS32–47 of SA2L. Deleting K34–K53 resulted in the localization of SA1Δ34–53 in the whole cell, which confirmed that the signal is necessary for SA1 nuclear import. When we fused 71 N-terminal amino acids of SA1 containing this signal to GFP, the fusion protein SA11–71-GFP localized to the nucleus, confirming that it contained a functional NLS (Figure 5).
Protein: DP03383 (UniProt Q8WVM7)
Region: residues 34	to 52
Annotation: localization (Biological process)
Evidence: microscopy evidence used in manual assertion
Supporting statements:
Since the SA1 protein was also nuclear in yeast, we asked whether the putative 19-amino acid-long bipartite NLS present in the N-terminal non-conserved part of this protein was responsible. The sequence 34KRKRGRPGRPPSTNKKPRK53 is specific to SA1 and is not homologous to the identified functional NLS32–47 of SA2L. Deleting K34–K53 resulted in the localization of SA1Δ34–53 in the whole cell, which confirmed that the signal is necessary for SA1 nuclear import. When we fused 71 N-terminal amino acids of SA1 containing this signal to GFP, the fusion protein SA11–71-GFP localized to the nucleus, confirming that it contained a functional NLS (Figure 5).
Protein: DP03385 (UniProt P20592)
Region: residues 599	to 621
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The Cryo-EM structure shows this region lacks electron density, indicating it is disordered. 
Cross-references: EMDB:8577
PDB:5UOT
Protein: DP03385 (UniProt P20592)
Region: residues 1	to 92
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The NTR, together with the MBP tag, is not resolved, probably because of their flexibility.
Cross-references: EMDB:8577
PDB:5UOT
Protein: DP03386 (UniProt Q9Y237-2)
Region: residues 1	to 59
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The carbon-associated 1H resonances of the Par17 N-terminus up to residue Gly59, however, are missing due to a very high degree of resonance degeneracy within this apparently unstructured region.
Signals belonging to the first 60 N-terminal residues of Par17 show a low amide proton resonance dispersion (between 8.55 and 8.01 ppm), indicating that this region of the protein is largely unstructured.
Subsequent chemical shift index analysis indicated that Par17 features a parvulin-type PPIase domain at the C-terminus, analogous to Par14, and an unstructured N-terminus encompassing the first 60 residues.
Cross-references: BMRB:18615
Protein: DP03386 (UniProt Q9Y237-2)
Region: residues 1	to 25
Annotation: localization (Biological process)
Evidence: co-localization evidence used in manual assertion
Supporting statements:
The Par17 protein differs from Par14 within the N-terminus by 25 additional amino acids.
Par17-RS- and -QR-EGFP co-localized with mitochondrial staining. Totals of 77 ± 5 and 63 ± 9% of EGFP fluorescence were measured to overlap with the MitoTracker signal for Par17-RS and -QR, respectively. Par14-EGFP fluorescence is equally distributed throughout the cytosol and partially enriched in the nucleus, as has been described previously. Co-localization values were far lower for Par14-EGFP (11 ± 6%) and EGFP alone (4 ± 1%). Therefore, the presequence seemed to be the determinant for mitochondrial targeting, and the question arose whether the Par17 N-terminus was necessary and/or sufficient for mitochondrial targeting.
Protein: DP03387 (UniProt Q9Y237-1)
Region: residues 1	to 35
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The hPar14 folds into aba3bab2 structure, and contains an unstructured 35-amino acid basic tail N-terminal to the catalytic core that replaces the WW domain of hPin1  homolog.
Poorly dispersed resonances of amino acid residues Lys4 to Gly35 within the amid region   of TOCSY and COSY-spectra point to the fact that these residues are localized in random  coil areas. Confirmation comes from the evaluation of NOESY spectra where only sequential NOEs of neighboring residues within this sequence were found. 
Cross-references: BMRB:4768
Protein: DP03388 (UniProt P0AB38)
Region: residues 21	to 80
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In agreement with the presence of 27 % Pro residues, the G1 to W64 segment is largely unstructured with Cα and CO chemical shifts close to random coil values and IUPred scores larger than 0.55.
We also provide evidence for a two-domain organization of LpoB and a largely disordered, 64 amino acid-long N-terminal domain.
The first four residues of the analyzed sequence construct belonged to a tag that replaced the signal peptide. Valine 21 was the first UniProt residue being part of the construct (equivalent to residue 5 in the construct).
Cross-references: BMRB:19681