Water mediating

Structural studies of a repressor-DNA complex have shown that helices 4 and 5 form a helix-turn-helix motif and that side chains from the recognition helix 5 form water-mediated interactions with bases in the major groove. 

Ezzaouia H, Heindl R, Parsons R, Tributsch H (1983) Visible light photo-oxidation of water with single-crystal RuS2 electrodes. J Electroanal Chem 145 279-292 Kiihne HM, Tributsch H (1983) Oxygen evolution from water mediated by infrared light on iron doped RuS2 electrodes. J Electrochem Soc 130 1448-1450... 

The reaction of an a-halo carbonyl compound with zinc, tin, or indium together with an aldehyde in water gave a direct cross-aldol reaction product (Eq. 8.90).226,227 A direct Reformatsky-type reaction occurred when an aromatic aldehyde reacted with an a-bromo ester in water mediated by zinc in low yields. Recently, it was found that such a reaction mediated by indium was successful and was promoted by son-ication (Eq. 8.91).228 The combination of BiCl3-Al,229 CdCl2-Sm,230 and Zn-Et3B-Eb0231 is also an effective mediator. Bismuth metal, upon activation by zinc fluoride, effected the crossed aldol reaction between a-bromo carbonyl compounds and aldehydes in aqueous media. The reaction was found to be regiospecific and syn-diastereoselective (Eq. 8.92).232... 

Further evidence for the OHb pairs is given in an STM movie recorded at approximately 187 K. The movie shows the OHb pairs separating across the Ob rows via proton exchange with water molecules [19]. Key frames from the movie are shown in Figure 8.5. This water-assisted OHb diffusion mechanism is supported by calculations, which show that the barrier to diffusion is lowered by the exchange with water. The same diffusion mechanism is also observed for isolated OHb and because of the misassignment of OHb and Ob-vacs by Schaub et al. [15], this water-mediated diffusion of OHb was incorrectly reported as oxygen-mediated diffusion of Ob-vacs [32, 33] via a mechanism inconsistent with subsequent isotope studies [34],... 

In addition to their work with solvent free systems, Wang and co-workers reported a water mediated Friedlander quinoline synthesis using hydrochloric acid and conventional heating to synthesize a variety of substituted quinolines in high yields <06TL1059>. 

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... 

Instead, the Lys side chains bond to Y position carbonyl groups of an adjacent chain, while one Glu directly interacts with a Hyp hydroxyl group. There was also a range of water-mediated interactions involving the polar side chains. In peptide T3-785, with the central region Gly-Ile-Thr-Gly-Ala-Arg-Gly-Leu-Ala, the Arg side... 

Figure 17 Water-mediated interchain hydrogen bond. The figure was created with the UCSF Chimera package coordinates from PDB structure 1QSU.

Figure 18 Molecular structure of IBP collagen (PDB accession number 1Q7D) showing a direct intrahelical ion bridge and a water-mediated interaction between Glu and Arg of different chains. The figure was generated using the UCSF Chimera package.

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...

Contacts with the catalytic residues, in combination with hydrophobic interactions, are also observed in the complex of an insect a-amylase with the Ragi bifunctional a-amylase/trypsin inhibitor (RBI) [174]. Conversely, the mechanism of inhibition of barley a-amylase by the barley a-amylase/subtilisin inhibitor (BASI) did not involve direct contact between inhibitor residues and the catalytic site [175]. The inhibitor sterically blocks the catalytic site, but does not extend into it. A cavity is created, which is occupied by a calcium ion coordinated by water-mediated interactions with the catalytic residues. 

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