User:Wayne Decatur/Sandbox

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<applet load='2hty2hu4_j.pdb' size='500' frame='true' align='right' caption='Morph of N1 alone (2hty) to N1 complexed with Tamiflu (2hu4). The position where Tamiflu will bind is shown translucent except when bound in the empirically-determined model.' scene='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/Morph_2hty_to_2hu4/2' />
<applet load='2hty2hu4_j.pdb' size='500' frame='true' align='right' caption='Morph of N1 alone (2hty) to N1 complexed with Tamiflu (2hu4). The position where Tamiflu will bind is shown translucent except when bound in the empirically-determined model.' scene='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/Morph_2hty_to_2hu4/2' />
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Tamiflu was designed to fit N2/N9, so it is serendipitous that it works on N1. In fact, when the structure of N1 was determined<ref name='Russell2006' />, the <font color='#e07000'><b>loop comprising residues 147-152</b></font> was not in a suitable position to participate in binding Tamiflu. However, the complex of N1 with Tamiflu revealed that this loop is pulled into proper contact with the drug in an [[Induced fit|induced fit]] manner<ref name='Russell2006' />. A [[Morphs|morph]] from N1 alone ([[2hty]]) to N1 complexed with Tamiflu ([[2hu4]])<ref>Chain A from [[2hty]] was morphed to chain A of [[2hu4]] by linear interpolation, inserting 6 intermediate interpolated frames, using the freely available [http://www.umass.edu/microbio/rasmol/pdbtools.htm#martz morph2 program].</ref> shows the change in position of this loop (<scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/Morph_2hty_to_2hu4/8'>replay initial morph</scene>).
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T
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s, <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/Morph_2hty_to_2hu4/7'>Asp151, Glu119</scene>, closer to the inhibitor.
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The binding of Tamiflu to N1 pulls the sidechains of two conserved residues, <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/Morph_2hty_to_2hu4/7'>Asp151, Glu119</scene>, closer to the inhibitor.
 
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<scene name='User:Wayne_Decatur/Sandbox/Test_animation/1'>Test animation I made/scene>
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<scene name='User:Wayne_Decatur/Sandbox/Test_animation/1'>TextToBeDisplayed</scene>
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<!--HOW TO MAKE AN ANIMATION USING PROTEOPEDIA SCREEN AUTHORING TOOLS AND THE CONSOLE
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model 0;select all; spacefill on;
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loaded 2hty2hu4_j.pdb using load molecule under Scene authoring tools
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then in console:
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select 1.8; spacefill 0.2;wireframe 0.1; color red;
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anim mode palindrome;
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anim on;
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anim fps 8; # frames per second -->

Revision as of 09:56, 19 November 2008

p19 complexed with siRNA

Drag the structure with the mouse to rotate

Here is a schematic illustration of the two strands of this silencing RNA (siRNA):
        5'-pCGUACGCGUCACGCGUACGUU-OH-3'
            |||||||||||||||||||
    3'-OH-UUGCAUGCGCACUGCGCAUGCp-5'


HOW TO MAKE AN ANIMATION USING PROTEOPEDIA SCREEN AUTHORING TOOLS AND THE CONSOLE

Morph of N1 alone (2hty) to N1 complexed with Tamiflu (2hu4). The position where Tamiflu will bind is shown translucent except when bound in the empirically-determined model.

Drag the structure with the mouse to rotate

T s, , closer to the inhibitor.


Proteopedia Page Contributors and Editors (what is this?)

Wayne Decatur

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