What matters for lac repressor search in vivo--sliding, hopping, intersegment transfer, crowding on DNA or recognition?
Bottom Line: Including a mechanism of inter-segment transfer between distant DNA segments does not bring down the 1D diffusion to the expected fraction of the in vitro value.This suggests a mechanism where transcription factors can slide less hindered in vivo than what is given by a simple viscosity scaling argument or that a modification of the model is needed.For example, the estimated diffusion rate constant would be consistent with the expectation if parts of the chromosome, away from the operator site, were inaccessible for searching.
Affiliation: Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden.Show MeSH
Mentions: The process by which two DNA segments diffuse within binding distance of a protein capable of transiently binding both segments and therefore transfer from one segment to the other without dissociation is called intersegment transfer. We take this mode into account using the approach of (5). For the combination of parameters having no analytic counterpart we used simulations to get the chi-squared values. We find that intersegment transfer rates below ca 100 s−1 have a negligible effect on the minimal acceptable D1 value (Figure 5). The reason for the small effect is that intersegment transfer disrupts the sliding process which weakens the correlations in the two-operator data effectively increasing the required D1 value. At the same time, intersegment transfer increases the specific association rate, effectively decreasing D1. For higher values of kIST, the fit becomes increasingly bad, pushing the minimal acceptable D1 higher (Supplementary Figure S8).
Affiliation: Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden.