Dielectric and Calorimetric Characteristics of Bound and Free Water in Surfactant-Based Systems

The hydration behavior of the system polyoxyethylene (10) oleylalcohol [C_18:1 (EO)₁₀ or Brij 97]/water/dodecane/butanol (model system B) was investigated along a dilution line for which the respective weight ratio of dodecane:butanol:Brij 97 is 3:3:4. Two experimental methods were applied: time domain dielectric spectroscopy (TDDS) and sub-zero temperature differential scanning calorimetry (SZT-DSC). Two types of bound water (with melting peaks at -25 and -11°C) were detected by SZT-DSC (using the endothermic mode), whereas TDDS revealed only one such type. Nevertheless, roughly the same total amount of bound water was estimated from these two techniques. The average number of bound water molecules per ethylene oxide (EO) group, N_W/EO is 2.3 (TDDS data) or 2.5 (SZT-DSC data) in good agreement with the observation that 1–2 water layers are formed in the hydration of ethoxylated surfactants. We have also shown that butanol is involved in the formation of the bound water that melts at -25°C. We suggest that butanol molecules occupy binding sites within the second hydration shell, thereby reducing the expected total bound water content.     

De novo ligand design with explicit water molecules: an application to bacterial neuraminidase

Most computer-aided drug design methods ignore the presence of crystallographically-determined water molecules in the binding site of a target protein. In this paper, our de novo ligand design methods are applied to the X-ray crystal structure of bacterial neuraminidase in the presence of some selected water molecules. We have found that, for this particular protein, the complete removal of all bound water molecules leads to difficulties in generating any potential ligands if the unsatisfied hydrogen-bonding sitepoints left by removing these water molecules are to be satisfied by a ligand. As more of the crystallographically determined water molecules are allowed in the binding site, it becomes much easier to generate ligands in larger numbers and with wider chemical diversity. This example shows that, in some cases, bound water molecules can be more accessible for hydrogen bonding to an incoming ligand than the actual protein binding sitepoints associated with them. From the point of view of de novo ligand design, water molecules can thus act as versatile amphiprotic hydrogen-bonding sitepoints and reduce the conformational constraints of a particular binding site.     

Hydration of small peptides

The results for the sequential hydration of small peptides (<15 residues) obtained in our group are reviewed and put in perspective with other work published in the literature where appropriate. Our findings are based on hydration equilibrium measurements in a high-pressure drift cell inserted into an electrospray mass spectrometer and on calculations employing molecular mechanics and density functional theory methods. It is found that the ionic functional groups typically present in peptides, the ammonium, guanidinium, and carboxylate groups, are the primary target of water molecules binding to peptides. Whereas the water–guanidinium binding energy is fairly constant at 9 ± 1 kcal/mol, the water binding energy of an ammonium group ranges from 7 to 15 kcal/mol depending on how exposed the ammonium group is. A five-residue peptide containing an ammonium group is in favorable cases large enough to fully self-solvate the charge, but a pentapeptide containing a guanidinium group is too small to efficiently shield the charge of this much larger ionic group. The water–carboxylate interaction amounts to 13 kcal/mol with smaller values for a shielded carboxylate group. Both water bound to water in a second solvation shell and charge remote water molecules on the surface of the peptide are bound by 7–8 kcal/mol. The presence of several ionic groups in multiply charged peptides increases the number of favorable hydration sites, but does not enhance the water–peptide binding energy significantly. Water binding energies measured for the first four water molecules bound to protonated bradykinin do not show the declining trend typically observed for other peptides but are constant at 10 kcal/mol, a result consistent with a molecule containing a salt bridge with several good hydration sites. Questions regarding peptide structural changes as a function of number of solvating water molecules are discussed. Not much is known at present about the effect of individual water molecules on the conformation of peptides and on the stability of peptide zwitterions.     

