LiteFold/DisProt huggingface dataset:
Protein: DP00118 (UniProt P05059)
Region: residues 1	to 449
Annotation: calcium ion binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The nature of the Ca2+-induced conformational changes of CGA was studied by circular dichroism in the presence and absence of Ca2+. As shown in Fig. 2, the CD spectrum of CGA at pH 5.5 was significantly changed in the presence of 15 mM Ca2+.
Protein: DP00118 (UniProt P05059)
Region: residues 1	to 449
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The nature of the Ca2+-induced conformational changes of CGA was studied by circular dichroism in the presence and absence of Ca2+. As shown in Fig. 2, the CD spectrum of CGA at pH 5.5 was significantly changed in the presence of 15 mM Ca2+.
Protein: DP00118 (UniProt P05059)
Region: residues 1	to 449
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
As shown in Fig. 1A, chromogranin A was proteolyzed into small fragments by trypsin at pH 5.5.
Protein: DP00118 (UniProt P05059)
Region: residues 1	to 449
Annotation: disorder to order (Structural transition)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
A with a  size of -60 kDa remained relatively intact at pH 7.5 whereas the same fragment was proteolyzed continuously by trypsin at pH 5.5, suggesting that the N-terminal core structure is more compact and better protected at pH 7.5.
Protein: DP00119 (UniProt P10163)
Region: residues 17	to 310
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Since the PRG CD spectrum differed from the poly-L-proline II helical structure and did not respond to CaCl1, the implication was that the proline present in PRG exists in a disordered state (i.e. a mixture of cis and/ or trans isomers).
Protein: DP00119 (UniProt P10163)
Region: residues 17	to 310
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
These data imply that all of the lysine residues in Dns-PRG are exposed to solvent in the native form.
Protein: DP00120 (UniProt P12957)
Region: residues 636	to 771
Annotation: calmodulin binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
This spectrum was calculated assuming that both proteins are completely involved into the complex formation and a difference between the measured CaD136‐CaM and CaM spectra are due to the partial folding of CaD136 rather than a partial unfolding of CaM; i.e., as [(CaD136‐CaM − 0.5 ÷ CaM)/0.5].
Figure 7 shows that the formation of CaD136–CaM complex led to a partial folding of the natively unfolded CaD136. As it was already pointed out, in the absence of CaM CaD136 possesses a far‐UV CD spectrum typical of an essentially unfolded polypeptide chain; i.e., a spectrum with an intense minimum in the vicinity of 200 nm, and the absence of characteristic bands in the 210–230 nm region. However, as the CaD136–CaM complex was formed, the minimum at 200 nm became less intense and shifted toward the longer wavelength, whereas the negative intensity of the spectrum around 222 nm increased, reflecting the formation of ordered secondary structure. Importantly, the extent of this folding was relatively low and CaD136 remained substantially unstructured even after the effective binding to CaM. Potentially, there is an alternative scenario of CaD136 binding to CaM, where CaD136 gains some sort of rigid but nonregular structure as a result of complex formation.
Protein: DP00120 (UniProt P12957)
Region: residues 636	to 771
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
To obtain information about the hydrodynamic dimensions of CaD136, the gel‐filtration behavior of this protein at neutral pH in the absence or in the presence of 6 M GdmCl was studied. Chromatographic analysis confirmed the results of other techniques and showed that CaD136 was essentially unfolded under the conditions of neutral pH. In fact, we have established that the hydrodynamic dimensions of CaD136 are relatively close to those measured in the presence of 6 M GdmCl (RS = 28.1 ± 0.8 and 35.3 ± 0.8 Å, respectively), confirming the fact that CaD136 is essentially unfolded even in the absence of denaturant.
We are showing in this article that the functionally important C‐terminal domain of CaD, CaD136, is an intrinsically unstructured. In fact, it shows large hydrodynamic dimensions (gel‐filtration and SAXS), does not have cooperatively melted tertiary structure (DSC), possesses absence of globular structure (SAXS), and is characterized by low content of ordered secondary structure (far‐UV CD).
Protein: DP00120 (UniProt P12957)
Region: residues 636	to 771
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
Figure 5(A) represents the results of Guinier analysis of the scattering data for CaD136. The linear Guinier plot indicates that the solution of this protein was homogeneous. The radius of gyration of a random coil, Rurn:x-wiley:08873585:media:PROT10481:tex2gif-stack-6, may be estimated from the corresponding Stokes radius, Rurn:x-wiley:08873585:media:PROT10481:tex2gif-stack-7, using the relation Rurn:x-wiley:08873585:media:PROT10481:tex2gif-stack-8/Rurn:x-wiley:08873585:media:PROT10481:tex2gif-stack-9 = 1.51.45 The observed Rg value for CaD136 (40.8 ± 0.8 Å) is smaller than that estimated for a random coil conformation for a protein of this size (51.9 Å), indicating that the natively unfolded conformation of this protein is in fact more compact than that of a random coil. Finally, analysis of the X‐ray scattering data in a form of the Kratky plot shows that CaD136 does not have any well‐developed globular structure [Fig. 5(B)]. 
