Hydration sites

Of course the interaction between water molecules and the hydration sites depends on their chemical nature. According to the results of IR-measurements the following order of decreasing affinity was given by Falk et al.160) and was accepted as being quite reasonable 161) ... 

On the other hand, according to Kopka et al.158), a zig-zag spine of hydration in the minor groove of the B-DNA 1561 is assumed to be mainly responsible for stabilizing its conformation and a 100% occupancy of the hydration sites in the A + T region has been found. Each first water molecule of this hydration-spine is close to two 0-1 atoms of desoxyribose-rings (Fig. 22). 

Bo is the measurement frequency. Rapid exchange between the different fractions is assumed the bulk, water at the protein surface (s) and interior water molecules, buried in the protein and responsible for dispersion (i). In fact, protons from the protein surface exchanging with water lead to dispersion as well and should fall into this category Bulk and s are relevant to extreme narrowing conditions and cannot be separated unless additional data or estimations are available (for instance, an estimation of fg from some knowledge of the protein surface). As far as quadrupolar nuclei are concerned (i.e., and O), dispersion of Rj is relevant of Eqs. (62) and (63) (this evolves according to a Lorentzian function as in Fig. 9) and yield information about the number of water molecules inside the protein and about the protein dynamics (sensed by the buried water molecules). Two important points must be noted about Eqs. (62) and (63). First, the effective correlation time Tc is composed of the protein rotational correlation time and of the residence time iw at the hydration site so that... 

Water binding varies with the number and type of polar groups (5 ). Other factors that affect the mechanism of protein-water interactions include protein conformation and environmental factors that affect protein polarity and/or conformation. Conformational changes in the protein molecules can affect the nature and availability of the hydration sites. Transition from globular to random coil conformation may expose previously buried amino acid side chains, thereby making them available to interact with aqueous medium. Consequently, an unfolded conformation may permit the protein to bind more water than was possible in the globular form ( ). 

Fig. 9. Hydration sites in cytosine.252 Energies given in kilocalories per mole. Heavy lines, preferred hydration sites full lines, coplanar arrangement of water and base half-dashed, perpendicular arrangement of water with respect to the plane of the base.

As concerns the hydration sites of thymine, the interaction energy (its electrostatic component) between thymine and water has been... 

In reverse to solubilization, soluble polysaccharides are made less soluble by removing branches or substituents to produce a more uniformly linear polysaccharide with improved possibility of intermolecular fit, by removing formal charges, by lessening the number of strong hydration sites, or by completely overcoming hydration effects by introducing hydrophobic substituents. 

Kvenvolden (Personal Communication, November 28, 2005) compiled 89 hydrate sites shown in Figure 7.2, with a complete listing in Tables 7.4 and 7.5. In those locations hydrates were either ... 

H2O] is the molarity of water in the protein solution, Tij,r and Tiw are the relaxation times for protons in the hydration spheres of the protein and in the bulk water, [Pr] is the protein concentration in mol/1, n the number of waters bound to each protein molecule, and rvr the residence time for water protons on the protein molecule. In writing Eq. (19) it was assumed for simplicity that there is only one type of hydration site with characteristic rpr and Tipr- It is seen that the relaxation enhancement through the presence of the protein is... 

Hu B, Lill MA (2012) Protein pharmacophore selection using hydration-site analysis. J Chem Inf Model 52(4)4046-1060... 

Fig. 3. SCF-MI optimised structure of the penta-hydrated CG pair with methylated bases. Dark circles represent average crystallographic hydration sites in B-DNA.

Molecular dynamics (MD) simulations [29-31], coupled with experimental observations, have played an important role in the understanding of protein hydration. They predicted that the dynamics of ordered water molecules in the surface layer is ultrafast, typically on the picosecond time scales. Most calculated residence times are shorter than experimental measurements reported before, in a range of sub-picosecond to 100 ps. Water molecules at the surface are very mobile and are in constant exchange with bulk water. For example, the trajectory study of myoglobin hydration revealed that among 294 hydration sites, the residence times at 284 sites (96.6% of surface water molecules) are less than lOOps [32]. Furthermore, the population time correlation functions... 

Figure 15-6. Hydration sites around the imidazole molecule. Numbers indicate calculated H-bond energy (kcal/mol) for each individual site [87]...

Table 15-8. Energetic cooperativity (kcal/mol) of hydration sites of imidazole...

Fig. 24.3. Preferred hydration sites in B-DNA derived from physicochemical studies. Numbers 7 to 5 illustrate strength of binding, in decreasing order. Around phosphate groups, about five water molecules are found, as indicated by larger circle [853]...

Crystallographically Determined Hydration Sites in A-, B-, Z-DNA. A Statistical Analysis... 

The most inclnsive definition of hydration shell describes it as consisting of all thermodynamically altered water molecnles in the vicinity of a solnte. From a thermodynamic standpoint, hydration can be viewed as binding of water molecnles to the hydration sites of a solnte. The energetics of this association is modulated by the type of solute-solvent interactions (electrostatic, hydrogen bonding, van der Waals) and by solnte-indnced solvent reorganization. The latter occnrs even in the absence of appreciable solute-solvent interactions becanse the eqnUib-rium distribution of hydrogen-bonded water networks of the bulk becomes disrupted at the solute surface. 

Figure 1 Chemical structures of GC (panel A) and AT (panel B) base pairs with schematic representation of potential hydration sites. The diagram specifies those functional groups of DNA, in the vicinity of which waters are observed frequently in X-ray crystallographic structures. The diagram does not reflect the relative occupancies and precise localizations of individual water molecules.

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