Molecular Playground/T7 RNAP Conformations: Difference between revisions
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<Structure load='1qln' size='400' frame ='true' align ='right' caption='T7 RNA polymerase' scene='User:Luis_E_Ramirez-Tapia/ | <Structure load='1qln' size='400' frame ='true' align ='right' caption='T7 RNA polymerase [[1qln]]' scene='User:Luis_E_Ramirez-Tapia/T7_RNA_polymerase/Transition/2'/> | ||
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= Conformational Changes on T7 RNA Polymerase = | = Conformational Changes on T7 RNA Polymerase = | ||
[http://en.wikipedia.org/wiki/Transcription_(genetics) Transcription] is a fundamental part of genetic regulation. The RNA polymerases that accomplish this function vary in structure, size and complexity, but must all carry out the same basic functions ([See[http://en.wikipedia.org/wiki/RNA_polymerase]''RNA polymerases''). The correct transcription of DNA to RNA depends of several factors and the complexity increases with the complexity of the organism. This makes the study of the transcriptional process complicated. The RNA polymerase of the [http://ecoliwiki.net/colipedia/index.php/Phage_T7 bacteriophage T7], is the perfect model for studying the transcription process given that T7 RNA polymerase is a single unit enzyme that processes RNA with the same effectivity as the polymerase from higher organisms. Nevertheless, there is plenty to learn from the transcription mechanism, such as the "abortive cycle" process that takes place during the <scene name='User:Luis_E_Ramirez-Tapia/Sandbox_3/Initiation/2'>INITIATION</scene> phase (Figure 1) remains poorly understood. | [http://en.wikipedia.org/wiki/Transcription_(genetics) Transcription] is a fundamental part of genetic regulation. The '''RNA polymerases''' that accomplish this function vary in structure, size and complexity, but must all carry out the same basic functions ([See[http://en.wikipedia.org/wiki/RNA_polymerase]''RNA polymerases''). The correct transcription of DNA to RNA depends of several factors and the complexity increases with the complexity of the organism. This makes the study of the transcriptional process complicated. The RNA polymerase of the [http://ecoliwiki.net/colipedia/index.php/Phage_T7 bacteriophage T7], is the perfect model for studying the transcription process given that T7 RNA polymerase is a single unit enzyme that processes RNA with the same effectivity as the polymerase from higher organisms. Nevertheless, there is plenty to learn from the transcription mechanism, such as the "abortive cycle" process that takes place during the <scene name='User:Luis_E_Ramirez-Tapia/Sandbox_3/Initiation/2'>INITIATION</scene> phase (Figure 1) remains poorly understood. | ||
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[[Image:Abortivecycling.png|thumb|400px|left|<b> Figure 1. Abortive Cycle during transcription initiation</b>]] | [[Image:Abortivecycling.png|thumb|400px|left|<b> Figure 1. Abortive Cycle during transcription initiation</b>]] | ||
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<p>The first striking observation is the conformational change of the <font color='magenta'>N-terminus</font> part of the enzyme and the <font color='orange'>helices C1-C2</font>. | <p>The first striking observation is the conformational change of the <font color='magenta'>N-terminus</font> part of the enzyme and the <font color='orange'>helices C1-C2</font>. | ||
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 [ | 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 [[1qln|(PDB ID:1qln)]], T7 intermediate state complex [[3e2e|(PDB ID:3e2e)]](1) and the T7 RNA polymerase elongation complex [[1msw|(PDB ID:1msw)]].</p> | ||
==3D structures of RNA polymerase== | |||
[[RNA polymerase]] | |||
=References= | =References= | ||