LiteFold/DisProt huggingface dataset:
Protein: DP04430 (UniProt P38829)
Region: residues 1	to 102
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
We noticed that both the IMAC purified dtCia2 and refolded Cia2 exhibited aberrantly slow migration in SDS-PAGE.
To determine if the N-terminus is disordered, we removed the first 102 residues (Δ102-Cia2) and refolded the protein from insoluble inclusions. Δ102-Cia2’s SDS-PAGE migration behavior normalized (Fig.2A, lane 3).
Protein: DP04431 (UniProt A0A936SUR2)
Region: residues 1	to 64
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H–15N HSQC spectrum shows a narrow spread of proton NMR signals, characteristic of an intrinsically disordered protein.
The 1H–15N HSQC reveals a narrow spread of amide signals in the proton dimension, a hallmark of disordered proteins (Fig. 1).
Cross-references: BMRB:51116
Protein: DP04432 (UniProt A0A3Q8IT45)
Region: residues 1	to 54
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The black dashed line on the left panel represents a most likely flexible 55-aa N-terminal tail (68-aa in TcKSRP), which remained unmodeled due to its lack of density.
Cross-references: PDB: 5OSG
Protein: DP04433 (UniProt P0DXF5)
Region: residues 1	to 250
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Here we present a comprehensive biophysical and spectroscopy analysis of FapA, FapB and FapC and provide insight into their molecular interactions. We show that all three proteins are primarily disordered with some regions with structural propensities for α-helix and β-sheet.
Protein: DP04433 (UniProt P0DXF5)
Region: residues 1	to 250
Annotation: amyloid fibril formation (Biological process)
Evidence: transmission electron microscopy evidence used in manual assertion
Supporting statements:
Negative-stained TEM was used to visualize the fibrils formed in the ThT assays, both FapB and FapC fibrils alone (Figure 5(A) and (B)) as well as FapB and FapC fibrillated with FapA (Figure 5(C) and (D)).
Protein: DP04433 (UniProt P0DXF5)
Region: residues 1	to 250
Annotation: amyloid fibril formation (Biological process)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Fibrils are clearly seen for all samples, as expected from the observed increase in ThT fluorescence (Figure 3(A), Figure 4(A)).
Protein: DP04433 (UniProt P0DXF5)
Region: residues 1	to 250
Annotation: disorder (Structural state)
Evidence: circular dichroism evidence used in manual assertion
Supporting statements:
CD data show FapA, FapB, and FapC have deep minima around 200 nm (Figure 1(A)), which is typical for a random coil structure.
Protein: DP04433 (UniProt P0DXF5)
Region: residues 1	to 250
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The fitting with the simple Gaussian random coil model is in accordance with the trend of primarily random coil seen in CD.
Protein: DP04434 (UniProt P0DXF3)
Region: residues 1	to 152
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
FapA is an intrinsically disordered chaperone for Pseudomonas functional amyloid FapC.
Protein: DP04434 (UniProt P0DXF3)
Region: residues 1	to 152
Annotation: negative regulation of amyloid fibril formation (Biological process)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
FapA inhibits FapC fibrillation by targeting the nucleation step, whereas for FapB the elongation step is modulated.
For both FapC concentrations, the ThT end level increased at larger FapA concentrations although FapA did not produce a ThT-positive signal in isolation (Figure 3(A)). This suggests that the interactions of ThT with fibrils has changed, most likely due to structural changes in the fibril surface structure.
Thus, from both experiments it can be concluded that FapA inhibits FapC fibrillation by increasing tLag but without influencing rElong.
Normalized data (Figure 4(B)) clearly show a systematic decrease in rElong (measured as the slope of the normalized curves from 1−4 hours for each triplicate) as a function of FapA concentration (inset of Figure 4(B)). Thus, FapA inhibits FapB fibrillation by reducing rElong but does not lead to a lag phase.
Protein: DP04434 (UniProt P0DXF3)
Region: residues 1	to 152
Annotation: disorder (Structural state)
Evidence: circular dichroism evidence used in manual assertion
Supporting statements:
CD data show FapA, FapB, and FapC have deep minima around 200 nm (Figure 1(A)), which is typical for a random coil structure.
Protein: DP04434 (UniProt P0DXF3)
Region: residues 1	to 152
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The fitting with the simple Gaussian random coil model is in accordance with the trend of primarily random coil seen in CD.
Protein: DP04435 (UniProt P0DXF4)
Region: residues 1	to 182
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Here we present a comprehensive biophysical and spectroscopy analysis of FapA, FapB and FapC and provide insight into their molecular interactions. We show that all three proteins are primarily disordered with some regions with structural propensities for α-helix and β-sheet.
Protein: DP04435 (UniProt P0DXF4)
Region: residues 1	to 182
Annotation: amyloid fibril formation (Biological process)
Evidence: transmission electron microscopy evidence used in manual assertion
Supporting statements:
Negative-stained TEM was used to visualize the fibrils formed in the ThT assays, both FapB and FapC fibrils alone (Figure 5(A) and (B)) as well as FapB and FapC fibrillated with FapA (Figure 5(C) and (D)).
Protein: DP04435 (UniProt P0DXF4)
Region: residues 1	to 182
Annotation: amyloid fibril formation (Biological process)
Evidence: thioflavin T based fluorescence spectroscopy evidence
Supporting statements:
Fibrils are clearly seen for all samples, as expected from the observed increase in ThT fluorescence (Figure 3(A), Figure 4(A)).
Protein: DP04435 (UniProt P0DXF4)
Region: residues 1	to 182
Annotation: disorder (Structural state)
Evidence: circular dichroism evidence used in manual assertion
Supporting statements:
CD data show FapA, FapB, and FapC have deep minima around 200 nm (Figure 1(A)), which is typical for a random coil structure.
Protein: DP04435 (UniProt P0DXF4)
Region: residues 1	to 182
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The fitting with the simple Gaussian random coil model is in accordance with the trend of primarily random coil seen in CD.