Water clustering and percolation in low hydration DNA shells

The hydrogen-bonded networks of water at the surface of a model DNA molecule are analyzed. At low hydrations, only small water clusters are attached to the DNA surface, whereas, at high hydrations, it is homogeneously covered by a spanning water network. The spanning water network is formed via a percolation transition at an intermediate hydration number of about 15 water molecules per nucleotide, which is very close to the midpoint of polymorphic transitions between A- and B-forms of the double helix. The percolation transition can occur in both A- and B-DNA hydration shells with nearly identical percolation thresholds. However, the mechanism of the percolation transition in A- and B-DNA is qualitatively different in regard to the roles played by the two opposite grooves of the double helix. Free ions can shift the percolation threshold by preventing some water molecules from hydrogen bond networking. The results corroborate the suggested relationship between water percolation and the low hydration polymorphism in DNA.     

Formation of spanning water networks on protein surfaces via 2D percolation transition

The formation of spanning hydrogen-bonded water networks on protein surfaces by a percolation transition is closely connected with the onset of their biological activity. To analyze the structure of the hydration water at this important threshold, we performed the first computer simulation study of the percolation transition of water in a model protein powder and on the surface of a single protein molecule. The formation of an infinite water network in the protein powder occurs as a 2D percolation transition at a critical hydration level, which is close to the values observed experimentally. The formation of a spanning 2D water network on a single rigid protein molecule can be described by adapting the cluster analysis of conventional percolation studies to the characterization of the connectivity of the hydration water on the surface of finite objects. Strong fluctuations of the surface water network are observed close to the percolation threshold. Our simulations also furnish a microscopic picture for understanding the specific values of the experimentally observed hydration levels, where different steps of increasing mobility in the hydrated powder are observed.     

Titration in silico of reversible B <=> A transitions in DNA

Reversible transitions between the A- and B-forms of DNA are obtained in free molecular dynamics simulations of a single double helix immersed in a water drop with Na(+) counterions. The dynamics of the transitions agrees with their supposed cooperative character. In silico titration of the transitions was carried out by smooth variation of the drop size. The estimated range of hydration numbers corresponding to the transition roughly agrees with experimental data. The chain length dependence was studied for double helices from 6 to 16 base pairs. It appeared that the B --> A transition is hindered for DNA shorter than one helical turn. With increased NaCl concentration in the drop, stabilization of the B-form is observed accompanied by the salt crystallization. The results strongly suggest that the B --> A transition at low hydration is caused by Na(+) ions sandwiched between phosphate strands in the major groove and is driven by direct medium range electrostatic interactions. The role of the reduced water shell apparently consists of increasing the counterion concentration in the opening of the major groove. Analysis of the available experimental data suggests that this mechanism is perhaps generally responsible for the A/B polymorphism in DNA.     

Negative Hydration of Ions

The negative hydration, that is the increase in the mobility of water molecules near sufficiently large single-charged ions, is studied by modeling, cold-neutron scattering, and computer modeling. Special attention is paid to the mechanism of negative hydration and the boundary of transition from positive to negative and from negative to hydrophobic hydration. Hypothetical ions with radii of approximately 1.1 and 3.3 Å correspond to these boundaries. Dynamic characteristics of hydration water in these ions are identical to those of water molecules in bulk water.     

Direct observation of essential DNA dynamics: melting and reformation of the DNA minor groove

The dynamics of bound water and ions present in the minor groove of a dodecamer DNA has been decoupled from that of the long-range twisting/bending of the DNA backbone, using the minor groove binder Hoechst 33258 as a fluorescence reporter in the picosecond-resolved time window. The bound water and ions are essential structural components of the minor groove and are destroyed with the destruction of the minor groove when the dodecamer melts at high temperatures and reforms on subsequent cooling of the melted DNA. The melting and rehybridization of the DNA has been monitored by the changes in secondary structure using circular dichroism (CD) spectroscopy. The change in the relaxation dynamics of the DNA has been studied with picosecond resolution at different temperatures, following the temperature-dependent melting and rehybridization profile of the dodecamer, using time-resolved emission spectra (TRES). At room temperature, the relaxation dynamics of DNA is governed by a 40 ps (30%) and a 12.3 ns (70%) component. The dynamics of bound water and ions present in the minor groove is characterized by the 40 ps component in the relaxation dynamics of the probe bound in the minor groove of the dodecamer DNA. Analyses of the TRES taken at different temperatures show that the contribution of this component decreases and ultimately vanishes with the destruction of the minor groove and reappears again with the reformation of the groove. The dynamical behavior of bound water molecules and ions of a genomic DNA (from salmon testes) at different temperatures is also found to be consistent with that of the dodecamer. The longer component of approximately 10 ns in the DNA dynamics is found to be associated with the long-range bending/twisting of the DNA backbone and the associated counterions. The transition from bound water to free water at the DNA surface, indicative of the change in the hydration number associated with each base pair, has also been ascertained in the case of the genomic DNA at different temperatures by employing densimetric and acoustic techniques.     

