Components and fractions for differently bound water molecules of dipalmitoylphosphatidylcholine-water system as studied by DSC and 2H-NMR spectroscopy

Differently bound water molecules of dipalmitoylphosphatidylcholine (DPPC)-H2O system were investigated with differential scanning calorimetry (DSC). According to a method previously reported by us, the ice-melting DSC curves of the DPPC-H2O samples of varying water contents were deconvoluted into multiple components, and the ice-melting enthalpies for the individual deconvoluted components were used to estimate average molar ice-melting enthalpies for freezable interlamellar and bulk waters, respectively. With these average molar ice-melting enthalpies, the numbers of differently bound water molecules of the DPPC-H2O system were calculated at varying water contents and were used to construct a water distribution diagram of this system. Furthermore, to evaluate the reliability of the present DSC deconvolution method, 2H-NMR T1 measurements of DPPC-2H2O system were carried out at 5 degrees C of the gel phase temperature, and components and fractions for differently bound water (2H2O) molecules were estimated from the analysis of nonexponential magnetization recovery curves.     

Crystallization of water in multilamellar vesicles

The two-step crystallization of water in multilamellar vesicles (MLVs) of phosphatidylcholines has been investigated. The main crystallization occurs near -15 degrees C and involves bulk water. Contrary to unilamellar vesicles, a sub-zero phase transition is observed for MLVs at -40 degrees C that corresponds to the crystallization of interstitial water, as proved by Fourier transform infrared absorption and differential scanning calorimetry (DSC) experiments. Furthermore, by means of the DSC method and, more specifically, using the enthalpy change values Delta H(sub) at the sub-zero transition, the number of water molecules per 1,2-dipalmitoylphosphatidylcholine (DPPC) molecule giving rise to this transition has been estimated for different H(2)O/DPPC molar ratios. The curve of the molecular fraction of water molecules involved in the sub-zero transition versus the H(2)O/DPPC molar ratio exhibits a maximum for H(2)O/DPPC equal to 27 (40% in mass of water) and tends towards zero for H(2)O/DPPC ratio values approaching that of the swelling limit of the membrane. A smaller enthalpy value of the sub-zero transition is found for 1-oleoyl-2-palmitoyl-3-phosphatidylcholine (OPPC) than for DPPC. This may be explained by the decrease of interstitial water's quantity when the lipid contains an unsaturated chain. When troxerutin, a hydrophilic drug, is added to the DPPC multilayers, the decrease of Delta H(sub) and melting enthalpy of bulk water is attributed to a decrease of the entropy of the liquid phase owing to the network of water molecules surrounding troxerutin molecules. In all cases, the experiments revealed that the sub-zero transition occurs only in the presence of excess water with respect to the swelling limit of membranes. This evidence could be, at least qualitatively, related to an increase of membrane pressure on interstitial water subsequent to bulk water crystallization.     

Molecular dynamics simulation of a synthetic ion channel.

A molecular dynamics simulation has been performed on a synthetic membrane-spanning ion channel, consisting of four alpha-helical peptides, each of which is composed of the amino acids leucine (L) and serine (S), with the sequence Ac-(LSLLLSL)3-CONH2. This four-helix bundle has been shown experimentally to act as a proton-conducting channel in a membrane environment. In the present simulation, the channel was initially assembled as a parallel bundle in the octane portion of a phase-separated water/octane system, which provided a membrane-mimetic environment. An explicit reversible multiple-time-step integrator was used to generate a dynamical trajectory, a few nanoseconds in duration for this composite system on a parallel computer, under ambient conditions. After more than 1 ns, the four helices were found to adopt an associated dimer state with twofold symmetry, which evolved into a coiled-coil tetrameric structure with a left-handed twist. In the coiled-coil state, the polar serine side chains interact to form a layered structure with the core of the bundle filled with H2O. The dipoles of these H2O molecules tended to align opposite the net dipole of the peptide bundle. The calculated dipole relaxation function of the pore H2O molecules exhibits two reorientation times. One is approximately 3.2 ps, and the other is approximately 100 times longer. The diffusion coefficient of the pore H2O is about one-third of the bulk H2O value. The total dipole moment and the inertia tensor of the peptide bundle have been calculated and reveal slow (300 ps) collective oscillatory motions. Our results, which are based on a simple united atom force-field model, suggest that the function of this synthetic ion channel is likely inextricably coupled to its dynamical behavior.     

