Hyper-mobile Water and Raman 2900 cm-1 Peak Band of Water Observed around Backbone Phosphates of Double Stranded DNA by High-Resolution Spectroscopies and MD Structural Feature Analysis of Water.

High-resolution measurements of microwave dielectric relaxation and Raman spectroscopies for waters in double-stranded (ds) 10-mer DNA solution revealed the presence of hyper-mobile water (HMW) and a marked OH stretching band appearing in the range from 2500 to 3100 cm-1, here called the LA band, at the low wavenumber tail of the major OH stretching band of water. Quantitation of the Raman scattering intensity for ds 10-mer DNA in phosphate or tris(hydroxymethyl)aminomethane (TRIS) buffers showed that the LA band was formed by 2000-3000 water molecules per ds 10-mer DNA, indicating collective OH stretching vibrations of water molecules around the backbone phosphate oxygen atoms. The LA band intensity of ds 10-mer DNA in 10 mM TRIS increased and decreased by 30% with the addition of 2 mM MgCl2 and 2 mM CaCl2, respectively. The LA band intensity and the effect of adding Mg(II) or Ca(II) ions to the band intensity were maintained in the presence of 0.14 M KCl; however, the changes induced by the divalent cations were reduced by half. Molecular dynamics calculations of water molecules around the backbone phosphate groups of ds 10-mer DNA indicate the presence of high-density water and broad regions of fluctuating water density, suggesting that they correspond to HMW and the LA band, respectively.

Physical driving force of actomyosin motility based on the hydration effect.

We propose a driving force hypothesis based on previous thermodynamics, kinetics and structural data as well as additional experiments and calculations presented here on water-related phenomena in the actomyosin systems. Although Szent-Györgyi pointed out the importance of water in muscle contraction in 1951, few studies have focused on the water science of muscle because of the difficulty of analyzing hydration properties of the muscle proteins, actin, and myosin. The thermodynamics and energetics of muscle contraction are linked to the water-mediated regulation of protein-ligand and protein-protein interactions along with structural changes in protein molecules. In this study, we assume the following two points: (1) the periodic electric field distribution along an actin filament (F-actin) is unidirectionally modified upon binding of myosin subfragment 1 (M or myosin S1) with ADP and inorganic phosphate Pi (M.ADP.Pi complex) and (2) the solvation free energy of myosin S1 depends on the external electric field strength and the solvation free energy of myosin S1 in close proximity to F-actin can become the potential force to drive myosin S1 along F-actin. The first assumption is supported by integration of experimental reports. The second assumption is supported by model calculations utilizing molecular dynamics (MD) simulation to determine solvation free energies of a small organic molecule and two small proteins. MD simulations utilize the energy representation method (ER) and the roughly proportional relationship between the solvation free energy and the solvent-accessible surface area (SASA) of the protein. The estimated driving force acting on myosin S1 is as high as several piconewtons (pN), which is consistent with the experimentally observed force.

Strong Dependence of Hydration State of F-Actin on the Bound Mg(2+)/Ca(2+) Ions.

Understanding of the hydration state is an important issue in the chemomechanical energetics of versatile biological functions of polymerized actin (F-actin). In this study, hydration-state differences of F-actin by the bound divalent cations are revealed through precision microwave dielectric relaxation (DR) spectroscopy. G- and F-actin in Ca- and Mg-containing buffer solutions exhibit dual hydration components comprising restrained water with DR frequency f2 (fw). The hydration state of F-actin is strongly dependent on the ionic composition. In every buffer tested, the HMW signal Dhyme (≡ (f1 - fw)δ1/(fwδw)) of F-actin is stronger than that of G-actin, where δw is DR-amplitude of bulk solvent and δ1 is that of HMW in a fixed-volume ellipsoid containing an F-actin and surrounding water in solution. Dhyme value of F-actin in Ca2.0-buffer (containing 2 mM Ca(2+)) is markedly higher than in Mg2.0-buffer (containing 2 mM Mg(2+)). Moreover, in the presence of 2 mM Mg(2+), the hydration state of F-actin is changed by adding a small fraction of Ca(2+) (∼0.1 mM) and becomes closer to that of the Ca-bound form in Ca2.0-buffer. This is consistent with the results of the partial specific volume and the Cotton effect around 290 nm in the CD spectra, indicating a change in the tertiary structure and less apparent change in the secondary structure of actin. The number of restrained water molecules per actin (N2) is estimated to be 1600-2100 for Ca2.0- and F-buffer and ∼2500 for Mg2.0-buffer at 10-15 °C. These numbers are comparable to those estimated from the available F-actin atomic structures as in the first water layer. The number of HMW molecules is roughly explained by the volume between the equipotential surface of -kT/2e and the first water layer of the actin surface by solving the Poisson-Boltzmann equation using UCSF Chimera.

