LiteFold/DisProt huggingface dataset:
Protein: DP00207 (UniProt P21513)
Region: residues 833	to 850
Annotation: protein binding (Molecular function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
Series B with a molecular mass of 93,158(±14) Da, corresponding to an enolase dimer with one peptide C bound, was the predominant species observed (theoretical mass of 93,089 Da). In addition we observe a charge state series C with a mass of 95,195(±12) Da, corresponding to one enolase dimer bound to two peptide C molecules (theoretical mass 95,131 Da). MS/MS analysis of the B+19 complex ion confirmed the composition of the species to be that of an enolase dimer bound to peptide C (Figure 8B).
Protein: DP00207 (UniProt P21513)
Region: residues 1021	to 1061
Annotation: protein binding (Molecular function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
Addition of Peptide D to PNPase in stoichiometric excess gave evidence for a charge series corresponding to a species with a molecular mass of 497,442(±15) Da, (Figure 9, red trace, series D). This is consistent with a dimer of PNPase trimers with six peptide D molecules bound, which equates to one peptide D per PNPase monomer (theoretical mass of 496,950 Da). Also, we observed a trimer of PNPase with three and four peptide D molecules bound (Figure 9, series B and C respectively).
Protein: DP00214 (UniProt P10451)
Region: residues 1	to 314
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The narrow spread of the peptide backbone amide NH peaks (7.8–8.6 ppm) and the side chain NH peaks (6.6–7.4 ppm) are indicative of a lack of ordered structures over the NMR time scale.
Furthermore, the average proton T2 relaxation times for both of these molecules were on the
order of 60 ms. This is fully consistent with the two proteins being extended and flexible in solution.
Therefore, both BSP and OPN, when purified and isolated in solution, are flexible along their entire length and have no significant regions that persist in a single structural environment for more than a few milliseconds.
Protein: DP00214 (UniProt P10451)
Region: residues 1	to 314
Annotation: protein binding (Molecular function)
Evidence: competitive binding evidence used in manual assertion
Supporting statements:
Furthermore, our current supply of antisera against OPN also appears to be unable to bind to the OPN when complexed with Factor H (data not shown). This all suggests that essentially
the full length of this SIBLING is tightly bound to either Factor H or to HA and that specific portions of OPN can bind to either of two independent cell surface receptors or to additional regions of Factor H.
Protein: DP00214 (UniProt P10451)
Region: residues 1	to 314
Annotation: protein binding (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
In addition to binding to integrins, OPN has been reported to be able to bind to CD44.
Protein: DP00214 (UniProt P10451)
Region: residues 1	to 314
Annotation: protein binding (Molecular function)
Evidence: competitive binding evidence used in manual assertion
Supporting statements:
The binding of biotin-labeled Opn to A31.C1 CD44 transfectants was dependent on dose, was specific, and was inhibited by an antibody to CD44 but not by an irrelevant antibody.
Protein: DP00214 (UniProt P10451)
Region: residues 1	to 314
Annotation: protein binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
We confirmed this by analyzing proteins that bound to recombinant glutathione-S- transferase (GST)-Opn (which lacks glycosyl moieties, including HA)
immobilized on Sepharose 4B. Coomassie-stained electrophoresis gels of the desalted eluate showed comigration of the most prominent band with CD44 purified from the same cell line.
Depletion of CD44 from cell lysates with antibody removed this band from the material eluted from the GST-Opn columns.
Protein: DP00214 (UniProt P10451)
Region: residues 1	to 314
Annotation: protein binding (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
The addition of tween  BSP  or  OPN  and  Factor  H  can  be  readily  studied  by intrinsic steady state fluorescence. Titration of purified human complement Factor H with rBSPor rOPN was followed by excitation at 295 nm and monitoring emission  between  300  and  450  nm.  The  emission  profile  of Factor H alone yields a peak at 347 nm. The addition of rBSP or rOPN in nanomolar increments causes a relative fluorescent  intensity  quenching.  Conversion  of  the  fluorescent intensity  titration  into  a  binding  curve  by  determining  the fraction of binding sites occupied as the fractional change influorescence quenching at 347 nm yields a saturable binding curves. By steady state fluorescence, the binding of BSP  and  OPN  by  Factor  H  are  saturable  and  possess  a  1:1 stoichiometry, have binding constants in the nanomolar range, given the serum concentration of Factor H (0.5 mg/ml), virtually all BSP and OPN in serum will be complexed with Factor H.