Quantitation of physical-chemical properties of the aqueous phase inside the phoE ionic channel.

The anion-specific channel of the phoE porine is a miniature body of water surrounded by peptide walls. The physical and chemical properties of the water in such a microscopic space were measured by monitoring the dynamics of a well-studied reaction--the protolytic dissociation of a strong acid. To attain this purpose, we allowed pyranine (8-hydroxypyrene-1,3,6-trisulfonate) to bind to the anion-specific channel. The dye is bound, with a 1:1 stoichiometry, with a delta G = -9.5 kcal/mol. Photoexcitation of the dye, to its first electronic singlet state (phi OH*), renders it very acidic and the hydroxyl proton dissociates to H+ and excited anion (phi O*-). We employed single photon-counting time-resolved fluorimetry, to monitor the reversible dissociation of pyranine as it proceeds within the channel and reconstructed the observed signal by a numerical integration of the differential diffusion equation pertinent for a proton within the channel. The most characteristic feature of the water-filled channel, is the intensified electrostatic interactions attained by the low dielectric constant of the diffusion space, epsilon eff = 24. For this reason, the electric field of a few positive charges is sufficient to ensure that an anion entering the channel will be effectively sucked in. The interaction of the water molecules with the peptide structure forming the channel affects the physical properties of the water. Their capacity to conduct proton, quantitated by the protons diffusion coefficient (4.5.10(-5) cm2/s), is reduced by 50% with respect to that of bulk water. The activity of the water in the channel is reduced to alpha H2O = 0.966. These observation are in accord with our previous studies of water in small defined cavities in proteins.     

Role of bulk water in hydrolysis of the rhodopsin chromophore

Rhodopsin (Rho) is a prototypical G protein-coupled receptor that changes from an inactive conformational state to a G protein-activating state as a consequence of its retinal chromophore isomerization, 11-cis-retinal → all-trans-retinal. The photoisomerized chromophore covalently linked to Lys(296) by a Schiff base is subsequently hydrolyzed, but little is known about this reaction. Recent research indicates a significant role for tightly bound transmembrane water molecules in the Rho activation process. Atomic structures of Rho and hydroxyl radical footprinting reveal ordered waters within Rho transmembrane helices that are located close to highly conserved and functionally important receptor residues, forming a hydrogen bond network. Using (18)O-labeled H(2)O, we now report that water from bulk solvent, but not tightly bound water, is involved in the hydrolytic release of chromophore upon Rho activation by light. Moreover, small molecules (and presumably, water) enter the Rho structure from the cytoplasmic side of the membrane. Thus, this work indicates two distinct origins of water vital for Rho function.     

Water and deuterium oxide permeability through aquaporin 1: MD predictions and experimental verification

