LiteFold/DisProt huggingface dataset:
Protein: DP01947 (UniProt O65934)
Region: residues 150	to 154
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR spectral perturbations resulting from the single-site phosphorylation of the T152A and T210A variants provided evi- dence for differential interactions of the two FHA domains and the two linker phospho-acceptors (Figures S10B and S10C). In the case of the Rv17471-213 constructs, phosphorylation at pT152 yielded only small chemical shift changes of diagnostic amides relative to the unmodified protein, whereas phosphorylation at pT210 caused changes resembling those resulting from double phosphorylation of the wild-type protein.
Phosphorylation site corresponding to T152.
Protein: DP01947 (UniProt O65934)
Region: residues 208	to 212
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR spectral perturbations resulting from the single-site phosphorylation of the T152A and T210A variants provided evi- dence for differential interactions of the two FHA domains and the two linker phospho-acceptors (Figures S10B and S10C). In the case of the Rv17471-213 constructs, phosphorylation at pT152 yielded only small chemical shift changes of diagnostic amides relative to the unmodified protein, whereas phosphorylation at pT210 caused changes resembling those resulting from double phosphorylation of the wild-type protein.
Phosphorylation site corresponding to T210.
Protein: DP01948 (UniProt Q9HZJ8)
Region: residues 1	to 42
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal residues of SulA (1–42), which were not ordered in the previous structure, are not ordered in the complex structure either.
Cross-references: PDB:1OFT
Protein: DP01950 (UniProt P21333)
Region: residues 1	to 36
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal extension of 36 residues (chain A) and 38 (chain
B) are not observed and are assumed to be disordered.
Cross-references: PDB:3HOP
Protein: DP01951 (UniProt P04083)
Region: residues 116	to 185
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Deconvolution of the far-UV CD spectrum of the isolated domain in aqueous solution, using the Yang reference, gave a secondary structure content of, at most, 25% alpha-helix, 75% coil, and no beta-structure. This helix content is quite far from the native content.
This fragment was studied by circular dichroism and by NMR. Both techniques clearly showed that the domain was poorly folded in pure aqueous solution although the residual helix structure is far from negligible.
Protein: DP01951 (UniProt P04083)
Region: residues 116	to 185
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
A first set of NMR experiments was performed on the domain solubilized in pure aqueous solution, in which the very weak spectral dispersion of the amide proton resonances (1.1 ppm) showed that the peptide is poorly folded.
This fragment was studied by circular dichroism and by NMR. Both techniques clearly showed that the domain was poorly folded in pure aqueous solution although the residual helix structure is far from negligible.
Protein: DP01951 (UniProt P04083)
Region: residues 2	to 12
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The annexin I N-terminal peptide is clearly visible in the complex, despite its high temperature factor.
Cross-references: PDB:1QLS
Protein: DP01951 (UniProt P04083)
Region: residues 2	to 12
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The annexin I N-terminal peptide is clearly visible in the complex, despite its high temperature factor.
The peptide forms an amphiphilic α helix, as predicted [20].
Cross-references: PDB:1QLS
Protein: DP01951 (UniProt P04083)
Region: residues 2	to 12
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The annexin I N-terminal peptide is clearly visible in the complex, despite its high temperature factor (Figure 2). Although the stoichiometry is one peptide bound to one S100C monomer, the binding zone on S100C is formed by regions of both molecules of the dimer: the C-terminal helix and the L2 linker region of one molecule and the N-terminal helix of the other molecule.
Cross-references: PDB:1QLS
Protein: DP01951 (UniProt P04083)
Region: residues 116	to 185
Annotation: lipid binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Nevertheless, the 15N chemical shift variations, Δδ15N, are good indicators of the course of the structural change, within the different segments of the domain, associated with DPC titration.
Protein: DP01951 (UniProt P04083)
Region: residues 116	to 185
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
As expected, addition of micelles led to a considerable increase in the helix content (Figure 10).
Protein: DP01951 (UniProt P04083)
Region: residues 116	to 185
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Nevertheless, the 15N chemical shift variations, Δδ15N, are good indicators of the course of the structural change, within the different segments of the domain, associated with DPC titration.
At high DPC concentration (150 mM), the NH spectral range was considerably larger than that observed in pure aqueous solution (1.7 ppm against 1.1 ppm for the pure aqueous solution).
