User:Chloe Paul/Sandbox 1: Difference between revisions

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== The Structure of RTP ==

<StructureSection <applet load='1bm9' size='500' side='right' caption='Structure of RTP (PDB entry [[1bm9]])' scene=''>RTP has been found to exist as a symmetric α+β protein in solution and a homomeric dimer through crystal structure determination <ref name="bussiere">PMID: 7867072</ref>.These identical monomers each contain four α helices (α1, α2, α3, α4), one β strand (β1) and two β ribbons(β2 and β3). Int also contains a distorted N-terminal region. When the two monomers come together and the two α4 helices bind, forming a dimer with an overall rectangle shape of 66Å x 35 Å x 30 Å <ref name="bussiere" />. The long C-terminal helices (α4) facilitate binding by establishing a hydrophobic core between the monomers (residues 93-103.) The helices form an antiparallel coiled-coil structure and additionally contribute an amino acid to the hydrophobic core of the other monomer (residue 122)<ref name="bussiere" />. Both monomers still remain structurally similar when they form the dimer in solution. It should be noted that when in solution the flexible loop between β2 and β3 are able to assume different conformation <ref name="bussiere" />. This later gives rise to the "wing-up, wing-down" conformation when bound to native DNA<ref name="vivian">PMID:17521668</ref>.</StructureSection>

<StructureSection <applet load='1bm9' size='500' side='right' caption='Structure of RTP (PDB entry [[1bm9]])' scene='Chloe_Paul/Sandbox_1/Basicrtp/1'>RTP has been found to exist as a symmetric α+β protein in solution and a homomeric dimer through crystal structure determination <ref name="bussiere">PMID: 7867072</ref>.These identical monomers each contain four α helices (α1, α2, α3, α4), one β strand (β1) and two β ribbons(β2 and β3). Int also contains a distorted N-terminal region. When the two monomers come together and the two α4 helices bind, forming a dimer with an overall rectangle shape of 66Å x 35 Å x 30 Å <ref name="bussiere" />. The long C-terminal helices (α4) facilitate binding by establishing a hydrophobic core between the monomers (residues 93-103.) The helices form an antiparallel coiled-coil structure and additionally contribute an amino acid to the hydrophobic core of the other monomer (residue 122)<ref name="bussiere" />. Both monomers still remain structurally similar when they form the dimer in solution. It should be noted that when in solution the flexible loop between β2 and β3 are able to assume different conformation <ref name="bussiere" />. This later gives rise to the "wing-up, wing-down" conformation when bound to native DNA<ref name="vivian">PMID:17521668</ref>.</StructureSection>

== RTP binding to DNA ==

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 == The Structure of RTP ==
-<StructureSection <applet load='1bm9' size='500' side='right' caption='Structure of RTP (PDB entry [[1bm9]])' scene=''>RTP has been found to exist as a symmetric α+β protein in solution and a homomeric dimer through crystal structure determination <ref name="bussiere">PMID: 7867072</ref>.These identical monomers each contain four α helices (α1, α2, α3, α4), one β strand (β1) and two β ribbons(β2 and β3). Int also contains a distorted N-terminal region. When the two monomers come together and the two α4 helices bind, forming a dimer with an overall rectangle shape of 66Å x 35 Å x 30 Å <ref name="bussiere" />. The long C-terminal helices (α4) facilitate binding by establishing a hydrophobic core between the monomers (residues 93-103.) The helices form an antiparallel coiled-coil structure and additionally contribute an amino acid to the hydrophobic core of the other monomer (residue 122)<ref name="bussiere" />. Both monomers still remain structurally similar when they form the dimer in solution. It should be noted that when in solution the flexible loop between β2 and β3 are able to assume different conformation <ref name="bussiere" />. This later gives rise to the "wing-up, wing-down" conformation when bound to native DNA<ref name="vivian">PMID:17521668</ref>.</StructureSection>
+<StructureSection <applet load='1bm9' size='500' side='right' caption='Structure of RTP (PDB entry [[1bm9]])' scene='Chloe_Paul/Sandbox_1/Basicrtp/1'>RTP has been found to exist as a symmetric α+β protein in solution and a homomeric dimer through crystal structure determination <ref name="bussiere">PMID: 7867072</ref>.These identical monomers each contain four α helices (α1, α2, α3, α4), one β strand (β1) and two β ribbons(β2 and β3). Int also contains a distorted N-terminal region. When the two monomers come together and the two α4 helices bind, forming a dimer with an overall rectangle shape of 66Å x 35 Å x 30 Å <ref name="bussiere" />. The long C-terminal helices (α4) facilitate binding by establishing a hydrophobic core between the monomers (residues 93-103.) The helices form an antiparallel coiled-coil structure and additionally contribute an amino acid to the hydrophobic core of the other monomer (residue 122)<ref name="bussiere" />. Both monomers still remain structurally similar when they form the dimer in solution. It should be noted that when in solution the flexible loop between β2 and β3 are able to assume different conformation <ref name="bussiere" />. This later gives rise to the "wing-up, wing-down" conformation when bound to native DNA<ref name="vivian">PMID:17521668</ref>.</StructureSection>
 == RTP binding to DNA ==