Determining the mechanisms of flux through protein channels requires a combination of structural data, permeability measurement, and molecular dynamics (MD) simulations. To further clarify the mechanism of flux through aquaporin 1 (AQP1), osmotic p(f) (cm(3)/s/pore) and diffusion p(d) (cm(3)/s/pore) permeability coefficients per pore of H(2)O and D(2)O in AQP1 were calculated using MD simulations. We then compared the simulation results with experimental measurements of the osmotic AQP1 permeabilities of H(2)O and D(2)O. In this manner we evaluated the ability of MD simulations to predict actual flux results. For the MD simulations, the force field parameters of the D(2)O model were reparameterized from the TIP3P water model to reproduce the experimentally observed difference in the bulk self diffusion constants of H(2)O vs. D(2)O. Two MD systems (one for each solvent) were constructed, each containing explicit palmitoyl-oleoyl-phosphatidyl-ethanolamine (POPE) phospholipid molecules, solvent, and AQP1. It was found that the calculated value of p(f) for D(2)O is approximately 15% smaller than for H(2)O. Bovine AQP1 was reconstituted into palmitoyl-oleoyl-phosphatidylcholine (POPC) liposomes, and it was found that the measured macroscopic osmotic permeability coefficient P(f) (cm/s) of D(2)O is approximately 21% lower than for H(2)O. The combined computational and experimental results suggest that deuterium oxide permeability through AQP1 is similar to that of water. The slightly lower observed osmotic permeability of D(2)O compared to H(2)O in AQP1 is most likely due to the lower self diffusion constant of D(2)O.     

Water and lipid relations in beech (Fagus sylvatica L.) seeds and its effect on storage behaviour

Beech (Fagus sylvatica L.) seeds indicate intermediate storage behaviour. Properties of water in seed tissues were studied to understand their requirements during storage conditions. Water sorption isotherms showed that at the same relative humidity (RH) the water content is significantly higher in embryo axes than cotyledons. This tendency maintains also after recalculating the water content for zero amount of lipids in tissues. Differential thermal analysis (DTA) indicated water crystallization exotherms in the embryo axes at moisture content (MC) higher than 29% and 16% in the cotyledons. In order to examine the occurrence of glassy state in the cytoplasm of beech embryos as a function of water content, isolated embryo axes were examined using electron spin resonance (ESR) of nitroxide TEMPO probe located inside axes cells. TEMPO molecules undergo fast reorientations with correlation time varied from 2 x 10(-9) s at 180 K to 2 x 10(-11) s at 315 K. Although the TEMPO molecules label mainly the lipid bilayers of cell membranes, they are sensitive to the dynamics and phase transformation of the cytoplasmic cell interior. The label motion is clearly affected by a transition between liquid and glassy state of the cytoplasm. The glass transition temperature (T(g)) raises from 253 to 293 K when water content decreases from 18% to 8%. Far from T(g) the motion is described by Arrhenius equation with very small activation energy E(a) in the liquid state and is relatively small in the glassy state where E(a)=1.5 kJ/mol for 28% H(2)O and E(a)=4.7 kJ/mol for 8% H(2)O or less. The optimal storage conditions of beech seeds are proposed in the range from 255 K for 15% H(2)O to 280 K for 9% H(2)O.     

Metal ion interactions with sugars. The crystal structure and FT-IR study of the NdCl3-ribose complex

The single-crystal structure of neodymium chloride-ribopyranose pentahydrate, NdCl3.C5H10O5.5H2O was determined to have Mr=490.80, a=9.138(11), b=8.830(10), c=9.811(11) A, beta=94.087(18) degrees, V=789.7(16) A3, P2(1), Z=2, mu=0.71073 A and R=0.0198 for 2075 observed reflections. The ligand of the title complex was observed in a disordered state and two molecular configurations of NdCl3.C5H10O5.5H2O were found in the single crystal as a pair of isomers. Both ligand moieties of the two molecules are ribopyranose forms, providing three hydroxyl groups in ax-eq-ax orientation for coordination. One ligand of the pair of isomers is beta-D-ribopyranose in the 1C4 conformation, and the other is alpha-D-ribopyranose in the 4C1 conformation. The Nd3+ ion is nine-coordinated with five Nd-O bonds from water molecules, three Nd-O bonds from hydroxyl groups of the ribopyranose and one Nd-Cl bond from chloride ion. The hydroxyl groups, water molecules, chloride ions form an extensive hydrogen-bond network. The IR spectral C-C,O-H,C-O and C-O-H vibrations were observed to be shifted in the complex and the IR results are in accordance with those of X-ray spectroscopy.     

