LiteFold/DisProt huggingface dataset:
Protein: DP01775 (UniProt P53632)
Region: residues 482	to 584
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Due to significant sample degradation during purification (Fig. S1), we were not able to isolate a complex consisting of full-length forms of Trf4p and Air2p. We therefore worked with Trf4p/Air2p subcomplexes, where the proteolytically sensitive N and C termini of both proteins were removed.
Protein: DP01775 (UniProt P53632)
Region: residues 482	to 584
Annotation: protein binding (Molecular function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Residues 573-584 bind to NDR1 (ref. PubMedID: 25066235).
Cross-references: imex : IM-26196-1
Protein: DP01776 (UniProt Q8GYN5)
Region: residues 1	to 211
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Consistent with the in silico prediction, full-length RIN4 circular dichroism spectra displayed a characteristic shape, including low ellipticity at 190 nm and strong negative ellipticity at 200 nm, consistent with an intrinsically disordered protein.
Protein: DP01776 (UniProt Q8GYN5)
Region: residues 1	to 211
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
RIN4 is a key accessory protein that associates with the plasma membrane localized NLRs, RPM1, and RPS2. The Arabidopsis protein RIN4 is targeted by multiple bacterial effectors, including HopF2, AvrPto, AvrRpt2, AvrB, and AvrRpm1.
Protein: DP01776 (UniProt Q8GYN5)
Region: residues 1	to 211
Annotation: phosphorylation display site (Disorder function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
RPM1-INDUCED PROTEIN KINASE (RIPK), a receptor-like cytoplasmic kinase, phosphorylates RIN4 at three residues: Thr-21, Ser-160, and Thr-166.
Protein: DP01777 (UniProt Q3LS93)
Region: residues 22	to 329
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In the absence of lipids, rSpTrf-E1 remained intrinsically disordered (~2% α helical) in agreement with a disordered structure in the absence of binding targets.
Protein: DP01777 (UniProt Q3LS93)
Region: residues 22	to 329
Annotation: lipid binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
we investigated possible interactions of rSpTrf-E1 and the recombinant fragments with phospholipids and identified specific binding to phosphatidic acid (PA) by the full-length protein and the rGly-rich and rHis-rich fragments. In addition, the rHis-rich fragment also binds to phosphatidyl inositol 4 phosphate [PtnIns(4)P], although with lower affinity.
Protein: DP01779 (UniProt Q05917)
Region: residues 146	to 199
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The NH resona1H, 13C and 15N resonance assignment of a 114-residue fragment of Engrailed 2 homeoprotein, a partially disordered proteinnces corresponding to homeodomain residues are well dispersed, while those belonging to the N-terminal extension are all in a narrow range between 7.6 and 8.6 ppm, which indicates intrinsic disorder in regions outside the homeodomain.
The weak dispersion in the proton dimension of the (1)H-(15)N HSQC spectrum indicates the presence of disordered regions that do not belong to the homeodomain. This work is a first step toward the NMR investigation of the structure and dynamics of Engrailed 2 protein that contains a well-structured globular domain and partially disordered regions.
The NH resonances corresponding to homeodomain residues are well dispersed, while those belonging to the N-terminal extension are all in a narrow range between 7.6 and 8.6 ppm (see Fig. 1) which indicates intrinsic disorder in regions outside the homeodomain.
Protein: DP01779 (UniProt Q05917)
Region: residues 146	to 199
Annotation: protein binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
This led us to investigate if Engrailed and Foxa2 interact directly. Direct interaction was confirmed by pull-down experiments, and the regions participating in this interaction were identified. In Foxa2 the interacting domain is the Forkhead box DNA-binding domain. In Engrailed, two independent interacting domains exist: the homeodomain and a region that includes the Pbx-binding domain.
As illustrated in Fig. 6B (left panel), fragment 146-199 (containing the Pbx-interacting domain) and the homeodomain bind Foxa2. The 146-199 domain was further sub-divided into fragments 146-167 and 168-199 (the latter containing only the EH2-EH3 Pbx-interacting domain). Fig.6B (right panel) shows that these two sub-fragments still retain Foxa2, although less efficiently than the entire sequence. It can thus be concluded that the homeodomain and a domain N-terminal to the homeodomain, including the Pbx-interacting domain, bind Foxa2
Protein: DP01779 (UniProt Q05917)
Region: residues 146	to 199
Annotation: molecular function regulator (Molecular function)
Evidence: luciferase reporter gene assay evidence used in manual assertion
Supporting statements:
Foxa2 physiologically interacts with Engrailed in regulating the MAP1B promoter ex vivo
At a higher dose (5 μg of plasmid), Foxa2 activates the MAP1B promoter and this activation is partially antagonized by the co-expression of low levels of Engrailed (2μg of plasmid) which have no significant effect per se (Fig.3C). Taken together these results suggest that Foxa2 and Engrailed physically interact and/or compete for overlapping DNA target sequences.
