T7 RNA Polymerase: Difference between revisions

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'''The initial bubble grows'''. From 2mer, the system progresses ->3mer->4mer->5mer->6mer ... During this time, the newly formed RNA-DNA duplex (hybrid) grows, from 2 bases, to <scene name='77/778917/T7rp_3mer_rna_backedout/1'>3 bases</scene>, to 4 bases, to 5 bases, to 6 bases, to<scene name='77/778917/T7rp_7mer_rna_backedout/1'> 7 bases</scene>, to <scene name='77/778917/T7rp_8mer_rna_backedout/1'>8 bases</scene>, etc., and during the time, the duplex is short and otherwise unstable.

'''The growing hybrid induces protein domain movement'''. Also note that the initial active site accommodates only about a 3 ~~base~~ RNA-DNA duplex, as the N-terminal domain lies in the path of that hybrid (remember that forward translocation of the polymerase is really reverse translocation of the RNA-DNA hybrid). Beyond about 3 bases, the <scene name='77/778917/Morph/1'>hybrid pushes on the N-terminal domain</scene>, inducing into to both translate backwards and rotate. This can be seen in structures of the complex with 7 and 8 ~~bases~~ of RNA synthesized.

'''The growing hybrid induces protein domain movement'''. Also note that the initial active site accommodates only about a 3 basepair RNA-DNA duplex, as the N-terminal domain lies in the path of that hybrid (remember that forward translocation of the polymerase is really reverse translocation of the RNA-DNA hybrid). Beyond about 3 bases, the <scene name='77/778917/Morph/1'>hybrid pushes on the N-terminal domain</scene>, inducing into to both translate backwards and rotate. This can be seen in structures of the complex with 7 and 8 nucleotides of RNA synthesized. In the morph shown <ref>The [[Jmol/Storymorph|Storymorph Jmol scripts]] were used to create the interpolation shown in the morph. [https://proteopedia.org/wiki/index.php/Image:Morph_timing_t7rnap.pdb|Coordinates] available on Proteopedia</ref>

, models of how the structure might look with 4, 5, and 6 nucleotides of RNA synthesized were interpolated from the existing structures with 3 and 7 nucleotides of RNA.

'''Transition to Elongation'''. Toward the end of the above rotation (at about a 9mer RNA), stress builds up in the promoter binding domain, leading to a weakening of some of the interactions with the upstream duplex promoter. This triggers promoter release, which now allows the N-terminal domain to rotate 220° in the ''other'' direction, to form the <scene name='77/778917/T7rp_elongation_cmplx_full_vw/1'>elongation complex</scene>.

T7 RNA Polymerase: Difference between revisions

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@@ Line 16: / Line 16: @@
 '''The initial bubble grows'''. From 2mer, the system progresses ->3mer->4mer->5mer->6mer ...  During this time, the newly formed RNA-DNA duplex (hybrid) grows, from 2 bases, to <scene name='77/778917/T7rp_3mer_rna_backedout/1'>3 bases</scene>, to 4 bases, to 5 bases, to 6 bases, to<scene name='77/778917/T7rp_7mer_rna_backedout/1'> 7 bases</scene>, to <scene name='77/778917/T7rp_8mer_rna_backedout/1'>8 bases</scene>, etc., and during the time, the duplex is short and otherwise unstable.
-'''The growing hybrid induces protein domain movement'''. Also note that the initial active site accommodates only about a 3 base RNA-DNA duplex, as the N-terminal domain lies in the path of that hybrid (remember that forward translocation of the polymerase is really reverse translocation of the RNA-DNA hybrid). Beyond about 3 bases, the <scene name='77/778917/Morph/1'>hybrid pushes on the N-terminal domain</scene>, inducing into to both translate backwards and rotate. This can be seen in structures of the complex with 7 and 8 bases of RNA synthesized.
+'''The growing hybrid induces protein domain movement'''. Also note that the initial active site accommodates only about a 3 basepair RNA-DNA duplex, as the N-terminal domain lies in the path of that hybrid (remember that forward translocation of the polymerase is really reverse translocation of the RNA-DNA hybrid). Beyond about 3 bases, the <scene name='77/778917/Morph/1'>hybrid pushes on the N-terminal domain</scene>, inducing into to both translate backwards and rotate. This can be seen in structures of the complex with 7 and 8 nucleotides of RNA synthesized. In the morph shown <ref>The [[Jmol/Storymorph|Storymorph Jmol scripts]] were used to create the interpolation shown in the morph. [https://proteopedia.org/wiki/index.php/Image:Morph_timing_t7rnap.pdb|Coordinates] available on Proteopedia</ref>
+, models of how the structure might look with 4, 5, and 6 nucleotides of RNA synthesized were interpolated from the existing structures with 3 and 7 nucleotides of RNA.
 '''Transition to Elongation'''. Toward the end of the above rotation (at about a 9mer RNA), stress builds up in the promoter binding domain, leading to a weakening of some of the interactions with the upstream duplex promoter. This triggers promoter release, which now allows the N-terminal domain to rotate 220° in the ''other'' direction, to form the <scene name='77/778917/T7rp_elongation_cmplx_full_vw/1'>elongation complex</scene>.