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To detect all cases of peptide-mediated protein interactions of known 3D structure, we first parsed the PDB (02/2007) and identified all those entries containing two or more interacting proteins.
We report here that forty-five of the eighty-eight TAP-tagged PKs can be purified in amounts sufficient for MS analysis, and thirteen of these have been isolated as complexes with one or more interacting proteins.
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It will certainly be interesting to identify more CTTNBP2 interacting proteins in neurons, which may elucidate how CTTNBP2 is enriched in dendritic spines.
In addition to histone modifications, chromatin can be remodelled by ATP-dependent chromatin remodelling complexes [ 77], which make use of ATP hydrolysis to alter the histone-DNA interaction so that nucleosomal DNA becomes much more accessible to interacting proteins [ 78].
These machines represent sets of 10 or more spatially positioned interacting proteins that undergo highly ordered movements in a machine-like assembly (Alberts, 2003).
Moreover, it is thought that several hundred more human PP1 interacting proteins have yet to be discovered (Hendrickx et al., 2009).
Since binding sites tend to occur more frequently in interacting proteins than in non-interacting proteins [ 40], we sought to detect over-represented domains or motifs by comparing their frequency of occurrence in the two different datasets.
It is possible that scFv-6E intrabody, by increasing aggregate load, might expand the protein-recruiting surface area of intracellular aggregates, which in turn could enhance toxicity by sequestering more aggregate-interacting proteins away from their native functions.
Here, we assume that whenever two given proteins possess one or more interacting domains between them, those proteins will interact.
It has been shown that pairs of genes that genetically interact are more likely to encode interacting proteins than random pairs of genes (Kelley and Ideker, 2005; Tong et al., 2004; Wong et al., 2004).
There is evidence that genes with similar expression profiles are more likely to encode interacting proteins [ 33, 34].
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