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Exploring the sequence determinants of amyloid structure using position-specific scoring matrices
TLDR
This work experimentally explored the sequence space of amyloid hexapeptides and used the derived data to build Waltz, a web-based tool that uses a position-specific scoring matrix to determine amyloids-forming sequences and allows users to identify and better distinguish between amyloidal sequences and amorphous β-sheet aggregates. Expand
Protein prenyltransferases
TLDR
Farnesyltransferase-inhibitor drugs have been developed as anti-cancer agents and may also be able to treat several other diseases, but the effects of these inhibitors are complicated, however, by the overlapping substrate specificities of geranylgeranyltransferase I and farnesyl transferase. Expand
TPR Subunits of the Anaphase-Promoting Complex Mediate Binding to the Activator Protein CDH1
TLDR
Biochemically characterized subcomplexes of the anaphase-promoting complex (APC) of the human APC suggest that the different TPR subunits of the APC might function as receptors that interact with the C termini of regulatory proteins such as CDH1, CDC20, and APC10. Expand
The WD40 propeller domain of Cdh1 functions as a destruction box receptor for APC/C substrates.
TLDR
It is shown that the D box directly interacts with an evolutionarily conserved surface on the predicted WD40 propeller structure of Cdh1 and that this interaction is essential for processive substrate ubiquitination. Expand
The Tudor domain 'Royal Family': Tudor, plant Agenet, Chromo, PWWP and MBT domains.
TLDR
This finding has been extended, using a combination of sequence- and structure-dependent approaches, to show that the three beta-stranded core regions of Tudor, PWWP, chromatin-binding (Chromo) and MBT domains are homologous because they originate from a common ancestor. Expand
Prediction of peroxisomal targeting signal 1 containing proteins from amino acid sequence.
TLDR
The refined PTS1 motif description was implemented in a prediction tool composed of taxon-specific functions (metazoa, fungi, remaining taxa), capable of recognising potential PTS1s in query sequences, and the tool can be applied for large-scale unsupervised sequence database annotation. Expand
SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants
TLDR
The new meta-analysis application allows plotting correlations between phenotypic features for a user-selected set of variants in a sequence- and structure-based bioinformatics tool, including automated structure modeling. Expand
Kleisins: a superfamily of bacterial and eukaryotic SMC protein partners.
TLDR
A superfamily of eukaryotic and prokaryotic proteins (kleisins) that includes ScpA, Scc1, Rec8, and Barren is described, suggesting that ring formation with SMC proteins may define this family. Expand
Design of multistable RNA molecules.
TLDR
It is argued that both the general properties of the sequence structure map of RNA secondary structures and the ease with which the design tool finds bistable RNAs strongly indicates that RNA switches are easily accessible in evolution. Expand
Enzymes and auxiliary factors for GPI lipid anchor biosynthesis and post-translational transfer to proteins.
TLDR
A structural proposal would explain the paradoxical properties of the GPI lipid anchor signal motif and of PIG-K/GPI8 orthologs without membrane insertion regions in some species. Expand
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