Sandbox Reserved 1063: Difference between revisions
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=== Helix-Turn-Helix Motif === | === Helix-Turn-Helix Motif === | ||
[[Image:Screen Shot 2017-04-18 at 11.56.32 PM.png|300 px|right|thumb|'''Figure 2'''. A generic protein representing the wHTH motif binding the major and minor groove of DNA similar to AdcR.]] | [[Image:Screen Shot 2017-04-18 at 11.56.32 PM.png|300 px|right|thumb|'''Figure 2'''. A generic protein representing the wHTH motif binding the major and minor groove of DNA similar to AdcR.]] | ||
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 <ref name="guerra" />. The <scene name='69/694230/Whth_4/7'>winged helix turn helix</scene> motif is made up of the <font color='blue'>α3</font> and <font color='blue'>α4 helices</font> along with <scene name='69/694230/Anti-parallel_beta_sheet/2'>anti-parallel β sheets</scene> on each side. There is one wHTH motif per monomer. The recognition helix, or the α4 helix, binds the major groove of DNA through [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bonding] and [https://en.wikipedia.org/wiki/Van_der_Waals_force Van der Waals interactions] between exposed bases <ref name="guerra" />. 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 β sheets contain several <scene name='69/694230/Positive_residues_on_wing_3/4'>Arginine, Asparagine, and Lysine residues</scene> that stabilize this interaction between DNA (The residues are only shown on one side because this same section of amino acids on the other protein monomer were not crystallized). The charge map down below highlights the dark blue tips of the wHTH motif consisting of lysine and arginine residues, which stabilize the negatively charged backbone of DNA. | 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 <ref name="guerra" />. The <scene name='69/694230/Whth_4/7'>winged helix turn helix</scene> motif is made up of the <font color='blue'>α3</font> and <font color='blue'>α4 helices</font> along with <scene name='69/694230/Anti-parallel_beta_sheet/2'>anti-parallel β sheets</scene> on each side. There is one wHTH motif per monomer. The recognition helix, or the α4 helix, binds the major groove of DNA through [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bonding] and [https://en.wikipedia.org/wiki/Van_der_Waals_force Van der Waals interactions] between exposed bases <ref name="guerra" />. 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 β sheets contain several <scene name='69/694230/Positive_residues_on_wing_3/4'>Arginine, Asparagine, and Lysine residues</scene> that stabilize this interaction between DNA (The residues are only shown on one side because this same section of amino acids on the other protein monomer <scene name='69/694230/Uncrystallized_loop/1'>were not crystallized</scene>). The charge map down below highlights the dark blue tips of the wHTH motif consisting of lysine and arginine residues, which stabilize the negatively charged backbone of DNA. | ||