Difference between revisions of "Fabry:Normal mode analysis"

From Bioinformatikpedia
(→‎WEBnm@)
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[[Fabry Disease]] » Normal_mode_analysis
  
[[Fabry Disease]] » Normal_mode_analysis
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<hr>
  
   
 
[[Category: Fabry Disease 2012]]
  
[[Category: Fabry Disease 2012]]
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== Introduction ==
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<div style="float: left">
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<figure id="fig:bindSite">
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[[File:FABRY_bindingSite3HG2-3.png|300px|thumb|left|<caption>...</caption>]]
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</figure>
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<figure id="fig:bindSitenoSUBS">
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[[File:FABRY_bindingSite3HG2-3_noSUBS.png|300px|thumb|left|<caption>...</caption>]]
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</figure>
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</div>
   
 
Maybe one of the first questions that can be asked in this task is, why we use ''low-frequency'' normal modes. This is explained in the paper of Marc Delarue and Philippe Dumas<ref>Marc Delarue and Philippe Dumas '''[http://www.pnas.org/content/101/18/6957.full.pdf On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models]''', Proc. Natl. Acad. Sci. (USA), 101, 6957-6962 (2004)</ref>, where they claim, that "many of the structural transitions (...) can be explained by just a few of the lowest-frequency normal modes". The normal modes can be used to generate the general motion of a system by superposition them. Thus we could in principle infer from our analysis in this task how the alpha-galactosidase A, which we examine hydrolyses the terminal alpha-galactosyl moiety of its substrate<ref>Normal mode [http://en.wikipedia.org/wiki/Normal_mode http://en.wikipedia.org/wiki/Normal_mode], July 5th, 2012</ref>.
  
Maybe one of the first questions that can be asked in this task is, why we use ''low-frequency'' normal modes. This is explained in the paper of Marc Delarue and Philippe Dumas<ref>Marc Delarue and Philippe Dumas '''[http://www.pnas.org/content/101/18/6957.full.pdf On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models]''', Proc. Natl. Acad. Sci. (USA), 101, 6957-6962 (2004)</ref>, where they claim, that "many of the structural transitions (...) can be explained by just a few of the lowest-frequency normal modes". The normal modes can be used to generate the general motion of a system by superposition them. Thus we could in principle infer from our analysis in this task how the alpha-galactosidase A, which we examine hydrolyses the terminal alpha-galactosyl moiety of its substrate<ref>Normal mode [http://en.wikipedia.org/wiki/Normal_mode http://en.wikipedia.org/wiki/Normal_mode], July 5th, 2012</ref>.
   
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<br style="clear:both">
 
== WEBnm@ ==
  
== WEBnm@ ==
   
 
[http://apps.cbu.uib.no/webnma/home WEBnm@] <ref>Hollup SM, Sælensminde G, Reuter N. ''WEBnm@: a web application for normal mode analysis of proteins'' BMC Bioinformatics. 2005 Mar 11;6(1):52 </ref>
  
[http://apps.cbu.uib.no/webnma/home WEBnm@] <ref>Hollup SM, Sælensminde G, Reuter N. ''WEBnm@: a web application for normal mode analysis of proteins'' BMC Bioinformatics. 2005 Mar 11;6(1):52 </ref>
   
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<div style="float:left; border:thin solid lightgrey; margin-right: 20px; width: 500px">
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<div style="float:left; border:thin solid lightgrey; margin-right: 20px; width: 650px">
 
<figtable id="tab:webnma_3hg2">
  
<figtable id="tab:webnma_3hg2">
 
<caption>In this table are the 6 modes shown, that were calculated by WEBnm@. Depicted is the structure 3HG2, which represents the Human α-galactosidase catalytic mechanism with empty active site in cyan and the substrate binding site at position 203 to 207 highlighted in red.<br><br></caption>
  
<caption>In this table are the 6 modes shown, that were calculated by WEBnm@. Depicted is the structure 3HG2, which represents the Human α-galactosidase catalytic mechanism with empty active site in cyan and the substrate binding site at position 203 to 207 highlighted in red.<br><br></caption>
 
{| style="border-style: none"
 
{| style="border-style: none"
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| [[File:FABRY_mode7.gif|right|300px|thumb| WEBnm@ mode 7of 3HG2]]
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| [[File:FABRY_mode7.gif|right|170px|thumb| WEBnm@ mode 7 of 3HG2]]
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| [[File:FABRY_mode8.gif|right|170px|thumb| WEBnm@ mode 8 of 3HG2]]
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| bla
  
