Hydration of biomolecules

Since hydration of biomolecules is of particular importance in molecular biology, uracil - water (U-W) complexes have been studied by many groups [98 JCS(F) 1277, 98JST307, 99JPC(A)1611, 00PCCP1281]. In the cyclic U-W complex the most stable hydrogen bond is formed at the site characterized by the lowest proton... 

Berndt M, Kwiatkowski JS (1986) Hydration of biomolecules. In N4ray-Szab6 G (ed) Theoretical chemistry of biological systems. Studies in physical and theoretical chemistry, vol. 41. Elsevier, Amsterdam, pp 349-422... 

It is possible to study step-by-step hydration of biomolecules as was first done by Gluckauf. The hydration is localized and connected to ionic binding. Thus, Gregor et al. found that the order of adsorption onto polystyrene was IT > Li" " > Na > K . 

Bemdt, M., and Kwiatkowski, J. S. (1986). In Theoretical Chemistry of Biological Systems (G. Naray-Szabo, ed.). Elsevier, Amsterdam (in press)—review on hydration of biomolecules including theoretical studies on the effect of solvation on tautomeric equilibria, bibliography of theoretical papers on this subject up to 1984. 

Wyttenbach T, Bowers MT (2009) Hydration of biomolecules. Chem Phys Lett 480 (1-3) 1-16... 

Effect of hydration on the properties of biosystems was extensively studied both experimentally and by computer simulations. We have already considered how biological activity and conformational dynamics of hydrated biomolecules (Section 6) as well as conductivity of biosystems (Section 7.1) develop upon hydration. Now we analyze some other physical properties of hydrated biosystems (first, their dynamical properties) in relation to the percolation transition of water. Typical biomolecular surface is characterized by heterogeneity (presence of strongly hydrophilic and strongly hydrophobic groups), roughness, and finite size (closed surface of a single biomolecule). These features determine several steps in the process of hydration of biomolecules. 

A second area of particular importance in biophysics is the determination of the structural consequences, or thermodynamics, of stepwise hydration of biomolecules. These... 

This bimodal dynamics of hydration water is intriguing. A model based on dynamic equilibrium between quasi-bound and free water molecules on the surface of biomolecules (or self-assembly) predicts that the orientational relaxation at a macromolecular surface should indeed be biexponential, with a fast time component (few ps) nearly equal to that of the free water while the long time component is equal to the inverse of the rate of bound to free transition [4], In order to gain an in depth understanding of hydration dynamics, we have carried out detailed atomistic molecular dynamics (MD) simulation studies of water dynamics at the surface of an anionic micelle of cesium perfluorooctanoate (CsPFO), a cationic micelle of cetyl trimethy-lainmonium bromide (CTAB), and also at the surface of a small protein (enterotoxin) using classical, non-polarizable force fields. In particular we have studied the hydrogen bond lifetime dynamics, rotational and dielectric relaxation, translational diffusion and vibrational dynamics of the surface water molecules. In this article we discuss the water dynamics at the surface of CsPFO and of enterotoxin. 

The problems being addressed in recent work carried out in various laboratories include the fundamental nature of the solute-water intermolecular forces, the aqueous hydration of biological molecules, the effect of solvent on biomolecular conformational equilibria, the effect of biomolecule - water interactions on the dynamics of the waters of hydration, and the effect of desolvation on biomolecular association 17]. The advent of present generation computers have allowed the study of the structure and statistical thermodynamics of the solute in these systems at new levels of rigor. Two methods of computer simulation have been used to achieve this fundamental level of inquiry, the Monte Carlo and the molecular dynamics methods. 

Recently, the investigations of nitrobenzisoxazoles mainly 6-nitrobenzisoxazole-3-carboxilate ions have received considerable interest due to their participation in reverse micellar systems [679-682], Reverse micelles are of considerable interest as reaction media because they are powerful models for biological compartmental-ization, enzymatic catalysis, and separation of biomolecules. Solutions of ionic surfactants in apolar media may contain reverse micelles, but they may also contain ion pairs or small clusters with water of hydration [679], Molecular design of nonlinear optical organic materials based on 6-nitrobenzoxazole chromophores has been developed [451],... 

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... 

The role of water in mediating binding differs between the biomolecules because of variations in the strength of the natural hydration of the interfaces, which approximates roughly to DNA > proteins > ligands. 

Jalkanen KJ, Jiirgensen VW, Claussen A, Rahim A, Jensen GM, Wade RC, Nardi F, Jung C, Degtyarenko IM, Nieminen RM, et al. Use of vibrational spectroscopy to study protein and DNA structure, hydration, and binding of biomolecules a combined theorehcal and experimental approach. Int. J. Quantum Chem. 2006 106 1160-1198. 

Thinking about the hydration of protein complexes is simplified by dividing water molecules into four classes bulk water molecules that are not directly in contact with the biomolecules, surface water hydrogen bonded to the protein or ligand, surface water associated with apolar biomolecular groups, and buried water molecules that have no direct connection to the bulk solvent. 

It is well known that water-mediated interaction stabilizes structure of biomolecules [1, 138, 247-250]. Therefore, several model molecular systems have been chosen to probe the water-mediated interactions in biomolecules and a large amount of experimental and theoretical work has been published over the years on this subject [78, 138, 251-258]. Since phenol is the simplest aromatic alcohol resembling chromophore of an aromatic amino acid, hydration of phenol molecules has been studied to understand H-bonding and solute-solvent interaction in biological systems. Several experimental and theoretical calculations have been made on the phenol-water clusters [259-273]. Recently, we have made a comprehensive analysis on structure, stability, and H-bonding interaction in phenol (P1-4), water (W1-4), and phenol-water (PmW (w = 1-3, n = 1-3, w + n < 4)) clusters using ab initio and DFT methods [245]. In this section, electronic structure calculations combined with AIM analysis on phenol-water clusters are presented. 

The origin of life in aqueous milieux and the necessity of the internal aqueous environment in living systems leads us to expect the hydration and swelling of biomolecules to be a central feature of their organization and function. Direct measurement of intermolecular forces in aqueous solutions now shows us new ways in which nature achieves the controlled swelling essential to living matter. 

Garcia AE, Stiller L Computation of the mean residence time of water in the hydration shells of biomolecules. J. Comp. Chem. 1993,14 1396-1406. 

O Neil CP, Demurtas TSD, Finka A, HubbeU JA (2009) A novel method for the encapsulation of biomolecules into polymersomes via direct hydration. Langmuir 25 9025-9029... 

Many biomolecules are characterized by surfaces containing extended polar regions and also extended non-polar regions. A well-known example is provided by beta-amyloid - the well-known Alzheimer protein. It has extended hydrophobic regions separated by hydrophilic regions, as discussed in Chapter 7. The hydration of extended non-polar planar surfaces may involve novel structures that are orien-tationally inverted relative to clathrate-hke hydration shells, where unsatisfied HBs are directed towards the hydrophobic surface. We have discussed these two geometric arrangements in the appendix to this chapter (Appendix 8.A). 

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