Relating structure and translational dynamics in aqueous dispersions of monoolein

The temperature dependence of the molecular diffusion in monoolein/water systems is investigated at several levels of hydration. Using the proton/deuteron selectivity, field gradient NMR allows the simultaneous determination of the diffusion constants of both, lipid and water molecules in the various lamellar and non-lamellar phases. Due to the mesoscopic structure of the monoolein/water phases, the diffusion coefficients are interpreted as 'reduced' or 'effective' diffusion coefficients, and are related to the microscopic molecular displacements by a so-called 'obstruction factor'. Changes in the microscopic structure at the phase transition from the bicontinuous cubic phases to the inverse hexagonal phase are reflected in the obstruction factor of the monoolein diffusion coefficients. The reduction of the water diffusion coefficients is too high to be explained by an obstruction factor only, implying a mechanism of molecular motion, which strongly differs from that of bulk water. Experiments on samples prepared with isotopic labeled water (2H(2)O and H(2)(17)O) indicate a chemical exchange of protons between the water molecules and the lipid headgroups on a millisecond timescale.     

Accelerated exchange of a buried water molecule in selectively disulfide-reduced bovine pancreatic trypsin inhibitor

Using magnetic relaxation dispersion (MRD), we have previously shown that the four internal water molecules in bovine pancreatic trypsin inhibitor (BPTI) exchange with bulk water on time scales between 10(-8) and 10(-4) s at room temperature. Because this exchange is controlled by the protein structure, internal water molecules can be used to probe rare conformational fluctuations. Here, we report (2)H and (17)O MRD data at three temperatures for wild-type BPTI and two BPTI variants where the 14-38 disulfide bond has been cleaved by a double Cys --> Ser mutation or by disulfide reduction and carboxamidomethylation. The MRD data show that the internal water molecules are conserved on disulfide cleavage. However, the exchange rate of the water molecule buried near the disulfide bond is enhanced by 2-4 orders of magnitude. The relation of water exchange to other dynamic processes in BPTI is discussed.     

Conformational analysis of an acyclic tetrapeptide: ab‐initio structure determination from X‐ray powder diffraction,Hirshfeld surface analysis and electronic structure

A terminally protected acyclic tetrapeptide has been synthesized, and the crystal structure of its hydrated form, Boc‐Tyr‐Aib‐Tyr‐Ile‐OMe·2H₂O ( 1 ), has been determined directly from powder X‐ray diffraction data. The backbone conformation of tetrapeptide ( 1 ) exhibiting two consecutive β‐turns is stabilized by two 4 → 1 intramolecular N―H · · · O hydrogen bonds. In the crystalline state, the tetrapeptide molecules are assembled through water‐mediated O―H · · · O hydrogen bonds to form two‐dimensional molecular sheets, which are further linked by intermolecular C―H · · · O hydrogen bonds into a three‐dimensional supramolecular framework. The molecular electrostatic potential (MEP) surface of ( 1 ) has been used to supplement the crystallographic observations. The nature of intermolecular interactions in ( 1 ) has been analyzed quantitatively through the Hirshfeld surface and two‐dimensional fingerprint plot. The DFT optimized molecular geometry of ( 1 ) agrees closely with that obtained from the X‐ray structure analysis. The present structure analysis of Boc‐Tyr‐Aib‐Tyr‐Ile‐OMe·2H₂O ( 1 ) represents a case where ab‐initio crystal structure of an acyclic tetrapeptide with considerable molecular flexibility has been accomplished from laboratory X‐ray powder diffraction data. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.     

Ab initio molecular dynamics study of proton transfer in a polyglycine analog of the ion channel gramicidin A.