Spatial-Decomposition Analysis of Energetics of Ionic Hydration.

Hydration energetics is analyzed for a set of ions. The analysis is conducted on the basis of a spatial-decomposition formula for the excess partial molar energy of the solute that expresses the thermodynamic quantity as an integral over the whole space of the solute-solvent and solvent-solvent interactions conditioned by the solute-solvent distance. It is observed for all the ionic solutes treated in the present work that the ion-water interaction is favorable at the expense of the water-water interaction and that the variations of the ion-water and water-water interactions with the ion-water distance compensate against each other beyond the contact distance. The extent of spatial localization of the excess partial molar energy is then assessed by introducing a cutoff into the integral expression and examining the convergence with respect to the change in the cutoff. It is found that the excess energy is not quantitatively localized within the first and second hydration layers, while its correlations over the variation of ions are good against the first-layer contribution.

Comparative study on the properties of hydration water of Na- and K-halide ions by Raman OH/OD-stretching spectroscopy and dielectric relaxation data.

Properties of hypermobile water (HMW) were studied by Raman OH-stretching spectroscopy. Hydration water properties measured by Raman OH-stretching spectra of NaX/KX (X: Cl, Br, I) solutions (0.05-0.2 M) were comparatively analyzed with the data by dielectric relaxation spectroscopy (DRS), NMR, and statistical mechanical studies. The Raman OH-stretching spectra were well-fitted with linear combinations of the spectra of pure water both at the same and the higher temperatures. The fitting analysis determined the "structure temperature" Tstr and mole fraction of the high Tstr water region, giving the hydration number Nhyd, for each electrolyte solution. The determined Tstr was much higher than the solution temperature of 293 K for each tested salt and was higher for larger halide ions, consistent with commonly known "structure-breaking" order Cl < Br < I. No significant differences in Nhyd were observed between NaX and KX and among even halide ion species within the experimental errors. Measured Nhyd values of 25-27 were much greater than the reported numbers by NMR chemical shift and (17)O NMR relaxation studies and comparable to the numbers of hypermobile water reported in the previous DRS studies. The results indicated that the hydration region around NaX or KX measured by the present Raman study was nearly overlapped with the region of HMW by DRS. It was also suggested that differences in the ion size effects on Tstr and the DR frequency resulted from the sensitivity difference to long-range many-body interactions among water molecules. High structure-temperature regions were also detected by the analysis of OH-stretching and OD-stretching bands for 0.2 M NaI in H2O/D2O mixed solvent of 50 mol %, and we found that both OH-stretching and OD-stretching bands have almost equivalent Tstr ≈ 330 K and mole fractions with each other.

Anion-dependence of fast relaxation component in Na-, K-halide solutions at low concentrations measured by high-resolution microwave dielectric spectroscopy.

High-resolution microwave dielectric spectra of NaX, KX (X: F, Cl, Br, I) aqueous solutions of c = 0.05 and 0.1 M measured in the frequency range 0.2-26 GHz at 10 °C are analyzed. The dielectric relaxation (DR) spectrum of each solution, which deviates slightly from the bulk-water spectrum, is mathematically divided into the bulk-water spectrum and the spectrum of solute particles covered with a water layer using a mixture theory by assuming the existence of continuous bulk-water phase. The solute spectra above 3 GHz are fitted with a linear series of pure water component (γ dispersion with DR frequency fw), fast Debye component-1 with DR frequency f1 (>fw), and slow Debye component-2 with DR frequency f2 (

Hydration-state change of horse heart cytochrome c corresponding to trifluoroacetic-acid-induced unfolding.

We investigate the hydration state of horse-heart cytochrome c (hh cyt c) in the unfolding process induced by trifluoroacetic acid (TFA). The conformation of hh cyt c changes from the native (N) state (2.9 < pH < 6.0) to the acid-unfolded (U(A)) state (1.7 < pH < 2.0) to the acid-induced molten globule (A) state (pH ∼1.2). Hydration properties of hh cyt c during this process are measured at 20°C by high-resolution dielectric relaxation (DR) spectroscopy, UV-vis absorbance, and circular dichroism spectroscopy. Constrained water of hh cyt c is observed at every pH as an ∼5-GHz Debye component (DC) (DR time, τ(D) ∼30 ps) and its DR amplitude (DRA) is increased by 77% upon N-to-U(A) transition, when pH changes from 6.0 to 2.0. Even in the N state, the DRA of the constrained-water component is found to be increased by 22% with decreasing pH from 6.0 to 2.9, suggesting an increase in the accessible surface area of native hh cyt c. Moreover, hypermobile water around native hh cyt c is detected at pH 6.0 as a 19-GHz DC (τ(D) ∼ 8.4 ps <τ(DW) = 9.4 ps), but is not found at other pH values. The DRA signal of constrained water is found to return to the pH 2.9 (N-state) level upon U(A)-to-A transition. Fast-response water (slightly slower than bulk) around A-state hh cyt c is detected at pH 1.2, and this suggests some accumulation of TFA(-) ions around the peptide chain. Thus, this high-resolution DR spectroscopy study reveals that hh cyt c exhibits significant hydration-state change in the TFA-unfolding process.

