[gmx-users] Peptide protonation inside membrane

Justin A. Lemkul jalemkul at vt.edu
Thu Feb 23 22:07:07 CET 2012

Ricardo O. S. Soares wrote:
> Dear Users,
> when using pdb2gmx with the -inter flag, how should one manage the 
> residues charges of a peptide which is fully embedded in a lipid bilayer?
> It seems that there are evidences that ARG residue remains protonated 
> inside the membrane (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275699/).
> How about the HIS, LYS etc?
> Sorry if it's a dull question, however I found very little comments on 
> the subject.

There is quite a lot in the literature about pKa shifting based on different 
microenvironments.  There are also a number of tools available to do pKa 
estimates, for instance:




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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