Water-mediated hydrogen bonds

The precise chemical interactions between an adhesin and its receptor are also important. For example, direct- and water-mediated hydrogen bonds are the most important interactions within the carbohydrate-recognition domain in carbohydrate-binding adhesins on the host cell surface (Weis and Drickamer, 1996). Nonpolar van der Waals interactions and hydrophobic "stacking of the receptor oligosaccharide rings with aromatic amino acid side chains of the bacterial adhesin protein also contribute to oligosaccharide-protein interactions. X-ray structural... 

Fig. 3 Interactions between the Fab and octapeptide or pentasaccharide. A Stereoview of octapeptide binding, which includes eight direct and nine one-water-mediated hydrogen bonds. B Stereoview of pentasaccharide binding, adapted from [82]. The two water molecules (Ow) hind solely to the sugar. C Comparison of the number of direct contacts of residues between the Fah and octapeptide or pentasaccharide. The numbers of direct hydrogen bonds and van der Waals contacts (<4 A) associated with peptide binding are 6 and 126, respectively, and with saccharide binding are 8 and 74, respectively. Reproduced from [80]. 2003 by The National Academy of Sciences of the USA...

Figure 2.21. Stabilization of collagen triple helix. The diagram shows hydrogen bonding between the amide hydrogen in position 4 on chain A and the carbonyl oxygen in position 2 on chain B. A second water-mediated hydrogen bond occurs when hydroxyproline is present in position 3 on chain A between the carbonyl oxygen in position 1 on chain A and the amide hydrogen in position 2 on chain B.

In addition to these repressor-operator interactions, there are six water-mediated hydrogen bonds, three bridging to the major groove functional groups of A5, G6, A7 (Fig. 20.18 b), and the other three to five phosphate oxygens. The water molecules can only be accommodated with G at position 6 and a purine at position 5, and a purine (adenine) at position 7. Recent studies have cast some doubts on the specifity of these interactions, however, and further experiments are necessary to show that this ternary complex is really of biological relevance [714]. 

Using the program GRASP (Nicholls ei al.. 1991). accessible surface area calculations based on the Shrake Rupley (1973) Hydrogen bonds in domain interfaces, with water-mediated hydrogen bonds in parentheses. 

The restriction endonuclease Mspl makes specific contacts with all eight bases in the four base pair recognition sequence (CCGG), by six direct and five water-mediated hydrogen bonds and 13 water-mediated links to the phosphates (30). Numerous... 

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