User:Chloe Paul/Replication Terminator Protein: Difference between revisions

<StructureSection <applet load='1bm9' size='500' side='right' caption='Structure of RTP (PDB entry [[1bm9]])' scene='Chloe_Paul/Sandbox_1/Basicrtp/1'>RTP has been found to exist as a symmetric α+β protein in solution and a homomeric dimer through crystal structure determination <ref name="bussiere">PMID: 7867072</ref>.These identical monomers each contain four α helices (α1, α2, α3, α4), one β strand (β1) and two β ribbons(β2 and β3). It also contains a distordered N-terminal region. When the two monomers come together and the two α4 helices bind, forming a dimer with an overall rectangle shape of 66Å x 35 Å x 30 Å <ref name="bussiere" />. The long C-terminal helices (α4) facilitate binding by establishing a hydrophobic core between the monomers (residues 93-103.) The helices form an antiparallel coiled-coil structure and additionally contribute an amino acid to the hydrophobic core of the other monomer (residue 122)<ref name="bussiere" />. Both monomers still remain structurally similar when they form the dimer in solution. It should be noted that when in solution the flexible loop between β2 and β3 are able to assume different conformations <ref name="bussiere" />. This later gives rise to the "wing-up, wing-down" conformation when bound to native DNA<ref name="vivian">PMID:17521668</ref>.</StructureSection>

<StructureSection load='1f4k' size='500' side='right' caption='RTP bound to symmetric DNA (PDB entry [[1f4k]])' scene=''>RTP has been of interest in terms of its specific binding to DNA because it doesn’t use the common DNA structural motifs such as a basic leucine zipper, zinc finger or helix-turn-helix motif. It has been established that RTP, like Tus, is sequence specific, as it binds as the Ter sites. These comprise two sequences that are imperfect inverted repeats <ref name="bussiere" /><ref name="vivian" />. This means that RTP needs to be able to recognise specific bases in the helical DNA structure by reading the exposed edges of the bases located in the major and minor grooves of DNA. Structurally RTP interacts with DNA through the α3 helices in the major grooves, its anti-parallel β-sheets (β2 and β3) in the minor grooves. The flexible N-terminal regions wrap with non-specific ionic interactions around the DNA <ref name=“wilce”>PMID:11224562</ref>. </StructureSection>

<StructureSection load='2efw' size='500' side='right' caption='RTP bound to native DNA (PDB entry [[2efw]])' scene=''>The RTP:DNA interaction has been shown to be able to induce two different conformations of RTP depending upon the nature of the DNA. Early experiments used to determine how they interacted, used symmetric DNA (sDNA) which resulted in RTP binding symmetrically. However in nature, RTP was found to have a polar mechanism which implied asymetric binding, leading to further investigations of how RTP bound to DNA. It was later shown that when RTP bound to native or non-symmetric DNA (nDNA) it induced an asymmetric "wing-up, wing-down" form of RTP with a two faces. One face, known as the “blocking” face acts to terminate the approaching replication fork. The other face is described as the “permissive” face as it allows the replication fork to proceed along the DNA.  These faces correspond to the A site and B site of the Ter sequence of DNA respectively. These DNA sites are the two halves of the pseudosymmetric palindromic sequence. The conformation and thus function of the RTP monomer depends on which site the RTP monomer binds to.  It is the concept of these two faces that give rise to the polar mechanism of RTP.</StructureSection>