Carbohydrate Primer
- Introduction
- Protein Chemistry
- MAN
- NAG
- Polysaccharides
- Protein links
Introduction
A carbohydrate is an organic compound with the empirical formula Cm(H2O)nwhere m could be different from
n. Synonym of saccharide. Saccharides have several characteristics that
differentiate them. These include
- placement of carbonyl group
- length of the carbon chain
- sequence of chiral centres
- handedness of the molecule
- linear or cyclic
Cyclic saccharides are classified as alpha or beta isomers based on the
position of the OH on the anomeric carbon relative to the large group on
the ring.
Protein Chemistry
If your protein was produced in an insect or yeast cell
line, you should only have NAG and MAN sugars, otherwise
you should look at both types of PDB files to see which
fits the density better (if you have any density past the
main, five sugar core).
MAN
Mannose is a common saccharide in protein chemistry. There are two
linear isomers and two cyclic forms of each. The PDB code for each is
different because of the different restraints require for each. A
leading form of error in protein models with carbohydrates is the use
of the three-letter code, MAN, which is for the alpha-D-mannose when
that vast majority of units in saccharides are beta-D-mannose or BMA.
NAG
NAG represents the beta form (the most common) and NDG is the alpha form. NAG
is interesting because it's a saccharide with a substitute attached to the
C2 carbon.
Polysaccharides
Saccharides polymerise into tree like structures that covalently bind to
proteins. The links between are generally between the anomeric carbon and
an oxygen on the "preceding" units moving from the protein outwards on the
chain. Consider the disaccharide, lactose.
Note that the left saccharide is linked with its anomeric carbon via an oxygen
to the C4 carbon. The left unit is β-D-galactose and the right is glucose.
The link is known as β-(1-4) because the "attaching" unit is β and the
it links C1 to C4.
Protein links
The most common link to proteins is the n-link which attaches to ASN in the
ASN-X-SER/THR motif.
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