User:Luis E Ramirez-Tapia/Sandbox 3
From Proteopedia
(→Conformational Changes on T7 RNA Polymerase) |
(→Conformational Changes on T7 RNA Polymerase) |
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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. The correct transcription of DNA to RNA depends of several factors like...., making the study of the transcriptional process more complicated, specially in higher organisms. The RNA polymerase of the bactereophage T7, is the perfect model for studying the transcription process, mainly because it is a single unit enzyme that processes RNA with the affectivity as the polymerase from higher organisms. Still much of the mechanism is unknown, for example, during the Initial steps of transcription GREEN LINK an event called abortive cycling occurs (Figure X), where the small RNA transcripts (less than 12 bases) fall from the complex. This event will continue until the enzyme/DNA/RNA complex reach the elongation GREEN LINK phase, where a more stable enzyme/DNA/RNA complex is form. A mayor contributor of the stability of the complex is the formation of the RNA exit tunnel GREEN LINK. | 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. The correct transcription of DNA to RNA depends of several factors like...., making the study of the transcriptional process more complicated, specially in higher organisms. The RNA polymerase of the bactereophage T7, is the perfect model for studying the transcription process, mainly because it is a single unit enzyme that processes RNA with the affectivity as the polymerase from higher organisms. Still much of the mechanism is unknown, for example, during the Initial steps of transcription GREEN LINK an event called abortive cycling occurs (Figure X), where the small RNA transcripts (less than 12 bases) fall from the complex. This event will continue until the enzyme/DNA/RNA complex reach the elongation GREEN LINK phase, where a more stable enzyme/DNA/RNA complex is form. A mayor contributor of the stability of the complex is the formation of the RNA exit tunnel GREEN LINK. | ||
| - | One of the most striking characteristics of this enzyme is the HUGE conformational change of the N-terminus part | + | ===Understanding the morph=== |
| - | + | One of the most striking characteristics of this enzyme is the<b>HUGE conformational change</b> of the <font color='magenta'>N-terminus part of the enzyme</font>. There has been good advances in solving how the <font color ="green">Subdomain H</font> (alfa-helices in green) and the <font color='yellow'>helices C1-C2</font> refolds, specially thanks to a new intermediate state structure (PDB ID:3e2e). You can see the transition between the <scene name='User:Luis_E_Ramirez-Tapia/Sandbox_3/Initiation/2'>INITIATION</scene> conformation and the intermediate state <scene name='User:Luis_E_Ramirez-Tapia/Sandbox_3/1mswcolor/2'>ELONGATION </scene>complex. Press the BUTTON <jmol> | |
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| - | <jmol> | + | |
<jmolButton> | <jmolButton> | ||
<script> | <script> | ||
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<text>Play Animation</text> | <text>Play Animation</text> | ||
</jmolButton> | </jmolButton> | ||
| - | </jmol> | + | </jmol> |
| + | Still there are some imporant details that are missing, If we try to use the three structures available for the <scene name='User:Luis_E_Ramirez-Tapia/Sandbox_3/T7wrongtransition/1'>conformational change.</scene> of T7 RNAP, an interesting event happen. Could you see what is the problem?. | ||
| + | Hopefully, someday we will have an intermediate state between the enzyme/DNA/RNA complex with a 7 mer transcript and the elongation complex. | ||
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| - | + | Using a energy minimization morphing software (Yale Morph), a morph between the INITIATION (PDB ID: 1qln) and the INTERMIDATE STATE (PDB ID: 3e2e) structures was created. | |
| - | <scene name='User:Luis_E_Ramirez-Tapia/Sandbox_3/T7wrongtransition/1'>TextToBeDisplayed</scene> | ||
<scene name='User:Luis_E_Ramirez-Tapia/Sandbox_3/Transition/1'>One</scene> | <scene name='User:Luis_E_Ramirez-Tapia/Sandbox_3/Transition/1'>One</scene> | ||
Revision as of 19:35, 27 April 2011
One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground
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Color code N-Terminus domain, Subdomain H, Helices C1 and C2, specificity loop, Non-template strand, template strand and the nascent RNA strand |
Conformational Changes on T7 RNA Polymerase
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. The correct transcription of DNA to RNA depends of several factors like...., making the study of the transcriptional process more complicated, specially in higher organisms. The RNA polymerase of the bactereophage T7, is the perfect model for studying the transcription process, mainly because it is a single unit enzyme that processes RNA with the affectivity as the polymerase from higher organisms. Still much of the mechanism is unknown, for example, during the Initial steps of transcription GREEN LINK an event called abortive cycling occurs (Figure X), where the small RNA transcripts (less than 12 bases) fall from the complex. This event will continue until the enzyme/DNA/RNA complex reach the elongation GREEN LINK phase, where a more stable enzyme/DNA/RNA complex is form. A mayor contributor of the stability of the complex is the formation of the RNA exit tunnel GREEN LINK.
Understanding the morph
One of the most striking characteristics of this enzyme is theHUGE conformational change of the N-terminus part of the enzyme. There has been good advances in solving how the Subdomain H (alfa-helices in green) and the helices C1-C2 refolds, specially thanks to a new intermediate state structure (PDB ID:3e2e). You can see the transition between the conformation and the intermediate state complex. Press the BUTTON Still there are some imporant details that are missing, If we try to use the three structures available for the of T7 RNAP, an interesting event happen. Could you see what is the problem?. Hopefully, someday we will have an intermediate state between the enzyme/DNA/RNA complex with a 7 mer transcript and the elongation complex.
Using a energy minimization morphing software (Yale Morph), a morph between the INITIATION (PDB ID: 1qln) and the INTERMIDATE STATE (PDB ID: 3e2e) structures was created.
