Molecular Playground/T7 RNAP Conformations: Difference between revisions
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The DNA with translucent colors is our reference point and the modeled DNA is part of the intermediate state structure. The <font color='magenta'>N-terminus</font> rotates around 47º, the RNA transcript has 7 bases, but the enzyme has not reached its final elongation conformation yet. The missing steps could be resolved if we morph the structures using the intermediate state and the elongation structures. The following <scene name='User:Luis_E_Ramirez-Tapia/Sandbox_3/T7wrongtransition/1'> most notorious conformational change</scene> shows a complete refolding of the <font color =green> sub-domain H</font> (alfa-helices in green) and the <font color = orange>helices C-1 C-2</font>. It uses the intermediate state and the elongation state. However, there is a problem. Can you see it?<b> Follow the movement of the green helices</b>. Indeed, it can not be the real transition. While there has been good advances in solving the correct transition [http://www.ncbi.nlm.nih.gov/pubmed/17472344 (2)], the optimal way is by producing structures of the transitional complexes from 9 and 10 mer transcripts. Another approach to study this transition would be by labeling the enzyme with fluorophores and then using [http://en.wikipedia.org/wiki/Förster_resonance_energy_transfer FRET], which could allow us to calculate the movement distances that occurs during the transition. This work is in progress... | The DNA with translucent colors is our reference point and the modeled DNA is part of the intermediate state structure. The <font color='magenta'>N-terminus</font> rotates around 47º, the RNA transcript has 7 bases, but the enzyme has not reached its final elongation conformation yet. The missing steps could be resolved if we morph the structures using the intermediate state and the elongation structures. The following <scene name='User:Luis_E_Ramirez-Tapia/Sandbox_3/T7wrongtransition/1'> most notorious conformational change</scene> shows a complete refolding of the <font color =green> sub-domain H</font> (alfa-helices in green) and the <font color = orange>helices C-1 C-2</font>. It uses the intermediate state and the elongation state. However, there is a problem. Can you see it?<b> Follow the movement of the green helices</b>. Indeed, it can not be the real transition. While there has been good advances in solving the correct transition [http://www.ncbi.nlm.nih.gov/pubmed/17472344 (2)], the optimal way is by producing structures of the transitional complexes from 9 and 10 mer transcripts. Another approach to study this transition would be by labeling the enzyme with fluorophores and then using [http://en.wikipedia.org/wiki/Förster_resonance_energy_transfer FRET], which could allow us to calculate the movement distances that occurs during the transition. This work is in progress... | ||
Finally, the morphs were produced using the energy minimization morphing software from the [http://molmovdb.mbb.yale.edu/molmovdb/morph/ Yale Morph Server]. The protein structures that were used in the server are the following: T7 RNA polymerase initiation complex [http://www.pdb.org/pdb/explore/explore.do?structureId=1QLN (PDB ID: 1qln)], T7 intermediate state complex [http://www.pdb.org/pdb/explore/explore.do?structureId=3E2E (PDB ID: 3e2e)](1) and the T7 RNA polymerase elongation complex [http://www.pdb.org/pdb/explore/explore.do?structureId=1MSW (PDB ID:1msw)].</p> | Finally, the morphs were produced using the energy minimization morphing software from the [http://molmovdb.mbb.yale.edu/molmovdb/morph/ Yale Morph Server]. The protein structures that were used in the server are the following: T7 RNA polymerase initiation complex [http://www.pdb.org/pdb/explore/explore.do?structureId=1QLN (PDB ID: 1qln)], T7 intermediate state complex [http://www.pdb.org/pdb/explore/explore.do?structureId=3E2E (PDB ID: 3e2e)](1) and the T7 RNA polymerase elongation complex [http://www.pdb.org/pdb/explore/explore.do?structureId=1MSW (PDB ID:1msw)].</p> | ||
==3D structures of RNA polymerase== | |||
[[RNA polymerase]] | |||
=References= | =References= | ||