LiteFold/DisProt huggingface dataset:
Protein: DP04191 (UniProt Q99P72)
Region: residues 1025	to 1090
Annotation: order (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The structure of Nogo-66 induced by DPC is a compact helical bundle consisting of five helices wrapping upon each other. Thirty-two of the 66 backbone amide hydrogens exchange slowly over a period of hours to days (Fig. S3B), indicating that Nogo-66 forms a stable fold on the DPC surface.
Cross-references: PDB:2KO2
Protein: DP04191 (UniProt Q99P72)
Region: residues 1025	to 1090
Annotation: lipid binding (Molecular function)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Using NMR diffusion measurements we find Nogo-66 is fully bound to DPC at the concentrations used in our NMR experiments.
Cross-references: PDB:2KO2
Protein: DP04191 (UniProt Q99P72)
Region: residues 1025	to 1090
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In an aqueous environment, we find that Nogo-66 is largely disordered based on the following data. The CD spectrum of aqueous Nogo-66 indicates very little secondary structure (Fig. 1A, Red Trace).
Protein: DP04191 (UniProt Q99P72)
Region: residues 1025	to 1090
Annotation: order (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To determine the structural influence of phosphocholine (PC) on the fold of Nogo-66, we prepared DMPC lipid vesicles and collected CD data (Fig. 1A, Black Trace). Notably, Nogo-66 becomes significantly ordered in the presence of lipid vesicles, calculated to be 88% helix.
Protein: DP04191 (UniProt Q99P72)
Region: residues 1025	to 1090
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To determine the structural influence of phosphocholine (PC) on the fold of Nogo-66, we prepared DMPC lipid vesicles and collected CD data (Fig. 1A, Black Trace). Notably, Nogo-66 becomes significantly ordered in the presence of lipid vesicles, calculated to be 88% helix.
Protein: DP04191 (UniProt Q99P72)
Region: residues 1025	to 1090
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The structure of Nogo-66 induced by DPC is a compact helical bundle consisting of five helices wrapping upon each other. Thirty-two of the 66 backbone amide hydrogens exchange slowly over a period of hours to days (Fig. S3B), indicating that Nogo-66 forms a stable fold on the DPC surface
Cross-references: PDB:2KO2
Protein: DP04192 (UniProt P69019)
Region: residues 50	to 65
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
After binding to lipid bilayers, in the steady-state far-UV CD again indicates similar ordered α-helix conformations are adopted by both peptides; in the absence of lipid both peptides adopt disordered conformations (Fig. S4).
Protein: DP04192 (UniProt P69019)
Region: residues 50	to 65
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
After binding to lipid bilayers, in the steady-state far-UV CD again indicates similar ordered α-helix conformations are adopted by both peptides; in the absence of lipid both peptides adopt disordered conformations (Fig. S4).
Protein: DP04192 (UniProt P69019)
Region: residues 50	to 65
Annotation: order (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In SDS, both the far-UV CD and the NMR structures agree that both peptides
adopt ordered α-helix conformations.
Cross-references: PDB:6GS9
BMRB:34284
Protein: DP04192 (UniProt P69019)
Region: residues 50	to 65
Annotation: lipid binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
This shows that, while secondary amphipathic α-helix conformations are a vital element in the binding and disruption of bacterial plasma membranes, individual amino acids in the distinct structures make important structural and dynamic contributions that determine the precise mechanism of action, potency and species selectivity of AMPs.
Protein: DP04192 (UniProt P69019)
Region: residues 50	to 65
Annotation: defense response to Gram-negative bacterium (Biological process)
Evidence: cell growth assay evidence used in manual assertion
Supporting statements:
In the present study, temporin L is shown to be more potent than aurein 2.5 against all strains included in both the Gram-positive and Gram-negative bacteria panels and Candida albicans (Table 2). For the Gram-positive strains, aurein 2.5 is outperformed by temporin L with, on average a 7.6-fold greater potency for the latter. For the Gram-negative strains, the difference between the potency of aurein 2.5 and temporin L is less, notably for both Acinetobacter baumannii isolates.
