Water molecules firmly bound

VIII. Clusters of Firmly Bound Water Molecules and Proton Transfer. 116... 

Several amino acid residues of H form electrostatically coupled clusters ofionizable residues near Qb (Lancaster et al., 1996). In the Rb. sphaeroides RC, Glu H173 is a member of a cluster which also includes Asp L213, a residue required for proton uptake by Qb (see below). Mutation of Glu HI 73 to Gin retards both the kinetics of the first electron transfer and of the proton-linked second electron transfer (Takahashi and Wraight, 1996). Another characteristic for the region proximal to and Qb are clusters of firmly bound water molecules (Abresch etal., 1998 Fritzsch etal., 1998). Several side chains... 

Considering these results and the contributions by Broos [125], Watanabe [126], and Ueji [55, 77], it may be concluded that the relation between enzyme flexibility and enanhoselective performance in organic solvents is now firmly established. Molecular dynamic simulations on the flexibility of subtilisin and the mobility of bound water molecules in carbon tetrachloride corroborate the idea that organic solvents reduce molecular flexibility via interactions at specific binding sites [127]. Whether predictive tools can be developed on the basis of this knowledge remains to be seen. 

By the same token, reaction with participation by one water molecule will be relatively slow when both reactive sites are firmly hydrated. In that case, we may observe fast reaction with participation of two water molecules. However, in no case is reaction with solvent participation expected to be fast unless the conformation of the firmly bound solvent molecule is favourable for proton transfer. Thus, the relatively small values of the rate constants for reaction of tris- -hydroxyethylamine compared to triethylamine in water (Table 1) and of N,N-diethyl-w-toluidine compared to p-toluidine in methanol (Table 2) suggest that polar substituents or centres of van der Waals attraction can modify the hydrogen-bonded structure in the solvation shell. 

Water occurs in glass-ionomer and related cements in at least two different states (Wilson McLean, 1988 Prosser Wilson, 1979). These states have been classified as evaporable and non-evaporable, depending on whether the water can be removed by vacuum desiccation over silica gel or whether it remains firmly bound in the cement when subjected to such treatment (Wilson Crisp, 1975). The alternative descriptions loosely bound and tightly bound have also been applied to these different states of water combination. In the glass-poly(acrylic acid) system the evaporable water is up to 5 % by weight of the total cement, while the bound water is 18-28 % (Prosser Wilson, 1979). This amount of tightly bound water is equivalent to five or six molecules of water for each acid group and associated metal cation. Hence at least ten molecules of water are involved in the hydration of each coordinated metal ion at a carboxylate site. 

Incorporation of the position of water molecules that are firmly bound to the protein can impart affinity and novelty to the designed ligand. A prime example is the design of a class of HIV protease cyclic urea inhibitors by DuPont scientists that incorporated a water molecule bound to both flaps of the enzyme into their ligand [32]. The crystal structure of the HIV protease-cyclic urea complex [32] shows the urea carbonyl oxygen substituting for the position of the water molecule. 

It is quite certain that the two cobalamin species with coordinated and free benzimidazole are in rapid equilibrium. However, the ligands bound to the lower coordination site are apparently not always easily displaced. As mentioned above, Brodie and Poe (130) have found that in DMSO, a water molecule is firmly bound to the sixth coordination position of alkyl cobinamides. Thus, even though DMSO is a good Lewis base, it will not easily displace water from the primary coordination sphere of the cobalt. 

Another zinc-utilizing enzyme is carbonate/dehydratase C (Kannan et al., 1972). Here, the zinc is firmly bound by three histidyl side chains and a water molecule or a hydroxyl ion (Fig. 27). The coordination is that of a distorted tetrahedron. Metals such as Cu(II), Co(Il), and Mn(ll) bind at the same site as zinc. Hg(II) also binds near, but not precisely at, this site (Kannan et al., 1972). Horse liver alcohol dehydrogenase (Schneider et al., 1983) contains two zinc sites, one catalytic and one noncatalytic. X-Ray studies showed that the catalytic Zn(II), bound tetrahedrally to two cysteines, one histidine, and water (or hydroxyl), can be replaced by Co(II) and that the tetrahedral geometry is maintained. This is also true with Ni(Il). Insulin also binds zinc (Adams etai, 1969 Bordas etal., 1983) and forms rhombohedral 2Zn insulin crystals. The coordination of the zinc consists of three symmetry-related histidines (from BIO) and three symmetry-related water molecules. These give an octahedral complex... 

At each step in the food web, organochlorine contaminants undergo biomagnification and remain firmly bound to lipid molecules. The term biomagnification is self-explanatory, whereby the minuscule levels of toxic chemicals in the water become concentrated in wildlife bodies, often ending up at high concentrations in organisms at the top of the food web.6-8... 

