The Role of Structural Water Molecules in Protein—Saccharide Complexes

Abstract

Polysaccharides have very diverse biological roles. The best-known among these roles are the less noble, such as those concerning their structural functions in bacteria and plant cell walls, and their storage functions in glycogen and starch. Nevertheless, structure and flexibility of saccharides are recognized as having a deep and specific influence in several biological processes: protein protection, maintenance of conformational integrity, and recognition events involving viruses, enzymes and lectins (Lis and Sharon, 1990; Walker, 1988; Diaz et al., 1989). According to Nathan Sharon (Sharon and Lis, 1986), ‘the specificity of many natural polymers is written in terms of sugar residues, not of amino acids or nucleotides’. Since carbohydrates are very hydrophilic molecules, the question addressed in this chapter is whether discrete water molecules, as seen in crystallographic structures of protein—carbohydrate complexes, play a significant role in these interactions. The presence of structural water molecules in proteins and nucleic acids is well documented (Malin et al., 1991; Westhof, 1988). Since a well-refined high-resolution structure contains hundreds of water molecules, the Protein Data Bank (Bernstein et al., 1977) provides a very large structural database of protein-bound water molecules. In nucleic acids, Westhof (1988) has shown that water molecules are an integral part of the structure.