LiteFold/DisProt huggingface dataset:
Protein: DP04003 (UniProt P0C746)
Region: residues 3	to 77
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
To elucidate the structural basis for the interactions among the HBZ AD, KIX, and the transactivation domain of c-Myb (residues 284–315), we determined the crystal
structures of the ternary complexes KIX:c-Myb:HBZ (3–77) and KIX:c-Myb:HBZ (3–56) at 2.35 Å and 2.80 Å, respectively (SI Appendix, Table S1).
Cross-references: PDB:6DMX
Protein: DP04003 (UniProt P0C746)
Region: residues 3	to 77
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Surprisingly, the intrinsically disordered HBZ AD folds upon binding to form a single continuous a-helix, where the N-terminal (AD1) and C-terminal (AD2) subdomains each bind to one molecule of KIX.
Cross-references: PDB:6DMX
Protein: DP04003 (UniProt P0C746)
Region: residues 33	to 56
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
The 1H-15N HSQC spectrum of fully bound 15N-labeled HBZ (33–56) shows increased dispersion in the 1H dimension compared with the free peptide, indicating folding of AD2 upon binding to KIX (SI Appendix, Fig. S4A).
Protein: DP04005 (UniProt Q9WID3)
Region: residues 1849	to 1870
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To further investigate the influence of disordered region of VPg on its secondary structure, the far-UV CD spectra of purified VPg and the truncated proteins were recorded. The CD profile of VPg (Fig. 5A) showed a negative peak at around 200 nm similar to that observed for IDPs (Rantalainen et al., 2009, Satheshkumar et al., 2005)with 11.53% α-helical content (Fig. 5A, inset) as per K2D2 analysis (Perez-Iratxeta and Andrade-Navarro, 2008).
Protein: DP04005 (UniProt Q9WID3)
Region: residues 1849	to 1870
Annotation: disorder (Structural state)
Evidence: co-sedimentation assay evidence used in manual assertion
Supporting statements:
The f/f0 value between 1.2 and 1.5 is an indicative of a well folded protein, between 1.5 and 2.5 define an intrinsically disordered protein while that above 3 indicates a highly elongated protein (Erickson, 2009).
Protein: DP04006 (UniProt Q9RV58)
Region: residues 104	to 245
Annotation: disorder (Structural state)
Evidence: circular dichroism evidence used in manual assertion
Supporting statements:
We compared four different HD orthologs from distant organisms: (i) DrHD from the extremophilic bacterium Deinococcus radiodurans; (ii) CeHD from the nematode Caenorhabditis elegans; (iii) YlHD from the yeast Yarrowia lipolytica; and (iv) BnHD from the plant Brassica napus. Circular dichroism spectroscopy showed that all four HDs were intrinsically disordered in phosphate buffer and
then folded into a-helical structures with the addition of glycerol or trifluoroethanol.
The residue boundaries of the investigated protein constructs were taken from Table 1 column 5.
The proteins were analysed by far-UV circular dichroism (CD) spectroscopy. The spectra of all four HDs had a negative peak at 198 nm in phosphate buffer, indicating that DrHD, CeHD, BnHD and YlHD are natively unstructured in solution (Fig. 1A).
Protein: DP04006 (UniProt Q9RV58)
Region: residues 104	to 245
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
However, according to the SDS-PAGE results, the HDs migrated to a higher molecular mass due to their hydrophilic character, which is often used to identify IDPs (Tompa, 2002; Chakrabortee et al., 2010).
Protein: DP04006 (UniProt Q9RV58)
Region: residues 104	to 245
Annotation: protein folding chaperone (Molecular function)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
It was clear to see that LDH marked aggregation subjected to cycles of desiccation (Fig. 3A), addition of HDs can significantly decrease the aggregation of LDH compared to BSA mixture and negative control (only LDH), respectively, even after four cycles of desiccation, suggesting their aggregation-preventing ability. Noticeably, DrHD displayed the better job inhibiting the aggregation of LDH. The enzymatic activity of LDH was impaired under the dry conditions, especially after four cycles, and < 20% of the undried LDH activity was retained. Conspicuously, the loss of LDH enzymatic activity was significantly neutralized with the additional HDs and BSA. DrHD and CeHD performed excellently, preserving up to 60% of the LDH activity, and even BnHD protected up to 40% of the activity, which was slightly higher than the 38% protected by BSA (Fig. 3B). The HD protection of LDH enzymatic activity under oxidation stress followed a trend similar to that in desiccation (Fig. S5). DrHD and CeHD clearly exhibited the strongest protection ability (over 65% of LDH activity retained) of the HDs.
