International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

International Tables for Crystallography (2006). Vol. F, ch. 23.2, pp. 579-580   | 1 | 2 |

Section 23.2.2. Protein–carbohydrate interactions

A. E. Hodela and F. A. Quiochob

aDepartment of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA, and  bHoward Hughes Medical Institute and Department of Biochemistry, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA

23.2.2. Protein–carbohydrate interactions

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The interaction between proteins and carbohydrates provides a prototypic example of how proteins specifically recognize small organic ligands. Protein-mediated recognition of carbohydrates is crucial in a diverse array of processes, including the transport, biosynthesis and storage of carbohydrates as an energy source, signal transduction through carbohydrate messengers, and cell–cell recognition and adhesion (Rademacher et al., 1988[link]). Many aspects of protein–carbohydrate recognition are observed in the interactions of proteins with other small-molecule ligands. For example, carbohydrate recognition is largely conferred through a combination of hydrogen bonding and van der Waals interactions with the protein (Quiocho, 1986[link]). These interactions are generally presented in a binding site that is highly complementary to the target ligand in shape and functionality. Carbohydrate-binding proteins also occasionally employ ordered water molecules and bound metal ions to facilitate ligand recognition (Quiocho et al., 1989[link]; Vyas, 1991[link]; Weis & Drickamer, 1996[link]). There are also many examples of `induced fit' recognition of carbohydrates, where the binding of the ligand induces a conformational change in the protein. This phenomenon of ligand-induced conformational change was observed in one of the first ligand–protein interactions visualized by X-ray crystallography, namely the binding of a carbohydrate substrate to lysozyme (Blake et al., 1967[link]). Since these early studies, a wide variety of carbohydrate–protein structures have been determined, and a number of general themes have emerged from this continually active field (Vyas, 1991[link]). These themes are further applicable in the general study of protein–ligand recognition.

Two general classes of carbohydrate-binding modes have been observed in their complexes with proteins (Quiocho, 1986[link]; Vyas, 1991[link]). The first group of proteins completely sequester the carbohydrate from the surrounding solvent. These proteins, including the periplasmic proteins and the catalytic site of glycogen phosphorylase, tend to have a high affinity for their ligand (Kd ≃ 10−6–10−7). The high affinity of these proteins can be attributed to the entropic gain of desolvating the protein and carbohydrate surfaces as well as the exceptionally high degree of functional complementarity in the ligand-binding site. The periplasmic proteins nearly saturate the hydrogen-bonding potential of their carbohydrate ligands (Quiocho, 1986[link]). The second group of proteins bind their ligands in shallow clefts in the solvent-exposed protein surface. This mode of binding, observed in the lectins, lysozyme and the storage site of glycogen phosphorylase, generally has a lower binding constant than the first class of binding proteins (Kd ≃ 10−3—10−6). Some members of this second class of proteins, such as the lectins, are able to increase the affinity for their ligands dramatically by clustering a number of low-affinity sites through the oligmerization of the polypeptides (Weis & Drickamer, 1996[link]). The specific arrangement of lectin oligomers allows them to discriminate between large cell-surface arrays of polysaccharides with high affinity and selectivity.

23.2.2.1. Carbohydrate recognition at the atomic level

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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[link]). 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)[link]. 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]

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[link]). (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)[link]. 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[link] ) and protein–ligand interactions (see below).

References

Blake, C. C. F., Mair, G. A., North, A. C. T., Phillips, D. C. & Sarma, V. R. (1967). On the conformation of the hen egg-white lysozyme molecule. Proc. R. Soc. London Ser. B Biol. Sci. 167, 365–377.Google Scholar
Quiocho, F. A. (1986). Carbohydrate-binding proteins: tertiary structures and protein–sugar interactions. Annu. Rev. Biochem. 55, 287–315.Google Scholar
Quiocho, F. A., Sack, J. S. & Vyas, N. K. (1989). Substrate specificity and affinity of a protein modulated by bound water molecules. Nature (London), 340, 404–407.Google Scholar
Rademacher, T. W., Parekh, R. B. & Dwek, R. A. (1988). Glycobiology. Annu. Rev. Biochem. 57, 785–838.Google Scholar
Vyas, N. K. (1991). Atomic features of protein–carbohydrate interactions. Curr. Opin. Struct. Biol. 1, 732–740.Google Scholar
Weis, W. I. & Drickamer, K. (1996). Structural basis of lectin–carbohydrate recognition. Annu. Rev. Biochem. 65, 441–473.Google Scholar
Werner, M. H., Gronenborn, A. M. & Clore, G. M. (1996a). Intercalation, DNA kinking, and the control of transcription. Science, 271, 778–784.Google Scholar








































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