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| [[File:FABRY_mode9.gif|right|170px|thumb| WEBnm@ mode 9 of 3HG2]]
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|-
  
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| [[File:FABRY_mode8.gif|right|300px|thumb| WEBnm@ mode 8of 3HG2]]
  
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| bla
  
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|-
  
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| [[File:FABRY_mode9.gif|right|300px|thumb| WEBnm@ mode 9of 3HG2]]
  
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| bla
  
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|-
  
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| [[File:FABRY_mode10.gif|right|300px|thumb| WEBnm@ mode 10of 3HG2]]
  
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| bla
  
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|-
  
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| [[File:FABRY_mode11.gif|right|300px|thumb| WEBnm@ mode 11of 3HG2]]
  
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| bla
  
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|-
  
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| [[File:FABRY_mode12.gif|right|300px|thumb| WEBnm@ mode 12of 3HG2]]
  
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| bla
  
 
|-
  
|-
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| [[File:FABRY_mode10.gif|right|170px|thumb| WEBnm@ mode 10 of 3HG2]]
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| [[File:FABRY_mode11.gif|right|170px|thumb| WEBnm@ mode 11 of 3HG2]]
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| [[File:FABRY_mode12.gif|right|170px|thumb| WEBnm@ mode 12 of 3HG2]]
 
|}
  
|}
 
</figtable>
  
</figtable>
 
</div>
  
</div>
   
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<div style="float:left; border:thin solid lightgrey; margin-right: 20px; width: 500px">
 +
<div style="float:left; border:thin solid lightgrey; margin-right: 20px; width: 650px">
 
<figtable id="tab:webnma_3hg3">
  
<figtable id="tab:webnma_3hg3">
 
<caption>In this table are the 6 modes shown, that were calculated by WEBnm@. Depicted is the structure 3HG3, which represents the Human α-galactosidase catalytic mechanism with bound substrate (green, α-D-Galactose with bound α-D-Glucose) in cyan and the substrate binding site at position 203 to 207 highlighted in red.</caption>
  
<caption>In this table are the 6 modes shown, that were calculated by WEBnm@. Depicted is the structure 3HG3, which represents the Human α-galactosidase catalytic mechanism with bound substrate (green, α-D-Galactose with bound α-D-Glucose) in cyan and the substrate binding site at position 203 to 207 highlighted in red.</caption>
 
{| style="border-style: none"
 
{| style="border-style: none"
−
| [[File:FABRY_mode7_3hg3.gif|right|300px|thumb| WEBnm@ mode 7of 3HG3]]
 +
| [[File:FABRY_mode7_3hg3.gif|right|170px|thumb| WEBnm@ mode 7 of 3HG3]]
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| [[File:FABRY_mode8_3hg3.gif|right|170px|thumb| WEBnm@ mode 8 of 3HG3]]
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| bla
  
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| [[File:FABRY_mode9_3hg3.gif|right|170px|thumb| WEBnm@ mode 9 of 3HG3]]
 
|-
  
|-
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| [[File:FABRY_mode8_3hg3.gif|right|300px|thumb| WEBnm@ mode 8of 3HG3]]
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| [[File:FABRY_mode10_3hg3.gif|right|170px|thumb| WEBnm@ mode 10 of 3HG3]]
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| [[File:FABRY_mode11_3hg3.gif|right|170px|thumb| WEBnm@ mode 11 of 3HG3]]
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| bla
  
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| [[File:FABRY_mode12_3hg3.gif|right|170px|thumb| WEBnm@ mode 12 of 3HG3]]
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|}
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</figtable>
  +
</div>
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<br style="clear:both">
  +
=== Average Energies ===
  +
<div style="float:left; border:thin solid lightgrey; margin: 0px 0px 0px 0px;">
  +
<figtable id="tab:AverageEnergies">
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<caption>ADD CAPTION HERE</caption>
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{| class="wikitable sortable" style="border-collapse: collapse; border-spacing: 0; border-width: 1px; border-style: solid; padding-left:5px; padding-right:5px; border-color: #000; padding: 0"
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! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| 3HG2
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! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| 3HG3
 
|-
  
|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 406.07
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| [[File:FABRY_mode9_3hg3.gif|right|300px|thumb| WEBnm@ mode 9of 3HG3]]
  