Protein: DP00214 (UniProt P10451)
Region: residues 1	to 314
Annotation: protein binding (Molecular function)
Evidence: competitive binding evidence used in manual assertion
Supporting statements:
Pretreatment of MEL cells with hyaluronan, anatural  ligand  for  CD44,  as  well  as  with  an anti-CD44 antibody also reduced the protective effect of added rOPN.
Protein: DP00214 (UniProt P10451)
Region: residues 158	to 162
Annotation: protein binding (Molecular function)
Evidence: competitive binding evidence used in manual assertion
Supporting statements:
For OPN, pretreatment with GRGDS peptide or the aVb3 antibody reduced cell survival, although the magnitude of reduction was not as great as that seen for BSP.
Protein: DP00214 (UniProt P10451)
Region: residues 1	to 314
Annotation: calcium ion binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Human milk OPN binds Ca2+with high affinity, and with similar strong exothermicsignal which reaches full saturation at ~90μM.
In separate experiments, a strong endothermic signal for human OPN interaction with Mg2+ was observed.
Protein: DP00214 (UniProt P10451)
Region: residues 17	to 314
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
As expected for an intrinsically disordered protein the proton chemical shift dispersion of the 1H–15N HSQC spectrum shows a narrow profile with chemical shift values close to random coil values.
Cross-references: BMRB:19999
Protein: DP00214 (UniProt P10451)
Region: residues 17	to 314
Annotation: phosphorylation display site (Disorder function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
The total sequence coverage of the MS/MS experiments is 68.5%, and 28 phosphorylation events are identified.
There were so many phosphosites identified that basically the whole protein is hyperphosphorylated.
Protein: DP00214 (UniProt P10451)
Region: residues 17	to 314
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Twentyeight phosphorylation events are identified on the basis of the 1HN downfield shifts.
There were so many phosphosites identified that basically the whole protein is hyperphosphorylated.
Protein: DP00214 (UniProt P10451)
Region: residues 17	to 314
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
1H–15N HSQC NMR spectra of OPN before (black) and after (red) phosphorylation by Fam20C.
Very narrow chemical shift dispersion is evident from the figure for both the unphosphorylated and phosphorylated osteopontin.
Cross-references: BMRB:50447
Protein: DP00214 (UniProt P10451)
Region: residues 85	to 116
Annotation: calcium ion binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
OPN shows Ca2+-binding mainly in the aspartate-rich regime (poly-D regime; 85–116), accompanied by less pronounced perturbations in the other negatively charged regions 70–79, 130–136, 178–188 and 245–260, revealing binding affinities in the lower millimolar range (4–16(3) mM).
Protein: DP00214 (UniProt P10451)
Region: residues 85	to 116
Annotation: small molecule binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Similar to the binding to Ca2+ cations, both OPN and OPNp show CSPs mainly in the negatively charged regions upon the interaction with HAP surfaces. Again, OPN binds to HAP predominantly in the poly-D regime (residues 85 ff.).
CSP stands for chemical shift perturbation, HAP stands for hydroxyapatite. The poly-D regime was already stated to be between residues 85 and 116 when the bindig of Ca2+ ions was investigated.
Protein: DP00214 (UniProt P10451)
Region: residues 1	to 314
Annotation: molecular adaptor activity (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
It has been proposed that osteoclasts use OPN to bridge between the integrins on the cell surface and the mineral phase during resorption of bone matrix. We have shown that Factor H also binds to OPN already complexed to either avb3 integrin or CD44 and this complex can stop the alternate complement lysis pathway.
