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-- Dr. Dean Cuebas, Associate Prof of Chemistry deancuebas.missouristate.edu, Ph 417-836-8567 FAX 417-836-5507 Dept. of Chemistry, Missouri State University Springfield, Missouri 65897 On 7/29/11 3:06 AM, "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 >> >> _______________________________________________ >> >> AMBER mailing list >> >> AMBER.ambermd.org >> >> http://lists.ambermd.org/mailman/listinfo/amber >> >> >> >_______________________________________________ >> >AMBER mailing list >> >AMBER.ambermd.org >> >http://lists.ambermd.org/mailman/listinfo/amber >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> >_______________________________________________ >AMBER mailing list >AMBER.ambermd.org >http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sat Jul 30 2011 - 16:00:03 PDT