Protein: DP04007 (UniProt G5EFU3)
Region: residues 226	to 702
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We compared four different HD orthologs from distant organisms: (i) DrHD from the extremophilic bacterium Deinococcus radiodurans; (ii) CeHD from the nematode Caenorhabditis elegans; (iii) YlHD from the yeast Yarrowia lipolytica; and (iv) BnHD from the plant Brassica napus. Circular dichroism spectroscopy showed that all four HDs were intrinsically disordered in phosphate buffer and then folded into a-helical structures with the addition of glycerol or trifluoroethanol.
The proteins were analysed by far-UV circular dichroism (CD) spectroscopy. The spectra of all four HDs had a negative peak at 198 nm in phosphate buffer, indicating that DrHD, CeHD, BnHD and YlHD are natively unstructured in solution (Fig. 1A).
The residue boundaries of the investigated protein constructs were taken from Table 1 column 5.
Protein: DP04007 (UniProt G5EFU3)
Region: residues 226	to 702
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
However, according to the SDS-PAGE results, the HDs migrated to a higher molecular mass due to their hydrophilic character, which is often used to identify IDPs (Tompa, 2002; Chakrabortee et al., 2010).
Protein: DP04007 (UniProt G5EFU3)
Region: residues 226	to 702
Annotation: protein folding chaperone (Molecular function)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
It was clear to see that LDH marked aggregation subjected to cycles of desiccation (Fig. 3A), addition of HDs can significantly decrease the aggregation of LDH compared to BSA mixture and negative control (only LDH), respectively, even after four cycles of desiccation, suggesting their aggregation-preventing ability. Noticeably, DrHD displayed the better job inhibiting the aggregation of LDH. The enzymatic activity of LDH was impaired under the dry conditions, especially after four cycles, and < 20% of the undried LDH activity was retained. Conspicuously, the loss of LDH enzymatic activity was significantly neutralized with the additional HDs and BSA. DrHD and CeHD performed excellently, preserving up to 60% of the LDH activity, and even BnHD protected up to 40% of the activity, which was slightly higher than the 38% protected by BSA (Fig. 3B). The HD protection of LDH enzymatic activity under oxidation stress followed a trend similar to that in desiccation (Fig. S5). DrHD and CeHD clearly exhibited the strongest protection ability (over 65% of LDH activity retained) of the HDs.
Protein: DP04008 (UniProt Q8S8Z3)
Region: residues 42	to 162
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We compared four different HD orthologs from distant organisms: (i) DrHD from the extremophilic bacterium Deinococcus radiodurans; (ii) CeHD from the nematode Caenorhabditis elegans; (iii) YlHD from the yeast Yarrowia lipolytica; and (iv) BnHD from the plant Brassica napus. Circular dichroism spectroscopy showed that all four HDs were intrinsically disordered in phosphate buffer and then folded into a-helical structures with the addition of glycerol or trifluoroethanol.
The proteins were analysed by far-UV circular dichroism (CD) spectroscopy. The spectra of all four HDs had a negative peak at 198 nm in phosphate buffer, indicating that DrHD, CeHD, BnHD and YlHD are natively unstructured in solution (Fig. 1A).
The residue boundaries of the investigated protein constructs were taken from Table 1 column 5.
Protein: DP04008 (UniProt Q8S8Z3)
Region: residues 42	to 162
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
However, according to the SDS-PAGE results, the HDs migrated to a higher molecular mass due to their hydrophilic character, which is often used to identify IDPs (Tompa, 2002; Chakrabortee et al., 2010).
Protein: DP04008 (UniProt Q8S8Z3)
Region: residues 42	to 162
Annotation: protein folding chaperone (Molecular function)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
It was clear to see that LDH marked aggregation subjected to cycles of desiccation (Fig. 3A), addition of HDs can significantly decrease the aggregation of LDH compared to BSA mixture and negative control (only LDH), respectively, even after four cycles of desiccation, suggesting their aggregation-preventing ability. Noticeably, DrHD displayed the better job inhibiting the aggregation of LDH. The enzymatic activity of LDH was impaired under the dry conditions, especially after four cycles, and < 20% of the undried LDH activity was retained. Conspicuously, the loss of LDH enzymatic activity was significantly neutralized with the additional HDs and BSA. DrHD and CeHD performed excellently, preserving up to 60% of the LDH activity, and even BnHD protected up to 40% of the activity, which was slightly higher than the 38% protected by BSA (Fig. 3B). The HD protection of LDH enzymatic activity under oxidation stress followed a trend similar to that in desiccation (Fig. S5). DrHD and CeHD clearly exhibited the strongest protection ability (over 65% of LDH activity retained) of the HDs.
