Multiple module definitions were used to avoid bias of a certain protein complex annotation and make sure that results obtained hold independent of various protein complex maps used.
For SGD protein complexes, we found 58 such proteins, with no significant difference in contributions of WGD and SSD duplication types for most of the protein complex maps (see additional file 1, Table S3).
Proteins specifically isolated in nuclear FAK protein complexes were mapped onto the interactome, and those with physical or predicted direct or indirect interactions with Ccl5 transcription factors were analyzed using the NetworkAnalyzer plugin in Cytoscape.
To define the interactions that mediate SEC assembly and to understand how HIV Tat recruits P-TEFb (Wei et al., 1998) in the context of these large protein complexes, we mapped contacts among SEC subunits (Chou et al., 2012).
KEGG defines entries and an entry type, which specifies if the entry corresponds to a protein, complex, small molecule, referenced pathway map, or some other type.
where the signals representing the density map of a known protein complex structure are correlated to the signals in the cryoET map.
The mechanism through which the Map-NHERF1 protein complex contributes to filopodia formation is not known.
Covalent labeling (surface mapping) together with protein complex homology modeling and docking of trimers to form hexamer are utilized with all the above information to propose the likely quaternary structure of TNH, with chemical cross-linking providing cross-links consistent with the proposed structure.
Interestingly, tubulin post-translational modifications were shown to influence the recruitment of protein complexes such as MAPs (i.e. Tau, MAP1B) or plus-end tracking proteins (p150Glued, EB1, CLIP170) onto microtubules (Verhey and Gaertig, 2007).
Differently from previous homology mapping approach, our methods integrate the PPI data information and protein complex information.