Proton transfer in biological systems is thought to often proceed through hydrogen-bonded chains of water molecules. The ion channel, gramicidin A (gA), houses within its helical structure just such a chain. Using the density functional theory based ab initio molecular dynamics Car-Parrinello method, the structure and dynamics of proton diffusion through a polyglycine analog of the gA ion channel has been investigated. In the channel, a proton, which is initially present as hydronium (H3O+), rapidly forms a strong hydrogen bond with a nearest neighbor water, yielding a transient H5O2+ complex. As in bulk water, strong hydrogen bonding of this complex to a second neighbor solvation shell is required for proton transfer to occur. Within gA, this second neighbor shell included not only a channel water molecule but also a carbonyl of the channel backbone. The present calculations suggest a transport mechanism in which a priori carbonyl solvation is a requirement for proton transfer.     

Molecular association of betaine and betaine hydrochloride in aqueous solutions – a study by Raman spectroscopy

Raman vibrational spectroscopy, at 298 K, has been used to study the hydration of betaine hydrochloride and betaine in the concentration range 0.5–2 M. The observed changes in the internal vibrations of the solutes, namely, in the CO, COO⁻ and C–H stretchings, and in the components of the O–H stretching band are consonant with anionic water–betaine and betaine hydrochloride dimeric species involving simultaneously hydrogen-bonding between two solute and water molecules. In both cases, betaine hydrochloride and ‘zwitterionic’ betaine behave like structure-makers promoting a larger association in the ‘bulk’ liquid water.     

The state of water in biological systems as studied by proton and deuterium relaxation.

Careful experiments on the measurement of the intensity of the deuterium NMR signal for 2-H2 O in muscle and in its distillate were performed, and they showed that all 2-H2 O muscle is "NMR visible". The spin-lattice relaxation time (T1) of the water protons in the muscle and liver of mice and in egg white has been studied at six frequencies ranging from 4.5 to 6.0 MHz over the temperature range of +37 to --70 degrees C. T1 values of deuterons in 2H2 O of gastrocnemius muscle and liver of mice have been measured at three frequencies (4.5, 9.21 and 15.35 MHz) over the temperature range of +37 to --20 degrees C. Calculations on T1 for both proton and deuteron have been made and compared with the experimental data. It is suggested that the reduction of the T1 values compared to pure water and the frequency dependence of T1 are due to water molecules in the hydration layer of the macromolecules, and that the bulk of water molecules in the biological tissues and egg white undergoes relaxation like ordinary liquid water.     

H/D isotope effects on protein hydration and interaction in solution

An approach has been suggested to study the H/D isotope effect on protein-water and protein-protein intermolecular interactions by determining the content of non-freezing water using low-temperature (1)H NMR in mixed (H2O/D2O) water solutions. Direct data are obtained on the amount of H2O adsorbed (absolute hydration) in presence of the heavy isotope (deuterium D), and isothermals of H2O/D2O fractionation at protein surface groups are presented for temperatures between -10 degrees C and -35 degrees C and solutions of varying composition. The fractionation factor, phi = [x/(1 - x)]/[x(0)/(1 - x(0))], where x and x(0) are the fractions of deuterons in hydration and bulk water, respectively, appeared to be extremely high: phi > 1 at 0.03 < x(0) < 0.10. The high values of phi indicate a decrease in apparent hydration of protein molecules. A probable reason of the effect can be an inter-protein molecular solvent-mediated interaction induced by D2O. The excess of phi over 1 appears to provide a quantitative estimate of the fraction of hydration water affected by such interaction.     