In future it is necessary that collection of D values outside the original set needs to be performed in order to test the new models more fully. Outliers have been identified which diffuse more slowly than predicted, and a possible cause has been identified. The hydrogen-bonded water molecules directly attached to a diffusant molecule may be firmly bound and effectively moving with it, or at least be increasing its effective size. 

It is not necessary to emphasize how important water is for living systems to maintain their life [24-26], No wonder that many scientists in the field of X-ray and neutron diffraction measurement have been trying to determine positions and orientations of water molecules around and inside biomolecules, or protein and DNA [27,28], However, it is not so easy even for modern experimental technology to locate the position of water molecules, partly due to the limited resolution of diffraction measurements in space as well as in time. This is because water molecules at the surface of protein are not necessarily bound firmly to some particular site of biomolecules, but exchange their positions quite frequently. Actually this flexibility and fluctuation of water molecules are essential for living systems to control their life. The diffraction measurement can identify only some water molecules that have long residence time at some particular position of the biomolecules. 

In aqueous solution metal ions are surrounded by water molecules.36 In some cases, such as the alkali ions, they are weakly bound, whereas in others, such as [Cr(H20)6]3+ or [Rh(H20)6]3+, they may be firmly bound and exchange with solvent water molecules only very slowly for the lanthanides water exchange decreases with decreasing ionic radii.37 Coordination numbers vary extensively, depending on the size of the metal ion. For example, coordination number four is common for lithium, six is most frequently found for transition metal ions 38 higher coordination numbers are not unusual for larger ions, e.g., Bi3+ can form Bi(H20)93+.39... 

Since the cages are made from the firmly hydrogen bonded water molecules, the size of cage is restricted to be distributed in a very narrow range. Thus, the size of guest species must have an upper bound. Because the attrac-... 

It appears that four atoms of zinc are present in one molecule of ADH apoenzyme. The zinc in these crystalline preparations is firmly bound the zinc/protein bond is maintained against competitive physical-chemical factors involved in fractionation, potentially capable of dissociating it. Eecrystallization or dialysis against water fails to remove zinc. In some preparations more than 0.2 % of zinc was found. In these instances, small amounts of zinc could be removed by relatively mild procedures such as dialysis against OP. Such dialyses have not, thus far, lowered the zinc content below 4 moles of zinc per mole of protein. 

R1-NH-CO-R2 + H2O - RI-NH2 + HOOC-R2 where R1 and R2 denote the rest of the protein chain. HIV protease achieves catalysis by a combined acid-base mechanism. There are two aspartic acid residues in the active site, only one of which is protonated. At the time of the reaction, the protein is firmly bound in the active site as is the water molecule which is to be split ("lytic water ). The role of the unprotonated aspartate is... 

Like cellulose, chitin occurs in more than one crystal form. The j3-chitin modification, which contains one firmly bound molecule of water of hydration per 2-acetamido-2-deoxy-D-glucose residue, is usually found in association with animal tissue of the collagen type. a-Chitin, which is more common, usually replaces tissue of the collagen type this form has been examined more thoroughly " than the p, and will be discussed in detail. A little studied derivative of chitin, called chitosan, can be obtained in crystalline, oriented form by deacetylating chitin membranes with concentrated sodium hydroxide. Naturally occurring, chitinous membranes, such as insect cuticle, show various degrees of uniplanar orientation. 

Coordinately bound water firmly held in the form of H2O molecules exists on nonhydroxyl centers of the Il-type these centers are coordinately unsaturated Si atoms on the surface of the sample. The concentration of the Il-type centers is small asi = 0.1-0.3 Si atoms per square nanometer. 

In the dihydrate structures, one of the water molecules is firmly held in the lattice, being coordinated to two barium ions and forming hydrogen bonds to two sulfonate oxygen atoms. The other water molecule is loosely bound, to one barium ion only, and has a relatively spacious environment it is this water molecule which in the solvates is replaced by acetone or tetrahydrofuran. The oxygen atom of the organic molecule is coordinated to a barium ion, like the oxygen atom of the replaced water molecule, and is located between the barium ion and the nearest layer interface, with the rest of the molecule directed towards the interface. In the dioxane solvate... 

From the relation between the activity coeffijjient ratios and the acidity function (Ho), it is concluded that the transition state must be effectively a conjugate acid of the olefin which is not firmly bound- to any water molecule. Since the reactants are olefin and hydronium ion, such a transition state can be formed only by the isomerization from one unstable intermediate to another. The unimolecular isomerization of the r complex to the carbonium ion fits the requirements and constitutes the rate-determining step. Water molecules do not enter the transition state, thus the molecularity of the reaction is zero with respect to the solvent water. 

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