Protein: DP01951 (UniProt P04083)
Region: residues 2	to 26
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In aqueous buffer, the CD spectrum of AnxIN26 showed a strong negative band at 200 nm and a broad band around 222 nm, indicating a predominantly random-coil conformation with a slight helical propensity [33,34].
Protein: DP01951 (UniProt P04083)
Region: residues 2	to 26
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of AnxIN26 in 10 mM SDS, which is above the critical micellar concentration of SDS [38], also showed a typical α-helix pattern.
Protein: DP01951 (UniProt P04083)
Region: residues 2	to 26
Annotation: lipid binding (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
The CD spectrum of AnxIN26 in 10 mM SDS, which is above the critical micellar concentration of SDS [38], also showed a typical α-helix pattern.
Thus, it can be suggested that the conformational transition of AnxIN26, from random-coil in aqueous buffer to α-helix in membrane-mimetic environments, reflects its binding to the membrane.
Protein: DP01951 (UniProt P04083)
Region: residues 4	to 19
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
As shown in Fig. 2, the presence of a typical α-helix from V4 to Q19 is supported, both in TFE/water and in SDS micelles, by the frequent observations of dNN(i,i+1), dNN(i,i+2), dαL(i,i+3), dαN(i,i+3) and dαN(i,i+4) NOE connectivities, and slowly exchanging amide protons.
Protein: DP01951 (UniProt P04083)
Region: residues 2	to 26
Annotation: calcium ion binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The C-terminal region of the AnxIN26 helix contains frequent glutamate residues (-E15-NE-E-Q-E20-; Fig. 4A). Thus, we suggest that Ca2-ions bind to the negatively charged glutamate-rich region of AnxIN26 and function as salt-bridges between the peptide and SDS micelle molecules. The calcium-bridge in this region seems to stabilize the helical conformation of AnxIN26 as a membrane-bound form, resulting in the intensification of CD signals as shown in Fig. 5.
Protein: DP01951 (UniProt P04083)
Region: residues 116	to 185
Annotation: localization (Biological process)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Calcium ions participate in the functional binding of annexin to membranes.
Nevertheless, the 15N chemical shift variations, Δδ15N, are good indicators of the course of the structural change, within the different segments of the domain, associated with DPC titration.
At high DPC concentration (150 mM), the NH spectral range was considerably larger than that observed in pure aqueous solution (1.7 ppm against 1.1 ppm for the pure aqueous solution).
Protein: DP01958 (UniProt Q63450)
Region: residues 1	to 11
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
11 residues at the N-terminus and 4 at the C-terminus that are also disordered
Cross-references: PDB:1A06
Protein: DP01958 (UniProt Q63450)
Region: residues 54	to 63
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
There are two regions of high conformational disorder within the catalytic core of CaMKI, with no observable electron density for the corresponding residues. The loop between β8 and αEF in the C-terminal domain...
Cross-references: PDB:1A06
Protein: DP01958 (UniProt Q63450)
Region: residues 164	to 181
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The disorder of another loop, between β3 and αC in the ATP-binding domain, may also be coupled to the activation state of the enzyme...
Cross-references: PDB:1A06
Protein: DP01961 (UniProt P38516)
Region: residues 43	to 95
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Crystals of TmaL4 contain full-length protein, as seen from SDS-PAGE analysis of dissolved experiments ... A void seen in the crystal packing could accomodate the unobserved part of the molecule in a folded conformation. All these observations suggest that a large portion of TmaL4 is internally disordered.
Cross-references: PDB:1DMG
Protein: DP01961 (UniProt P38516)
Region: residues 43	to 95
Annotation: DNA binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The putative RNA interaction surface can be subdivided into two spatially separated regions. The first is made up mainly of the N-terminal part of helix alpha3. It is preceded by the 55 residue disordered loop, which is the most conserved portion in prokaryotic L4 proteins and displays many basic residues. The loop may therefore be the central element of this RNA-binding patch.
Protein: DP01963 (UniProt P19619)
Region: residues 1	to 40
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although we observe the large conformational change in the core domain that was anticipated upon calcium binding, we were not be able to model residues 1–40 in the full-length annexin A1 structure. The mass spectrum shows without a doubt that the crystals do contain the full-length protein, however the N-terminal domain is disordered in the X-ray structure.
