Section 23.2.2.1. Carbohydrate recognition at the atomic level

An early review of protein–carbohydrate interactions revealed several atomic level interactions that continue to appear ubiquitously in the structures of protein–carbohydrate complexes (Quiocho, 1986). A generic cyclic sugar in mono- or oligosaccharides appears to be recognized as a disc that displays two flat non-polar surfaces surrounded by a ring of polar hydroxyls. Proteins recognize these features by hydrogen bonding to the ring of polar hydroxyls while stacking flat aromatic side chains against the non-polar disc faces.

Cooperative hydrogen bonding, where the hydroxyl group of a carbohydrate participates as both a donor and acceptor of hydrogen bonds, is often observed in the direct interactions between proteins and carbohydrate ligands (Fig. 23.2.2.1). The sp³-hybridized oxygen atom of a carbohydrate hydroxyl may act as both an acceptor of two hydrogen bonds through the two lone pairs of electrons as well as a donor of a single hydrogen bond. Cooperative hydrogen bonding generally follows a simple pattern in which the carbohydrate hydroxyl accepts a hydrogen bond from a protein amide group while simultaneously donating a hydrogen bond to a protein carbonyl oxygen. Hydrogen bonding to protein hydroxyl groups is observed only infrequently. This pattern is thought to be a result, in part, of the entropic cost of fixing a freely rotating protein hydroxyl group while simultaneously fixing the ligand hydroxyl group. Amides and carbonyls are usually fixed in a planar geometry and thus do not require as much energy to compensate for their loss of entropy in ligand binding.

Figure 23.2.2.1| top | pdf | The atomic recognition of carbohydrates by a protein. The environment of glucose bound to the galactose/glucose binding protein is shown (Vyas et al., 1988). (a) The ring of hydrogen bonds around the polar edge of the sugar molecule. Note the `bidentate' hydrogen bonds with Asp236, Arg158 and Asn91. As the hydroxyl groups 1, 2 and 3 simultaneously donate and accept hydrogen bonds from protein side chains, they are involved in `cooperative' hydrogen bonds. (b) Two aromatic protein side chains, Phe16 and Trp183, `stack' on the non-polar faces of the carbohydrate.

The vicinal hydroxyl groups of carbohydrates provide an ideal geometry for the formation of `bidentate' hydrogen bonds, where the pair of hydroxyls interacts with two functional groups of a single amino-acid side chain or the main-chain amide groups of two consecutive residues (Fig. 23.2.2.1). These interactions occur when the adjacent carbohydrate hydroxyls are either both equatorial, or one is equatorial and the other axial. The interatomic distance for the carbohydrate hydroxyl oxygens is ∼2.8 Å in these cases, allowing for a bidentate interaction with the planar side chains of aspartate, asparagine, glutamate, glutamine and arginine. Bidentate hydrogen bonds have not been observed for consecutive axial hydroxyls where the oxygen–oxygen distance increases to ∼3.7 Å.

Carbohydrates often present a disc-like face of non-polar aliphatic hydrogen atoms which proteins recognize through the use of aromatic side chains. The protein aromatic groups are `stacked' on the flat face of the carbohydrate, thus generating both specificity and binding energy through van der Waals interactions. Tryptophan, the aromatic amino acid with the largest surface area and highest electronegativity, is the most common side chain employed in van der Waals `stacking' with carbohydrates. The infrequent use of aliphatic groups in the binding of the non-polar carbohydrate faces suggests that the aromatic moieties are employed in a specific manner. The electron-rich electron clouds of the aromatic side chains may provide a strong electrostatic interaction with the aliphatic carbohydrate protons that could not be satisfied by protein aliphatic groups. The anionic character of aromatic side chains is observed in a number of protein–intramolecular (Chapter 22.2 ) and protein–ligand interactions (see below).