LiteFold/DisProt huggingface dataset:
Protein: DP00287 (UniProt P40337)
Region: residues 72	to 78
Annotation: amyloid fibril formation (Biological process)
Evidence: atomic force microscopy evidence used in manual assertion
Supporting statements:
Here we report that using in silico approaches, we identified six (3-9 residues long) fragments predicted to harbor propensity to form amyloid fibrils. By a series of complementary biophysical techniques, including ThT binding assay, CD spectroscopy, Congo Red birefringence, transmission electron microscopy (TEM), atomic force microscopy (AFM), and X-ray diffraction, we found that two of the fragments, 72SQVIFCN78 and 147IFANITL153 , self-assembled in vitro and formed canonical amyloid fibrils β-sheets rich structures.
Furthermore, we performed AFM imaging to get additional details regarding the structural parameters such as height and diameter of the amyloid fibrils. Representative AFM images of amyloids formed by SN7 and IL7 are shown in Figure 2e, 2f, respectively. The amyloids of SN7 appeared as clusters of intercalated fibrils with a height of 5-10 nm and of diameter ~30 nm (n=30). The IL7 amyloids were observed to be of 3-13 nm height with a diameter of ~46 nm and varying length (n=30).
Protein: DP00287 (UniProt P40337)
Region: residues 72	to 78
Annotation: amyloid fibril formation (Biological process)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Here we report that using in silico approaches, we identified six (3-9 residues long) fragments predicted to harbor propensity to form amyloid fibrils. By a series of complementary biophysical techniques, including ThT binding assay, CD spectroscopy, Congo Red birefringence, transmission electron microscopy (TEM), atomic force microscopy (AFM), and X-ray diffraction, we found that two of the fragments, 72SQVIFCN78 and 147IFANITL153 , self-assembled in vitro and formed canonical amyloid fibrils β-sheets rich structures.
Among all the six peptides, two heptapeptides, namely 72SQVIFCN78 and 147IFANITL153 (hereafter termed SN7 and IL7, respectively) Figure. 1d exhibited a significant increase in ThT intensity compared to the other peptides when used at 100 µM, indicating their high propensity to self-assemble into amyloids.
To obtain deeper insights on the SN7 and IL7 aggregation kinetics, the two peptides were subjected to aggregation assay for 48 hours, using ThT as a real-time monitoring probe at physiological pH and temperature in 20 mM sodium phosphate buffer. As shown in Figure. 1e, both peptides displayed rapid aggregation kinetics, with an undetectable lag phase, reaching a plateau after 24-27 hours.
To obtain deeper insights on the SN7 and IL7 aggregation kinetics, the two peptides were subjected to aggregation assay for 48 hours, using ThT as a real-time monitoring probe at physiological pH and temperature in 20 mM sodium phosphate buffer. As shown in Figure. 1e, both peptides displayed rapid aggregation kinetics, with an undetectable lag phase, reaching a plateau after 24-27 hours.
Protein: DP00287 (UniProt P40337)
Region: residues 147	to 153
Annotation: amyloid fibril formation (Biological process)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Here we report that using in silico approaches, we identified six (3-9 residues long) fragments predicted to harbor propensity to form amyloid fibrils. By a series of complementary biophysical techniques, including ThT binding assay, CD spectroscopy, Congo Red birefringence, transmission electron microscopy (TEM), atomic force microscopy (AFM), and X-ray diffraction, we found that two of the fragments, 72SQVIFCN78 and 147IFANITL153 , self-assembled in vitro and formed canonical amyloid fibrils β-sheets rich structures.
Among all the six peptides, two heptapeptides, namely 72SQVIFCN78 and 147IFANITL153 (hereafter termed SN7 and IL7, respectively) Figure. 1d exhibited a significant increase in ThT intensity compared to the other peptides when used at 100 µM, indicating their high propensity to self-assemble into amyloids.
To obtain deeper insights on the SN7 and IL7 aggregation kinetics, the two peptides were subjected to aggregation assay for 48 hours, using ThT as a real-time monitoring probe at physiological pH and temperature in 20 mM sodium phosphate buffer. As shown in Figure. 1e, both peptides displayed rapid aggregation kinetics, with an undetectable lag phase, reaching a plateau after 24-27 hours.
To obtain deeper insights on the SN7 and IL7 aggregation kinetics, the two peptides were subjected to aggregation assay for 48 hours, using ThT as a real-time monitoring probe at physiological pH and temperature in 20 mM sodium phosphate buffer. As shown in Figure. 1e, both peptides displayed rapid aggregation kinetics, with an undetectable lag phase, reaching a plateau after 24-27 hours.