Cross-references: PDB:1MCX
Protein: DP01963 (UniProt P19619)
Region: residues 1	to 41
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal domain of annexin 1 contains 41 residues.
Cross-references: PDB:1HM6
Protein: DP01963 (UniProt P19619)
Region: residues 1	to 41
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Annexin 1 is active in membrane aggregation and its refined 1.8 Å structure shows an alpha-helical N-terminal domain connected to the core domain by a flexible linker.
Protein: DP01965 (UniProt P0CE48)
Region: residues 43	to 63
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
X-ray diffraction data extending to a maximum resolution of 2.5 Å were collected and the structure of the Qβ core replicase was determined by molecular replacement ... disordered are the ... EF-Tu residues 1–8 and 42–63
Cross-references: PDB:3MMP
Protein: DP01965 (UniProt P0CE48)
Region: residues 43	to 63
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure is complete except for residues constituting ... the switch I region 42–63 of EF-Tu
Cross-references: PDB:4R71
Protein: DP01965 (UniProt P0CE48)
Region: residues 44	to 64
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In EF-Tu, we have not modelled residues 42-63, including the effector loop (some scattered densities are visible)
Cross-references: PDB:1EFU
Protein: DP01967 (UniProt P0CF51)
Region: residues 102	to 112
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
...the mobile CDR3γ loop in the unligated state became ordered upon CD1d–α-GalCer engagement.
Cross-references: PDB:4LHU
Protein: DP01967 (UniProt P0CF51)
Region: residues 102	to 112
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
...the mobile CDR3γ loop in the unligated state became ordered upon CD1d–α-GalCer engagement.
Protein: DP01967 (UniProt P0CF51)
Region: residues 102	to 112
Annotation: small molecule binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Within the 9C2 γδ TCR ternary complex, Arg103γ and Tyr111γ contacted directly the galactose moiety...
Protein: DP01967 (UniProt P0CF51)
Region: residues 102	to 112
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Tyr111γ and the main chain of the CDR3γ loop also formed van der Waals contacts with Trp153, a CD1d residue...
Protein: DP01968 (UniProt A4C1A5)
Region: residues 1	to 86
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far-UV CD spectra of CspBNPi show a minimum close to 200 nm and weak ellipticity around 222 nm (Fig. 3B), which are also typical of a random coil conformation.
Protein: DP01969 (UniProt P27058)
Region: residues 1	to 200
Annotation: disorder (Structural state)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
By means of light scattering studies, the hydrodynamic properties of Prosys were elucidated, showing that, in solution, the prohormone occurs as a monomeric protein, with a molecular mass of 23.7 ± 0.1 kDa [Fig. 1(C)], and an apparent hydrodynamic radius of 5.61 ± 0.01 nm of the monodisperse peak, which is indicative of a protein with low compactness.
Protein: DP01969 (UniProt P27058)
Region: residues 1	to 200
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
As assessed by SDS-PAGE, Prosys showed an aberrant migration with an apparent molecular mass of 40 kDa, exceeding the expected molecular mass of 26 kDa (inclusive of the His-tag)...
Protein: DP01969 (UniProt P27058)
Region: residues 1	to 200
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Elution from the SEC column occurred as a sharp peak with an apparent molecular mass (MM app) of about 71 kDa [Fig. 1(B)], as estimated by the calibration curve [inset Fig. 1(B)]. This value was well above the expected value (MM theo) and was not compatible with a monomeric globular structure.
Protein: DP01969 (UniProt P27058)
Region: residues 1	to 200
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Prosys, incubated with different E:S ratio and at different time intervals, was readily digested already after 1 h of incubation (Fig. S1).
Protein: DP01969 (UniProt P27058)
Region: residues 1	to 200
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Prosys spectrum at neutral pH showed low ellipticity at 190 nm and a large negative ellipticity at 198 nm, typically observed for proteins in a largely disordered conformation.
Protein: DP01969 (UniProt P27058)
Region: residues 1	to 200
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1D [1H] NMR spectrum together with the 2D [1H,1H] TOCSY and 2D [1H,1H] NOESY experiments of Prosys presented the canonical features of the unstructured proteins, being dominated by a poor spectral dispersion, typical of IDPs.
Protein: DP01969 (UniProt P27058)
Region: residues 1	to 178
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Indeed, CD spectra revealed a disorder content (Figure 2), a reversible temperature-induced behavior, and a capability to increase secondary structure content in the presence of TFE co-solvent (Figure S4a,b).