Structural transition in the OH<Superscript>−</Superscript>(H<Subscript>2</Subscript>O)<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> cluster in water vapors

The hydration of hydroxyl ion in water vapors at temperatures corresponding to seasonal variations in natural air medium is studied by the Monte Carlo simulation in grand canonical statistical ensemble using the detailed model of intermolecular forces that takes into account many-particle covalent interactions, polarization, and charge transfer. An increase in the number of water molecules in a cluster is accompanied by a structural transition from strongly asymmetric ion environment of water molecules to the formation of enveloping shell composed of these molecules. This transition is accompanied by an abrupt increase in cluster size and qualitative changes in its structural characteristics. The displacement of ion on the surface of clusters with extremely small sizes is an entropy effect. Results of simulation are compared with data on the hydration of hydroxonium at which similar structural transition is not observed, and with data of quantum-chemical calculations.     

The Electrostatic Origin of Low‐Hydration Polymorphism in DNA

In recent years, significant progress has been made towards uncovering the physical mechanisms of low‐hydration polymorphism in double‐helical DNA. The effect appears to be mechanistically similar in different biological systems, and it is due to the ability of water to form spanning H‐bonded networks around biomacromolecules via a quasi‐two‐dimensional percolation transition. In the case of DNA, disintegration of the spanning H‐bonded network leads to electrostatic condensation of DNA strands because, below the percolation threshold, water loses its high dielectric permittivity, whereas the concentration of neutralizing counterions becomes high. In this Concept article arguments propose that this simple electrostatic mechanism represents the universal origin of low‐hydration polymorphism in DNA.     

Two-dimensional hydration shells of alkali metal ions at a hydrophobic surface

We study the hydration shell formation of alkali metal ions at a graphite surface. Two-dimensional shell structures are found in the initial stage of hydration, in contrast to the three-dimensional structures in bulk water and clusters. Comparison of vibrational spectra with experiments identifies the shell structures and the thermally induced transition from the first to the second shell. We also found intriguing competition between hydration and ion-surface interaction, leading to different solvation dynamics between K and Na. Implications of these results in ionic processes at interfaces are elaborated.     

Hofmeister effects in the restabilization of IgG--latex particles: testing Ruckenstein's theory

The hydration interaction is responsible for the colloidal stability observed in protein-coated particles at high ionic strengths. The origin of this non-DLVO interaction is related not only to the local structure of the water molecules located at the surface but also to the structure of those molecules involved in the hydration of the ions that surround the colloidal particles. Ruckenstein and co-workers have recently developed a new theory based on the coupling of double-layer and hydration interactions. Its validity was contrasted by their fitting of experimental data obtained with IgG-latex particles restabilized at high salt concentration. The theory details the important role played by the counterions in the stability at high salt concentrations by proposing an ion pair reaction forming surface dipoles. These surface dipoles are responsible of repulsive interactions between two approaching surfaces. This paper checks the theory with recent data where some ions associated with the Hofmeister series (NO(3)(-), SCN(-) and Ca(2+)) restabilize the same kind of IgG-latex systems by means of hydration forces. Surprisingly, these ions induce stability acting even as co-ions, likely by modifying the water structure at the surface, but not forming surface ion pairs. Therefore, this experimental evidence would question Ruckenstein's theory based on the surface dipole formation for explaining the observed restabilization phenomena.     

