LiteFold/DisProt huggingface dataset:
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 409	to 616
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Figure 5 shows the far-UV CD and HSQC spectra of the first set of four fragments P1-P4 spanning over the Nogo-A residues 201–1016. Similar to those observed for Nogo-B, all four fragments had far-UV CD spectra typical of disordered proteins and their HSQC spectra showed sharp resonance peaks distributed within very narrow spectral dispersions. Therefore the results indicated that this set of fragments owned no populated secondary structures and tight tertiary packing. Moreover, the second group of the fragments P5-P8 dissected in a very different way also gave rise to far-UV CD and HSQC spectra characteristic of disordered proteins (Fig. 6), again indicating that the second group of fragments were also largely disordered.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 617	to 824
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Figure 5 shows the far-UV CD and HSQC spectra of the first set of four fragments P1-P4 spanning over the Nogo-A residues 201–1016. Similar to those observed for Nogo-B, all four fragments had far-UV CD spectra typical of disordered proteins and their HSQC spectra showed sharp resonance peaks distributed within very narrow spectral dispersions. Therefore the results indicated that this set of fragments owned no populated secondary structures and tight tertiary packing. Moreover, the second group of the fragments P5-P8 dissected in a very different way also gave rise to far-UV CD and HSQC spectra characteristic of disordered proteins (Fig. 6), again indicating that the second group of fragments were also largely disordered.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 825	to 1016
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Figure 5 shows the far-UV CD and HSQC spectra of the first set of four fragments P1-P4 spanning over the Nogo-A residues 201–1016. Similar to those observed for Nogo-B, all four fragments had far-UV CD spectra typical of disordered proteins and their HSQC spectra showed sharp resonance peaks distributed within very narrow spectral dispersions. Therefore the results indicated that this set of fragments owned no populated secondary structures and tight tertiary packing. Moreover, the second group of the fragments P5-P8 dissected in a very different way also gave rise to far-UV CD and HSQC spectra characteristic of disordered proteins (Fig. 6), again indicating that the second group of fragments were also largely disordered.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 210	to 358
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Figure 5 shows the far-UV CD and HSQC spectra of the first set of four fragments P1-P4 spanning over the Nogo-A residues 201–1016. Similar to those observed for Nogo-B, all four fragments had far-UV CD spectra typical of disordered proteins and their HSQC spectra showed sharp resonance peaks distributed within very narrow spectral dispersions. Therefore the results indicated that this set of fragments owned no populated secondary structures and tight tertiary packing. Moreover, the second group of the fragments P5-P8 dissected in a very different way also gave rise to far-UV CD and HSQC spectra characteristic of disordered proteins (Fig. 6), again indicating that the second group of fragments were also largely disordered.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 359	to 566
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Figure 5 shows the far-UV CD and HSQC spectra of the first set of four fragments P1-P4 spanning over the Nogo-A residues 201–1016. Similar to those observed for Nogo-B, all four fragments had far-UV CD spectra typical of disordered proteins and their HSQC spectra showed sharp resonance peaks distributed within very narrow spectral dispersions. Therefore the results indicated that this set of fragments owned no populated secondary structures and tight tertiary packing. Moreover, the second group of the fragments P5-P8 dissected in a very different way also gave rise to far-UV CD and HSQC spectra characteristic of disordered proteins (Fig. 6), again indicating that the second group of fragments were also largely disordered.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 567	to 774
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Figure 5 shows the far-UV CD and HSQC spectra of the first set of four fragments P1-P4 spanning over the Nogo-A residues 201–1016. Similar to those observed for Nogo-B, all four fragments had far-UV CD spectra typical of disordered proteins and their HSQC spectra showed sharp resonance peaks distributed within very narrow spectral dispersions. Therefore the results indicated that this set of fragments owned no populated secondary structures and tight tertiary packing. Moreover, the second group of the fragments P5-P8 dissected in a very different way also gave rise to far-UV CD and HSQC spectra characteristic of disordered proteins (Fig. 6), again indicating that the second group of fragments were also largely disordered.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 775	to 1016
