User:Luis E Ramirez-Tapia/Sandbox 3

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One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground]
One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground]
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<table align="right" width="300" border="0" style="background-color:#e0e0e0;"><tr><td>
<table align="right" width="300" border="0" style="background-color:#e0e0e0;"><tr><td>
<Structure load='1qln' size='450' frame ='true' align ='right' caption='T7 RNA polymerase' scene='User:Luis_E_Ramirez-Tapia/Sandbox_3/Initiation/2'/>
<Structure load='1qln' size='450' frame ='true' align ='right' caption='T7 RNA polymerase' scene='User:Luis_E_Ramirez-Tapia/Sandbox_3/Initiation/2'/>
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<b>T7 RNA Polymerase</b>,
<b>T7 RNA Polymerase</b>,
Colors are as follow
Colors are as follow
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startint with the <font color='magenta'><b>N-Terminus domain</b></font>,
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startint with the <font color='magenta'><b>N-Terminus domain</b></font>, <font color='orange'><b>Helices C1 and C2</b></font>, the <font color='green'><b>Sub-domain H</b></font> and <font color='Proline 266'>,also the DNA <font color='x6060ff'><b>template strand</b></font>, <font color='x00ff00'><b>non-template strand</b></font>and nascent <font color='red'><b>RNA</b></font>;
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*<font color='orange'><b>helices C1 and C2</b></font>
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* the <font color='green'><b>Sub-domain H</b></font>
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*and <font color='Proline 266'>,
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* also the DNA <font color='x6060ff'><b>template strand</b></font>,
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*<font color='x00ff00'><b>non-template strand</b></font> and nascent <font color='red'><b>RNA</b></font>
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</td></tr>
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</table>
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{{Template:ColorKey_Element_C}}
{{Template:ColorKey_Element_C}}
<font color="white">'''H'''</font>
<font color="white">'''H'''</font>
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<scene name='User:Luis_E_Ramirez-Tapia/Sandbox_3/Transition-win98/3'>TextToBeDisplayed</scene>
<scene name='User:Luis_E_Ramirez-Tapia/Sandbox_3/Transition-win98/3'>TextToBeDisplayed</scene>
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==See Also==
==See Also==
*[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]
*[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]

Revision as of 18:53, 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

T7 RNA polymerase

Drag the structure with the mouse to rotate

T7 RNA Polymerase, Colors are as follow startint with the N-Terminus domain, Helices C1 and C2, the Sub-domain H and ,also the DNA template strand, non-template strandand nascent RNA; C H O N Se

</td></tr></table>

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.

One of the most striking characteristics of this enzyme is the HUGE conformational change of the N-terminus part GREEN LINK of the enzyme. There has been good advances in solving how the Subdomain H (alfa-helices in green) and the helices C1-C2 (yellow) refolds, specially thanks to a new intermediate state structure (PDB ID:3e2e) between the conformation and the complex, still there are some imporant details that are missing.

Using a energy minimization morphing software (Yale Morph), a morph between the INITIATION and the INTERMIDATE STATE structures was created. Press the BUTTON

If we try to use the three structures of the conformation change, an interesting event happen, Could you see what is the problem?. Hopefully someday we will be able to have a intermediate state between the enzyme/DNA/RNA complex with a 7 mer transcript and the elongation complex.


See Also

Proteopedia Page Contributors and Editors (what is this?)

Luis E Ramirez-Tapia

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