Hydration of black foam films made of amphiphilic cyclodextrins

We investigate the interfacial behavior of a new type of amphiphilic cyclic oligosaccharide obtained by grafting a phospholipid onto a methylated cyclodextrin. These compounds are able to form stable black foam films, the structure of which can be determined using X-ray reflectivity. These films consist of a highly hydrated bilayer of modified cyclodextrins which are remarkably thick due to their abundant hydration core. In the present paper, we explore the influence of cyclodextrin hydration on the film structure. The hydration rate of the films is tuned by changing the cyclodextrin methylation, by binding the modified cyclodextrins to various molecules (complex formation) and by exposing the films to IR radiation. In addition, we show that the gas permeability of these phospholipidyl-cyclodextrin films is governed by their central layer of bound water, which is an efficient barrier against gas permeation.     

Difference spatial distribution function analysis of aqueous solutions. II. Hydration structures of dimethyl ether, 180 degrees ethyl methyl ether and 0 degree ethyl methyl ether solutions

Monte Carlo simulations are systematically presented to demonstrate the influence of the hydrophobic group's steric bulk on hydration structure. We have simulated a dimethyl ether (DME), two conformations for ethyl methyl ether (0 degree EME and 180 degrees EME), and 0 degree ethanol solutions. Spatial distribution function (SDF), goo(x,y,z) and difference SDF (DSDF), delta goo(x,y,z), obtained from MC simulation in an infinitely dilute aqueous solution of ether show the three-dimensional probability of an atom-atom pair distribution between solute and solvent atoms. Based on the results of SDF in an infinitely dilute aqueous solution of ether, the distribution of hydration water molecules can be divided into hydrogen acceptor (HA) and hydrophobic hydration (HH), regions, and the spatial orientation of the hydrogen-bonded water in the HA region is found to form a triple-layer structure, as it does in alcohol solutions. From the results of an analysis of the DSDF delta goo(x,y,z) between the SDFs of EME and DME, it is apparent that the distribution changes of hydration water molecules in ether solutions are essentially similar to those in the alcohol solutions. Further, we show that the hydration water molecules are distributed mainly in the stable area in the binding energy's (BE) contour maps for each region.     

A theoretical study on the hydration of B- and Z-DNA double helices

A theoretical study on the hydration of B- and Z-DNA double helices has been carried out using empirical potential energy functions. The interaction energy between water and the model compounds has been computed considering only the first hydration shell.The results show the number of binding water molecules to be thirty-six and twenty-five in B- and in Z-DNA, respectively. The water molecules in the first hydration shell of B-DNA are very well ordered along the phosphate groups of the backbone whereas those of Z-DNA are more disordered than in B-DNA and are more strongly bound. The water molecules near the first hydration shell of Z-DNA are thought to move more freely than those of B-DNA.     

Structural transition to electrolyte-water solvent and changes in the molecular dynamics of water and properties of solutions

A model of concentration transition “ions and complexes in a water structure → ionic and ionicaqueous clusters → polymer structures of salt and crystal hydrate melts” is suggested. The appearance of cluster nanostructures outside the first zone of a waterlike structure is regarded as a general characteristic of solutions. The characteristics of solutions, phase equilibria, and salts of complex composition are interpreted based on this model. Investigation of the complex dielectric constant of electrolytic solutions in the SHF and EHF bands (7–119 GHz) at high concentrations showed that there are two dispersion regions in which the relaxation times differ by a factor of 5–10. Relaxation processes are separated, the numbers of molecules in hydration shells are calculated, and relaxation times are determined for bulky tetrahedral water with hydration shells of ions, for clusters, and for ionicaqueous polymer chains. It is shown that the two structure subsystems of water molecules in concentrated solutions may be described using the limited rotator/generalized diffusion molecular model. Translated fromZhumal Strukturnoi Khimii, Vol. 39, No. 5, pp. 851–863, September–October, 1998.     

