User:Karen Lee/Sandbox 1

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-		+	What is interesting about RTP? Two different RTP B sites have been found to interact with RTP. These are the symmetrical RTP B (sRB) site from TerI (the first Ter site that the clockwise replication fork encounters) and the native RTP B (nRB) site from TerI. These sequences differ only in 6 base pairs – three at the downstream end and three at the upstream end. The downstream changes have no bearing on the structure of RTP since the protein binds the downstream region in both sRB and nRB sequences with similar conformation. Additionally, no base-specific interactions are made in this region. However, the three upstream changes are all located in the major groove of the dsDNA. This is where the α3 helix binds which underlies RTP binding specificity [3]. Therefore, in binding of RTP monomers to the Ter site, there is a differential binding affinity in A and B sites, due to changes in the nRB site.
		+	This leads into the fact that RTP binds asymmetrically across the nRB site and therefore allows the complex to act as a polar barrier to the replication fork. When the fork approaches the B site (with tight RTP-DNA binding) the fork is unable to progress and is paused. Approaching from the A site does not impede its progress. This polarity can be explained by both the differential binding affinity as explained above and the cooperative binding affect of the RTP monomers. The complex formed between an RTP molecule and the B site facilitates cooperative binding of another RTP monomer to the A site to form a complete RTP-Ter complex [3].

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Revision as of 04:04, 4 May 2011

What is interesting about RTP? Two different RTP B sites have been found to interact with RTP. These are the symmetrical RTP B (sRB) site from TerI (the first Ter site that the clockwise replication fork encounters) and the native RTP B (nRB) site from TerI. These sequences differ only in 6 base pairs – three at the downstream end and three at the upstream end. The downstream changes have no bearing on the structure of RTP since the protein binds the downstream region in both sRB and nRB sequences with similar conformation. Additionally, no base-specific interactions are made in this region. However, the three upstream changes are all located in the major groove of the dsDNA. This is where the α3 helix binds which underlies RTP binding specificity [3]. Therefore, in binding of RTP monomers to the Ter site, there is a differential binding affinity in A and B sites, due to changes in the nRB site. This leads into the fact that RTP binds asymmetrically across the nRB site and therefore allows the complex to act as a polar barrier to the replication fork. When the fork approaches the B site (with tight RTP-DNA binding) the fork is unable to progress and is paused. Approaching from the A site does not impede its progress. This polarity can be explained by both the differential binding affinity as explained above and the cooperative binding affect of the RTP monomers. The complex formed between an RTP molecule and the B site facilitates cooperative binding of another RTP monomer to the A site to form a complete RTP-Ter complex [3].