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 318.52
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| bla
  
 
|-
  
|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 580.11
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| [[File:FABRY_mode10_3hg3.gif|right|300px|thumb| WEBnm@ mode 10of 3HG3]]
  
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 508.88
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| bla
  
 
|-
  
|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 1062.04
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| [[File:FABRY_mode11_3hg3.gif|right|300px|thumb| WEBnm@ mode 11of 3HG3]]
  
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 1078.20
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| bla
  
 
|-
  
|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 1703.56
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| [[File:FABRY_mode12_3hg3.gif|right|300px|thumb| WEBnm@ mode 12of 3HG3]]
  
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 1621.95
−
| bla
  
  +
|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 1808.92
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 1827.08
  +
|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 2227.10
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 2019.97
  +
|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 2541.59
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 2481.89
  +
|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3109.43
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 2695.35
  +
|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3345.86
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3321.12
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3842.69
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3588.18
  +
|-
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 4868.07
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3782.94
  +
|-
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 5178.29
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 4404.61
  +
|-
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 6119.79
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 5349.94
  +
|-
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 5940.89
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 6027.59
 
|-
  
|-
 
|}
  
|}
 
</figtable>
  
</figtable>
 
</div>
  
</div>
  +
<br style="clear:both">
 
<br style="clear:both">
  
<br style="clear:both">
   
 
== ElNemo ==
  
== ElNemo ==
  +
−
== ElNemo ==
  
  +
<br style="clear:both">
   
 
== References ==
  
== References ==

Revision as of 09:10, 9 July 2012

Fabry Disease » Normal_mode_analysis

Introduction

<figure id="fig:bindSite">

...

</figure> <figure id="fig:bindSitenoSUBS">

...

</figure>

Maybe one of the first questions that can be asked in this task is, why we use low-frequency normal modes. This is explained in the paper of Marc Delarue and Philippe Dumas<ref>Marc Delarue and Philippe Dumas On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models, Proc. Natl. Acad. Sci. (USA), 101, 6957-6962 (2004)</ref>, where they claim, that "many of the structural transitions (...) can be explained by just a few of the lowest-frequency normal modes". The normal modes can be used to generate the general motion of a system by superposition them. Thus we could in principle infer from our analysis in this task how the alpha-galactosidase A, which we examine hydrolyses the terminal alpha-galactosyl moiety of its substrate<ref>Normal mode http://en.wikipedia.org/wiki/Normal_mode, July 5th, 2012</ref>.


WEBnm@

WEBnm@ <ref>Hollup SM, Sælensminde G, Reuter N. WEBnm@: a web application for normal mode analysis of proteins BMC Bioinformatics. 2005 Mar 11;6(1):52 </ref>

<figtable id="tab:webnma_3hg2"> In this table are the 6 modes shown, that were calculated by WEBnm@. Depicted is the structure 3HG2, which represents the Human α-galactosidase catalytic mechanism with empty active site in cyan and the substrate binding site at position 203 to 207 highlighted in red.

WEBnm@ mode 7 of 3HG2
WEBnm@ mode 8 of 3HG2
WEBnm@ mode 9 of 3HG2
WEBnm@ mode 10 of 3HG2
WEBnm@ mode 11 of 3HG2
WEBnm@ mode 12 of 3HG2

</figtable>

<figtable id="tab:webnma_3hg3"> In this table are the 6 modes shown, that were calculated by WEBnm@. Depicted is the structure 3HG3, which represents the Human α-galactosidase catalytic mechanism with bound substrate (green, α-D-Galactose with bound α-D-Glucose) in cyan and the substrate binding site at position 203 to 207 highlighted in red.

WEBnm@ mode 7 of 3HG3
WEBnm@ mode 8 of 3HG3
WEBnm@ mode 9 of 3HG3
WEBnm@ mode 10 of 3HG3
WEBnm@ mode 11 of 3HG3
WEBnm@ mode 12 of 3HG3

</figtable>


Average Energies

<figtable id="tab:AverageEnergies"> ADD CAPTION HERE

3HG2 3HG3
406.07 318.52
580.11 508.88
1062.04 1078.20
1703.56 1621.95
1808.92 1827.08
2227.10 2019.97
2541.59 2481.89
3109.43 2695.35
3345.86 3321.12
3842.69 3588.18
4868.07 3782.94
5178.29 4404.61
6119.79 5349.94
5940.89 6027.59

</figtable>



ElNemo


References

<references/>

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