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GLYCAM-L  June 2016

GLYCAM-L June 2016

Subject:

Re: problems with SO3 derivation

From:

Lachele Foley <[log in to unmask]>

Reply-To:

Users of GLYCAM & GLYCAM-Web <[log in to unmask]>

Date:

Mon, 13 Jun 2016 10:57:46 -0400

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (77 lines)

This is the updated page:

http://glycam.org/docs/help/2014/04/04/adding-chemical-derivatives-to-glycam-residues/

On Mon, Jun 13, 2016 at 4:18 AM, Xiaocong Wang <[log in to unmask]> wrote:
> Hi Manuel,
>
>
> Please see the following documentation page on glycam.org.  We have
> protocols of altering charges when sugars are sulfated.
>
>
> http://glycam.org/docs/help/2014/04/04/sulfating-glycam-residues/
>
>
> This should solve your problem.
>
>
> Best,
>
>
> Xiao
>
>
>
> Xiaocong Wang
> Complex Carbohydrate Research Center
> The University of Georgia
> 315 Riverbend Road,
> Athens, GA, 30602
> Tel: (706) 254-7958
> E-mail: [log in to unmask]
> ________________________________
> From: Users of GLYCAM & GLYCAM-Web <[log in to unmask]> on behalf of
> mmaestre <[log in to unmask]>
> Sent: Monday, June 13, 2016 4:01:09 AM
> To: [log in to unmask]
> Subject: problems with SO3 derivation
>
> Dear Glycam users,
>
> I'm having a bit of trouble building sulfo sialil-lacnac. To be clear, the
> structure I'm trying to build is the following:
>
> NeuAc-alpha-2-3-Gal-beta-1-4-(6S)-GlcNac-Beta-1-ROH
>
> Written in Glycam06 compatible form (sort of):
>
> ROH-UYB(SO3)-3LB-0SA
>
> My problem is that I am not getting integral charges. I would expect to get
> an overall charge of -2 from xleap, however, I'm getting -2.031.
> I've checked all the units, and these are the individual charges:
> ROH: -0.194
> UYB: -0.194
> 3LB: 0
> 0SA: -0.806
> SO3: -0.837
>
> Ok, so, if I add all of it, indeed, I get -2.031. What's really annoying,
> though, is that it looks like the problem is on the SO3 or the UYB. I mean,
> if I construct any 6-sulfo-monoglycan, I'm going to be using a glycan
> fragment with net charge 0, an roh fragment with net charge -0.194, and an
> SO3 fragment with charge -0.837. Together, that's always going to be -1.031,
> which means that the charge will never ever be integral.
> Does anyone have any ideas? What am I doing wrong here?
>
> Thank you very much,
> Manuel



-- 
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA

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