Protein: DP01780 (UniProt P21736)
Region: residues 1	to 54
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In contrast, the 1H–15N HSQC spectrum of the full-length E7 of HPV45 contained additional signals only in a very narrow chemical shift range, whereas the signals arising from the C-terminus remained virtually unaffected (Figure 2a). Such a spectral ‘fingerprint’ indicates an unstructured and flexible N-terminus (a.a. 1–54) and, importantly so, that the C-terminus of E7 folds autonomously into a well-structured domain
Protein: DP01781 (UniProt O75112-6)
Region: residues 229	to 283
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
After trypsin digestion, analysis of the main digestion product by mass spectrometry indicated a main product with mass of 26 648 Da corresponding to residues 1−228. Minor processing was observed at residues 217, 218, and 224, indicating a hot spot region consistent with high arginine content. The processed C-terminal sequence includes exon 9 (residues 252−282).
Protein: DP01781 (UniProt O75112-6)
Region: residues 85	to 283
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The HSQC spectrum of ZASP-S is indicative of a largely unstructured species with well-folded regions, as shown by the low dispersion of resonances in the center of the spectrum together with the highly dispersed peaks surrounding them. Comparison of the spectrum with that of the isolated PDZ domain shows that the dispersed peaks mostly belong to the PDZ domain (residues 1-84).
Protein: DP01781 (UniProt O75112-6)
Region: residues 85	to 283
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Addition of ZASP-S to skeletal muscle G-actin resulted in the formation of F-actin (filaments). The PDZ domain was not required for array formation as ABRΔ10, both WT and mutant, formed similar arrays when mixed with F-actin.
Protein: DP01782 (UniProt Q53GG5)
Region: residues 107	to 273
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum suggested that ALP107-273 is mostly unfolded. No features characteristic of either α-helical or β-sheet structures were seen.
Protein: DP01782 (UniProt Q53GG5)
Region: residues 107	to 273
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Size exclusion chromatography showed that ALP107-273 eluted faster than expected based on its calculated monomer molecular weight (18 265 Da).
Protein: DP01782 (UniProt Q53GG5)
Region: residues 107	to 273
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 15N-HSQC spectrum measured in normal buffer conditions from uniformly 15N-labeled ALP107-273 was in line with the CD measurements as it showed the collapsed spectrum characteristic of an unfolded protein. When the 13C chemical shift values were compared to those of the random coil conformation, no clear indications of either α helix or β sheet secondary structures were observed.
Protein: DP01782 (UniProt Q53GG5)
Region: residues 107	to 273
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The NMR titration studies suggested that structure of ALP107-273 was partially stabilized by the interaction with the α-actinin rod region.
Protein: DP01782 (UniProt Q53GG5)
Region: residues 107	to 273
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
To test whether ALP107-273 was functional, we measured the interaction of the purified protein fragment with α-actinin by surface plasmon resonance (SPR). A clear interaction was observed in both experimental setups and the apparent dissociation equilibrium constants (Kd) were in the low micromolar range.
Protein: DP01783 (UniProt Q2JIZ5)
Region: residues 1	to 30
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The final NMR model (Protein Data Bank (PDB) code 2K2N) is absent the C-terminal 6His tag and the first 30 amino acids, which include the RIT consensus motif present in many members of the PAS-less Cph subfamily.12 Both regions are highly dynamic and largely unstructured, which broadened out most of their NMR signals.
Cross-references: PDB:2K2N
PDB:2LB9
BMRB:15717
Protein: DP01784 (UniProt Q86UX7)
Region: residues 142	to 224
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 15N-1H HSQC spectrum of the 83-residue loop region of kindlin-3 showed limited chemical shift dispersion, ~ 0.8 ppm, of the amide proton resonances, whereas 15N chemical shifts of the amino acids were better dispersed. These spectral features are typically observed for natively unfolded proteins and denatured proteins. The NOE pattern also suggests an absence of stably folded conformations.
Protein: DP01784 (UniProt Q86UX7)
Region: residues 142	to 224
Annotation: lipid binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR 15N-1H HSQC titration experiments were performed to demonstrate residue specific interactions of F1 loop region with liposomes containing zwitterionic lipid POPC, negatively charged lipids POPS or POPG. Membrane specific association of kindlin-3 by its large loop region is a key requirement for the activation of integrins.
Protein: DP01784 (UniProt Q86UX7)
Region: residues 142	to 224
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
UV CD spectra (240–190 nm) of the kindlin-3 loop in detergent free solutions and in solutions containing 50 mM detergents showed a relatively intense band at 208 nm and a less pronounced band around 222–225 nm.
