Sandbox Reserved 1063: Difference between revisions

The binding of Zinc allows for the conformational change that induces the binding of DNA in order to activate genes. The binding of Zinc metals creates a hydrogen bond network within the protein that connects the metal binding sites and the [https://en.wikipedia.org/wiki/DNA-binding_domain DNA binding domain]. Most importantly, the hydrogen bonding network connects the metal binding pockets to the alpha 4 helix. Alpha 4 helix plays a crucial role in binding DNA because it acts as the recognition helix. The specific sequence of DNA that is recognized by alpha helix 4 is unknown at the moment; however, scientists believe that the hydrogen bond network acts as an allosteric activator for the protein to bind DNA. The hydrogen bond network connects the alpha 2 and alpha 4 helix via hydrogen bonding between specific residues. After zinc is bound, a glutamate (<font color='blue'>E24</font>) residue from a random coil accepts a hydrogen bond from the carboxamide end of an asparagine (<font color='green'>N38</font>) residue from the alpha 2 helix. Then, a glutamine (<font color='gold'>Q40</font>) residue from alpha 2 helix accepts a hydrogen bond from a serine (<font color='red'>S74</font>) residue from the alpha 4 helix. The color coding in the previous sentence represents the <scene name='69/694230/Hydrogen_bonding_1/1'>Hydrogen Bonding Network</scene>, which is seen across the MarR family as a whole. Now the protein is ready to bind DNA.

[[Image:Charge_map.jpg |300 px|right|thumb| A charge map of AdcR shows the general triangular shape and the positive charged (blue) area on HTH domains]]

=== Helix-Turn-Helix Domain ===

The AdcR MarR transcriptional regulator's structure resembles the other proteins in the same family as mentioned before; however, the most notable differences are found in the winged helix-turn-helix (wHTH) motif that assists in binding DNA. Although AdcR is a highly alpha helical protein, the "wings" of the DNA binding domain consist of two anti parallel beta strands that are made up of several positively charged residues such as Arg. The major groove of DNA is bound to the recognition helix while the wings grip onto the minor grooves. The charge map on the right highlights the <font color='blue'>positively</font> charged areas, which stabilize the negatively charged backbone of the major and minor grooves of DNA. There is one on each domain of the protein.

The <scene name='69/694230/Whth/1'>winged helix-turn-helix</scene> domain is made up of the alpha 2 and alpha 4 helices along with anti-parallel beta sheets on each side. These structures can been seen in the java applet as all green structures in the rainbow scheme for clarity purposes. Only one monomer is shown. The recognition helix, or the alpha 4 helix, binds the major groove of DNA through hydrogen bonding and Van der Waals interactions between exposed bases. The wings of the helix bind the minor groove of DNA while the other helices stabilize the DNA and Protein upon binding. The two anti parallel beta sheets contain several <scene name='69/694230/Positive_residues_on_wing/1'>Arginine, Asparagine, and Lysine residues</scene> that stabilize this interaction between DNA.

</StructureSection>

== References ==

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