Protein: DP04192 (UniProt P69019)
Region: residues 50	to 65
Annotation: defense response to Gram-positive bacterium (Biological process)
Evidence: cell growth assay evidence used in manual assertion
Supporting statements:
In the present study, temporin L is shown to be more potent than aurein 2.5 against all strains included in both the Gram-positive and Gram-negative bacteria panels and Candida albicans (Table 2). For the Gram-positive strains, aurein 2.5 is outperformed by temporin L with, on average a 7.6-fold greater potency for the latter. For the Gram-negative strains, the difference between the potency of aurein 2.5 and temporin L is less, notably for both Acinetobacter baumannii isolates.
Protein: DP04192 (UniProt P69019)
Region: residues 50	to 65
Annotation: pore formation in membrane of another organism (Biological process)
Evidence: combinatorial experimental and curator inference evidence used in manual assertion
Supporting statements:
In the present study, temporin L is shown to be more potent than aurein 2.5 against all strains included in both the Gram-positive and Gram-negative bacteria panels and Candida albicans (Table 2). For the Gram-positive strains, aurein 2.5 is outperformed by temporin L with, on average a 7.6-fold greater potency for the latter. For the Gram-negative strains, the difference between the potency of aurein 2.5 and temporin L is less, notably for both Acinetobacter baumannii isolates.
In contrast, in the present study both aurein 2.5 and temporin L were found to be capable of inducing channel like activity (Fig. 6). For aurein 2.5 this was observed in both membrane types (Fig. 6A,B) whereas for temporin L this was only found when challenging membranes formed from DPhPG (Fig. 6D).
This shows that, while secondary amphipathic α-helix conformations are a vital element in the binding and disruption of bacterial plasma membranes, individual amino acids in the distinct structures make important structural and dynamic contributions that determine the precise mechanism of action, potency and species selectivity of AMPs.
Protein: DP04192 (UniProt P69019)
Region: residues 50	to 65
Annotation: channel activity (Molecular function)
Evidence: electrophysiology assay evidence used in manual assertion
Supporting statements:
Similar to aurein 2.5, temporin L has channel like activity when challenging DPhPG membranes.
In contrast, in the present study both aurein 2.5 and temporin L were found to be capable of inducing channel like activity (Fig. 6). For aurein 2.5 this was observed in both membrane types (Fig. 6A,B) whereas for temporin L this was only found when challenging membranes formed from DPhPG (Fig. 6D).
Protein: DP04193 (UniProt P12969)
Region: residues 55	to 74
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The remainder of the peptide on the C-terminal end from
Gly24–Tyr37 is predominantly disordered.
This difference in backbone rmsd clearly shows that the 5–17 region of rat IAPP is relatively stable and that the helical region from residues 18–23 is more disordered.
Numbering is not according to Uniprot reference.
Cross-references: PDB:2KJ7
BMRB:16314
Protein: DP04193 (UniProt P12969)
Region: residues 38	to 74
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The chemical shift dispersion was typical of a disordered peptide, yet there was sufficient resolution to identify all resonances.
Cross-references: BMRB:7311
Protein: DP04193 (UniProt P12969)
Region: residues 38	to 54
Annotation: order (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Taken together, the NOE and CSI data support the presence of a predominantly α-helical structure within the Ala5–Leu23 region, with the stretch of residues from Ala5–Val17 and Ser20–Leu23 acting as a more stable core.
Numbering is not according to Uniprot reference.
Cross-references: BMRB:16314
PDB:2KJ7
Protein: DP04193 (UniProt P12969)
Region: residues 38	to 54
Annotation: lipid binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectra suggested
that the rIAPP–DPC micelle was quite stable even after several months and the peptide had
significant helical structure in micelles, indicating that rIAPP remained bound to the DPC
micelle.
Protein: DP04193 (UniProt P12969)
Region: residues 38	to 54
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Taken together evidences from pmid:19456151 and pmid:17123962 it seems that rIAAP undergoes structural transition in DPC micelles.
