Substrate binding, hydration

The rate of attack of water upon the tri-/>-anisylmethyl cation is unaffected by binding of this cation to anionic micelles of sodium dodecyl sulfate (SDS) (Bunton and Huang, 1972) and equilibrium constants for aldehyde hydration are only slightly reduced by binding to micelles (Albrizzio and Cordes, 1979). These observations are also consistent with substrate binding at a wet micellar surface rather than in the interior of the micelle. 

Hydration and/or dehydration reactions are frequently catalyzed by metallopro-teins. Examples are proteins containing nickel (urease), zinc (e.g., peptidases), molybdenum (the hydratase partial reaction of formate oxidoreductase), tungsten (acetylene hydratase). An obvious difference between Ni, Zn, on the one hand, and Fe, Mo, W, on the other, is that the first are directly coordinated to the protein whereas the latter are also part of a cofactor. With reference to the Fe/S cluster in aconitase it has been suggested that cofactor coordination may provide an added flexibility to the active site, in particular to the substrate binding domain [15],... 

There is evidence that the a-cyclodextrin macrocycle can adjust its cavity diameter, within certain limits, to accommodate either two hydrate water molecules in the collapsed or tense form, or a nonaqueous guest molecule in the round or relaxed form. This is the concept of the induced fit [576] which has been applied to comparable conformational changes observed with several enzymes upon substrate binding. 

Hydration water molecules indicate substrate-binding sites. In crystal structures of native proteins, the active sites are usually hydrated if they are not in direct contact with symmetry-related protein molecules. Since the substrates or inhibitors are recognized by the protein and bound to its active site by hydrogen bonds and/or by insertion of hydrophobic residues into hydrophobic pockets, it is not surprising to find, in the native protein, water associated in positions which are the... 

Fig. 7. —Suggested Mechanisms for o/pho-Amylose Action, [a. Front-side displacement, where X and Y are substrate-binding groups, and N represents part of an imidazolium ring b. double displacement " and c. stereospecific hydration of a carbonium ion. ]...

Reuterin is a neutral broad-spectrum antimicrobial substance formed during anaerobic growth of Lactobacillus reuteri in the presence of glycerol (Axelsson et al., 1989). Reuterin is an equilibrium mixture of monomeric, hydrated monomeric, and cyclic dimeric forms of (Vhydroxypropionalde-hyde. The inhibitory effect of reuterin has been associated with its action on DNA synthesis by acting as an inhibitor of the substrate binding subunit of ribonucleotide reductase. 

High hydrostatic pressure alters any process that proceeds with a volume change. This affects enzyme catalysis because both substrate binding and associated protein conformational changes proceed with changes in the hydration state of amino acid residues that alter the total volume of the water-protein-ligand system (Low and Somero, 1975). Therefore, animals adapted to the deep sea require changes to the amino acid composition of enzymes that create pressure-insensitive kinetic parameters and pressure-resistant structures. 

Of special significance are the catalytic properties of small metal clusters. At their surface such clusters have a large number of atoms with a low coordination number to which substrates bind. Catalytic reactions are being studied in hydrogenation, hydrosilylation, hydration, and the Heck reaction. Metal clusters are also of importance with regard to redox and electron transfer processes such as the photochemical decomposition of water (fuel cells) and photocatalytic hydrogenation. 

Such instances present a somewhat static picture of water s roles in substrate binding. In reality, of course, this is a dynamic process that involves a continuous change in molecular conformations as binding and/or catalysis proceeds. It seems that this involves an extraordinarily subtle and anticipatory use of hydration water. Grossman et al. have shown that, as a zinc metalloprotease binds its substrate to form the Michaelis complex, the water motions are retarded by coupling to the... 

It should be emphasized that under these conditions the surface structure of Si(lOO) is substantially different from oxidized Si(lOO) which is polar and in effect hydrophilic [359]. This is nicely demonstrated in Fig, 14.7, where for SI and S3 the cPAC values are shown for bare and oxidized Si(lOO) samples. These data were obtained from AFM experiments of the peptides SI and S3 interacting with Si(lOO) and GaAs(lOO) substrates in solution [340]. The main result is that the binding of SI to oxidized GaAs(lOO) and Si(lOO) surfaces is virtually independent of the substrate type which is widely screened by the top oxygen layer. The different adhesion propensities to the bare (hydrated) substrates lead to the conclusion that oxidation does not strongly progress on timescales of the peptide adsorption process. 

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