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
--
========================================
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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