[gmx-users] Peptide protonation inside membrane

[Justin A. Lemkul]

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:

http://biophysics.cs.vt.edu/

-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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