We are showing in this article that the functionally important C‐terminal domain of CaD, CaD136, is an intrinsically unstructured. In fact, it shows large hydrodynamic dimensions (gel‐filtration and SAXS), does not have cooperatively melted tertiary structure (DSC), possesses absence of globular structure (SAXS), and is characterized by low content of ordered secondary structure (far‐UV CD).
Protein: DP00120 (UniProt P12957)
Region: residues 636	to 771
Annotation: disorder (Structural state)
Evidence: differential scanning calorimetry evidence used in manual assertion
Supporting statements:
The effect of temperature on CaD136 structure was further analyzed by DSC. We have established that CaD136 is characterized by the absence of distinct heat sorption peaks within the temperature region from 10°C to 110°C, indicative of the absence of rigid tertiary structure for the protein.
We are showing in this article that the functionally important C‐terminal domain of CaD, CaD136, is an intrinsically unstructured. In fact, it shows large hydrodynamic dimensions (gel‐filtration and SAXS), does not have cooperatively melted tertiary structure (DSC), possesses absence of globular structure (SAXS), and is characterized by low content of ordered secondary structure (far‐UV CD).
Protein: DP00120 (UniProt P12957)
Region: residues 636	to 771
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Figure 2 represents tryptophan fluorescence spectra of CD136. It is clearly seen that the spectrum of free CaD136 has maximum at about 350.2 nm; i.e., it is close to that of tryptophan in water (351.5 nm). This indicates that the CaD136 tryptophan residues are almost totally exposed to water.
Protein: DP00120 (UniProt P12957)
Region: residues 636	to 771
Annotation: calmodulin binding (Molecular function)
Evidence: experimental evidence used in manual assertion
Supporting statements:
Chicken gizzard CaD contains five tryptophan residues per protein molecule; three of them, Trp674, Trp707, and Trp737, are located within the CaD136 domain. On the other hand, CaM does not have any Trp residues. This implies changes in the CaD136 intrinsic tryptophan fluorescence as fast and easy method to detect CaD‐CaM complex formation.
Figure 2 compares the tryptophan fluorescence spectra (excitation at 296.7 nm) of CaD136 measured in the absence or presence of CaM. Notably, excess of Ca2+ (5 mM CaCl2) was used to saturate CaM by calcium, which is a necessary condition of effective binding of CaM by CaD.11 The temperature was kept at 20°C in order to distance from thermal transition of Ca2+‐loaded CaM. It can be seen that CaM binding to CaD136 led to the considerable (1.9‐fold) increase in the fluorescence quantum yield and an essential (17 nm) blue shift of the CaD136 fluorescence spectrum, reflecting the transfer of tryptophans into the less mobile and polar environment.
This most likely reflects some CaM‐induced compaction of a polypeptide chain at least in the vicinity of tryptophans or these changes in fluorescence are due to the insertion of Trp into a hydrophobic binding pocket on the CaM. These observations have been used to evaluate the binding parameters of CaD136‐CaM complex (see Fig. 6). It should be noted that the characteristic bend of the CaM‐titration curve in Figure 6, corresponding to saturation of CaD136 by CaM, takes place around CaM to CaD136 ratio about 1, which is an evidence of the binding of a single CaM molecule per CaD136 molecule
Protein: DP00120 (UniProt P12957)
Region: residues 636	to 771
Annotation: pre-molten globule (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Figure 1(A) represents far‐UV CD spectra of CaD136 measured at different temperatures. At low temperature this protein is characterized by a far‐UV CD spectrum typical of an essentially unfolded polypeptide chain. On the other hand, more detailed analysis of far UV CD spectrum shows that CaD136, being considerably distorted, is still far from to be completely unfolded and preserves some residual structure [e.g., [θ]222 ∼ −2500° cm2 dmol−1, the minimum is located at 200, rather than at 196–198 nm; see Fig. 1(A)].
It has been noted that such structure forming effect of heating, being typical of the intrinsically unstructured proteins, might be ascribed to the heat‐induced intensification of the hydrophobic interactions.
As it was already pointed out, in the absence of CaM CaD136 possesses a far‐UV CD spectrum typical of an essentially unfolded polypeptide chain; i.e., a spectrum with an intense minimum in the vicinity of 200 nm, and the absence of characteristic bands in the 210–230 nm region.