Protein: DP04009 (UniProt O64820)
Region: residues 1	to 92
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
 In solution the spectrum of LEA15 (Fig. 2A) showed typical features of a largely unstructured protein with a well defined minimal ellipticity at around 200 nm.
Protein: DP04009 (UniProt O64820)
Region: residues 1	to 92
Annotation: disorder (Structural state)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
The Amide I peaks from all hydrated proteins were situated between 1646 and 1650 cm−1 in agreement with the CD spectra indicating them to be largely unstructured.
Protein: DP04010 (UniProt Q94K79)
Region: residues 1	to 83
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In solution the spectrum of LEA15 (Fig. 2A) showed typical features of a largely unstructured protein with a well defined minimal ellipticity at around 200 nm.
After drying the spectrum was massively changed, indicating a gain of structure. However, the CD spectrum of LEA15 did not exhibit the double minimum at 208 and 222 nm characteristic of predominantly a-helical proteins. The CD spectra of the other investigated LEA proteins, both in the hydrated and dry state, were
similar to those presented in Fig. 2A and are therefore not shown.
Secondary structure estimates derived from these CD spectra indicated that the hydrated LEA proteins were between 61% (LEA17) and 68% (LEA20) unstructured (Fig. 2B). In addition, they contained around 20% b-sheet and only a negligible fraction of a-helices.
Based on the statement of the authors and figure 2B, the structural composition of the five investigated LEA proteins are similar to each other, both in the hydrated and dry state.
Protein: DP04010 (UniProt Q94K79)
Region: residues 1	to 83
Annotation: disorder (Structural state)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
The Amide I peaks from all hydrated proteins were situated between 1646 and 1650 cm−1 in agreement with the CD spectra indicating them to be largely unstructured.
Protein: DP04011 (UniProt O23658)
Region: residues 1	to 71
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In solution the spectrum of LEA15 (Fig. 2A) showed typical features of a largely unstructured protein with a well defined minimal ellipticity at around 200 nm.
After drying the spectrum was massively changed, indicating a gain of structure. However, the CD spectrum of LEA15 did not exhibit the double minimum at 208 and 222 nm characteristic of predominantly a-helical proteins. The CD spectra of the other investigated LEA proteins, both in the hydrated and dry state, were
similar to those presented in Fig. 2A and are therefore not shown.
Secondary structure estimates derived from these CD spectra indicated that the hydrated LEA proteins were between 61% (LEA17) and 68% (LEA20) unstructured (Fig. 2B). In addition, they contained around 20% b-sheet and only a negligible fraction of a-helices.
Based on the statement of the authors and figure 2B, the structural composition of the five investigated LEA proteins are similar to each other, both in the hydrated and dry state.
Protein: DP04011 (UniProt O23658)
Region: residues 1	to 71
Annotation: disorder (Structural state)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
The Amide I peaks from all hydrated proteins were situated between 1646 and 1650 cm-1 in agreement with the CD spectra indicating them to be largely unstructured.
Protein: DP04012 (UniProt Q02973)
Region: residues 1	to 92
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In solution the spectrum of LEA15 (Fig. 2A) showed typical features of a largely unstructured protein with a well defined minimal ellipticity at around 200 nm. After drying the spectrum was massively changed, indicating a gain of structure. However, the CD spectrum of LEA15 did not exhibit the double minimum at 208 and 222 nm characteristic of predominantly a-helical proteins. The CD spectra of the other investigated LEA proteins, both in the hydrated and dry state, were similar to those presented in Fig. 2A and are therefore not shown.
Secondary structure estimates derived from these CD spectra indicated that the hydrated LEA proteins were between 61% (LEA17) and 68% (LEA20) unstructured (Fig. 2B). In addition, they contained around 20% b-sheet and only a negligible fraction of a-helices.
Based on the statement of the authors and figure 2B, the structural composition of the five investigated LEA proteins are similar to each other, both in the hydrated and dry state.
Protein: DP04012 (UniProt Q02973)
Region: residues 1	to 92
Annotation: disorder (Structural state)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
The Amide I peaks from all hydrated proteins were situated between 1646 and 1650 cm−1 in agreement with the CD spectra indicating them to be largely unstructured.
Protein: DP04014 (UniProt Q9LL46)
Region: residues 1	to 82
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To test the disordered nature predicted for PvLEA6 protein, its secondary structure in aqueous solution at pH 8.0 (10 mM potassium phosphate) was explored by CD spectroscopy in the far-UV light. The spectrum showed a strong minimum ellipticity around 200 nm, indicative of a largely unordered conformation (Fig. 2B).
