Water networks, hydration

The NMR study by Wiithrich and coworkers has shown that there is a cavity between the protein and the DNA in the major groove of the Antennapedia complex. There are several water molecules in this cavity with a residence time with respect to exchange with bulk water in the millisecond to nanosecond range. These observations indicate that at least some of the specific protein-DNA interactions are short-lived and mediated by water molecules. In particular, the interactions between DNA and the highly conserved Gin 50 and the invariant Asn 51 are best rationalized as a fluctuating network of weak-bonding interactions involving interfacial hydration water molecules. 

More recent work with cosolvency in dilute systems seems to indicate that the magnitude of the solubility enhancement is linear up to some 10-20% cosolvent fraction [55,172,184,250-262]. At very low concentrations of cosolvent, the assumption of non-interaction between the cosolvent and water cannot hold. In dilute solutions the individual cosolvent molecules will be fully hydrated and, as a result, will disrupt the water network structure. If the total volume disrupted is regarded as the extended hydration shell, and if Sc is the average solubility within this shell, then the overall solubility Sm in the water-cosolvent mixture will be approximated by... 

Water is considered to be supercooled when it exists as a liquid at lower temperatures than its melting point, for example, at less than 0°C at atmospheric pressure. In this state, the supercooled water is metastable. The properties of supercooled water have been examined in detail in excellent reviews by Angell (1982, 1983) and Debenedetti (1996, 2003). A brief review of the properties of supercooled pure liquid water and the different liquid water models are discussed in this section. These structures comprise hydrogen-bonded water networks and/or water clusters ( cages ) that are the starting points to hydrate formation. 

The response range of the local environment to the excited Trp-probe is mainly within 10 A because the dipole-dipole interaction at 10 A to that at —3.5 A of the first solvent shell drops to 4.3%. This interaction distance is also confirmed by recent calculations [151]. Thus, the hydration dynamics we obtained from each Trp-probe reflects water motion in the approximately three neighboring solvent shells. About seven layers of water molecules exist in the 50-A channel, and we observed three discrete dynamic structures. We estimated about four layers of bulk-like free water near the channel center, about two layers of quasi-bound water networks in the middle, and one layer of well-ordered rigid water at the lipid interface. Because of lipid fluctuation, water can penetrate into the lipid headgroups, and one more trapped water layer is probably buried in the headgroups. As a result, about two bound-water layers exist around the lipid interface. The obtained distribution of distinct water structures is also consistent with —15 A of hydration layers observed by X-ray diffraction studies from White and colleagues [152, 153], These discrete water stmctures in the nanochannel are schematically shown in Figure 21, and these water molecules are all in dynamical equilibrium. 

Figure 46. A unified molecular mechanism of protein hydration dynamics and coupled water-protein fluctuations. The initial ultrafast dynamics in a few picoseconds (ii) represents local collective orientation or small translation motions, which mainly depend on local electrostatic interactions. On the longer time (12), the water networks undergo structural rearrangements in the layer, which are strongly coupled with both protein fluctuations and bulk-water dynamic exchange.

Fig. 23.12. Results of computer studies simulating the hydration of amino acids, (top) self-bridging loops of hydrogen-bonded water molecules around alanine (center) polar bridging chains between polar solute atoms of threonine (bottom) water networks associated with the apolar groups of leucine [847]...

Water networks around apolar solute atoms (methyl groups), or further from polar solute atoms (second and higher hydration layers) consistently included pentagonal motifs. 

Masson, P. Clery, C., Guerra, P., Redslob, A., Alharet, C., Fortier, P-L. (1999). Hydration change during the aging of phosphorylated human bytyrylcholinesterase importance of residues D70 and El97 in the water network as probed hy hydrostatic and osmotic pressures. Biochem. J. 343 361-9. 

Despite the above generalizations, hydration water likely participates in the transition state for certain reactions. X-Ray diffraction results have identihed, for some enzymes, bound solvent that may enter into the transition state, for example, lysozyme (Blake et al., 1983), DNase I (Oefner and Suck, 1986), and the aspartic proteinase from Rhizoptts chi-nensis (Suguna et al., 1987). Meyer et al. (1988) suggested the participation of water organized in a network or tunnellike structure in the... 

Figure 5. Snapshots of the final configurations of the bulk hydrated Nafion ionomer with the ionomers made invisible at hydration levels (a) X = 4.4, and (b) X = 9.6. A more connected water network is found at the higher water content.

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. 

The formation of spanning H-bonded water networks on the surface of biomolecules has been connected with the widely accepted view that a certain amount of hydration water is necessary for the dynamics and function of proteins. Its percolative nature had been suggested first by Careri et al. (59) on the basis of proton conductivity measurements on lysozyme this hypothesis was later supported by extensive computer simulations on the hydration of proteins like lysozyme and SNase, elastine like peptides, and DNA fragments (53). The extremely interesting... 

Oleinikova A, Brovchenko I. Percolation transition of hydration water in bio-systems. Mol. Phys. 2006 104 3841-3855. Oleinikova A, Brovchenko I. Percolating networks and liquid-liquid transitions in supercooled water. J. Phys. Cond. Matter 2006 18 S2247-S2259. 

This behavior reflects a competition between the energy needed to break the bulk hydrogen-bonded structure and the strength of the ion-water interaction. From 298 to 373 K, it is increasingly easier for water molecules to leave the ionic first shell (Cl, K+ and Rb+) than to break the tight H-bond water network. At T > 373 K, the behavior reverses. The water H-bond network is disrupted and the water-ion attraction becomes again predominant over the water-water interactions. For Na", on the other hand, the ratio of residence times remains approximately constant in spite of the increase in temperature due to the strong ion-water interaction. Dynamic hydration numbers reflect these trends, as seen in Table 11. 

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