Cross-references: PDB:2KJ7
BMRB:16314
Protein: DP04195 (UniProt Q4WE50)
Region: residues 159	to 186
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Main chain chemical shifts indicated that residues 159–186 are likely random coil whereas 212–228 and 195–208 formed helices corresponding to H1 and H2 (supplemental Fig. 2B).
Residues 159–185 did not converge to a consistent structure due to a lack of interresidue NOE-derived distance restraints and were omitted from the final structure calculation.
Protein: DP04196 (UniProt Q12285)
Region: residues 152	to 175
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The main chain chemical shifts (1HN, 15NN, 13CCO, 13Cα, 13Cβ, and 1Hα) of residues 152–175 have random coil character, whereas those of 179–190 and 194–210 are characteristic of helices (supplemental Fig. S2A).
Relaxation rates and heteronuclear NOE values also indicate rapid motions for residues 152–175.
Protein: DP04196 (UniProt Q12285)
Region: residues 152	to 177
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence used in manual assertion
Supporting statements:
Consistent with this secondary structure, 1HN of residues 182–187 and 200–208 were the most protected from solvent deuterium exchange whereas residues 152–177 readily exchanged. Therefore, we concluded that residues 152–175 were unstructured and not significantly contributing to the stability of the folded dimerization domain.
Protein: DP04197 (UniProt P35187)
Region: residues 1	to 125
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Using nuclear magnetic resonance spectroscopy, we show that the N-terminal 125 residues of Sgs1 are disordered and contain a transient α-helix that extends from residue 25 to 38.
The NHNOE values observed for Sgs11−125 are consistent with a mostly disordered protein that contains two transiently ordered regions centered on residues F30 and E92 (Figure 3a).
Protein: DP04197 (UniProt P35187)
Region: residues 25	to 33
Annotation: chromosome organization (Biological process)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
To determine if the inability of Sgs1 to interact with Top3 and Rmi1 also leads to increased genome instability, we tested the ability of D25P, K26P, V29P, F30P and I33P mutants of full-length Sgs1 expressed from a CEN/ARS plasmid to suppress the elevated GCR rate of an sgs1Δ mutant. Mirroring the results of the HU hypersensitivity assay, D25P, V29P, F30P and I33P were unable to complement the defects of sgs1Δ cells, whereas cells expressing the K26P mutant accumulated GCRs at a similar rate as cells expressing wild-type Sgs1 (Table 1).
Protein: DP04197 (UniProt P35187)
Region: residues 34	to 169
Annotation: disorder (Structural state)
Evidence: intrinsic disorder prediction evidence used in manual assertion
Supporting statements:
MobiDB shows this region is considered as disordered, and it aligns with other predictors results regarding the flexible character of this region.
Protein: DP04197 (UniProt P35187)
Region: residues 243	to 572
Annotation: disorder (Structural state)
Evidence: intrinsic disorder prediction evidence used in manual assertion
Supporting statements:
MobiDB shows this region is considered as disordered, and it aligns with other predictors results regarding the flexible character of this region.
Protein: DP04197 (UniProt P35187)
Region: residues 27	to 31
Annotation: DNA repair (Biological process)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
Cells expressing the mutant helicases were plated on media containing 100 mM of the DNA-damaging agent HU (Figure 4). While the sgs1-V29P and sgs1-F30P mutants were as sensitive to HU as the sgs1Δ mutant, neither the W92P nor the L93P mutation caused increased sensitivity (Figure 4a and b), indicating that the α-helical structure centered on V29 and F30 contributes to Sgs1’s role in DNA damage repair, whereas that centered on W92 and L93 does not.
Protein: DP04197 (UniProt P35187)
Region: residues 9	to 30
Annotation: DNA topoisomerase binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
When we introduced L9P, H13P, K17P, D25P, V29P and F30P mutations into the Sgs11−250 fragment, its ability to pull down Top3 from cell extracts was diminished, whereas the T21P and K26P mutants were still able to bind Top3 (Figure 7g).