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Figure 5 shows the far-UV CD and HSQC spectra of the first set of four fragments P1-P4 spanning over the Nogo-A residues 201–1016. Similar to those observed for Nogo-B, all four fragments had far-UV CD spectra typical of disordered proteins and their HSQC spectra showed sharp resonance peaks distributed within very narrow spectral dispersions. Therefore the results indicated that this set of fragments owned no populated secondary structures and tight tertiary packing. Moreover, the second group of the fragments P5-P8 dissected in a very different way also gave rise to far-UV CD and HSQC spectra characteristic of disordered proteins (Fig. 6), again indicating that the second group of fragments were also largely disordered.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 210	to 408
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Figure 5 shows the far-UV CD and HSQC spectra of the first set of four fragments P1-P4 spanning over the Nogo-A residues 201–1016. Similar to those observed for Nogo-B, all four fragments had far-UV CD spectra typical of disordered proteins and their HSQC spectra showed sharp resonance peaks distributed within very narrow spectral dispersions. Therefore the results indicated that this set of fragments owned no populated secondary structures and tight tertiary packing. Moreover, the second group of the fragments P5-P8 dissected in a very different way also gave rise to far-UV CD and HSQC spectra characteristic of disordered proteins (Fig. 6), again indicating that the second group of fragments were also largely disordered.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 409	to 616
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Figure 5 shows the far-UV CD and HSQC spectra of the first set of four fragments P1-P4 spanning over the Nogo-A residues 201–1016. Similar to those observed for Nogo-B, all four fragments had far-UV CD spectra typical of disordered proteins and their HSQC spectra showed sharp resonance peaks distributed within very narrow spectral dispersions. Therefore the results indicated that this set of fragments owned no populated secondary structures and tight tertiary packing. Moreover, the second group of the fragments P5-P8 dissected in a very different way also gave rise to far-UV CD and HSQC spectra characteristic of disordered proteins (Fig. 6), again indicating that the second group of fragments were also largely disordered.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 617	to 824
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Figure 5 shows the far-UV CD and HSQC spectra of the first set of four fragments P1-P4 spanning over the Nogo-A residues 201–1016. Similar to those observed for Nogo-B, all four fragments had far-UV CD spectra typical of disordered proteins and their HSQC spectra showed sharp resonance peaks distributed within very narrow spectral dispersions. Therefore the results indicated that this set of fragments owned no populated secondary structures and tight tertiary packing. Moreover, the second group of the fragments P5-P8 dissected in a very different way also gave rise to far-UV CD and HSQC spectra characteristic of disordered proteins (Fig. 6), again indicating that the second group of fragments were also largely disordered.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 825	to 1016
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Figure 5 shows the far-UV CD and HSQC spectra of the first set of four fragments P1-P4 spanning over the Nogo-A residues 201–1016. Similar to those observed for Nogo-B, all four fragments had far-UV CD spectra typical of disordered proteins and their HSQC spectra showed sharp resonance peaks distributed within very narrow spectral dispersions. Therefore the results indicated that this set of fragments owned no populated secondary structures and tight tertiary packing. Moreover, the second group of the fragments P5-P8 dissected in a very different way also gave rise to far-UV CD and HSQC spectra characteristic of disordered proteins (Fig. 6), again indicating that the second group of fragments were also largely disordered.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 210	to 358
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Figure 5 shows the far-UV CD and HSQC spectra of the first set of four fragments P1-P4 spanning over the Nogo-A residues 201–1016. Similar to those observed for Nogo-B, all four fragments had far-UV CD spectra typical of disordered proteins and their HSQC spectra showed sharp resonance peaks distributed within very narrow spectral dispersions. Therefore the results indicated that this set of fragments owned no populated secondary structures and tight tertiary packing. Moreover, the second group of the fragments P5-P8 dissected in a very different way also gave rise to far-UV CD and HSQC spectra characteristic of disordered proteins (Fig. 6), again indicating that the second group of fragments were also largely disordered.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 359	to 566
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Figure 5 shows the far-UV CD and HSQC spectra of the first set of four fragments P1-P4 spanning over the Nogo-A residues 201–1016. Similar to those observed for Nogo-B, all four fragments had far-UV CD spectra typical of disordered proteins and their HSQC spectra showed sharp resonance peaks distributed within very narrow spectral dispersions. Therefore the results indicated that this set of fragments owned no populated secondary structures and tight tertiary packing. Moreover, the second group of the fragments P5-P8 dissected in a very different way also gave rise to far-UV CD and HSQC spectra characteristic of disordered proteins (Fig. 6), again indicating that the second group of fragments were also largely disordered.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 567	to 774