Thermal breaking of spanning water networks in the hydration shell of proteins

The presence of a spanning hydrogen-bonded network of water at the surface of biomolecules is important for their conformational stability, dynamics, and function. We have studied by computer simulations the clustering and percolation of water in the hydration shell of a small elastinlike peptide (ELP) and the medium-size protein staphylococcal nuclease (SNase), in aqueous solution. We have found that in both systems a spanning network of hydration water exists at low temperatures and breaks up with increasing temperature via a quasi-two-dimensional percolation transition. The thermal breaking of the spanning water network occurs at biologically relevant temperatures, in the temperature range, which is close to the temperature of the "inverse temperature transition" of ELP and the unfolding temperature of SNase, respectively.     

Influence of electrolytes on the microenvironment of F127 triblock copolymer micelles: a solvation and rotational dynamics study of coumarin dyes

Dynamic Stokes' shift and fluorescence anisotropy measurements of coumarin 153 (C153) and coumarin 151 (C151) as fluorescence probes have been carried out to understand the influence of electrolytes (NaCl and LiCl) on the hydration behavior of aqueous (ethylene oxide)100-(propylene oxide)70-(ethylene oxide)100 (EO100-PO70-EO100, F127) block copolymer micelles. A small blue shift in the fluorescence spectra of C153 has been observed in presence of electrolytes due to the dehydration of the oxyethylene chains in the PEO-PPO region, although fluorescence spectra of C151 remain unaltered. The close vicinity of bulk water for C151 probably negates the effect of dehydration in the PEO region. Fluorescence anisotropy measurements indicate a gradual increase in microviscosity with electrolyte concentrations. The partial collapse of copolymer blocks in the presence of electrolytes has been suggested as a reason for the increase in microviscosity along with the strong hydration of ions in the corona region. The interplay between the ion hydration and the mechanically trapped water content, and specific interaction of ions, such as complexation of Li+ ions with the copolymer block, is found to control solvation dynamics in the corona region. In addition to that, it has been established that Na+ ions reside deep into the corona region whereas Li+ ions prefer to reside closer to the surface. Owing to its higher lyotropicity, LiCl influences the corona hydration to a greater extent than NaCl and sets in micelle-micelle interaction above the 2 M LiCl concentration, as reflected in the saturation of solvation time constants. The formation of larger clusters of F127 micelles above 2 M LiCl has been confirmed by dynamic light scattering measurements; however, such cluster formation is not evident with NaCl.     

Experimental evidence of fragile-to-strong dynamic crossover in DNA hydration water

We used high-resolution quasielastic neutron scattering spectroscopy to study the single-particle dynamics of water molecules on the surface of hydrated DNA samples. Both H(2)O and D(2)O hydrated samples were measured. The contribution of scattering from DNA is subtracted out by taking the difference of the signals between the two samples. The measurement was made at a series of temperatures from 270 down to 185 K. The relaxing-cage model was used to analyze the quasielastic spectra. This allowed us to extract a Q-independent average translational relaxation time of water molecules as a function of temperature. We observe clear evidence of a fragile-to-strong dynamic crossover (FSC) at T(L)=222+/-2 K by plotting log versus T. The coincidence of the dynamic transition temperature T(c) of DNA, signaling the onset of anharmonic molecular motion, and the FSC temperature T(L) of the hydration water suggests that the change of mobility of the hydration water molecules across T(L) drives the dynamic transition in DNA.     

Thermodynamic origin of hofmeister ion effects

Quantitative interpretation and prediction of Hofmeister ion effects on protein processes, including folding and crystallization, have been elusive goals of a century of research. Here, a quantitative thermodynamic analysis, developed to treat noncoulombic interactions of solutes with biopolymer surface and recently extended to analyze the effects of Hofmeister salts on the surface tension of water, is applied to literature solubility data for small hydrocarbons and model peptides. This analysis allows us to obtain a minimum estimate of the hydration b1 (H2O A(-2)), of hydrocarbon surface and partition coefficients Kp, characterizing the distribution of salts and salt ions between this hydration water and bulk water. Assuming that Na+ and SO4(2-) ions of Na2SO4 (the salt giving the largest reduction in hydrocarbon solubility as well as the largest increase in surface tension) are fully excluded from the hydration water at hydrocarbon surface, we obtain the same b1 as for air-water surface (approximately 0.18 H2O A(-2)). Rank orders of cation and anion partition coefficients for nonpolar surface follow the Hofmeister series for protein processes, but are strongly offset for cations in the direction of exclusion (preferential hydration). By applying a coarse-grained decomposition of water accessible surface area (ASA) into nonpolar, polar amide, and other polar surface and the same hydration b1 to interpret peptide solubility increments, we determine salt partition coefficients for amide surface. These partition coefficients are separated into single-ion contributions based on the observation that both Cl- and Na+ (also K+) occupy neutral positions in the middle of the anion and cation Hofmeister series for protein folding. Independent of this assignment, we find that all cations investigated are strongly accumulated at amide surface while most anions are excluded. Cation and anion effects are independent and additive, allowing successful prediction of Hofmeister salt effects on micelle formation and other processes from structural information (ASA).     

