[MMTK] ENM normal mode analysis question

Liz Kellogg lizkellogg at gmail.com
Sat Jun 1 07:37:32 UTC 2013


Hi Konrad,

thanks for the response! I am considering three different structures of 
the same protein sequence. The structures are very similar to one 
another, around 1 Angstrom rmsd, and the structures are large, around 
850 aa.
When I say "resolving" the structural changes, I mean this: Because the 
structures are so similar (yet have visible shifts when I align one on 
the others) it's difficult to see what is changing. I was hoping normal 
mode analysis could decompose the structural changes into something that 
is easier to parse visually (i.e. look at the structural differences 
between the three).
Also, the three structures represent three distinct states. Is it 
possible to sample the conformational transition from one state to 
another with normal modes? (this question here is how does one structure 
turn into the other?)

Thanks a lot,

Liz

On 6/1/13 12:10 AM, Konrad Hinsen wrote:
> Liz Kellogg writes:
>
>   > I'm new to the group, and I've been searching all over google to see if
>   > what i want to do is possible in MMTK. Perhaps someone here can answer.
>   > I have 3 different protein structures, and I want to perform normal mode
>   > analysis on the C-alphas (I think I need to use the elastic network
>   > model) to try and resolve the structural changes going from one
>   > conformation to the other. How do I go about doing this in MMTK?
>   > Do I read in the pdbs as a trajectory and create a universe from that,
>   > then perform normal mode analysis on the universe?
>
> This is definitely doable with MMTK, but if you want more precise
> guidance, we need more details about you want to do. In particular,
> are you considering three different structures for the same protein,
> or three different but somehow related proteins? And what exactly
> do you mean by "resolving" the structural changes?
>
> Konrad.




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