Hydration properties of adenosine phosphate series as studied by microwave dielectric spectroscopy.

Hydration properties of adenine nucleotides and orthophosphate (Pi) in aqueous solutions adjusted to pH=8 with NaOH were studied by high-resolution microwave dielectric relaxation (DR) spectroscopy at 20 °C. The dielectric spectra were analyzed using a mixture theory combined with a least-squares Debye decomposition method. Solutions of Pi and adenine nucleotides showed qualitatively similar dielectric properties described by two Debye components. One component was characterized by a relaxation frequency (f(c)=18.8-19.7 GHz) significantly higher than that of bulk water (17 GHz) and the other by a much lower f(c) (6.4-7.6 GHz), which are referred to here as hyper-mobile water and constrained water, respectively. By contrast, a hydration shell of only the latter type was found for adenosine (f(c)~6.7 GHz). The present results indicate that phosphoryl groups are mostly responsible for affecting the structure of the water surrounding the adenine nucleotides by forming one constrained water layer and an additional three or four layers of hyper-mobile water.

Measurement of the dielectric relaxation property of water-ion loose complex in aqueous solutions of salt at low concentrations.

Electrolytes and their dissociated ions are thought to form positive or negative hydration layers around them. In this study, we have developed a method to determine the volume and the dielectric relaxation property (relaxation frequency f c, dispersion intensity delta) of the water hydrating ions in salt solutions. The method consists of four steps: (1) By use of a high-resolution microwave dielectric spectroscopy technique, the dielectric spectra of sample salt solution and bulk water are measured in pair. (2) The dielectric spectrum of solutes (ions) with water layers for a given volume fraction varphi is then calculated from each pair of dielectric spectra of a sample salt solution and reference water according to the Hanai mixture theory. (3) Each spectrum of solutes with water layers at a given varphi is decomposed into a few Debye relaxation functions and the bulk water component. (4) The volume fraction varphi is operationally decreased from 0.5, and steps (2) and (3) are repeated at each varphi until the bulk water component vanished. Then the volume fraction of the hydrated solutes (ions) in solution is determined. The method was applied to NaF and NaCl solutions. As a result the different spectral intensity was nearly proportional to the salt concentration below 0.2 M in the frequency range of 3-26 GHz. The hydration number N h and the dielectric relaxation property of the hydration layer for each salt solution was successfully determined as ( f c1, delta 1, N h)= (18.7, 44.9, 27.9) for NaCl and ( f c1, delta 1, f c2, delta 2, N h) = (26.0, 6.70, 5.64, 19.2) for NaF.

Cooperative structural change of actin filaments interacting with activated myosin motor domain, detected with copolymers of pyrene-labeled actin and acto-S1 chimera protein.

Acto-S1 chimera proteins CP24 and CP18 carry the entire actin sequence, inserted in loop 2 of the motor domain of Dictyostelium myosin II, and have MgATPase activity close to that of natural Dictyostelium actomyosin [M.S.P. Siddique, T. Miyazaki, E. Katayama, T.Q.P. Uyeda, M. Suzuki, Evidence against essential roles of subdomain 1 of actin in actomyosin sliding movements, Biochem. Biophys. Res. Commun. 332 (2005) 474-481]. Here, we examined and detected cooperative structural change of actin filaments accompanying interaction with myosin motor domain in the presence of ATP using copolymer filaments consisting of pyrene-labeled skeletal actin (SA) and either CP24 or CP18. Upon addition of ATP, the fluorescence intensity increased over the range from 380 to 480nm using 365-nm excitation. The relative increases of fluorescence intensity at 390nm were 14%, 46%, and 77% for the copolymer filaments with the CP24 to actin molar ratios of 0.0625, 0.143, and 0.333, respectively, and demonstrated a sigmoid behavior. Stoichiometric analysis indicates that each CP24 molecule appears to affect four actin molecules, on average, in SA-CP24 copolymers, and each CP18 molecule appears to affect three actin molecules in SA-CP18 copolymers.