Sandbox Reserved 1063: Difference between revisions

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OCA, Zach LaRoche, Paxton Schowe, Geoffrey C. Hoops, Alexi Zaniker, Shandeep Singh, Isaac C. Gluesenkamp

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 === Hydrogen Bond Network ===
-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]. More importantly, the hydrogen bonding network connects the metal binding pockets to the alpha 4 helix. Alpha 4 helix on each monomer plays a crucial role in binding DNA because it acts as the recognition helix. <scene name='69/694230/Recognition_helix/2'>Specific residues</scene> in the recognition helix recognize a sequence of DNA that is unknown at the moment; however, scientists do know 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 <ref>PMID:22085181</ref>. The color coding in the previous sentence represents the <scene name='69/694230/Hydrogen_bonding_1/3'>hydrogen bond network</scene> (<scene name='69/694230/Hydrogen_bonding_2/2'>with measurements</scene>), which is seen across the MarR family as a whole.
+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]. More importantly, the hydrogen bonding network connects the metal binding pockets to the alpha 4 helix. Alpha 4 helix on each monomer plays a crucial role in binding DNA because it acts as the recognition helix. <scene name='69/694230/Recognition_helix/2'>Specific residues</scene> in the recognition helix recognize a sequence of DNA that is unknown at the moment; however, scientists do know 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 (E24) residue from a random coil accepts a hydrogen bond from the carboxamide end of an asparagine (N38) residue from the alpha 2 helix. Then, a glutamine (Q40) residue from alpha 2 helix accepts a hydrogen bond from a serine (S74) residue from the alpha 4 helix <ref>PMID:22085181</ref>. The <scene name='69/694230/Hydrogen_bonding_1/3'>hydrogen bond network</scene> (<scene name='69/694230/Hydrogen_bonding_2/2'>with measurements</scene>) is represented by each atom type in the 3D model. The hydrogen bond network is characteristic of the MarR family as a whole.
 [[Image:H Bonding of DNA.png|300 px|left|thumb|The Hydrogen Bonding Network is shown with dotted green lines approximately 2.8 angstroms between residues. The network consists of 4 major residues as follows from right to left: E24, N38, Q40, S74.  ]]