An alternative and likely explanation for the temperature induced changes in the rPvLEA6 far-UV CD spectra is the formation of secondary structure promoted by the increasing temperatures, which has been proposed to be driven by hydrophobic interactions and has also been reported for various IDPs (43, 44).
In this report, analysis by circular dichroism (CD) and nuclear magnetic resonance (NMR) shows the disordered structure of the PvLEA6 protein in aqueous solution, as well as the potential of this protein to acquire up to 40% α-helix.
Protein: DP04014 (UniProt Q9LL46)
Region: residues 1	to 82
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The low level of chemical shift dispersion apparent in the 1H dimension clustered between 7.7 and 8.5 ppm (Fig. 5A) was indicative of structural disordered state for this protein under native conditions in aqueous solution.
In this report, analysis by circular dichroism (CD) and nuclear magnetic resonance (NMR) shows the disordered structure of the PvLEA6 protein in aqueous solution, as well as the potential of this protein to acquire up to 40% α-helix.
Protein: DP04014 (UniProt Q9LL46)
Region: residues 1	to 82
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
The differences between the molecular masses estimated by SDS-PAGE (see above) and gel filtration chromatography with those obtained by mass spectrometry suggested that oligomeric forms maintain the monomer structural disorder.
The first indications of the unstructured nature of PvLEA6 were observed during initial characterization of the protein. rPvLEA6 protein was produced and purified from E. coli, from which a highly pure native protein was obtained that migrated in SDS-PAGE with an apparent molecular mass of 14 kDa (Fig. 2A; see “Experimental Procedures” for details). The molecular mass and amino acid sequence of the purified rPvLEA protein were proven by LC-MS, showing a molecular mass of 8.76 kDa (data not shown), in agreement with informatic predictions, and the same amino acid sequence as that deduced from its open reading frame, as reported previously (18). Therefore, indicating that the difference in its molecular mass obtained by SDS-PAGE migration or by LC-MS is likely due to the absence of hydrophobic clusters and therefore a low interaction with SDS (Fig. 1), and it is consistent with its predicted structural disorder, which usually gives rise to large protein hydrodynamic dimensions (34).
Protein: DP04014 (UniProt Q9LL46)
Region: residues 1	to 82
Annotation: identical protein binding (Molecular function)
Evidence: matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in manual assertion
Supporting statements:
To have a more precise determination of the molecular mass of these rPvLEA6 oligomers, a cross-linked sample was subjected to MALDI-TOF-MS analysis. The spectrum, obtained only for protein molecules smaller than 50,000 Da, showed three peaks at 8760, 17,520, and 26,280 Da, corresponding to monomer, dimer, and trimer, respectively (Fig. 8C).
Protein: DP04014 (UniProt Q9LL46)
Region: residues 1	to 82
Annotation: identical protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
The measurements (carried out in triplicate) yielded a Kd = 60 ± 20 μm and a dissociation enthalpy, ΔHd, = 1.0 ± 0.3 kcal/mol. This information allowed estimation of the following thermodynamic parameters for dimer formation (30 °C): ΔGa = −5.9 kcal/mol; ΔHa = −1.0 kcal/mol; and TΔSa = 4.9 kcal/mol, consistent with a low affinity, mainly entropically driven interaction between rPvLEA6 monomers under these conditions.
Protein: DP04014 (UniProt Q9LL46)
Region: residues 1	to 82
Annotation: identical protein binding (Molecular function)
Evidence: yellow fluorescent protein fusion protein localization evidence used in manual assertion
Supporting statements:
As shown in Fig. 11, fluorescence was detected only when the mixture containing the YFPN43-PvLEA6 and YFPC43-PvLEA6 was infiltrated but not when any of these were individually introduced into plant cells, indicating that the two nonfluorescent YFP fragments were brought together by the interaction between PvLEA6 monomers, hence forming a fluorescent complex.
Protein: DP04015 (UniProt Q9ZPQ7)
Region: residues 50	to 189
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.
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: DP04015 (UniProt Q9ZPQ7)
Region: residues 50	to 189
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: DP04015 (UniProt Q9ZPQ7)
Region: residues 50	to 189
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: DP04015 (UniProt Q9ZPQ7)
Region: residues 50	to 189
Annotation: response to cold (Biological process)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Therefore, we analyzed the stability of liposomes modeling the lipid composition of inner chloroplast membranes (ICMM) after a freeze/thaw cycle and a dehydration/rehydration cycle in the ethylene glycolpresence of all six LEA_4 proteins at different LEA protein: lipid mass ratios (Figure 13).