[gmx-users] Rg

Justin A. Lemkul jalemkul at vt.edu
Tue May 24 20:18:24 CEST 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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