DNA-protein interactions: Difference between revisions
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==DNA-Protein interactions== | ==DNA-Protein interactions== | ||
<StructureSection load='1d66' size='340' side='right' caption='Gal4 transcriptional activator interacting with its target DNA | <StructureSection load='1d66' size='340' side='right' caption='Gal4 transcriptional activator interacting with its target DNA (PDB code [[1d66]])'> | ||
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While DNA contains all the genetic material in a cell, proteins play an important role in regulating the transcription of DNA to RNA, not to mention replication, repair and packaging.. The interactions between [[DNA]] and proteins are important in this process. Most sequence specific interactions occur in the <scene name='71/711660/Grooves/1'>major grove</scene>, as the <scene name='71/711660/Base_exposure/1'>bases are exposed</scene> in this groove. In contrast, the <scene name='71/711660/Grooves/1'>minor grove</scene> contains more of the <scene name='71/711660/Base_exposure/1'>carbohydrate portions</scene> of DNA. | While DNA contains all the genetic material in a cell, proteins play an important role in regulating the transcription of DNA to RNA, not to mention replication, repair and packaging.. The interactions between [[DNA]] and proteins are important in this process. Most sequence specific interactions occur in the <scene name='71/711660/Grooves/1'>major grove</scene>, as the <scene name='71/711660/Base_exposure/1'>bases are exposed</scene> in this groove. In contrast, the <scene name='71/711660/Grooves/1'>minor grove</scene> contains more of the <scene name='71/711660/Base_exposure/1'>carbohydrate portions</scene> of DNA. | ||
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== Leucine zippers == | == Leucine zippers == | ||
The Basic Leucine Zipper Domain (<scene name='71/711660/Creb/1'>bZIP domain</scene>) is found in many DNA binding eukaryotic proteins, especially transcription factors such as the cAMP Responsive Element Binding (CREB) protein . One part of the domain contains a region that mediates sequence specific DNA binding properties via <scene name='71/711660/Creb_charge/2'>basic amino acids</scene> such as arginine and lysine. Since these basic amino acids would usually repel, the <scene name='71/711660/Creb_leu/1'>leucine zipper segment</scene> allows for dimerization of the protein. Notice the spacing of the leucine residues; they are spaced by 3, 4, or 7 amino acids, causing them to be on the same face of the alpha helix. this hydrophobic set of "zipper teeth" allows this region to interact with another monomer unit, pairing with the exact same residues to form a <scene name='71/711660/Creb_hydrophobic/1'>hydrophobic core</scene>, shown in grey. | The Basic Leucine Zipper Domain (<scene name='71/711660/Creb/1'>bZIP domain</scene>) is found in many DNA binding eukaryotic proteins, especially transcription factors such as the cAMP Responsive Element Binding (CREB) protein . One part of the domain contains a region that mediates sequence specific DNA binding properties via <scene name='71/711660/Creb_charge/2'>basic amino acids</scene> such as arginine and lysine. These basic residues can either interact ionically with the <scene name='71/711660/Creb_arg_p/1'>negatively charged backbone phosphate groups</scene> or via <scene name='71/711660/Creb_arg_hbond/1'>hydrogen bonds</scene> with the bases. | ||
Since these basic amino acids would usually repel, the <scene name='71/711660/Creb_leu/1'>leucine zipper segment</scene> allows for dimerization of the protein. Notice the spacing of the leucine residues; they are spaced by 3, 4, or 7 amino acids, causing them to be on the same face of the alpha helix. this hydrophobic set of "zipper teeth" allows this region to interact with another monomer unit, pairing with the exact same residues to form a <scene name='71/711660/Creb_hydrophobic/1'>hydrophobic core</scene>, shown in grey. At the base of the leucine zipper, where the protein meets the DNA, is positioned a <scene name='71/711660/Creb__mg/1'>magnesium ion</scene>. While you would expect a divalent cation to be surrounded by negatively charged amino acids from the protein or backbone phosphates from the DNA, its inner chelation sphere is completely composed of <scene name='71/711660/Creb_h2o_mg/1'>water molecules</scene>. The next sphere of interactions include <scene name='71/711660/Creb_lys304/1'>two lysine residues</scene> (one from each protein chain) | |||
== Zinc fingers == | == Zinc fingers == | ||
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</StructureSection> | </StructureSection> | ||
==See Also== | |||
*[[Lac repressor]] which explains specific and non-specific binding of the repressor protein to DNA, animates the transition between these kinds of binding (a [[Morphs|morph]]), how proteins recognize specific sequences in the major and minor grooves, and the differences between bends and kinks in DNA. | |||
== References == | == References == | ||
<references/> | <references/> | ||