[gmx-users] Protonation state of the ionisable residues

[Justin A. Lemkul]

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

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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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