Mish,
I don't know enough about your system to give you a definite answer on the protonation state of sialic acid in your protein complex however it is likely to be deprotonated. If you are unsure then you should look at the local environment carefully and consider the experimental/biological conditions under which the complex is formed.
If you were to do ensemble averaged charges for the neutral sugar then the reference for the method is in the AMBER manual and on our website but I would ask you to email me off list to discuss the specific considerations for Neu5Ac development.
Matthew B. Tessier
CCRC - UGA
matthew.tessier.gmail.com
706-542-3508
mish <smncbr.gmail.com> wrote:
>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 - 06:00:03 PDT