Protein: DP01785 (UniProt Q87P35)
Region: residues 1	to 125
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Alone, the spectrum of His-Gβ1-VopR (residues 1–125) chiefly contained peaks that could be attributed to the N-terminal Gβ1 domain; most of the remaining peaks originating from VopR 1–125 had heterogenous line widths and poor 1H chemical shift dispersion, consistent with unfolding.
Protein: DP01785 (UniProt Q87P35)
Region: residues 1	to 125
Annotation: lipid binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
These results indicated that the BPDVopR is unstructured in solution without a phosphoinositide ligand, but that specific binding of PIP2 induces its folding. Further analysis using circular dichroism (CD) spectroscopy revealed a PIP2-dependent increase in secondary structure within His-Gβ1-VopR1–125, corroborating these findings.
Protein: DP01785 (UniProt Q87P35)
Region: residues 1	to 125
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
These results indicated that the BPDVopR is unstructured in solution without a phosphoinositide ligand, but that specific binding of PIP2 induces its folding. Further analysis using circular dichroism (CD) spectroscopy revealed a PIP2-dependent increase in secondary structure within His-Gβ1-VopR1–125, corroborating these findings.
Protein: DP01786 (UniProt D2JX42)
Region: residues 1	to 143
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The secondary structure of MpASR was revealed by CD spectroscopy. The far-UV CD spectrum of recombinant MpASR has a maximum negative ellipticity at 200.8 nm and low ellipticity around 215–229 nm , which indicates a disordered protein structure.
Protein: DP01786 (UniProt D2JX42)
Region: residues 1	to 143
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
By SDS–PAGE analysis, MpASR showed a characteristic low mobility. The predicted molecular mass of MpASR is 16.2 kDa, but it ran at 22 kDa. This high apparent molecular mass is caused by a highly hydrophilic property which is often characteristic of IDPs.
Protein: DP01786 (UniProt D2JX42)
Region: residues 1	to 143
Annotation: disorder (Structural state)
Evidence: temperature-induced protein unfolding evidence used in manual assertion
Supporting statements:
MpASR proteins were heat stable, suggesting that compared with globular proteins such as BSA, MpASR is not likely to collapse and aggregate during high temperature treatment or boiling.
Protein: DP01786 (UniProt D2JX42)
Region: residues 1	to 143
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Incubation of recombinant MpASR with 200 ng trypsin for 1 h resulted in a large amount of low molecular weight proteolytic products.
Protein: DP01786 (UniProt D2JX42)
Region: residues 1	to 143
Annotation: disorder to order (Structural transition)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
In the presence of Zn2+, MpASR was less susceptible to proteolysis in a zinc concentration-dependent manner.
Protein: DP01786 (UniProt D2JX42)
Region: residues 1	to 143
Annotation: zinc ion binding (Molecular function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Desiccation and zinc binding can induce structure and homodimerization in ASR1 protein. ASR1 protein also possess zinc-dependent DNA-binding activity. In the presence of Zn2+, MpASR was less susceptible to proteolysis in a zinc concentration-dependent manner.
Protein: DP01787 (UniProt A0A1Z3GD05)
Region: residues 1	to 138
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
By comparing the experimentally determined Stokes radius (RS obs) of HvASR1 and TtASR1 with the Stokes radii expected for various conformational states (native, molten globule, pre-molten globule, and denaturant-unfolded), the two proteins were found to have an RS higher than the value expected for a monomeric, natively folded form (~20 Å) (Table 2).
Protein: DP01787 (UniProt A0A1Z3GD05)
Region: residues 1	to 138
Annotation: disorder (Structural state)
Evidence: temperature-induced protein unfolding evidence used in manual assertion
Supporting statements:
As shown in Supplementary Fig. S4, the experimentally observed profiles for HvASR1 and TtASR1 are consistent with lack of a stable 3D structure, as judged from their rather high basal fluorescence at 20 °C and from the flatness of their profile.
Protein: DP01787 (UniProt A0A1Z3GD05)
Region: residues 1	to 138
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Both HvASR1 and TtASR1 exhibit an abnormally slow migration in SDS-PAGE, with an apparent molecular mass (MM) comprised between 20 and 25 kDa (expected MM ~16 kDa) (Fig. 2).
The aberrant electrophoretic migration of HvASR1 and TtASR1 proteins constitutes the first experimental hint of their disordered nature.
Protein: DP01787 (UniProt A0A1Z3GD05)
Region: residues 1	to 138
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The experimental Rg values are therefore in very good agreement with the expected Rg values using parameters inferred from IDPs, while they are three times smaller that those expected for fully unfolded forms.
Protein: DP01787 (UniProt A0A1Z3GD05)
Region: residues 1	to 138
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Under native conditions and neutral pH, both proteins present spectra typical of proteins lacking any stable organized secondary structure, as judged from their large negative ellipticity at 200 nm, low amplitude in the 210–230 nm region, and low ellipticity at 190 nm (Fig. 5A). Spectral deconvolution revealed a high content (>60%) of unordered structure in both ASR1 proteins (see insets in Fig. 5A).
