DNA Origami Assembly for the Tar Chemoreceptor: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Dominique Kiki Carey, Michal Harel

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-==Your Heading Here (maybe something like 'Structure')==
+==DNA Origami as an Assembly Method for Tar Chemoreceptor==
-<StructureSection load='Image:ICons4noduplicatePDB.pdb.gz' size='340' side='right' caption='DNA Origami Chemoreceptor complex' scene=''>
+<StructureSection load='' size='340' side='right' caption='Human chemotaxis protein CheA complex with chemotaxis protein CheW and methyl-accepting chemotaxis protein 2 (PDB code [[3ja6]])' scene=''>
-This is a default text for your page '''DNA Origami Assembly for the Tar Chemoreceptor'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
+This project centers around the idea of using DNA origami to assemble the <scene name='80/800127/3ja6_centered_3/1'>Tar chemoreceptor</scene>. This assembly method would provide novel opportunities to investigate how this receptor works previously untestable using other assembly methods.
-You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
 == Introduction to Chemotaxis ==
-Chemotaxis is the process by which bacteria sense chemicals in their environment. This is done through the use of chemoreceptors to sense a chemical gradient that they can follow towards higher concentrations of food or away from higher concentrations of poisons or other unfavorable conditions. The Tar chemoreceptor is involved with the sensing of aspartate, a common amino acid, by binding aspartate in the extracellular portion of the protein and then propagates a signal down the receptor to activate a pathway to alter movement. '''[Add picture of chemoreceptor here? Are there any that are open source?]'''
+Chemotaxis is the process by which bacteria sense chemicals in their environment. This is done through the use of chemoreceptors to sense a chemical gradient that they can follow towards higher concentrations of food or away from higher concentrations of poisons or other unfavorable conditions. The '''Tar chemoreceptor''' is involved with the sensing of aspartate, a common amino acid, by binding aspartate in the extracellular portion of the protein and then propagates a signal down the receptor to activate a pathway to alter movement.
 == Possible Applications of Chemotaxis ==
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 == DNA Origami ==
-This project involves using a DNA tetrahedron as a scaffold for the Tar chemoreceptor complex ''in vitro''. In this model, receptor dimers are attached at three vertices of the DNA tetrahedron to make the native trimer of dimers structure seen ''in vivo''. At the other end of the receptor, two proteins are shown: CheA, a kinase, shown in dark blue, and CheW, a coupling protein, shown in cyan.
+This project involves using a DNA tetrahedron as a scaffold for the Tar chemoreceptor complex ''in vitro''. In this model, receptor dimers are attached at three vertices of the DNA tetrahedron to make the native <scene name='80/800127/Entire_trimer_of_dimers_color/1'>trimer of dimers</scene> structure seen ''in vivo''. At the other end of the receptor, two proteins are shown: CheA, a kinase, shown in blue, and CheW, a coupling protein, shown in cyan.
-<scene name='80/800127/Entire_trimer_of_dimers/2'>trimer of dimers</scene>
 ==Attachment to DNA==
-The protein receptor dimer is attached to the DNA tetrahedron using NTA-functionalized DNA. This means that the DNA has an NTA, or nitrilotriaceticacid, is able to coordinate with nickel ions, shown in green, which is also able to coordinate with histidines. The Tar chemoreceptor has six histidines added to the N-terminus of the protein ''in vitro'', which should be able to coordinate with the nickel ion as well, creating a coordination complex.
+The protein receptor dimer is <scene name='80/800127/Zoomed_in_connection_color_ct/1'>attached to tetrahedron</scene> using NTA-functionalized DNA. This means that the DNA has an NTA, or nitrilotriaceticacid, is able to coordinate with nickel ions, shown in green, which is also able to coordinate with histidines. The Tar chemoreceptor has six histidines added to the N-terminus of the protein ''in vitro'', which should be able to coordinate with the nickel ion as well, creating a coordination complex. One of monomers, shown in black, in each dimer is coordinated with the nickel atom.
-<scene name='80/800127/Zoomed_in_connection/1'>DNA-protein linkage</scene>
-== Structural highlights ==
-This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
+==Significance of Assembly Method==
+This assembly method will allow this receptor to be investigated in ways not previously possible. These ways include expanding the trimer of dimers by changing the size of the DNA tetrahedron as well as having more control of dimer position in the trimer of dimers. With these new experiments possible, more information can be gained about bacterial movement.
 </StructureSection>
 == References ==
 <references/>