Balance between asymmetry and abundance in multi-domain DNA-binding proteins may regulate the kinetics of their binding to DNA

摘要

Optimal recognition of proteins to DNA is governed by various factors among them the thermodynamics, kinetics and specificity of the protein-DNA complex. Multi-domain DNA-binding proteins are expected to have higher affinity and specificity due to the extensive interface they form with DNA. However, larger interface may result with higher friction when these proteins scan the DNA for the target site via the sliding mechanism. A way to overcome this drawback is to have asymmetry in the protein so that the interface with DNA is smaller. Alternatively, higher abundance can also increase the search speed. Here, using computational analysis of large data set of multi-domain zinc finger DNA-binding proteins, we report a trade-off between asymmetry and abundance.