Sandbox20: Difference between revisions

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===DNA Binding===

[[Image:RTP a3 DNA binding.png | thumb | upright=1.2| left| DNA-binding interactions of the a3 helix of RTP.]]

[[Image:RTP a3 DNA binding.png | thumb | upright=1.2| left| DNA-binding interactions of the α3 helix of RTP.]]

When an RTP dimer binds to a TerA or TerB site, the basic residues of the α3 helix are positioned in the major groove, and the β-ribbon rests within the minor groove. Non-specific ionic interactions between the N-terminus and the DNA backbone stabilise the complex.

It is known with some certainty that the RTP dimer adopts an asymmetric arrangement upon binding of the TerB site. In the [[2efw| C110S mutant]] complexed with the native TerB sequence, the two subunits interact differently with the DNA bases to produce wing-up and wing-down conformations. These can be distinguished by the angle the a2 helix makes with the a3 helix indicated in this <scene name='Sandbox20/2efw/14'>model</scene>. It is likely that asymmetry is also introduced when the RTP dimer binds to the TerA site, but the crystal structure of this complex has not been solved.

It is known with some certainty that the RTP dimer adopts an asymmetric arrangement upon binding of the TerB site. In the [[2efw| C110S mutant]] complexed with the native TerB sequence, the two subunits interact differently with the DNA bases to produce wing-up and wing-down conformations. These can be distinguished by the angle the α2 helix makes with the α3 helix indicated in this <scene name='Sandbox20/2efw/14'>model</scene>. It is likely that asymmetry is also introduced when the RTP dimer binds to the TerA site, but the crystal structure of this complex has not been solved.

The dissociation constant of the RTP-TerA complex is greater than that of RTP-TerB, indicating an inherently a lower binding affinity. However, following the binding of RTP to TerA, a positive cooperative effect facilitates the binding of RTP to TerA (Reference!). It has been proposed that RTP bends the DNA at the TerB site in a manner that favours RTP binding at TerA. The RTP dimer at TerB may also present a surface for stabilising interactions with the dimer at TerA through its β1 loop and β3 strand.

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@@ Line 33: / Line 33: @@
 ===DNA Binding===
 <Structure load='2EFW' size='300' frame='true' align='right' caption='RTP' scene='Sandbox20/2efw/3' />
-[[Image:RTP a3 DNA binding.png | thumb | upright=1.2| left| DNA-binding interactions of the a3 helix of RTP.]]
+[[Image:RTP a3 DNA binding.png | thumb | upright=1.2| left| DNA-binding interactions of the α3 helix of RTP.]]
 When an RTP dimer binds to a TerA or TerB site, the basic residues of the α3 helix are positioned in the major groove, and the β-ribbon rests within the minor groove. Non-specific ionic interactions between the N-terminus and the DNA backbone stabilise the complex.
-It is known with some certainty that the RTP dimer adopts an asymmetric arrangement upon binding of the TerB site. In the [[2efw| C110S mutant]] complexed with the native TerB sequence, the two subunits interact differently with the DNA bases to produce wing-up and wing-down conformations. These can be distinguished by the angle the a2 helix makes with the a3 helix indicated in this <scene name='Sandbox20/2efw/14'>model</scene>. It is likely that asymmetry is also introduced when the RTP dimer binds to the TerA site, but the crystal structure of this complex has not been solved.
+It is known with some certainty that the RTP dimer adopts an asymmetric arrangement upon binding of the TerB site. In the [[2efw| C110S mutant]] complexed with the native TerB sequence, the two subunits interact differently with the DNA bases to produce wing-up and wing-down conformations. These can be distinguished by the angle the α2 helix makes with the α3 helix indicated in this <scene name='Sandbox20/2efw/14'>model</scene>. It is likely that asymmetry is also introduced when the RTP dimer binds to the TerA site, but the crystal structure of this complex has not been solved.
 The dissociation constant of the RTP-TerA complex is greater than that of RTP-TerB, indicating an inherently a lower binding affinity. However, following the binding of RTP to TerA, a positive cooperative effect facilitates the binding of RTP to TerA (Reference!). It has been proposed that RTP bends the DNA at the TerB site in a manner that favours RTP binding at TerA. The RTP dimer at TerB may also present a surface for stabilising interactions with the dimer at TerA through its β1 loop and β3 strand.