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I need help with domELNEDIN. >.<
- yipy0005
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Thanks.
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- Clement
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- yipy0005
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- Clement
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In fact, it just depends on how you define the elastic network in the first place: for each of your subunits separately or for the entire protein. If no strings are linking the two subunits, you'll observe "conformational changes" and slight modification of the interactions between them.
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- yipy0005
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What I'm actually trying to do now is I wish to see the internal dynamics of a large protein (E.g. PPAR) where I hope to see more intense movements between the helices. I tried the AA approach, but due to the time scale, there's absolutely no way to visualize such internal motions. That's why I'm resorting to CG and ELNEDIN. So if I apply ELNEDIN throughout the whole protein, what are the chances I will get to see the more intense internal dynamics of the protein?
Thanks. =)
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- Clement
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What do you mean by "see more intense movements between the helices"? Remember you're using an elastic network...
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- yipy0005
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I have protein with 2 subunits, so if I want to see if they interact, then it's advised I "strung" them up in each subunit but not between them, and with the time scale advantage provided by CG, I may just be able to observe some conformational changes BETWEEN the 2 subunits, and not within.
So now, instead of a protein with 2 subunits, I have a protein that consists of let's say, 20 helices linked from N- to C-terminus. Using an AA approach, it would take me ages to obtain a simulation whereby I see the helices interacting with each other within the protein. So, in this case, since it's a time-scale problem, do I simply run it using CG without ELNEDIN?
Hopefully, I ain't confusing you too much with the way I phrase. >.<
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- Clement
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That's it.I have protein with 2 subunits, so if I want to see if they interact, then it's advised I "strung" them up in each subunit but not between them, and with the time scale advantage provided by CG, I may just be able to observe some conformational changes BETWEEN the 2 subunits, and not within.
Either you do that, either you try to remove the elastic network between each helices (keeping the elastic network internal to each helix). But all in all, the effects you want to observe here might be too fine to be seen in CG... To be tested.So now, instead of a protein with 2 subunits, I have a protein that consists of let's say, 20 helices linked from N- to C-terminus. Using an AA approach, it would take me ages to obtain a simulation whereby I see the helices interacting with each other within the protein. So, in this case, since it's a time-scale problem, do I simply run it using CG without ELNEDIN?
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- yipy0005
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- Clement
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