Protein: DP01787 (UniProt A0A1Z3GD05)
Region: residues 1	to 138
Annotation: zinc ion binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We then recorded the far-UV CD spectra in the presence of zinc (Fig. 10). The addition of 2.5 mM ZnSO4 does not trigger a gain in α-helical structure, but rather, leads to a decrease in the amplitude of the negative peak at 200 nm, consistent with a decrease in disorder content.
By combining 10% TFE and 2 mM ZnSO4, a much more pronounced gain of structure is observed (Fig. 10), resulting in an increase in α-helical content, as judged from the appearance of the characteristic double minima at 208 and 222 nm (Fig. 10).
Protein: DP01787 (UniProt A0A1Z3GD05)
Region: residues 1	to 138
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
In the absence of TFE, the two proteins are readily degraded after an incubation as short as one hour, and entirely digested after 6 hours (Fig. 8), a behavior that is consistent with an overall high solvent accessibility and disordered nature.
Protein: DP01787 (UniProt A0A1Z3GD05)
Region: residues 1	to 138
Annotation: disorder to order (Structural transition)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
Near-UV CD studies further support this conclusion (Supplementary Text 5). For both proteins, the addition of 2 mM ZnSO4 results in a spectral modification, consistent with the gain of some tertiary structure (Fig. 5D).
Protein: DP01787 (UniProt A0A1Z3GD05)
Region: residues 1	to 138
Annotation: zinc ion binding (Molecular function)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
Near-UV CD studies further support this conclusion (Supplementary Text 5). For both proteins, the addition of 2 mM ZnSO4 results in a spectral modification, consistent with the gain of some tertiary structure (Fig. 5D).
Protein: DP01787 (UniProt A0A1Z3GD05)
Region: residues 1	to 138
Annotation: zinc ion sequestering activity (Molecular function)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
Near-UV CD studies further support this conclusion (Supplementary Text 5). For both proteins, the addition of 2 mM ZnSO4 results in a spectral modification, consistent with the gain of some tertiary structure (Fig. 5D).
Protein: DP01787 (UniProt A0A1Z3GD05)
Region: residues 1	to 138
Annotation: zinc ion sequestering activity (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We then recorded the far-UV CD spectra in the presence of zinc (Fig. 10). The addition of 2.5 mM ZnSO4 does not trigger a gain in α-helical structure, but rather, leads to a decrease in the amplitude of the negative peak at 200 nm, consistent with a decrease in disorder content.
By combining 10% TFE and 2 mM ZnSO4, a much more pronounced gain of structure is observed (Fig. 10), resulting in an increase in α-helical content, as judged from the appearance of the characteristic double minima at 208 and 222 nm (Fig. 10).
Protein: DP01787 (UniProt A0A1Z3GD05)
Region: residues 1	to 138
Annotation: disorder (Structural state)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
Both proteins reached their maximum exchange after 10 sec of labeling, indicating that HvASR1 and TtASR1 are predominantly unfolded in their native state.
Both ASR1 proteins are intrinsically disordered in their native state.
Protein: DP01787 (UniProt A0A1Z3GD05)
Region: residues 1	to 138
Annotation: zinc ion sequestering activity (Molecular function)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
The addition of 2 mM ZnSO4 induced a weak dynamic HDX-MS behavior, indicative of structure formation, throughout the entire polypeptide chain of both proteins (Panels C, Fig. 11). Notably, the addition of both 10% TFE and 2 mM ZnSO4 in a combined fashion resulted in an more pronounced change in magnitude of HDX dynamics (Panels D, Fig. 11).
Protein: DP01787 (UniProt A0A1Z3GD05)
Region: residues 1	to 138
Annotation: disorder to order (Structural transition)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
The addition of 2 mM ZnSO4 induced a weak dynamic HDX-MS behavior, indicative of structure formation, throughout the entire polypeptide chain of both proteins (Panels C, Fig. 11). Notably, the addition of both 10% TFE and 2 mM ZnSO4 in a combined fashion resulted in an more pronounced change in magnitude of HDX dynamics (Panels D, Fig. 11).
Protein: DP01787 (UniProt A0A1Z3GD05)
Region: residues 1	to 138
Annotation: zinc ion binding (Molecular function)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
The addition of 2 mM ZnSO4 induced a weak dynamic HDX-MS behavior, indicative of structure formation, throughout the entire polypeptide chain of both proteins (Panels C, Fig. 11). Notably, the addition of both 10% TFE and 2 mM ZnSO4 in a combined fashion resulted in an more pronounced change in magnitude of HDX dynamics (Panels D, Fig. 11).