Protein: DP00287 (UniProt P40337)
Region: residues 147	to 153
Annotation: amyloid fibril formation (Biological process)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Here we report that using in silico approaches, we identified six (3-9 residues long) fragments predicted to harbor propensity to form amyloid fibrils. By a series of complementary biophysical techniques, including ThT binding assay, CD spectroscopy, Congo Red birefringence, transmission electron microscopy (TEM), atomic force microscopy (AFM), and X-ray diffraction, we found that two of the fragments, 72SQVIFCN78 and 147IFANITL153 , self-assembled in vitro and formed canonical amyloid fibrils β-sheets rich structures.
To further validate the ThT results, we performed CD analysis of these peptides before (t=0 hours) and after the aggregation (t=48 hours) to detect the amyloid-specific secondary structural changes. The concentration used for recording CD spectra was 400 µM to obtain a better signal-to-noise ratio. The CD spectra exhibited a negative ellipticity at 195 nm for IL7 and 200 nm for SN7 at the beginning of the aggregation (t=0), suggesting that the peptides possessed random coil conformation in their monomeric form. At the end of the aggregation period (t=48 hours), the individual peaks shifted to 220-224 nm, which is indicative of the β-sheet rich structures by both peptides (Figure. 2a). β-sheet formation is a characteristic hallmark of amyloid structures, thus substantiating the findings from ThT analysis, suggestive of self-assembly of the heptapeptides to form amyloids.
Protein: DP00287 (UniProt P40337)
Region: residues 72	to 78
Annotation: amyloid fibril formation (Biological process)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Here we report that using in silico approaches, we identified six (3-9 residues long) fragments predicted to harbor propensity to form amyloid fibrils. By a series of complementary biophysical techniques, including ThT binding assay, CD spectroscopy, Congo Red birefringence, transmission electron microscopy (TEM), atomic force microscopy (AFM), and X-ray diffraction, we found that two of the fragments, 72SQVIFCN78 and 147IFANITL153 , self-assembled in vitro and formed canonical amyloid fibrils β-sheets rich structures.
To further validate the ThT results, we performed CD analysis of these peptides before (t=0 hours) and after the aggregation (t=48 hours) to detect the amyloid-specific secondary structural changes. The concentration used for recording CD spectra was 400 µM to obtain a better signal-to-noise ratio. The CD spectra exhibited a negative ellipticity at 195 nm for IL7 and 200 nm for SN7 at the beginning of the aggregation (t=0), suggesting that the peptides possessed random coil conformation in their monomeric form. At the end of the aggregation period (t=48 hours), the individual peaks shifted to 220-224 nm, which is indicative of the β-sheet rich structures by both peptides (Figure. 2a). β-sheet formation is a characteristic hallmark of amyloid structures, thus substantiating the findings from ThT analysis, suggestive of self-assembly of the heptapeptides to form amyloids.
Protein: DP00287 (UniProt P40337)
Region: residues 72	to 78
Annotation: amyloid fibril formation (Biological process)
Evidence: particle scattering evidence used in manual assertion
Supporting statements:
Here we report that using in silico approaches, we identified six (3-9 residues long) fragments predicted to harbor propensity to form amyloid fibrils. By a series of complementary biophysical techniques, including ThT binding assay, CD spectroscopy, Congo Red birefringence, transmission electron microscopy (TEM), atomic force microscopy (AFM), and X-ray diffraction, we found that two of the fragments, 72SQVIFCN78 and 147IFANITL153 , self-assembled in vitro and formed canonical amyloid fibrils β-sheets rich structures.
This observation was further corroborated by collecting an X-ray diffraction pattern for the self-assembly of both peptides. Classical amyloid fibrils exhibit a characteristic diffraction pattern that displays the inter-strand distance of 4.5-4.8 Å and inter-sheet distance of 10-11Å, due to the specific arrangement of β-sheets in an amyloid fiber.
Protein: DP00287 (UniProt P40337)
Region: residues 147	to 153
Annotation: amyloid fibril formation (Biological process)
Evidence: particle scattering evidence used in manual assertion
Supporting statements:
Here we report that using in silico approaches, we identified six (3-9 residues long) fragments predicted to harbor propensity to form amyloid fibrils. By a series of complementary biophysical techniques, including ThT binding assay, CD spectroscopy, Congo Red birefringence, transmission electron microscopy (TEM), atomic force microscopy (AFM), and X-ray diffraction, we found that two of the fragments, 72SQVIFCN78 and 147IFANITL153 , self-assembled in vitro and formed canonical amyloid fibrils β-sheets rich structures.