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Figure 5 shows the far-UV CD and HSQC spectra of the first set of four fragments P1-P4 spanning over the Nogo-A residues 201–1016. Similar to those observed for Nogo-B, all four fragments had far-UV CD spectra typical of disordered proteins and their HSQC spectra showed sharp resonance peaks distributed within very narrow spectral dispersions. Therefore the results indicated that this set of fragments owned no populated secondary structures and tight tertiary packing. Moreover, the second group of the fragments P5-P8 dissected in a very different way also gave rise to far-UV CD and HSQC spectra characteristic of disordered proteins (Fig. 6), again indicating that the second group of fragments were also largely disordered.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 775	to 1016
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Figure 5 shows the far-UV CD and HSQC spectra of the first set of four fragments P1-P4 spanning over the Nogo-A residues 201–1016. Similar to those observed for Nogo-B, all four fragments had far-UV CD spectra typical of disordered proteins and their HSQC spectra showed sharp resonance peaks distributed within very narrow spectral dispersions. Therefore the results indicated that this set of fragments owned no populated secondary structures and tight tertiary packing. Moreover, the second group of the fragments P5-P8 dissected in a very different way also gave rise to far-UV CD and HSQC spectra characteristic of disordered proteins (Fig. 6), again indicating that the second group of fragments were also largely disordered.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 567	to 748
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To explore whether Nogo‐A(567–748) had any specific interaction with metal ions, we utilized CD measurements to monitor conformational changes induced by the addition of metal ions, including Ca2+, Mg2+, Cu2+, Ni2+ and Zn2+. Only Zn2+ was able to induce a significant conformational change in the polypeptide. As shown in Fig. 3A, the CD spectrum of Nogo‐A(567–748) with dual negative signals at ≈206 and 221nm in the presence of 4mm Zn2+ resembles that for a typical helical protein. The results indicate that Zn2+ could specifically induce, to a significant degree, the polypeptide to assume a helical conformation.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 567	to 748
Annotation: metal ion binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To explore whether Nogo‐A(567–748) had any specific interaction with metal ions, we utilized CD measurements to monitor conformational changes induced by the addition of metal ions, including Ca2+, Mg2+, Cu2+, Ni2+ and Zn2+. Only Zn2+ was able to induce a significant conformational change in the polypeptide. As shown in Fig. 3A, the CD spectrum of Nogo‐A(567–748) with dual negative signals at ≈206 and 221nm in the presence of 4mm Zn2+ resembles that for a typical helical protein. The results indicate that Zn2+ could specifically induce, to a significant degree, the polypeptide to assume a helical conformation.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 567	to 748
Annotation: metal ion binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Interestingly, upon addition of 4mm Zn2+, no new HSQC peaks appeared but the intensities of the existing peaks became stronger (spectrum not shown). This observation suggests that although the introduction of Zn2+ was able to significantly enhance the helical structure of Nogo‐A(567–748) as detected by CD, it was not sufficient to make the tertiary packing as tight as those found in a well‐structured protein.
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 567	to 748
Annotation: molten globule (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
As shown in Fig. 3B, the poor chemical dispersions of the spectrum at both 1H and 15N dimensions indicated that Nogo‐A(567–748) did not have a tight side‐chain packing. In particular, the number of observed NMR cross peaks was only about 35, much less than expected for a 182 residue protein, thus indicating that slow conformational exchanges existed over most regions of the protein. Usually, slow conformational exchange would result in significant line‐broadening for HSQC peaks and make these peaks undetectable. The manifested HSQC peaks in Fig. 3B most likely resulted from the unstructured and flexible regions of the Nogo‐A(567–748), while the peaks for the regions undergoing slow conformational changes were undetectable. The results above indicated that Nogo‐A(567–748) was partially structured, probably with some properties characteristic of molten globule states [[24-27]].
Protein: DP01855 (UniProt Q9NQC3-1)
Region: residues 1055	to 1094
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of Nogo‐40 in the aqueous buffer has a negative peak at ≈198nm, indicating that Nogo‐40 had no stable conformation in aqueous buffer [[23]]. Interestingly, with the introduction of methanol, the CD spectra of Nogo‐40 undergo dramatic changes. The CD spectra of Nogo‐40 in the presence of methanol at a concentration of 74% or above show one positive peak at ≈198nm and two negative peaks at ≈208 and 222nm, respectively. This observation clearly indicates that Nogo‐40 adopts a well‐formed helical conformation in the presence of 74% or higher percentages of methanol. Similarly, as shown in Fig. 5B, TFE is also able to stabilize the helical conformation of Nogo‐40. It appears that 50% TFE is sufficient to stabilize a full helical conformation for the peptide.