ProSys(1-178) recombinant protein is intrinsically disordered. The Far-UV CD spectrum was recorded from 260 to 190 nm at 20 °C in 10 mM phosphate buffer pH 7.4 at a protein concentration of 6.8 µM.
Protein: DP01970 (UniProt M1GUG5)
Region: residues 1	to 86
Annotation: disorder (Structural state)
Evidence: synchrotron radiation circular dichroism evidence used in manual assertion
Supporting statements:
The SRCD measurements confirm experimentally that MEG-14 should be classified as an IDP.
Protein: DP01970 (UniProt M1GUG5)
Region: residues 1	to 86
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
For the protein MEG-14, as a result of its quite flexible and almost fully disordered state (Lopes et al. 2013), no spectral bands were observed at ~225-nm region (lacking any ordered content), but a negative peak of ~198 nm with similar shape was observed (Suppl. Figure 2a).
Protein: DP01970 (UniProt M1GUG5)
Region: residues 1	to 86
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
The molecular mass of the recombinant MEG-14 was determined to be 10,613 ± 7 Da by MS (...) whereas SDS-PAGE analyses gave an apparent molecular mass of 13.7 kDa (Fig. 1 b). As observed for other IDPs (34, 35), the discrepancies between the sequence and hydrodynamic methods are a consequence of the extended (not globular) conformation of MEG-14 in solution and its high content of hydrophilic amino acids, which reduce its mobility on polyacrylamide gels because it binds less SDS.
Protein: DP01970 (UniProt M1GUG5)
Region: residues 1	to 86
Annotation: disorder (Structural state)
Evidence: synchrotron radiation circular dichroism evidence used in manual assertion
Supporting statements:
Moreover, a small band at ~184 nm could be observed in the SRCD spectra of IDPs, appearing as a shoulder for STI and a small positive peak for MEG-14 (Suppl. Figure 2c). This spectral band can also be attributed to the unordered content of the protein (Wallace and Janes 2009; Lopes et al. 2013).
Protein: DP01970 (UniProt M1GUG5)
Region: residues 1	to 86
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The SRCD spectrum of sMEG-14 in aqueous solution is typical of a disordered protein with high flexibility, aspreviously described
Protein: DP01970 (UniProt M1GUG5)
Region: residues 1	to 86
Annotation: protein binding (Molecular function)
Evidence: yeast 2-hybrid evidence used in manual assertion
Supporting statements:
To that end, a yeast two hybrid screening was performed using as bait the soluble portion of MEG-14
isoform 1 (previously defined in [6]) and human leukocyte cDNA library as prey.d
Using these criteria, only two clones remained as positives, one containing a
cDNA encoding S100A9 and another encoding the C2 Freud-1 domain from the
CC2D1A protein.
Protein: DP01970 (UniProt M1GUG5)
Region: residues 1	to 86
Annotation: protein binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
It was only possible to recover sMEG-14 in the fraction bound to the resin, after the washing steps, when this protein was incubated with S100A9-GST immobilized in a glutathionesepharose resin in the presence of calcium.
Protein: DP01970 (UniProt M1GUG5)
Region: residues 1	to 86
Annotation: protein binding (Molecular function)
Evidence: surface plasmon resonance evidence used in manual assertion
Supporting statements:
Figure 3A shows a sensorgram indicating that both proteins interact immediately after S100A9 solution is applied onto the sensor chip surface in which sMEG-14 was covalently immobilized and that the intensity of the signal obtained is dependent on the concentration of S100A9 in the solution.
Experimental binding curves were fit in a plain 1:1 Langmuir binding model
and the dissociation constant (Kd) calculated under this model for the MEG-14/S100A9 complex was 1.89 µM.
The interaction of sMEG14 with the heterodimer
S100A9/S100A8 was also investigated by SPR, and although it was possible to observe interaction (Figure 3B), the affinity (Kd = 44.1 µM) has shown to be much lower than the observed for S100A9 alone.
Protein: DP01970 (UniProt M1GUG5)
Region: residues 1	to 86
Annotation: protein binding (Molecular function)
Evidence: microscale thermophoresis evidence used in manual assertion
Supporting statements:
A profile suggestive of interaction between sMEG-14 and S100A9 was also obtained by performing an experiment of microscale thermophoresis (Supplementary Figure 3)