RTP and Tus: Difference between revisions

[[Image:RTP_DBA_Model2.jpg|300px|right|thumb| Differential Binding Affinity Model proposed by Kralicek ''et al.'' in 1997.

Image from Duggin ''et al.'', 2004. ]]

In 1997, Kralicek ''et al.'' proposed an alternate theory of RTP arrest known as the '''Differential Binding Affinity''' Model. This model also involves the idea of a “molecular clamp”, and states that the polar arrest mechanism can be explained purely based on the differential binding affinities of RTP to the A and B termination sites. The theory is based on the assumption that the affinity of RTP for the B site in the complete complex is much greater than the affinity of for the A site in the complete complex, or the affinity of a single RTP monomer to the B site alone. According to the model, only the affinity of the complex RTP for the ''Ter''-B (K3 in Figure X) is sufficient to prevent the removal of RTP from DNA when the replication fork moves along the DNA; therefore, if the replisome approaches from the B site, the RTP is not removed from the DNA and the replication fork is arrested. Similarly, when the replication fork approaches from the A site the binding affinity (K4 in Figure X) is not sufficient to prevent the removal of RTP and the replisome is able to pass.<ref>Kralicek, AV, Wilson PK, Ralston GB, Wake RG, King GF (1997) Reorganization of terminator DNA upon binding replication terminator protein: implications for the functional replication fork arrest complex. ''Nucleic Acids Research'' 25(3): 590-596.</ref>