Protein: DP00217 (UniProt P05221)
Region: residues 153	to 171
Annotation: importin-alpha family protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The bipartite NLS (154VKRPAATKKAGQAKKKKLD172) of Xenopus nucleoplasmin binds along the surface groove of Kapα50 with the upstream basic cluster (residues 155–156) at the small site and the downstream basic cluster (residues 167–170) at the large site.
Cross-references: PDB:1EE5
Protein: DP00217 (UniProt P05221)
Region: residues 120	to 200
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The spectrum of the full-length protein (dotted line) displays a minimun at 198 nm, that has been related with nonregular conformations. In contrast, that of the truncated protein is located at 213 nm, being the ellipticity value at 198 nm positive (solid line).
Protein: DP00217 (UniProt P05221)
Region: residues 1	to 10
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
A truncated N-terminal domain of Np was produced by proteolysis
N-terminal sequencing and mass spectrometry indicated that native Np-core extended from Lys10-Tyr124.
Protein: DP00217 (UniProt P05221)
Region: residues 125	to 200
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
A truncated N-terminal domain of Np was produced by proteolysis
N-terminal sequencing and mass spectrometry indicated that native Np-core extended from Lys10-Tyr124.
Protein: DP00219 (UniProt O60927)
Region: residues 1	to 126
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
The recombinant protein behaved anomalously on SDS−PAGE with a relative molecular mass of 23 kDa, much higher than its estimated molecular mass of 14 kDa (Figure 4). This may be due to the high content of hydrophilic amino acids in the polypeptide, which could result in a lower binding of SDS and a lower motility on SDS−PAGE.
Protein: DP00219 (UniProt O60927)
Region: residues 1	to 126
Annotation: protein phosphatase inhibitor activity (Molecular function)
Evidence: radioisotope quantification assay evidence used in manual assertion
Supporting statements:
Both forms of PP1 are potently inhibited by inhibitor-3 in the nanomolar range. However the recombinant Co(II)-PP1 is inhibited ca. 20-fold more strongly than the Mn2+-dependent PP1 (Figure 6). The IC50s for Co(II)-PP1 and Mn2+ PP1 were found to be 0.3 and 6 nM, respectively (mean of two determinations with different preparations of I-3 and PP1).
Protein: DP00219 (UniProt O60927)
Region: residues 14	to 126
Annotation: phosphatase binding (Molecular function)
Evidence: yeast 2-hybrid evidence used in manual assertion
Supporting statements:
 A human brain cDNA expression library expressing the proteins fused with the GAL4 activation domain was used for the screening of PP1-binding proteins by the yeast two-hybrid system (Experimental Procedures).
Clone 45 was completely sequenced and found to consist of 768 base pairs that were identical to the cDNA for HCG V, except for a 138 bp deletion at the 5‘ end, such that it starts at amino acid 14 of the encoded sequence, and a 614 bp deletion in the 3‘-noncoding region (662−1275) (Figure 1).
Protein: DP00219 (UniProt O60927)
Region: residues 1	to 126
Annotation: disorder (Structural state)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
The protein also behaved anomalously on HPLC gel filtration, with an apparent molecular weight of 55 000 (Figure 5).
Protein: DP00219 (UniProt O60927)
Region: residues 1	to 126
Annotation: phosphatase binding (Molecular function)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
To confirm that the clone 45/HCG V protein binds to PP1, the crude bacterial lysate expressing the GST−HCG V fusion protein was chromatographed on a PP1−Sepharose column. The results are shown in Figure 3. The 43 kDa protein was bound to PP1−Sepharose while the GST protein (29 kDa) did not bind to the column.
Protein: DP00220 (UniProt P17810)
Region: residues 284	to 346
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
These findings demonstrate that the C-terminus is relatively accessible to limited proteolysis and are consistent with the extensive regions of disorder predicted by structure modeling.