Protein: DP01857 (UniProt P09012)
Region: residues 102	to 117
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The backbone resonances for residues Val102 to Glu117 have very narrow linewidths, suggesting considerable flexibility in this C-terminal region and facilitating assignment through strong dαN connectivities, characteristic of
an extended conformation.
Cross-references: PDB:1fht
Protein: DP01857 (UniProt P09012)
Region: residues 102	to 117
Annotation: DNA binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
This region was not included in the isolated crystal structure of the U1-A N-terminal RRM-SL2 complex (Oubridge et al, 1994) and was disordered in the absence of RNA in an NMR-structure of a U1-A fragment spanning residues 1–117 (Avis et al, 1996), demonstrating that its fold is induced on RNA binding.
Cross-references: PMID:21113136
Protein: DP01857 (UniProt P09012)
Region: residues 115	to 207
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
a second RRM at the C terminus of the U1-A protein (residues 208–282), which is connected to the N-terminal RRM by a flexible linker (residues 115–207)
Cross-references: PDB:3PGW
Protein: DP01857 (UniProt P09012)
Region: residues 115	to 207
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
a second RRM at the C terminus of the U1-A protein (residues 208–282), which is connected to the N-terminal RRM by a flexible linker (residues 115–207)
Cross-references: PDB:3PGW
Protein: DP01857 (UniProt P09012)
Region: residues 99	to 117
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The   N terminus  (residues  2  to  7)  and  the  C  terminus (residues 99 to 117) are poorly ordered and show no long-range  NOE  connectivity  to  the  rest  of  the protein
The backbone resonances for  residues  Val102  to  Glu117  have  very  narrow line widths,   suggesting   considerable   flexibility   in this  C-terminal  region
Cross-references: PDB:1FHT
Protein: DP01858 (UniProt Q96270)
Region: residues 1	to 169
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of the hydrated protein indicated a low content of stable secondary structures, with a well defined minimal ellipticity around 200 nm
Protein: DP01858 (UniProt Q96270)
Region: residues 1	to 169
Annotation: disorder (Structural state)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
The minimum at 1642 cm− 1 indicating unstructured elements in the protein is the most prominent. This is in good agreement with the CD spectra, which also indicate that the unstructured components of LEA7 dominate in its hydrated state.
Protein: DP01858 (UniProt Q96270)
Region: residues 1	to 169
Annotation: disorder (Structural state)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
We therefore monitored secondary structure of the six LEA_4 proteins in response to decreasing relative humidity (RH) using the Amide I band of Fourier-transform infrared (FTIR) spectra (Figure 6). This absorbance band mainly results from the C=O stretching vibration and is directly related to the protein backbone conformation. A maximum at 1650–1640 cm-1 indicated that all proteins were mainly disordered at 100% RH, which is in line with the CD data.
Protein: DP01858 (UniProt Q96270)
Region: residues 1	to 169
Annotation: disorder (Structural state)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
Simultaneous static and dynamic light scattering (SLS/DLS) measurements were conducted to determine the apparent average single particle mass (Mapp) and the apparent average hydrodynamic radius (RS) of the proteins in solution as a function of concentration (Figure S4, [30]). Absolute molecular mass and RS were obtained by extrapolation of apparent molecular mass and RS to infinite dilution. All investigated LEA proteins are essentially monomeric under fully hydrated conditions. Compared to globular proteins, RS of all investigated LEA proteins was rather large, indicating their expanded, non-compact nature.
Protein: DP01858 (UniProt Q96270)
Region: residues 1	to 169
Annotation: disorder to order (Structural transition)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
Figure S5 shows FTIR spectra of the six LEA_4 proteins in EG concentrations ranging from 0 to 12 osM. Similar to decreasing RH, increasing osmolarity induces coil-helix transitions, indicated by a shift of the Amide I maxima to higher wavenumbers.
Protein: DP01858 (UniProt Q96270)
Region: residues 1	to 169
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
All proteins showed typical random coil spectra in dilute solution. With increasing concentrations of each of the co-solvents, the changes in the spectral shape report on the formation of ordered secondary structure.