[gmx-users] Rg

[Justin A. Lemkul]

simon sham wrote:
> Hi,
> I have a question of using Radius of Gyration to analyze my simulation 
> data for a protein at a temperature that it would unfold.
> My understanding is that when a protein in an unfolded state, it still 
> have some structure and is not a random coil. So, my question is:
> Will the Rg value for a unfolded protein be completely different from 
> that of folded one?
> 

In general, probably.  It depends entirely upon what the "unfolded" state is for 
the protein in question - is it elongated, with little secondary structure, or 
does it collapse into a disordered globule that doesn't resemble the native 
state?  If the latter, then Rg can be misleading.  At extremely high 
temperature, though, I would expect just about any protein to be very elongated, 
unless it has lots of disulfides to keep it compact.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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