James Starlight wrote:
Thanks Justin.
Your aproach is very usefull indeed.
I've just one relative question about CAPPING of the termi in the case
of simulation of the membrane receptors. In that proteins both of N and
C termi are in the water polar layer. In the literature I've found
nothing about capping of the termi as well as changing of protonated
state of that fragments. What advantages might have such capping of the
termni of that protein?
Probably none. If termini are exposed to solvent, they are generally assumed to
be in their predominant (ionized) form. Capping is typically used when a
polypeptide fragment is being modeled, such that residues that are normally
present at the N- or C-termini are not present in the simulation. Neutralizing
the charges by adding amide caps is a more realistic representation in such cases.
-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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