We are showing in this article that the functionally important C‐terminal domain of CaD, CaD136, is an intrinsically unstructured. In fact, it shows large hydrodynamic dimensions (gel‐filtration and SAXS), does not have cooperatively melted tertiary structure (DSC), possesses absence of globular structure (SAXS), and is characterized by low content of ordered secondary structure (far‐UV CD).
Moreover, our data are consistent with the conclusion that CaD136 is not completely unfolded, belonging to the subclass of the native premolten globules, according to its hydrodynamic properties and far‐UV CD spectrum.
Protein: DP00122 (UniProt P15146)
Region: residues 1	to 135
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The spectra of the two halves in this case are very similar, and their sum reproduces the spectrum of the full-length protein within experimental error. This finding is consistent with the overall random structure of MAP2c and the lack of appreciable long-range interactions between its two halves.
Protein: DP00122 (UniProt P15146)
Region: residues 298	to 467
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The spectra of the two halves in this case are very similar, and their sum reproduces the spectrum of the full-length protein within experimental error. This finding is consistent with the overall random structure of MAP2c and the lack of appreciable long-range interactions between its two halves.
Protein: DP00122 (UniProt P15146)
Region: residues 136	to 297
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The spectrum of MAP2c also shows a characteristic minimum at 200 nm and is compatible with a random-coil conformation (Figure 5B).
Protein: DP00122 (UniProt P15146)
Region: residues 136	to 297
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Limited proteolysis of MAP2c (Figure 2) also results in a nonrandom cleavage, demonstrating different accessibility of its large number of potentially vulnerable sites.
Protein: DP00123 (UniProt P01730)
Region: residues 396	to 433
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In the absence of TFE, the initial shallow negative CD curve with a minimum at ca. 200 nm and a very small negative ellipticity value at 220 nm was characteristic of a disordered peptide conformation with very little evidence of stable secondary structure (Figure 1).
Protein: DP00123 (UniProt P01730)
Region: residues 403	to 415
Annotation: lipid binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Our CD analysis indicates that CD4CYTO adopts a stable secondary structure only when a membrane-like environment was present.
Protein: DP00123 (UniProt P01730)
Region: residues 372	to 395
Annotation: order (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Nearly complete resonance assignment of DPC micelle-inserted CD4mut has been reported earlier [32]. Secondary chemical shift analysis predicted a transmembrane α-helix from 372 to 395 and a short α-helix from residue 407 to 412.
Cross-references: PDB:2KLU
Protein: DP00123 (UniProt P01730)
Region: residues 372	to 395
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Nearly complete resonance assignment of DPC micelle-inserted CD4mut has been reported earlier [32]. Secondary chemical shift analysis predicted a transmembrane α-helix from 372 to 395 and a short α-helix from residue 407 to 412.
Cross-references: PDB:2KLU
Protein: DP00123 (UniProt P01730)
Region: residues 372	to 395
Annotation: lipid binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Nearly complete resonance assignment of DPC micelle-inserted CD4mut has been reported earlier [32]. Secondary chemical shift analysis predicted a transmembrane α-helix from 372 to 395 and a short α-helix from residue 407 to 412.
Cross-references: PDB:2KLU
Protein: DP00128 (UniProt P40357)
Region: residues 401	to 651
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The spectra for Sec9c and Snc1 are very similar to each other and are suggestive of largely random coil conformation.
Protein: DP00128 (UniProt P40357)
Region: residues 401	to 651
Annotation: protein binding (Molecular function)
Evidence: native protein gel electrophoresis evidence used in manual assertion
Supporting statements:
Sso1, the purified binary complex of Sso1 and Sec9c, and the purified ternary complex of Sso1, Sec9c, and Snc1 all migrate as well-defined bands on the native gel.
Protein: DP00129 (UniProt Q04207)
Region: residues 295	to 304
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final ten amino acids of p65dd are disordered in the structure.
Protein: DP00129 (UniProt Q04207)
Region: residues 295	to 304
Annotation: entropic chain (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final ten amino acids of p65dd are disordered in the structure.
Protein: DP00130 (UniProt P22531)
Region: residues 2	to 20
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Together, these data suggest that only the central peptide repeat domain of SPR2 proteins possesses an organized structure.
Protein: DP00130 (UniProt P22531)
Region: residues 2	to 20
Annotation: flexible N-terminal tail (Disorder function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Together, these data suggest that only the central peptide repeat domain of SPR2 proteins possesses an organized structure.
Protein: DP00130 (UniProt P22531)
Region: residues 48	to 72
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Together, these data suggest that only the central peptide repeat domain of SPR2 proteins possesses an organized structure.
Protein: DP00130 (UniProt P22531)
Region: residues 48	to 72
Annotation: flexible C-terminal tail (Disorder function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Together, these data suggest that only the central peptide repeat domain of SPR2 proteins possesses an organized structure.
Protein: DP00132 (UniProt P07221)
Region: residues 376	to 395
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-terminal region is missing from the crystal structure.
