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 Thu Jul 28 2011 - 11:30:04 PDT
