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These helices form two repeat units that span part of the binding groove, where most protein interactions occur [ 18].
However, for most protein interactions in E. coli, there are not yet enough sequences available to allow the use of just one pair per genome, as the complex may not necessarily occur in all bacteria.
Since the vast majority of hypothetical fusion events would modify existing assembly pathways, this helps to rationalize why most protein interactions are not predicted by fusion-based methods (e.g., only 3.7% of the nonredundant subunit pairs in our data set are associated with evolutionary fusion events).
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In spite of the scale-free degree distribution that characterizes most protein interaction networks (PINs), it is common to define an ad hoc degree scale that defines "hub" proteins having special topological and functional significance.
It is likely that most protein-protein interactions would occur on the β-propeller domains of these proteins [ 54].
Most protein-protein interactions are mediated through specific domains that recognize other domains, motifs or modifications on other proteins [ 1].
Also included are detailed methods and experimental protocols that can be applied toward studying most protein-protein interactions.
These are the most significant protein interactions found for upregulated genes, and the most significant annotation of this group is "DNA-repair" and "response to DNA damage stimulus".
Three of the most conserved protein interactions in rice between DNA polymerase catalytic subunit and DNA polymerase subunit B, small nuclear ribonucleoproteins SmD2 and F and self-interaction of UTP-glucose-1-phosphate uridyltransferase were also among the most conserved in Arabidopsis (Geisler-Lee et al., 2007).
Furthermore, the most significant protein interactions in the data suggested that DNA-repair complexes are activated by EWS-FLI1.
As an extreme example, the ability of heparin to bind to antithrombin III is dependent on the presence of a rare pentasaccharide structure [10], whereas most other protein interactions seem to involve less stringent criteria [3], [5], [9], [12].
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