Hydration-dependent protein dynamics revealed by molecular dynamics simulation of crystalline staphylococcal nuclease

Molecular dynamics simulations of crystalline Staphylococcal nuclease in full and minimal hydration states were performed to study hydration effects on protein dynamics at temperatures ranging from 100 to 300 K. In a full hydration state (hydration ratio in weight, h=0.49), gaps are fully filled with water molecules, whereas only crystal waters are included in a minimal hydration state (h=0.09). The inflection of the atomic mean-square fluctuation of protein as a function of temperature, known as the glass-like transition, is observed at approximately 220 K in both cases, which is more significant in the full hydration state. By examining the temperature dependence of residual fluctuation, we found that the increase of fluctuations in the loop and terminal regions, which are exposed to water, is much greater than that in other regions in the full hydration state, but the mobilities of the corresponding regions are relatively restricted in the minimal hydration state by intermolecular contact. The atomic mean-square fluctuation of water molecules in the full hydration state at 300 K is 1 order of magnitude greater than that in the minimal hydration state. Above the transition temperature, most water molecules in the full hydration state behave like bulk water and act as a lubricant for protein dynamics. In contrast, water molecules in the minimal hydration state tend to form more hydrogen bonds with the protein, restricting the fluctuation of these water molecules to the level of the protein. Thus, intermolecular interaction and solvent mobility are important to understand the glass-like transition in proteins.     

Breakdown of hydration repulsion between charged surfaces in aqueous Cs+ solutions

Using a surface force balance, we have measured the normal and shear forces between mica surfaces across aqueous caesium salt solutions (CsNO(3) and CsCl) up to 100 mM concentrations. In contrast to all other alkali metal ions at these concentrations, we find no evidence of hydration repulsion between the mica surfaces on close approach: the surfaces appear to be largely neutralized by condensation of the Cs ions onto the charged lattice sites, and are attracted on approach into adhesive contact. The contact separation at adhesion indicates that the condensed Cs ions protrude by 0.3 +/- 0.2 nm from each surface, an observation supported both by the relatively weak adhesion energies between the surfaces, and the relatively weak frictional yield stress when they are made to slide past each other. These observations show directly that the hydration shells about the Cs(+) ions are removed as the ions condense into the charged surface lattice. This effect is attributed to the low energies-resulting from their large ionic radius-required for dehydration of these ions.     

Approaches to hydration, old and new: Insights through Hofmeister effects

Hydration effects in colloidal interactions or problems involving electrolytes are usually taken care of by effective electrostatic potentials that subsume notions like hydrated ion size, Gurney potentials, soft and hard, chaotropic and cosmotropic ions, and inner and outer Helmholtz planes. Quantum fluctuation (dispersion) forces between ions and between ions and surfaces are missing from classical theories, at least not explicit in standard approaches to hydration. This paper outlines an evolving back-to-basics approach that allows these ion specific forces to be included in theories quantitatively. In this approach ab initio quantum mechanics is used to calculate dynamic polarisabilities of ions and to quantify bare ion radii. The ionic dispersion potentials between ions, and between ions and surfaces in water can then be given explicit analytic form from an extension of Lifshitz theory. They are included in the theory along with electrostatic potentials. In a first stage the primitive (continuum solvent) model provides a skeletal theory on which to build in hydration. Extension of the ab initio calculations to include “dressed” ions, i.e. water hydration shells for cosmotropic ions, quadrupolar and octupolar polarisability contributions and; for colloids, allowance for a surface hydration layer, permits quantification of Hofmeister effects and Gurney potentials. With these extensions, primary hydration forces (short range repulsion) arise due to an interplay between surface hydration layers and specific ion interactions. Apparent longer range “secondary hydration forces” are shown to be a consequence of ion-surface dispersion interactions and are not true “hydration forces”.     

