User:Eric Martz/Sandbox 8: Difference between revisions

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~~===Neuraminidase Structure and Conserved Amino Acids===~~

*Influenza neuraminidase is a homotetramer<ref>The tetramer is one of two [[Biological Unit|biological units]] in the [[Asymmetric Unit|asymmetric unit]] of [[2hu4]].</ref> (<scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_tetramer/1'>restore initial scene</scene>).

*Each of the four protein chains in the tetramer has a catalytic site, indicated in <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_tetramer/10'>this scene</scene> by the positions of the bound <font color='red'>'''Tamiflu'''</font> inhibitors.

*The <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_monomer/2'>substrate binding site</scene> involves only a single protein chain, being distant from neighboring chains.

*The <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_monomer_sec_struct/1'>secondary structure</scene> is mostly beta, consisting of several beta sheets with three short alpha helices ({{Template:ColorKey_Strand}}, {{Template:ColorKey_Helix}}).

*The residues contacting the <font color='red'>'''Tamiflu inhibitory substrate analog'''</font> are <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_monomer_consurf/1'>highly conserved</scene><ref>See [[Evolutionary Conservation]]. Coloring by ConSurf on chain A of 2hu4 based on 100 unique homologs using default conditions, done on September 23, 2008.</ref>.

~~<center>{{Template:ColorKey_ConSurf}}</center>~~

*These highly conserved residues include some known to be crucial to binding sialic acid substrate: Arg 118, Arg 292 and Arg 371 bind the carboxylate; Arg 152 interacts with the acetamido substituent; and Glu 276 forms hydrogen bonds with the 8- and 9-hydroxyl groups of the substrate. These residues are <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_monomer_activesite/1'>highlighted here</scene> in contact with the sialic acid substrate analog Tamiflu. In this scene, atoms and bonds in Tamiflu and the highlighted residues are colored by element: {{Template:ColorKey_Element_C}}, {{Template:ColorKey_Element_O}}, {{Template:ColorKey_Element_N}}.

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 <applet load='2hu4_1.pdb' size='500' frame='true' align='right' caption='Influenza Neuraminidase N1 (2hu4).' scene='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_tetramer/1' />
-===Neuraminidase Structure and Conserved Amino Acids===
-*Influenza neuraminidase is a homotetramer<ref>The tetramer is one of two [[Biological Unit|biological units]] in the [[Asymmetric Unit|asymmetric unit]] of [[2hu4]].</ref> (<scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_tetramer/1'>restore initial scene</scene>).
-*Each of the four protein chains in the tetramer has a catalytic site, indicated in <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_tetramer/10'>this scene</scene> by the positions of the bound <font color='red'>'''Tamiflu'''</font> inhibitors.
-*The <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_monomer/2'>substrate binding site</scene> involves only a single protein chain, being distant from neighboring chains.
-*The <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_monomer_sec_struct/1'>secondary structure</scene> is mostly beta, consisting of several beta sheets with three short alpha helices ({{Template:ColorKey_Strand}}, {{Template:ColorKey_Helix}}).
-*The residues contacting the <font color='red'>'''Tamiflu inhibitory substrate analog'''</font> are <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_monomer_consurf/1'>highly conserved</scene><ref>See [[Evolutionary Conservation]]. Coloring by ConSurf on chain A of 2hu4 based on 100 unique homologs using default conditions, done on September 23, 2008.</ref>.
-<center>{{Template:ColorKey_ConSurf}}</center>
-*These highly conserved residues include some known to be crucial to binding sialic acid substrate: Arg 118, Arg 292 and Arg 371 bind the carboxylate; Arg 152 interacts with the acetamido substituent; and Glu 276 forms hydrogen bonds with the 8- and 9-hydroxyl groups of the substrate. These residues are <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_monomer_activesite/1'>highlighted here</scene> in contact with the sialic acid substrate analog Tamiflu. In this scene, atoms and bonds in Tamiflu and the highlighted residues are colored by element: {{Template:ColorKey_Element_C}}, {{Template:ColorKey_Element_O}}, {{Template:ColorKey_Element_N}}.