This observation was further corroborated by collecting an X-ray diffraction pattern for the self-assembly of both peptides. Classical amyloid fibrils exhibit a characteristic diffraction pattern that displays the inter-strand distance of 4.5-4.8 Å and inter-sheet distance of 10-11Å, due to the specific arrangement of β-sheets in an amyloid fiber.
Protein: DP00287 (UniProt P40337)
Region: residues 147	to 153
Annotation: amyloid fibril formation (Biological process)
Evidence: cell staining evidence used in manual assertion
Supporting statements:
Here we report that using in silico approaches, we identified six (3-9 residues long) fragments predicted to harbor propensity to form amyloid fibrils. By a series of complementary biophysical techniques, including ThT binding assay, CD spectroscopy, Congo Red birefringence, transmission electron microscopy (TEM), atomic force microscopy (AFM), and X-ray diffraction, we found that two of the fragments, 72SQVIFCN78 and 147IFANITL153 , self-assembled in vitro and formed canonical amyloid fibrils β-sheets rich structures.
We subsequently investigated the amyloidogenic nature of SN7 and IL7 aggregates using the amyloid-specific Congo Red (CR) dye. CR is a histopathological dye routinely used to diagnose amyloids formed in vitro and in tissue biopsies. [18] The dye can bind to the cross-β-sheets of amyloids, and this interaction results in the exhibition of apple-green birefringence when observed under cross-polarized light.
Protein: DP00287 (UniProt P40337)
Region: residues 72	to 78
Annotation: amyloid fibril formation (Biological process)
Evidence: cell staining evidence used in manual assertion
Supporting statements:
Here we report that using in silico approaches, we identified six (3-9 residues long) fragments predicted to harbor propensity to form amyloid fibrils. By a series of complementary biophysical techniques, including ThT binding assay, CD spectroscopy, Congo Red birefringence, transmission electron microscopy (TEM), atomic force microscopy (AFM), and X-ray diffraction, we found that two of the fragments, 72SQVIFCN78 and 147IFANITL153 , self-assembled in vitro and formed canonical amyloid fibrils β-sheets rich structures.
We subsequently investigated the amyloidogenic nature of SN7 and IL7 aggregates using the amyloid-specific Congo Red (CR) dye. CR is a histopathological dye routinely used to diagnose amyloids formed in vitro and in tissue biopsies. [18] The dye can bind to the cross-β-sheets of amyloids, and this interaction results in the exhibition of apple-green birefringence when observed under cross-polarized light.
Protein: DP00287 (UniProt P40337)
Region: residues 1	to 213
Annotation: protein binding (Molecular function)
Evidence: immunoprecipitation evidence used in manual assertion
Supporting statements:
We confirmed the physical interaction of DJ-1 and VHL proteins in SH-SY5Y cells by immunoprecipitating VHL using VHL antibody and mouse IgG-conjugated beads and probing for endogenous DJ-1 (Fig. 1A). We observed that endogenous DJ-1 was coimmunoprecipitated with endogenous VHL
Protein: DP00287 (UniProt P40337)
Region: residues 1	to 213
Annotation: protein binding (Molecular function)
Evidence: protein mass spectrometry evidence used in manual assertion
Supporting statements:
VHL was one of the baits and analysis of the dataset suggested DJ-1 as one of its interacting candidates with the interaction confidence score of 0.31 an unbiased mass spectrometry screen, which indicated Von Hippel Lindau (VHL) protein as a potential interacting partner.
Protein: DP00287 (UniProt P40337)
Region: residues 59	to 213
Annotation: protein binding (Molecular function)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
In vitro-translated 35 S-labeled VHL interacted with GST–HDAC-1, GST–HDAC-2, and GST–HDAC-3 fusion proteins but not with GST (Fig. 7A).
VHL
residues 1–213 or 1–155 bound to the GST–HDAC fusion
proteins whereas VHL(1–58) and VHL(1–57) did not (Fig.
7B).
Protein: DP00287 (UniProt P40337)
Region: residues 1	to 213
Annotation: transcription corepressor activity (Molecular function)
Evidence: luciferase reporter gene assay evidence used in manual assertion
Supporting statements:
In vitro-translated 35 S-labeled VHL interacted with GST–HDAC-1, GST–HDAC-2, and GST–HDAC-3 fusion proteins but not with GST (Fig. 7A).
