On Monday 18 January 2010, Engin Ozkan wrote:
> Hi everybody,
>
> I have a question regarding glycosidic bonds. This relates to refmac,
> phenix and cns, so I thought the best forum to pose this was here.
>
> We have these very nifty link descriptions, such as BETA1-4, ALPHA1-6,
> etc. that come with refmac and phenix. These essentially describe a
> chiral center and torsion angles around position C1. However, the way a
> glycosidic linkage is defined as alpha or beta does not solely depend on
> the C1 chiral center (see below if interested, and see if I am right).
> An ALPHA1-3 link in refmac or phenix works for a alpha-D-mannose, but it
> forces my alpha-L-fucoses to become beta, no matter what I do.
I do not know what options are available in phenix, but in the refmac
dictionaries you have the option of specifying the chiral volume of the
anomeric carbon as "both" rather than as "negativ" or "postive".
This will preserve the chirality of the model as input.
So long as you provide the correct anomer in your input model,
you should be OK. Caveat: I have used this successfully for to handle
anomers of GLU, GAL, NAG, and SIA, but I can't rule out a bug of some sort
that hits other sugars.
Ethan
> And by
> the way, secreted and membrane proteins you make in insect cells will
> have ALPHA1-3 and ALPHA1-6 linkages to fucose, and in mammals, ALPHA1-6
> to fucose; this should be a very common occurrence (and problem).
>
> This seems to be a fucose-specific problem, since it is the only
> standard sugar residue, that's an L sugar, so the defined links will
> result in incorrect stereoisomers.
>
> I would be very happy if anyone can check the logic here, and please
> correct me (it has been 12 years since I learnt and soon forgot what an
> anomer is!).
>
> Best,
> Engin
>
> P.S. Alpha or beta: How a sugar is designated as an alpha or beta
> "anomer" is actually complicated, and requires one to draw a Fischer
> projection. IUPAC says:
>
> Relative stereodescriptors used in carbohydrate nomenclature to describe
> the configuration at the anomeric carbon by relating it to the anomeric
> reference atom. For simple cases the anomeric reference atom is the same
> as the configurational reference atom. Thus in ?-d-glucopyranose the
> reference atom is C-5 and the OH at C-1 is on the same side as the OH at
> C-5 in the Fischer projection.
>
> Simply checking wikipedia:anomer can show that an alpha or beta anomer
> can have opposite chiral centers depending on the identity of the sugar.
> Also, the current versions of FUC-a-L in the monomer libraries of refmac
> and phenix seem to be beta indeed. Garib Murshudov knows about this. See
> http://www.flickr.com/photos/46544...@n03/4274285327/
> HIC-UP has it right: http://xray.bmc.uu.se/hicup/FUC/
>
>