WATsite: Hydration site prediction program with PyMOL interface

Water molecules that mediate protein–ligand interactions or are released from the binding site on ligand binding can contribute both enthalpically and entropically to the free energy of ligand binding. To elucidate the thermodynamic profile of individual water molecules and their potential contribution to ligand binding, a hydration site analysis program WATsite was developed together with an easy‐to‐use graphical user interface based on PyMOL. WATsite identifies hydration sites from a molecular dynamics simulation trajectory with explicit water molecules. The free energy profile of each hydration site is estimated by computing the enthalpy and entropy of the water molecule occupying a hydration site throughout the simulation. The results of the hydration site analysis can be displayed in PyMOL. A key feature of WATsite is that it is able to estimate the protein desolvation free energy for any user specified ligand. The WATsite program and its PyMOL plugin are available free of charge from http://people.pnhs.purdue.edu/~mlill/software . © 2014 Wiley Periodicals, Inc.     

Including tightly-bound water molecules in de novo drug design. Exemplification through the in silico generation of poly(ADP-ribose)polymerase ligands

Different strategies for the in silico generation of ligand molecules in the binding site of poly(ADP-ribose)polymerase (PARP) were studied in order to observe the effect of the targeting and displacement of tightly bound water molecules. Several molecular scaffolds were identified as having better interactions in the binding site when targeting one or two tightly bound water molecules in the NAD binding site. Energy calculations were conducted in order to assess the ligand-protein and ligand-water-protein interactions of different functional groups of the generated ligands. These calculations were used to evaluate the energetic consequences of the presence of tightly bound water molecules and to identify those that contribute favorably to the binding of ligands.     

AquaBridge: A novel method for systematic search of structural water molecules within the protein active sites

We have developed a novel method for calculation of the water bridges that can be formed in the active sites of proteins in the absence or in the presence of small‐molecule ligands. We tested its efficiency on a representative set of human ATP‐binding proteins, and show that the docking accuracy of ligands can be substantially improved when water bridges are included in the modeling of protein–ligand interactions. Our analysis of binding pocket hydration can be a useful addition to the in silico approaches of Drug Design. © 2015 Wiley Periodicals, Inc.     

Investigation of the hydration of nonfouling material poly(sulfobetaine methacrylate) by low-field nuclear magnetic resonance

The strong surface hydration layer of nonfouling materials plays a key role in their resistance to nonspecific protein adsorption. Poly(sulfobetaine methacrylate) (polySBMA) is an effective material that can resist nonspecific protein adsorption and cell adhesion. About eight water molecules are tightly bound with one sulfobetaine (SB) unit, and additional water molecules over 8:1 ratio mainly swell the polySBMA matrix, which is obtained through the measurement of T(2) relaxation time by low-field nuclear magnetic resonance (LF-NMR). This result was also supported by the endothermic behavior of water/polySBMA mixtures measured by differential scanning calorimetry (DSC). Furthermore, by comparing both results of polySBMA and poly(ethylene glycol) (PEG), it is found that (1) the hydrated water molecules on the SB unit are more tightly bound than on the ethylene glycol (EG) unit before saturation, and (2) the additional water molecules after forming the hydration layer in polySBMA solutions show higher freedom than those in PEG. These results might illustrate the reason for higher resistance of zwitterionic materials to nonspecific protein adsorptions compared to that of PEGs.     

Ligand-protein docking with water molecules

The presence of water molecules plays an important role in the accuracy of ligand-protein docking predictions. Comprehensive docking simulations have been performed on a large set of ligand-protein complexes whose crystal structures contain water molecules in their binding sites. Only those water molecules found in the immediate vicinity of both the ligand and the protein were considered. We have investigated whether prior optimization of the orientation of water molecules in either the presence or absence of the bound ligand has any effect on the accuracy of docking predictions. We have observed a statistically significant overall increase in accuracy when water molecules are included during docking simulations and have found this to be independent of the method of optimization of the orientation of water molecules. These results confirm the importance of including water molecules whenever possible in a ligand-protein docking simulation. Our findings also reveal that prior optimization of the orientation of water molecules, in the absence of any bound ligand, does not have a detrimental effect on the improved accuracy of ligand-protein docking. This is important, given the use of docking simulations to predict the binding modes of new ligands or drug molecules.     