Taken together with
the cotransfection assays, these studies demonstrate that
VHL functions as a corepressor by recruiting HDACs to
HIF-1 alpha.
In addition, we
demonstrate that FIH-1 binds to VHL and that VHL also functions as a transcriptional corepressor that
inhibits HIF-1alpha transactivation function by recruiting histone deacetylases.
Protein: DP00287 (UniProt P40337)
Region: residues 1	to 213
Annotation: protein binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
To demonstrate binding directly and to localize the
region of FIH-1 that interacted with VHL and with HIF-
1 alpha, 35 S-labeled FIH-1 that was either full length (1–349)
or lacking N-terminal residues (126–349) was synthesized and tested for interaction with FLAG-tagged VHL
or GST–HIF1 alpha (531–826). FIH-1(1–349) bound to FLAG–VHL or GST–HIF-1 alpha (531–826), whereas FIH-1(126–349)
bound only to GST–HIF-1 alpha (531–826) 
Whereas VHL residues
1–155 were sufficient for binding to FIH-1, residues
1–213 were required for efficient binding to HIF-1 alpha (Fig.
4C). These studies indicate the presence of distinct bind-
ing sites that allow the simultaneous interaction of FIH-
1, HIF-1 alpha, and VHL.
Protein: DP00287 (UniProt P40337)
Region: residues 1	to 155
Annotation: protein binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
To demonstrate binding directly and to localize the
region of FIH-1 that interacted with VHL and with HIF-
1 alpha, 35 S-labeled FIH-1 that was either full length (1–349)
or lacking N-terminal residues (126–349) was synthesized and tested for interaction with FLAG-tagged VHL
or GST–HIF-1 alpha (531–826). FIH-1(1–349) bound to FLAG–VHL or GST–HIF-1 alpha (531–826), whereas FIH-1(126–349)
bound only to GST–HIF-1 alpha (531–826) 
Whereas VHL residues
1–155 were sufficient for binding to FIH-1, residues
1–213 were required for efficient binding to HIF-1 alpha (Fig.
4C). These studies indicate the presence of distinct bind-
ing sites that allow the simultaneous interaction of FIH-
1, HIF-1 alpha, and VHL.
Protein: DP00287 (UniProt P40337)
Region: residues 1	to 213
Annotation: regulation of gene expression (Biological process)
Evidence: green fluorescent protein immunolocalization evidence used in manual assertion
Supporting statements:
Regarding the expression of various factors, that of CD133 was decreased in the VHL transfectants and those of STAT3, JAK2 and Elongin A were eliminated.  However, the expression of PTEN and of VHL was upregulated.
VHL inhibited STAT3, JAK2 and Elongin A.
In addition, VHL upregulated PTEN expression.
Protein: DP00287 (UniProt P40337)
Region: residues 1	to 213
Annotation: regulation of gene expression (Biological process)
Evidence: northern blot evidence used in manual assertion
Supporting statements:
The restoration of VHL function in vitro in the VHL-deficient CC-RCC cell lines was found to reinstate PL6 expression, thus establishing a direct link between VHL and PL6.
We found that functional VHL inactivation caused down-regulation of PL6 expression, thus suggesting transcriptional regulation of PL6 by pVHL.
Northern blot analysis demonstrated that PL6 expression was significantly lower in cell lines with mutated VHL as compared to their wtVHL-transfected counterparts or to KRC/Y and 293T cell lines
Protein: DP00287 (UniProt P40337)
Region: residues 1	to 213
Annotation: regulation of gene expression (Biological process)
Evidence: immunolocalization evidence used in manual assertion
Supporting statements:
The restoration of VHL function in vitro in the VHL-deficient CC-RCC cell lines was found to reinstate PL6 expression, thus establishing a direct link between VHL and PL6.
Immunostaining analysis of VHL-deficient tumours (CC-RCC, haemangioblastoma and epididymal adenocarcinoma) showed no PL6 positivity compared to matched normal tissues and was in line with regulation of PL6 expression by pVHL.
Immunostaining of these cells with anti-PL6 antibodies showed no PL6 protein in VHL-deficient cells, while their wtVHL-transfected derivatives were positive for the PL6 protein. KRC/Y and 293T, cell lines with intact VHL gene, had a high PL6 protein level.
Protein: DP00287 (UniProt P40337)
Region: residues 1	to 213
Annotation: protein binding (Molecular function)
Evidence: yeast 2-hybrid evidence used in manual assertion
Supporting statements:
To identify low occupancy VHL protein partners with potential relevance to renal cancer, we screened a human kidney library against human VHL p30 using a yeast two-hybrid approach. Jade-1 (gene for Apoptosis and Differentiation in Epithelia) encodes a previously uncharacterized 64-kDa protein that interacts strongly with VHL protein and is most highly expressed in kidney.
