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User:Eric Martz/Sandbox 8

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===Neuraminidase Structure and Conserved Amino Acids===
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==Chemistry of Water and Its Hydrogen Bonds==
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Prepared in collaboration with [[User:Gabriel Pons]].
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*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>).
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===One Molecule===
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<applet size='400' frame='true' align='right' caption='Insert caption here'
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scene='User:Eric_Martz/Sandbox_8/Water/2' />
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*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.
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*(<scene name='User:Eric_Martz/Sandbox_8/Water/2'>restore initial scene</scene>)
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*<scene name='User:Eric_Martz/Sandbox_8/Water/4'>partial charge values</scene>
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*<scene name='User:Eric_Martz/Sandbox_8/Water/6'>shape of the molecule (spacefilling)</scene> (van der Waals radii)
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*<scene name='User:Eric_Martz/Sandbox_8/Water/5'>translucent surface colored by molecular electrostatic potential</scene> <font color="blue"><b>Positive (+)</b></font>, <font color="red"><b>Negative (-)</b></font>
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*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.
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----
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===Technical Information===
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*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}}).
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The following scene demonstrates a problem with greek letters in labels in Jmol
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*<scene name='User:Eric_Martz/Sandbox_8/Water/3'>partial charges</scene> (using &delta; in the label, it gets corrupted)
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*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>.
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Script for translucent MEP colored surface:
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<center>{{Template:ColorKey_ConSurf}}</center>
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<pre>
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{hydrogen}.partialCharge = 0.41
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{oxygen}.partialCharge = -0.82
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*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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# IMPORTANT: the SOLVENT version of isosurface
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# IGNORES WATER UNCONDITIONALLY! We must us MOLECULAR!
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#isosurface resolution 6 MOLECULAR colorscheme "rwb" map MEP
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isosurface resolution 6 MOLECULAR map MEP
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# Higher values of resolution make a choppier surface that rotates
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# more jerkily. 6 is good.
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color isosurface "rwb" range -0.2 0.2
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# chose this range by trial and error.
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# default is -0.1 0.1 as reported by the isosurface command.
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color isosurface translucent 2
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# or the partial charges could be in the PDB file using
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# this command to transfer the values.
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# {*}.partialCharge = {*}.temperature.all
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</pre>
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Possible script for large translucent hbonds:
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<pre>
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select all
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calculate hbonds
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hbonds 0.3
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color hbonds white
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color hbonds translucent 6
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</pre>

Current revision

Chemistry of Water and Its Hydrogen Bonds

Prepared in collaboration with User:Gabriel Pons.

One Molecule

Insert caption here

Drag the structure with the mouse to rotate
  • ()
  • (van der Waals radii)
  • Positive (+), Negative (-)

Technical Information

The following scene demonstrates a problem with greek letters in labels in Jmol

  • (using δ in the label, it gets corrupted)

Script for translucent MEP colored surface: 

{hydrogen}.partialCharge = 0.41
{oxygen}.partialCharge = -0.82

# IMPORTANT: the SOLVENT version of isosurface
# IGNORES WATER UNCONDITIONALLY! We must us MOLECULAR!
#isosurface resolution 6 MOLECULAR colorscheme "rwb" map MEP
isosurface resolution 6 MOLECULAR map MEP
# Higher values of resolution make a choppier surface that rotates
# more jerkily. 6 is good.

color isosurface "rwb" range -0.2 0.2
# chose this range by trial and error.
# default is -0.1 0.1 as reported by the isosurface command.

color isosurface translucent 2

# or the partial charges could be in the PDB file using
# this command to transfer the values.
# {*}.partialCharge = {*}.temperature.all

Possible script for large translucent hbonds: 

select all
calculate hbonds
hbonds 0.3
color hbonds white
color hbonds translucent 6

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

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