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We hope that using "binding cooperativity" rather than "coupling" in the revised manuscript eliminates the ambiguity.
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The Tim8 Tim13 complex contained approximately six binding sites and showed a complex binding interaction indicative of positive cooperativity rather than a simple bimolecular interaction.
More recently, Macdonald and Pike have presented evidence that high- and low-affinity binding can be explained by negative cooperativity, rather than by the existence of two distinct populations of receptor [8].
High- and low-affinity binding sites therefore occur in the same receptor dimer and result from negative cooperativity rather than from distinct populations of receptor.
Literature data suggests that activity is marked by positive cooperativity rather than no cooperativity or negative cooperativity.
The de novo evolution of active homo-oligomers is likely to be rare, making causality more plausible in the opposite direction, at least under the cooperativity rather than the sequestration explanation of our results.
To our knowledge, analysis of large-scale studies has provided relatively little evidence supporting a major role for true cooperativity among TFs in gene regulation— i.e., that transcript levels are controlled by logical combinations of TF binding events, rather than a simpler aggregative or combinatorial effect.
We use TF binding data rather than binding motifs as predictor variables.
Quantitative analysis indicates a competitive binding rather than a screening binding during egg-box dimerization, which is responsible for the inhibitory effect in the lower Ca concentration regime.
In this way and depending on the binding affinities of the TF, binding cooperativity may occur, leading to a higher exponent than the one corresponding to the degree of the multimer employed.
A slight but insignificant decrease in binding cooperativity was also observed.
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