User:Cameron Ball/Sandbox 1: Difference between revisions

<scene name='User:Cameron_Ball/Sandbox_1/Rtp_dna_complex/1'>RTP binds DNA</scene> through interactions between the <scene name='User:Cameron_Ball/Sandbox_1/Rtp_alpha_helices_and_dna_/1'>alpha helices</scene> and the major groove of DNA. Two possible mechanisms were originally proposed to explain it's activity; The "differential binding affinity" model (DBA), where RTP's different affinity for the A and B sites gives rise to the polarity, and the "interaction" model, where there is some protein-protein interaction between RTP's non-permissive face and the approaching replisome unit. Recent data has shown that RTP-Ter contact is not sufficient to cause arrest, suggesting the interaction model is the best approximation. <ref>Duggin, I.G., Mathews, J.M., Dixon, N.E., Wake, R.G., Mackay, J.P., A Complex Mechanism Determines Polarity of DNA Replication Fork Arrest by the Replication Terminator Complex of ''Bacillus subtilis'' 2005 The Journal of Biological Chemistry, 280, 13105-13113.</ref><ref> Kaplan, D.L and Bastia, D, Mechanisms of polar arrest of a replication fork, Molecular Microbiology 2009:72:2), pp 279-285 </ref> Additionally, in 2006 Ian Duggin showed that the fork arrest efficiency of RTP can be lowered by attaching peptides that would block any protein-protein interaction from occurring, while not affecting the RTP-DNA binding affinity<ref> Duggin, I.G., DNA replication fork arrest by the Bacillus subtilis RTP-DNA complex involves a mechanism that is independent of the affinity of RTP-DNA binding ''J Mol Biol'' '''361:'''1-6</ref>.