Protein: DP04197 (UniProt P35187)
Region: residues 9	to 30
Annotation: protein binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
When we introduced L9P, H13P, K17P, D25P, V29P and F30P mutations into the Sgs11−250 fragment, its ability to pull down Top3 from cell extracts was diminished, whereas the T21P and K26P mutants were still able to bind Top3 (Figure 7g). Mutations of Sgs1 that disrupted binding to Top3 also disrupted binding to Rmi1 (Figure 7h).
Protein: DP04197 (UniProt P35187)
Region: residues 9	to 30
Annotation: RecQ family helicase-topoisomerase III complex (Cellular component)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
When we introduced L9P, H13P, K17P, D25P, V29P and F30P mutations into the Sgs11−250 fragment, its ability to pull down Top3 from cell extracts was diminished, whereas the T21P and K26P mutants were still able to bind Top3 (Figure 7g). Mutations of Sgs1 that disrupted binding to Top3 also disrupted binding to Rmi1 (Figure 7h).
Protein: DP04198 (UniProt P26663)
Region: residues 2950	to 2989
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Therefore, as judged by its CD, 1D and HSQC spectra, the isolated
C-linker appears to be predominantly disordered in solution, lacking of any well-formed
secondary structures and tight tertiary packing.
Protein: DP04198 (UniProt P26663)
Region: residues 2950	to 2989
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Therefore, as judged by its CD, 1D and HSQC spectra, the isolated
C-linker appears to be predominantly disordered in solution, lacking of any well-formed
secondary structures and tight tertiary packing.
Protein: DP04198 (UniProt P26663)
Region: residues 2950	to 2989
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
These results together decipher that the C-linker of the HCV NS5B plays a central role in binding the MSP domain of
the human VAPB.
Protein: DP04198 (UniProt P26663)
Region: residues 2950	to 2989
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
By contrast, as shown in Fig 2A, the C-linker peptide has a far-UV CD spectrum typical of a highly-disordered protein with the maximal negative signal at 198 nm, and lacking any positive signal at 190 nm.
Protein: DP04198 (UniProt P26663)
Region: residues 2950	to 2989
Annotation: flexible linker (Disorder function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
By contrast, as shown in Fig 2A, the C-linker peptide has a far-UV CD spectrum typical of a highly-disordered protein with the maximal negative signal at 198 nm, and lacking any positive signal at 190 nm.
Therefore, as judged by its CD, 1D and HSQC spectra, the isolated C-linker appears to be predominantly disordered in solution, lacking of any well-formed secondary structures and tight tertiary packing.
Protein: DP04199 (UniProt Q9C7W1)
Region: residues 1	to 178
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
Consistent with the CD spectra, the Rg/Rh ratio of 1.2 to 1.3 (compared to a compact protein ratio of 0.8) and subsequent dimensionless Kratky plot (Fig. S7A) demonstrate that PARCL is an IDP.
Protein: DP04199 (UniProt Q9C7W1)
Region: residues 1	to 178
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The measurements showed that both proteins are highly unstructured with no detectable β-sheets and an α-helix content below 5% (Table 1 and Fig. S9).
Protein: DP04199 (UniProt Q9C7W1)
Region: residues 1	to 178
Annotation: zinc ion binding (Molecular function)
Evidence: affinity chromatography evidence used in manual assertion
Supporting statements:
Since many RBPs need divalent metal ions for their interaction with RNA (30, 60, 61), we performed metal affinity chromatography experiments indicating that PARCL binds Zn2+, Ni2+, Cu2+, and Co2+, but not Mg2+, Ca2+, Fe3+, or Cd2+ (Fig. S10).
Protein: DP04199 (UniProt Q9C7W1)
Region: residues 1	to 178
Annotation: nickel cation binding (Molecular function)
Evidence: affinity chromatography evidence used in manual assertion
Supporting statements:
Since many RBPs need divalent metal ions for their interaction with RNA (30, 60, 61), we performed metal affinity chromatography experiments indicating that PARCL binds Zn2+, Ni2+, Cu2+, and Co2+, but not Mg2+, Ca2+, Fe3+, or Cd2+ (Fig. S10).
