Alberto Sergio Garay wrote:
Dear all
I am preparing the topology for my enzyme molecule using pdb2gmx tool.
But first of all, I run a PROPKA program in order to assign the correct
protonation state for my molecule. As a result of this calculation I
obtained a pair of cysteines which should be deprotonated at pH 7
(fisiological pH), and others which should be protonated (the most of
them).
Should they be deprotonated such that they bear a net -1 charge, or connected
via disulfide bond?
I have two questions: 1) Is it a correct aproximation to accept the
protonation state obtained by these kind of methods to assign the
charges of my enzyme's residues?
I suppose that depends on the inherent approximations or limitations of the pKa
calculation method. Certainly considering pKa values makes for a more accurate
model than blindly assuming certain protonation states, but probably the primary
literature of the calculation method(s) will describe advantages, limitations,
approximations, etc. You can probably make an argument either way based on
what's published.
2) How can I manage to select which cysteines are deprotonated and which
are not, using pdb2gmx tool?
The first consideration is whether or not you want to use a force field for
which parameters have been derived for this species. As far as I know, only the
AMBER force fields (by default) contain parameters for a cysteine that bears a
net -1 charge. There may be parameters out there for other force fields,
though. Using the AMBER force fields (after installing the ffamber ports) will
require that you name the residues appropriately in the input coordinate file
when running pdb2gmx. That is, your deprotonated CYS would have to be named CYM
to be interpreted correctly.
-Justin
Any help will appreciated.
--
========================================
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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