Protein: DP00220 (UniProt P17810)
Region: residues 284	to 346
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
We measured intrinsic tryptophan fluorescence of CTER under a variety of solution conditions and found this to be so. Fig. 6A (solid line) shows an emission spectrum of CTER, using an excitation wavelength of 295 nm. The characteristic broad peak at 348 nm suggested to us that the two tryptophans contained within this domain were rather solvent exposed, as had been predicted by the SEC and AUC results.
Protein: DP00220 (UniProt P17810)
Region: residues 284	to 346
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
The rigorous determination that CTER is monomeric (by AUC) combined with a substantially retarded hydrodynamic elution position (observed by SEC) suggests that CTER possesses an extended conformation and may have a weak affinity for the SEC matrix.
Overall these results suggest that CTER structure, like that in other disordered domains is not affected by macromolecular crowding effects [22], but is appreciably increased in the presence of a hydrophobic environment.
Protein: DP00220 (UniProt P17810)
Region: residues 284	to 346
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
As expected from SEC, AUC, intrinsic tryptophan fluorescence and previous CD measurements, the spectra also indicate strong contributions from random coil elements (estimated here at ~36%).
Overall these results suggest that CTER structure, like that in other disordered domains is not affected by macromolecular crowding effects [22], but is appreciably increased in the presence of a hydrophobic environment.
Protein: DP00220 (UniProt P17810)
Region: residues 284	to 346
Annotation: disorder (Structural state)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
The rigorous determination that CTER is monomeric (by AUC) combined with a substantially retarded hydrodynamic elution position (observed by SEC) suggests that CTER possesses an extended conformation and may have a weak affinity for the SEC matrix.
Overall these results suggest that CTER structure, like that in other disordered domains is not affected by macromolecular crowding effects [22], but is appreciably increased in the presence of a hydrophobic environment.
Protein: DP00222 (UniProt P32499)
Region: residues 1	to 720
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Analyses of the Nup2p structure by far-UV circular dichroism (CD) spectroscopy, Fourier transform infrared (FTIR) spectroscopy, protease sensitivity, gel filtration, and sedimentation velocity experiments indicate that Nup2p is a "natively unfolded protein," belonging to a class of proteins that exhibit little secondary structure, high flexibility, and low compactness.
Protein: DP00222 (UniProt P32499)
Region: residues 1	to 720
Annotation: disorder (Structural state)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
Analyses of the Nup2p structure by far-UV circular dichroism (CD) spectroscopy, Fourier transform infrared (FTIR) spectroscopy, protease sensitivity, gel filtration, and sedimentation velocity experiments indicate that Nup2p is a "natively unfolded protein," belonging to a class of proteins that exhibit little secondary structure, high flexibility, and low compactness.
Protein: DP00222 (UniProt P32499)
Region: residues 1	to 720
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Analyses of the Nup2p structure by far-UV circular dichroism (CD) spectroscopy, Fourier transform infrared (FTIR) spectroscopy, protease sensitivity, gel filtration, and sedimentation velocity experiments indicate that Nup2p is a "natively unfolded protein," belonging to a class of proteins that exhibit little secondary structure, high flexibility, and low compactness.
Protein: DP00222 (UniProt P32499)
Region: residues 1	to 720
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Analyses of the Nup2p structure by far-UV circular dichroism (CD) spectroscopy, Fourier transform infrared (FTIR) spectroscopy, protease sensitivity, gel filtration, and sedimentation velocity experiments indicate that Nup2p is a "natively unfolded protein," belonging to a class of proteins that exhibit little secondary structure, high flexibility, and low compactness.
Protein: DP00222 (UniProt P32499)
Region: residues 1	to 720
Annotation: protein binding (Molecular function)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
A second chromatography step was sufficient  to  obtain  purified  Nup2p  in  complex  with  its  binding partner  Kap60p  (data  not  shown).
