Difference between revisions of "Fabry:Normal mode analysis"

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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
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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.
 
Why do we use low frequency
 
   
 
== WEBnm@ ==
 
== WEBnm@ ==

Revision as of 14:34, 5 July 2012

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.

WEBnm@

WEBnm@

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

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

</figtable>


References

<references/>