Sandbox Reserved 1063: Difference between revisions
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=== Hydrogen Bond Network === | === 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]. Most importantly, the hydrogen bonding network connects the metal binding pockets to the alpha 4 helix, which is known as the recognition helix. Alpha 4 helix plays a crucial role in binding DNA. 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='yellow'>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'>Hyrdogen Bonding Network</scene>, which is seen across the MarR family as a whole. Now the protein is ready to bind DNA. [[Image:H Bonding of DNA.png|300 px|left|thumb|<font size="3.5"><div style="text-align: center;">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. ]] | 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, which is known as the recognition helix. Alpha 4 helix plays a crucial role in binding DNA. 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='yellow'>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'>Hyrdogen Bonding Network</scene>, which is seen across the MarR family as a whole. Now the protein is ready to bind DNA. [[Image:H Bonding of DNA.png|300 px|left|thumb|<font size="3.5"><div style="text-align: center;">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. ]] === Helix-Turn-Helix Domain === | ||
=== Helix-Turn-Helix Domain === | |||
The AdcR MarR transcriptional regulator's structure resembles the other proteins in the same family; however, the most notable differences are found in the winged helix-turn-helix (wHTH) motif that assists in binding DNA. This wHTH motif is consistent among all marR family proteins that bind DNA. Although AdcR is a highly alpha helical protein, the "wings" of the DNA binding domain consist of two anti parallel beta strands. There is one on each domain of the protein. | The AdcR MarR transcriptional regulator's structure resembles the other proteins in the same family; however, the most notable differences are found in the winged helix-turn-helix (wHTH) motif that assists in binding DNA. This wHTH motif is consistent among all marR family proteins that bind DNA. Although AdcR is a highly alpha helical protein, the "wings" of the DNA binding domain consist of two anti parallel beta strands. There is one on each domain of the protein. | ||