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. 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/
--
Engin Özkan
Post-doctoral Scholar
Laboratory of K. Christopher Garcia
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111