Formation and interaction of hydrated alkali metal ions at the graphite-water interface

Ion hydration at a solid surface ubiquitously exists in nature and plays important roles in many natural processes and technological applications. Aiming at obtaining a microscopic insight into the formation of such systems and interactions therein, we have investigated the hydration of alkali metal ions at a prototype surface-graphite (0001), using first-principles molecular dynamics simulations. At low water coverage, the alkali metal ions form two-dimensional hydration shells accommodating at most four (Li, Na) and three (K, Rb, Cs) waters in the first shell. These two-dimensional shells generally evolve into three-dimensional structures at higher water coverage, due to the competition between hydration and ion-surface interactions. Exceptionally K was found to reside at the graphite-water interface for water coverages up to bulk water limit, where it forms an "umbrellalike" surface hydration shell with an average water-ion-surface angle of 115 degrees . Interactions between the hydrated K and Na ions at the interface have also been studied. Water molecules seem to mediate an effective ion-ion interaction, which favors the aggregation of Na ions but prevents nucleation of K. These results agree with experimental observations in electron energy loss spectroscopy, desorption spectroscopy, and work function measurement. In addition, the sensitive dependence of charge transfer on dynamical structure evolution during the hydration process, implies the necessity to describe surface ion hydration from electronic structure calculations.     

Hydration water and bulk water in proteins have distinct properties in radial distributions calculated from 105 atomic resolution crystal structures

Water plays a critical role in the structure and function of proteins, although the experimental properties of water around protein structures are not well understood. The water can be classified by the separation from the protein surface into bulk water and hydration water. Hydration water interacts closely with the protein and contributes to protein folding, stability, and dynamics, as well as interacting with the bulk water. Water potential functions are often parametrized to fit bulk water properties because of the limited experimental data for hydration water. Therefore, the structural and energetic properties of the hydration water were assessed for 105 atomic resolution (相似文献   

Computational investigation of the role of hydration in nucleic acid structure and function

The results of the Monte Carlo Metropolis simulation of water structure and of the hydration of nucleic acid fragments, complementary base pairs and mispairs, base pair stacks, and duplex fragments have been summarized. Systematic investigations suggest some general conclusions: (1) the hydration shell structure of the major and minor grooves of the duplex depends significantly on DNA conformation (or stack configuration) and nucleotide sequence, while global hydration characteristics (average energy, the number of water–water and water–base H-bonds) are only slightly dependent on these factors, (2) hydration economy takes place in the B–A transition due to an increase of the number of water molecules forming hydrogen bonds with two or more atoms of bases (water bridging), and (3) the hydration of the duplex could contribute to nucleic acid functioning via water-bridged mispair formation and stabilization of specific conformations.     

The role of water H-bond imbalances in B-DNA substate transitions and peptide recognition revealed by time-resolved FTIR spectroscopy

The conformational substates B(I) and B(II) of the phosphodiester backbone in B-DNA are thought to contribute to DNA flexibility and protein recognition. We have studied by rapid scan FTIR spectroscopy the isothermal B(I)-B(II) transition on its intrinsic time scale. Correlation analysis of IR absorption changes occurring within seconds after a reversible incremental growth of the DNA hydration shell identifies water populations w(1) (PO(2)(-)-bound) and w(2) (non-PO(2)(-)-bound) exhibiting weaker and stronger H-bonds, respectively, than those dominating in bulk water. The B(II) substate is stabilized by w(2). The water H-bond imbalance of 3-4 kJ mol(-1) is equalized at little enthalpic cost upon formation of a contiguous water network (at 12-14 H(2)O molecules per DNA phosphate) of reduced ν(OH) bandwidth. In this state, hydration water cooperatively stabilizes the B(I) conformer via the entropically favored replacement of w(2)-DNA interactions by additional w(2)-water contacts, rather than binding to B(I)-specific hydration sites. Such water rearrangements contribute to the recognition of DNA by indolicidin, an antimicrobial 13-mer peptide from bovine neutrophils which, despite little intrinsic structure, preferentially binds to the B(I) conformer in a water-mediated induced fit. The FTIR spectra resolve sequential steps leading from PO(2)(-)-solvation to substate transition and eventually to base stacking changes in the complex. In combination with CD-spectral titrations, the data indicate that, in the absence of a bulk aqueous phase, as in molecular crowded environments, water relocation within the DNA hydration shell allows for entropic contributions similar to those assigned to water upon DNA ligand recognition in solution.