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=== Hydrogen Bond Network === | === Hydrogen Bond Network === | ||
[[Image:Charge_map.jpg |300 px|right|thumb|'''Figure 3'''. A charge map of AdcR shows the general triangular shape and the positive charged (blue) area on HTH domains]] | [[Image:Charge_map.jpg |300 px|right|thumb|'''Figure 3'''. A charge map of AdcR shows the general triangular shape and the positive charged (blue) area on HTH domains]] | ||
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 name="guerra" /> | 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.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 name="guerra" />. | ||
[[Image:H Bonding of DNA.png|300 px|left|thumb|'''Figure 3'''. 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.]] | [[Image:H Bonding of DNA.png|300 px|left|thumb|'''Figure 3'''. 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.]] | ||