In other words, the order of Ca2+-CaM-target complex assembly, the number of bound Ca2+ ions, target specific Ca2+-CaM cooperative affinities, in addition to unique CaM-target interaction interfaces, all allow CaM to achieve its highly versatile intracellular multifunctionality.
The newly discovered genomic targets that contain a binding motif are generally contacted by Ss-LrpB through non-cooperative low-affinity binding, in contrast to the local gene targets.
The only differences between these models were the values of the parameters describing protein affinities of cooperative DNA binding - the affinity of either KorA or KorB to DNA-KorB or DNA-KorA complexes, respectively.
Despite the high-affinity, cooperative binding to multiple binding sites in vitro, no enrichment of this genomic region has been detected in the ChIP-chip assay.
These may include favoring high-affinity cooperative TF binding and lateral diffusion of TF binding along regulatory regions, or simply increasing of the local TF concentration in the vicinity of these regions and thereby increase the probability of functional interactions [ 38– 40].
DOI: http://dx.doi.org/10.7554/eLife.00960.014 10.7554/eLiFigure60.015 Figure 4 figure supplement 2. Cheaters with a much higher affinity for cooperative benefits than cooperators can destroy heterotypic cooperation even in a spatial environment.
The PWWP domain is demonstrated here to bind DNA in a cooperative manner with μM affinity.
The inclusion or removal of these SLiMs can switch the subcellular localisation of an isoform, promote cooperative associations, refine the affinity of an interaction, coordinate phase transitions within the cell, and even create isoforms of opposing function.
It is also possible, in principle, for nearest neighbor interactions to result in cooperative gains, thereby improving affinity beyond what would be predicted by thermodynamic additivity, such cooperative interactions were not observed here.