The structure of water in the hydration shell of cations from x-ray Raman and small angle x-ray scattering measurements

X-ray Raman scattering (XRS) spectroscopy and small angle x-ray scattering (SAXS) are used to study water in aqueous solutions of NaCl, MgCl(2), and AlCl(3) with the particular aim to provide information about the structure of the hydration shells of the cations. The XRS spectra show that Na(+) weakens the hydrogen bonds of water molecules in its vicinity, similar to the effect of increased temperature and pressure. Mg(2+) and Al(3+), on the other hand, cause the formation of short and strong hydrogen bonds between the surrounding water molecules. The SAXS data show that Mg(2+) and Al(3+) form tightly bound hydration shells that give a large density contrast in the scattering data. From the form factors extracted from the SAXS data, we found that Mg(2+) and Al(3+) have, respectively, an equivalent of one and one and a half stable hydration shells that appear as a density contrast. In addition, we estimated that the density of water in the hydration shells of Mg(2+) and Al(3+) is, respectively, ～61% and ～71% higher than in bulk water.     

Raman study on conformational equilibria of fluoroacetone in aqueous solutions

The effects of water and heavy water on conformational equilibria of fluoroacetone have been investigated via Raman spectroscopy. Additional Raman bands have been observed in the C-F stretching and the C-C-C symmetric stretching regions for the aqueous solutions. Based on enthalpy and volume differences between the conformers, these bands are assigned to the syn conformer which has hydrogen bonds between the fluorine atom and water molecules (syn' conformer). The number of H2O molecules binding to the syn' conformer is estimated to be 2.4 from the concentration dependence of the spectrum. The enthalpy and the volume differences between the cis and syn conformers in the aqueous solutions show anomalous values in comparison with those in organic solvents. We discuss these thermodynamic behaviors from the viewpoint of the hydration structures of fluoroacetone.     

A molecular dynamics study of the dielectric properties of aqueous solutions of alanine and alanine dipeptide

Molecular dynamics simulations were used to compute the frequency-dependent dielectric susceptibility of aqueous solutions of alanine and alanine dipeptide. We studied four alanine solutions, ranging in concentration from 0.13-0.55 mol/liter, and two solutions of alanine dipeptide (0.13 and 0.27 mol/liter). In accord with experiment we find a strong dielectric increment for both solutes, whose molecular origin is shown to be the zwitterionic nature of the solutes. The dynamic properties were analyzed based on a dielectric component analysis into solute, a first hydration shell, and all remaining (bulk) waters. The results of this three component decomposition were interpreted directly, as well as by uniting the solute and hydration shell component to a "suprasolute" component. In both approaches three contributions to the frequency-dependent dielectric properties can be discerned. The quantitatively largest and fastest component arises from bulk water [i.e., water not influenced by the solute(s)]. The interaction between waters surrounding the solute(s) (the hydration shell) and bulk water molecules leads to a relaxation process occurring on an intermediate time scale. The slowest relaxation process originates from the solute(s) and the interaction of the solute(s) with the first hydration shell and bulk water. The primary importance of the hydration shell is the exchange of shell and bulk waters; the self-contribution from bound water molecules is comparatively small. While in the alanine solutions the solute-water cross-terms are more important than the solute self-term, the solute contribution is larger in the dipeptide solutions. In the latter systems a much clearer separation of time scales between water and alanine dipeptide related properties is observed. The similarities and differences of the dielectric properties of the amino acid/peptide solutions studied in this work and of solutions of mono- and disaccharides and of the protein ubiquitin are discussed.     

