Hi:
What Oliver says abou -COOH group is very much correct but I am only afraid
that, can sugar molecules be charged in physiological condition ?. Just to
clear the condition, I am running MD of protein complexed with this
saccharides. I am using modeled structure
(A-D-Neu5Ac-(2-3)-B-D-Galp-(1-4)-B-D-Glcp-(1-1)-OH) of ligand as such. Yes I
added counter ions to balance the charge in complex. Do you think this makes
sense ? I can not see anything strange in simulation but the question is if
having charges sugar is not a theoretical mistake. Whats you opinion on this
? ? If its not correct, then I would like to ask how to generate ensemble
averaged charges for the neutral sugar.
Sincerely
mish
On Thu, Jul 28, 2011 at 8:13 PM, Matthew Tessier
<matthew.tessier.gmail.com>wrote:
> Mish,
> The charges for sialic acids are developed for the anionic glycans so you
> can't simply replace the charges with those of ROH. You will need to
> generate ensemble averaged charges for the neutral sugar to use this in MD
> simulations. We can discuss this if you'd like to go down that path but we
> have no immediate plans to generate these charges.
>
> Matthew B. Tessier
> CCRC - UGA
> matthew.tessier.gmail.com
> 706-542-3508
>
> Oliver Grant <olivercgrant.gmail.com> wrote:
>
> >Hi Mish,
> >
> >At physiological pH the carboxylate group will have a negative charge
> which
> >will be shared between the two oxygens. It is common to represent the
> >structure as (COOH) with all the valencies filled but in solution that
> >proton will come off. Again it is common to represent that as O=C-O with a
> >negative charge on the right hand side oxygen but really that charge is
> >shared between the two oxygens. It's called resonance hybridization. The
> >double bond you see is probably put there by whatever visualizer/builder
> you
> >are using.
> >
> >Oliver
> >
> >On 28 July 2011 10:29, mish <smncbr.gmail.com> wrote:
> >
> >> Hi all:
> >>
> >> My question is related to preparing the structure of 3' Sialyllactose
> using
> >> GLYCAM. In databse (http://www.hmdb.ca/metabolites/HMDB00825) I can see
> >> that
> >> this structure is nothing but tri-saccharides linked in fallowing way.
> >> A-D-Neu5Ac-(2-3)-B-D-Galp-(1-4)-B-D-Glcp-(1-1)-OH
> >> I modeled the structure in GLYCAM web interface but I can see a
> difference
> >> in the structure of Neu5Ac (0SA) residue. C1 of 0SA has two oxygens O1A
> >> and
> >> O1B making double bond with C1. This makes the sugar charged. Whereas if
> we
> >> look for the structure published in article or in the same data base its
> >> just a -COOH group. Can you please correct me if I am going in wrong
> >> direction or whats is the possible way to overcome ? Replacing O1A or
> O1B
> >> with ROH should be fine or I have to be careful about something else ?
> >>
> >> Sincerely
> >> Mish
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Received on Fri Jul 29 2011 - 01:30:03 PDT