Cross-references: PDB:1A8Y
Protein: DP00132 (UniProt P07221)
Region: residues 1	to 395
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Fig. 1 shows the 270-MHz 1H NMR spectrum of calsequestrin in the calcium-free form. The spectrum is characteristic of a protein known to be largely in the random coil conformation in the apo form (5, 7, 8, 10), in the sense that there is no dispersion of chemical shifts of the resonances of any of the amino acids from their random coil positions in the spectrum and the resonances are relatively narrow for a protein of this size (Mr = 44,000).
Protein: DP00132 (UniProt P07221)
Region: residues 1	to 395
Annotation: calcium ion binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The addition of KCl to calsequestrin (Fig. 3) resulted in the broadening and concomitant loss of intensity of resonances throughout both the aromatic and
aliphatic regions of the spectrum. This broadening was dependent on the concentration of KCl and there was no evidence of any selective changes in the NMR spectrum (Fig. 3, A and B). This is consistent with K+ binding to several sites on the extended structure of calsequestrin (7).
The addition of CaCl2 to calsequestrin (Fig. 4) had the same general effect as KCI; that is, a broadening of the resonances and loss of intensities throughout the NMR spectrum.
Unlike the KCl titration curve (Figs. 3 and 6), which showed binding to a single class of independent sites, the calcium titration curve showed a flatter region at the initial stages of the titration (Fig. 4C, curves a and b). This type of curve indicates the presence of some positive cooperativity for the binding of calcium to calsequestrin (10).
Protein: DP00132 (UniProt P07221)
Region: residues 1	to 395
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The addition of KCl to calsequestrin (Fig. 3) resulted in the broadening and concomitant loss of intensity of resonances throughout both the aromatic and
aliphatic regions of the spectrum. This broadening was dependent on the concentration of KCl and there was no evidence of any selective changes in the NMR spectrum (Fig. 3, A and B). This is consistent with K+ binding to several sites on the extended structure of calsequestrin (7).
The addition of CaCl2 to calsequestrin (Fig. 4) had the same general effect as KCI; that is, a broadening of the resonances and loss of intensities throughout the NMR spectrum.
Protein: DP00132 (UniProt P07221)
Region: residues 1	to 395
Annotation: potassium ion binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The addition of KCl to calsequestrin (Fig. 3) resulted in the broadening and concomitant loss of intensity of resonances throughout both the aromatic and
aliphatic regions of the spectrum. This broadening was dependent on the concentration of KCl and there was no evidence of any selective changes in the NMR spectrum (Fig. 3, A and B). This is consistent with K+ binding to several sites on the extended structure of calsequestrin (7).
The addition of CaCl2 to calsequestrin (Fig. 4) had the same general effect as KCI; that is, a broadening of the resonances and loss of intensities throughout the NMR spectrum.
Unlike the KCl titration curve (Figs. 3 and 6), which showed binding to a single class of independent sites, the calcium titration curve showed a flatter region at the initial stages of the titration (Fig. 4C, curves a and b). This type of curve indicates the presence of some positive cooperativity for the binding of calcium to calsequestrin (10).
Protein: DP00132 (UniProt P07221)
Region: residues 1	to 395
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum obtained for calsequestrin in this study (Fig. 5A) is similar to the published CD spectra of this protein (8, 10) which indicate that the calcium-free protein is predominantly in the random coil form.
Protein: DP00132 (UniProt P07221)
Region: residues 1	to 395
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The addition of calcium to the protein results in an increase in the a-helix content (8-10) to 35% in the calcium-saturated form (Fig. 5, A and B). The shape of the calcium titration curve obtained from the CD experiments (Fig. 5B) is very similar to that obtained from the NMR studies (Fig. 4C, curves a and b), with a region at the low calcium concentrations which is indicative of positive cooperativity.
Protein: DP00132 (UniProt P07221)
Region: residues 1	to 395
Annotation: metal ion binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The addition of calcium to the protein results in an increase in the a-helix content (8-10) to 35% in the calcium-saturated form (Fig. 5, A and B). The shape of the calcium titration curve obtained from the CD experiments (Fig. 5B) is very similar to that obtained from the NMR studies (Fig. 4C, curves a and b), with a region at the low calcium concentrations which is indicative of positive cooperativity.
Protein: DP00132 (UniProt P07221)
Region: residues 1	to 395
Annotation: calcium ion binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The addition of calcium to the protein results in an increase in the a-helix content (8-10) to 35% in the calcium-saturated form (Fig. 5, A and B). The shape of the calcium titration curve obtained from the CD experiments (Fig. 5B) is very similar to that obtained from the NMR studies (Fig. 4C, curves a and b), with a region at the low calcium concentrations which is indicative of positive cooperativity.