Some opinions of an innocent bystander regarding the Hofmeister series

Hofmeister's “water absorbing effect” of ions is quantified. A clear definition is provided for the term “hydration number” as the average number of water molecules bound to the solute more strongly (by at least 13.3 kcal mol^− 1) than are bound to other waters. Such hydration numbers are reported for various ions of electrolytes along with the extent of ion pair formation of each salt. Experimental measurements of various colligative properties demonstrate that the hydration numbers and extents of ion pair formation remain constant over large ranges of concentration and that solutions behave “ideally” up to the point where about 50% of the total water is strongly bound to the solute and is not available to act as solvent for additional solute.     

Molecular dynamics study of the solvation of calcium carbonate in water

We performed molecular dynamics simulations of diluted solutions of calcium carbonate in water. To this end, we combined and tested previous polarizable models. The carbonate anion forms long-living hydrogen bonds with water and shows an amphiphilic character, in which the water molecules are expelled in a region close to its C(3) symmetry axis. The calcium cation forms a strongly bound ion pair with the carbonate. The first hydration shell around the CaCO(3) pair is found to be very similar to the location of the water molecules surrounding CaCO(3) in ikaite, the hydrated mineral.     

The investigation on the relative stability of different clusters of thiourea dioxide in water using gas phase quantum chemical calculations

The relative stability of different clusters of thiourea dioxide (TDO) in water is examined using gas phase quantum chemical calculations at the MP2 and B3LYP level with 6‐311++G(d,p) basis set. The possible equilibrium structures and other energetic and geometrical data of the thiourea dioxide clusters, TDO‐(H₂O)_n (n is the number of water molecules), are obtained. The calculation results show that a strong interaction exists between thiourea dioxide and water molecules, as indicated by the binding energies of the TDO clusters progressively increased by adding water molecules. PCM model is used to investigate solvent effect of TDO. We obtained a negative hydration energy of ?20.6 kcal mol^?1 and free‐energy change of ?21.0 kcal mol^?1 in hydration process. On the basis of increasing binding energies with adding water molecules and a negative hydration energy by PCM calculation, we conclude thiourea dioxide can dissolve in water molecules. Furthermore, the increases of the C? S bond distance by the addition of water molecules show that the strength of the C? S bonds is attenuated. We find that when the number of water molecules was up to 5, the C? S bonds of the clusters, TDO‐(H₂O)₅ and TDO‐(H₂O)₆ were ruptured. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration

Continuum solvation methods are frequently used to increase the efficiency of computational methods to estimate free energies. In this paper, we have evaluated how well such methods estimate the nonpolar solvation free-energy change when a ligand binds to a protein. Three different continuum methods at various levels of approximation were considered, viz., the polarized continuum model (PCM), a method based on cavity and dispersion terms (CD), and a method based on a linear relation to the solvent-accessible surface area (SASA). Formally rigorous double-decoupling thermodynamic integration was used as a benchmark for the continuum methods. We have studied four protein-ligand complexes with binding sites of varying solvent exposure, namely the binding of phenol to ferritin, a biotin analogue to avidin, 2-aminobenzimidazole to trypsin, and a substituted galactoside to galectin-3. For ferritin and avidin, which have relatively hidden binding sites, rather accurate nonpolar solvation free energies could be obtained with the continuum methods if the binding site is prohibited to be filled by continuum water in the unbound state, even though the simulations and experiments show that the ligand replaces several water molecules upon binding. For the more solvent exposed binding sites of trypsin and galectin-3, no accurate continuum estimates could be obtained, even if the binding site was allowed or prohibited to be filled by continuum water. This shows that continuum methods fail to give accurate free energies on a wide range of systems with varying solvent exposure because they lack a microscopic picture of binding-site hydration as well as information about the entropy of water molecules that are in the binding site before the ligand binds. Consequently, binding affinity estimates based upon continuum solvation methods will give absolute binding energies that may differ by up to 200 kJ/mol depending on the method used. Moreover, even relative energies between ligands with the same scaffold may differ by up to 75 kJ/mol. We have tried to improve the continuum solvation methods by adding information about the solvent exposure of the binding site or the hydration of the binding site, and the results are promising at least for this small set of complexes.