The human Jade-1 gene was
identified as a particularly strong VHL-interacting clone in a
yeast two-hybrid screen of human VHL p30
Protein: DP00287 (UniProt P40337)
Region: residues 1	to 213
Annotation: protein binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Jade-1 immunoprecipitation of these same cell lysates permitted coimmunoprecipitation of VHL with full-length Jade-1, dd, and del1, but not with del2 (Fig. 3F). Likewise, VHL immunoprecipitation allowed coimmunoprecipitation of full-length Jade-1, dd, and del1, but not del2 (Fig. 3G). The VHL interaction with del1 did appear reduced, even taking into account lower del1 expression. As expected, immunoprecipitation in the absence of either partner did not show the interaction (Fig. 3, F and G, end lanes).Thus, these experiments demonstrate that the Jade-1 carboxyl terminus and PHD regions themselves are not absolutely required and that the amino terminus and the inter-PHD region in particular may be most important for interaction with VHL. These findings also support the specificity of the VHL-Jade-1 interaction.
Protein: DP00287 (UniProt P40337)
Region: residues 1	to 213
Annotation: regulation of gene expression (Biological process)
Evidence: Affymetrix GeneChip evidence used in manual assertion
Supporting statements:
We identiﬁed 30 genes (0.2 of total genes analysed) that demonstrated a >=X2-fold difference between VHL+ and VHL- cells in both experiments and in the three different clones.
Protein: DP00287 (UniProt P40337)
Region: residues 1	to 213
Annotation: regulation of gene expression (Biological process)
Evidence: quantitative polymerase chain reaction evidence used in manual assertion
Supporting statements:
Expression of target genes was normalized tob-actin and results for the 11 genes analysed are shown in Table 1. Real-time PCR analysis confirmed the results of the microarray analysis for all 11 genes.
Genes regulated by VHL: MLC2, GPR56, CDKN1C, P311, GLS, DOC-2/DAB2, GNG4, Claudin 4, SPARC, MCT3, E3, VEGF, PAI-1, beta-actin.
We transiently transfected empty vector (pCDNA3.1, In-vitrogen) or the wild-type pVHL (pCDNA 3.1-VHL (1–213) HA) into RCC4 cells to determine whether theresults of transient transfection were consistent withthose for stable transfection. The expression of fourgenes was analysed (CDKN1C, P311, Claudin 4 and E3) by real-time PCR and these demonstrated similar resultsin transient and stable transfections.
Protein: DP00287 (UniProt P40337)
Region: residues 1	to 213
Annotation: regulation of gene expression (Biological process)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
To determine whether pVHL regulation of target gene transcripts was reﬂected in protein levels, Western blots of RCC4/VHL+ and RCC4/VHL- protein extracts were probed with anti-CDKNIC and anti CT-3 antibodies. In each case the effect of pVHL on the transcripts was mirrored by the effect on protein levels. Thus pVHL upregulated CDKNIC and downregulated MCT3 protein expression (Figure 2).
Protein: DP00287 (UniProt P40337)
Region: residues 1	to 213
Annotation: regulation of gene expression (Biological process)
Evidence: cell transfection experiment evidence used in manual assertion
Supporting statements:
The relationship between pVHL regulation of target genes in an isogenic cell line and in primary RCC with VHL inactivation (somatic VHL mutation73p25 allele loss) was analysed in up to nine paired normal–tumour pairs. For CDKN1C (n=8), GNG4 (n=8), GPR56 (n=8), GPR56 (n=8),  MCT3 (n=4), MLC2 (n=6), P311(n=8) and SPARC (n=7), all tumours tested demonstrated altered expression consistent with the cell line data (results showed threshold of X2-fold differential expression).For DOC-2/DAB26/7  clear  cell  RCC  with VHL inactivation  demonstrated  downregulation  comparedto matched normal tissue. However, E3 and CDN4 demonstrated altered expression in only a minority of the primary tumours tested (4/9 and 1/3, respectively)(data not shown).
Protein: DP00287 (UniProt P40337)
Region: residues 1	to 213
Annotation: protein binding (Molecular function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
VHL was one of the baits and analysis of the dataset suggested DJ-1 as one of its interacting candidates with the interaction confidence score of 0.31 an unbiased mass spectrometry screen, which indicated Von Hippel Lindau (VHL) protein as a potential interacting partner.