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No antagonism or indeterminate interactions were identified.
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It is important to note that biological networks usually are indeterminate; for instance, the interactions of proteins often exist at certain probability.
Indeed, many of the peptide-SH2 interactions that fall in the indeterminate set are likely to be real binders.
To probe this complexity further we chose to study the model rhizobial symbiont genome Sinorhizobium meliloti [ 4]. S. meliloti is a model bacterium that can engage in a symbiotic interaction by infecting the roots of members of the genera Medicago and Melilotus, being the S. meliloti-Medicago truncatula interaction the model system for indeterminate type nodules [ 5].
Peptides with signal intensities between 1X and 3X mean were scored as "indeterminate" and ascribed as neither array positive binding interactions nor array-negative non-binders.
A statically indeterminate structure was modeled with inner redundant forces, where the interactions between the girder and diaphragms were indicated by a distortional moment.
The indeterminate pairs, as well as 6 additional pairs that involved interactions between two autoactivators, were excluded from further analyses.
Probing arrays with 50 SH2 domains identifies a total of 529 array-positive interactions, together with 5949 array-negative and 1122 indeterminate SH2-ligand pairs.
Among them is the "derivation" of all reality from the interaction of two opposite principles, "the One" and "the indeterminate dyad".
Non-array-positive literature-reported interactions tend to fall into three categories: 1) low affinity interactions; 2) near misses that are array-indeterminate and thus just below threshold; or 3) cases where orthogonal measurement confirms no interaction at the level of the individual SH2 domain and 11-mer phosphopeptide.
Its future is indeterminate.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com