it's not really an answer to your question, but have you considered
the size box you need to hold the unfolded state? how large is your
box? it may be that the protein is interacting strongly with its
periodic images, stabilizing specific structures.
regarding the "how long does it take"- proteins vary widely in this.
is there experimental data for unfolding rate? that might give some
clue, though of course it can't be done at 500K. there are other ways,
such as adding denaturant, but keep in mind that unfolded states and
pathways depend on the process sued to unfold it, and so what you do
depends on what you want to learn. In my opinion, an unfolded protein
at 500K doesn't really tell me much that has biological relevance.
On Thu, Jun 7, 2012 at 11:17 PM, Chinh Su Tran To
<chinh.sutranto.gmail.com> wrote:
> Dear Amber users,
>
> I am doing unfolding for a 270-residue protein using Amber 9. By heating it
> at 500K (dt=1.5fs), I observe its unfolded states (mostly by visualization
> using VMD).
> It's been running for 276 ns, but its active site is still somehow
> "maintained" (not much changed --> I calculated distances among C-alpha
> atoms of these active residues, the values are not very much different
> among the unfolded states, e.g. the 6ns-state and the 240ns-state).
> The overall RMSD significantly differ though.
>
> This may be a "silly" question 'cause it is not a technical one, but I am
> interested in it.
> - I didnt put any restraint for the whole system during the unfolding, but
> using iwrap=1 to keep it in the solvent box. Does this iwrap parameter
> somewhat give any restraint per se?
> - Im a newbie in unfolding such a big protein, how long normally does it
> take to totally get unfolded protein? One of my professors folded a protein
> in ms or second scale, how about unfolding?
> - aside from heating, any other ways to unfold the protein? Is 500K an
> appropriate value?
>
> Thank you for any help. Any recommended papers are also very much
> appreciated.
>
> Regards,
> Chinh
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Received on Fri Jun 08 2012 - 03:00:03 PDT