Protein: DP00222 (UniProt P32499)
Region: residues 1	to 720
Annotation: disorder (Structural state)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
Analyses of the Nup2p structure by far-UV circular dichroism (CD) spectroscopy, Fourier transform infrared (FTIR) spectroscopy, protease sensitivity, gel filtration, and sedimentation velocity experiments indicate that Nup2p is a "natively unfolded protein," belonging to a class of proteins that exhibit little secondary structure, high flexibility, and low compactness.
Protein: DP00222 (UniProt P32499)
Region: residues 185	to 527
Annotation: entropic chain (Disorder function)
Evidence: deletion mutation phenotypic evidence used in manual assertion
Supporting statements:
Our finding that FxFG domains of nuclear basket nups (Nup1, Nup2, and Nup60) are functional elements of the NPC permeability barrier (Figure 7B) supports the virtual-gate model because these FG domains behave as noncohesive filaments (Figures 2 and 5A).
Contrary to a central prediction made by the selective-phase model (i.e., that all FG domains of nups interact by virtue of their FG motifs), we demonstrated here in vivo and in vitro that some FG domains of nups are not cohesive, including the FxFG domains of Nsp1, Nup1, Nup2, and Nup60 and the SAFGxPSFG domain of Nup159 (Figure 2, Figure 3, Figure 4, Figure 5 and S4). This finding supports the notion that some FG domains of nups function exclusively as repulsive bristles due to Brownian motion, consistent with the virtual-gate model (Rout et al., 2000).
We also demonstrate that the FG domains of nups are structural components of the NPC permeability barrier in vivo.
The virtual-gate model proposes that FG domains are noncohesive, entropic bristles that repel the entry of non-karyophilic proteins into the NPC through Brownian motion.
The integrity of the NPC permeability barrier was tested in ΔFG yeast lacking the GLFG domain of Nup116 or Nup100, the SAFGxPSFG domain of Nup42, or the FxFG domain of Nsp1, Nup60, Nup1, or Nup2.
Protein: DP00222 (UniProt P32499)
Region: residues 562	to 720
Annotation: protein binding (Molecular function)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
We find that Nup60p binds to Nup2p and serves as a docking site for Kap95p-Kap60p heterodimers and Kap123p.
First, Nup60p binds to Nup2p in the absence of additional proteins (KD ∼396 nM) (Fig. 3, A and D) and in crude yeast extracts in the presence of thousands of competitor proteins (Figs. 1 B and 3 C).
Additional evidence suggests that the association between Nup2p and Nup60p at the NPC is dynamic. First, Nup2p fails to copurify with other Nups during the isolation of NPCs (Rout et al., 2000), implying that Nup2p dissociates readily from the NPC. Second, Nup2p–GFP accumulates in the nucleoplasm and cytoplasm of yeast lacking Nup60p (Fig. 2 A, middle), raising the possibility that Nup2p shuttles in and out of the nucleus and uses Nup60p as a rest-stop. Third, Nup2p can be tethered (indirectly) to a subset of FG Nups (Nup42p, Nup49p, Nup57p, Nup100p, and Nup116p) via the Kap95p–Kap60p heterodimer (Allen et al., 2001 and data not shown), suggesting that Nup2p moves across the NPC in a Kap95p–Kap60p-dependent manner.
Protein: DP00223 (UniProt P14635)
Region: residues 1	to 78
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The lack of dispersion seen for the amide chemical shifts in the WATERGATE spectra indicates a very similar environment for all amide hydrogen atoms in the proteins and therefore a random coil state for the polypeptide. Further indication of the unfolded state of both N-terminal fragments comes from examination of the methyl proton region of the spectra. As shown in Fig. 4B, the methyl protons display little dispersion. Furthermore, the methyl proton peaks are clustered in the region of ∼1.0–0.8 ppm, whereas peaks from methyl protons in a hydrophobic environment typically are shifted upfield to ∼0.5–0.0 ppm. Thus, 1H-NMR studies strongly indicate a largely unfolded conformation for both N-terminal fragments.
Of the observable NOEs, almost all have negative values, indicating fast tumbling and local flexibility. Thus, 1H,15N NOE analysis provides little indication of stable structure.