Protein: DP04199 (UniProt Q9C7W1)
Region: residues 1	to 178
Annotation: cupric ion binding (Molecular function)
Evidence: affinity chromatography evidence used in manual assertion
Supporting statements:
Since many RBPs need divalent metal ions for their interaction with RNA (30, 60, 61), we performed metal affinity chromatography experiments indicating that PARCL binds Zn2+, Ni2+, Cu2+, and Co2+, but not Mg2+, Ca2+, Fe3+, or Cd2+ (Fig. S10).
Protein: DP04199 (UniProt Q9C7W1)
Region: residues 1	to 178
Annotation: cobalt ion binding (Molecular function)
Evidence: affinity chromatography evidence used in manual assertion
Supporting statements:
Since many RBPs need divalent metal ions for their interaction with RNA (30, 60, 61), we performed metal affinity chromatography experiments indicating that PARCL binds Zn2+, Ni2+, Cu2+, and Co2+, but not Mg2+, Ca2+, Fe3+, or Cd2+ (Fig. S10).
Protein: DP04199 (UniProt Q9C7W1)
Region: residues 1	to 178
Annotation: non-membrane-bounded organelle assembly (Biological process)
Evidence: confocal laser scanning microscopy evidence used in manual assertion
Supporting statements:
To analyze the subcellular localization of PARCL and the effect of mutations in the PLD or the C-terminus, N-terminally eYFP-tagged fusion constructs of PARCL were transiently expressed in Nicotiana benthamiana, and leaves were examined by confocal microscopy. In most cells, the eYFP-wildtype PARCL fusion (PARCLWT) appeared as condensates in the cytosol, in nuclei and nucleoli (Fig. 4, A and B).
Protein: DP04199 (UniProt Q9C7W1)
Region: residues 1	to 178
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: confocal laser scanning microscopy evidence used in manual assertion
Supporting statements:
To further validate the phase separation properties of PARCL, in vitro assays were performed. Here, phase separation could be induced under physiological conditions in 10% PEG 3350 and low salt regime (<150 mM NaCl) at neutral pH (Fig. 5). Condensates started to emerge at PARCL concentrations higher than 1 μM (Fig. 5A). Higher protein concentrations first increased the number of condensates and at concentrations above 6 μM, their size increased (Fig. 5A).
Protein: DP04199 (UniProt Q9C7W1)
Region: residues 1	to 178
Annotation: RNA binding (Molecular function)
Evidence: microscale thermophoresis evidence used in manual assertion
Supporting statements:
C, difference in RNA binding of unphosphorylated and phosphorylated AtPARCL against labeled miR164 as measured by MST. Addition of multiple negative charges within the PLD (PARCLPLD Y-E) did not affect RNA-binding affinities, whereas a C-terminal hyperphosphorylation led to an entire loss of RNA binding within the measured concentration range.
Protein: DP04199 (UniProt Q9C7W1)
Region: residues 165	to 178
Annotation: RNA binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
However, phosphorylation of PARCL by CKII at the predicted phosphorylation site at the S-rich C terminus (Fig. 1B) that was confirmed by mutating the S-segment serine to alanine residues (PARCLC-term S-A, Fig. S5) strongly reduced RNA-binding activity (Fig. 2C). These observations suggest that the C-terminus and not the PLD domain is involved in protein:RNA interactions.
Protein: DP04199 (UniProt Q9C7W1)
Region: residues 165	to 178
Annotation: phosphorylation display site (Disorder function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
The S-rich region was stepwise mutated until all possible phosphorylation sites were replaced by alanines (PARCLC-term S-A). AtPARCL could be phosphorylated in vitro by CKII whereas the alanine mutant could not, indicating the S-segment as a phosphorylation target for CKII.
According to the results the serines residues at position 165, 169, 171, 172, 173, 175 and 177 are display sites for phosphorylation.