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STITCHER: Dynamic assembly of likely amyloid and prion β-structures from secondary structure predictions.

Bryan AW, O'Donnell CW, Menke M, Cowen LJ, Lindquist S, Berger B - Proteins (2011)

Bottom Line: Putative structural heterogeneity can be inferred from sequence regions that compose poorly.We put forward predicted structures for the yeast prion Sup35, suggesting N-terminal structural stability enabled by tyrosine ladders, and C-terminal heterogeneity.Predictions for the Rnq1 prion and alpha-synuclein are also given, identifying a similar mix of homogenous and heterogeneous secondary structure elements.

View Article: PubMed Central - PubMed

Affiliation: Harvard/MIT Division of Health Science and Technology, Bioinformatics and Integrative Genomics, E25-519 Cambridge, Massachusetts 02139; Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142; MIT Computer Science and Artificial Intelligence Laboratory, The Stata Center, Cambridge, Massachusetts 02139.

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STITCHER results for Sup35p (m = 3) in three species. (A) C. albicans, (B) S. cerevisiae, and (C) Y. lipolytica. At left, a contact map of the 50 highest-scoring folds. At right, the top-scoring structure. For S. cerevisiae, the highest-scoring structures for n = 2 and n = 3 are presented. For description of colors, numbers, and lines, see the caption to Figure 1.
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fig03: STITCHER results for Sup35p (m = 3) in three species. (A) C. albicans, (B) S. cerevisiae, and (C) Y. lipolytica. At left, a contact map of the 50 highest-scoring folds. At right, the top-scoring structure. For S. cerevisiae, the highest-scoring structures for n = 2 and n = 3 are presented. For description of colors, numbers, and lines, see the caption to Figure 1.

Mentions: We used STITCHER to computationally investigate the amyloidogenic impact of minor sequence differences in homologs proteins. Three homologs of the yeast prion Sup35p were chosen, taken from Candida albicans, Saccharomyces cerevisiae, and Yarrowia lipolytica. The outputs of these predictions are shown in Figure 3.


STITCHER: Dynamic assembly of likely amyloid and prion β-structures from secondary structure predictions.

Bryan AW, O'Donnell CW, Menke M, Cowen LJ, Lindquist S, Berger B - Proteins (2011)

STITCHER results for Sup35p (m = 3) in three species. (A) C. albicans, (B) S. cerevisiae, and (C) Y. lipolytica. At left, a contact map of the 50 highest-scoring folds. At right, the top-scoring structure. For S. cerevisiae, the highest-scoring structures for n = 2 and n = 3 are presented. For description of colors, numbers, and lines, see the caption to Figure 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3298606&req=5

fig03: STITCHER results for Sup35p (m = 3) in three species. (A) C. albicans, (B) S. cerevisiae, and (C) Y. lipolytica. At left, a contact map of the 50 highest-scoring folds. At right, the top-scoring structure. For S. cerevisiae, the highest-scoring structures for n = 2 and n = 3 are presented. For description of colors, numbers, and lines, see the caption to Figure 1.
Mentions: We used STITCHER to computationally investigate the amyloidogenic impact of minor sequence differences in homologs proteins. Three homologs of the yeast prion Sup35p were chosen, taken from Candida albicans, Saccharomyces cerevisiae, and Yarrowia lipolytica. The outputs of these predictions are shown in Figure 3.

Bottom Line: Putative structural heterogeneity can be inferred from sequence regions that compose poorly.We put forward predicted structures for the yeast prion Sup35, suggesting N-terminal structural stability enabled by tyrosine ladders, and C-terminal heterogeneity.Predictions for the Rnq1 prion and alpha-synuclein are also given, identifying a similar mix of homogenous and heterogeneous secondary structure elements.

View Article: PubMed Central - PubMed

Affiliation: Harvard/MIT Division of Health Science and Technology, Bioinformatics and Integrative Genomics, E25-519 Cambridge, Massachusetts 02139; Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142; MIT Computer Science and Artificial Intelligence Laboratory, The Stata Center, Cambridge, Massachusetts 02139.

Show MeSH
Related in: MedlinePlus