An evaluation of the hydration of lysozyme by an NMR titration method

In this study a new titration method is proposed to study the motional properties of water molecules in conjunction with globular proteins using proton NMR relaxation measurements. The method was applied to the study of the interaction of water with lysozyme and allowed identification of four water fractions-superbound water, polar-bound water, structured water and bulk water - in exchanged equilibrium. The titration demonstrated that 193 water molecules are hydrogen bonded directly to the lysozyme molecule. The combination of structured and bound water extends to 1.4 g H2O per g lysozyme and approx. two to three layers from the surface of the macromolecule. It is proposed that this structured water is related to non-isotropic water rotation in conjunction with hydrophobic patches and directly related to 'hydrophobic bonding' changes. Water amounts greater than 1.4 g H2O per g lysozyme are sufficiently distant from the macromolecule for motion to revert to that typical of water in bulk. The typical correlation times for water motion in the four fraction are: over 10(-6) s (superbound); 10(-9) s (polar bound); 10(-11) s (structured) and 10(-12) s (bulk). These results correlate well with results from other measurement techniques found in the literature.     

Characterisation of germinating and non-germinating wheat seeds by nuclear magnetic resonance (NMR) spectroscopy

Experiments were conducted to characterise the changes, especially of water status in germinating and non-germinating wheat seeds by nuclear magnetic resonance (NMR) spectroscopy. NMR relaxation time (T₂) measurements showed tri-phasic or bi-phasic characteristics during different stages of hydration, depending on the seed's ability to germinate. Component analysis of T₂ data revealed the existence of only two components, bound and bulk water, in dry seeds. In contrast, both the germinating and non-germinating wheat seeds had a three-component water proton system (bound, bulk and free water) in phase I of hydration. During the lag phase (phase II) of hydration, bulk water component of non-germinating seeds disappeared completely, resulting in a two component water proton system. Nevertheless, the three component water proton system was observed in the germinating seeds in phase II. Following phase II, rapid hydration (phase III) was observed in germinating seeds only. Water protons were re-organised and there were increases in bulk and free water but decreases in bound water concomitantly. Comparison of the physical state of water in these seeds by NMR spectroscopy with that of tissue leachate conductivity measurement suggests that the seed membrane system was affected more evidently in non-germinating seeds, leading to the disorganised cell structure. The present study provides evidence that the reorganisation of physical state of water in germinating wheat seeds during hydration is essential for its subsequent event of germination.     

Thermotropic properties of bipolar lipids of Sulfolobus solfataricus and of their mixtures with dipalmitoylphosphatidylcholine

The thermotropic properties of the bipolar lipids, glycerol dialkylglycerol tetraether (GDGT) and glycerol dialkylnonitol tetraether (GDNT), were determined at different degrees of hydration and in mixtures with dipalmitoylphosphatidylcholine (DPPC). The number of water molecules rendered unfreezable by the GDNT molecule is 10+/-1.5 and that by the GDGT molecule 2.8+/-0.7 or about 1.1-1.5 H2O molecules per OH group. Binding of water molecules causes randomization of the two polar heads from the oriented form prevailing in the dry state. The hydration seems to be a cooperative process extending over a whole lipid domain. DPPC added in small amounts to GDNT interacts preferentially with the nonitol halves of the molecules separating them from the glycerol half molecules. In the cooperative interaction domain each DPPC molecule is surrounded by up to six GDNT molecules. Cooperative domains formed during the interaction of DPPC with GDGT are less pronounced. In both cases they affect the thermotropic properties of the system.     

Crystal structures and spectroscopic studies of ternary compounds of Ni(II) with ethylenediamine and 5'GMP and 5'IMP

Two metal complexes [Ni(en)5'GMPH)2(H2O)2] (en).6.5H2O and [Ni(en)(5'IMPH)2(H2O)2].13H2O have been synthesized in the form of suitable crystals for x-ray crystallography (en = ethylenediamine, 5'GMP = guanosine 5'-monophosphate, 5'IMP = inosine 5'-monophosphate). The 5'GMP complex crystallizes in a monoclinic space group P21 (Z = 4) with a = 12.317(2), b = 28.417(4), c = 12.290(2)A, beta (deg) = 89.59(2). The 5'IMP complex is tetragonal, space group P4122 (Z = 4), with a = 12.119(3), b = 12.119(3), c = 28.560(4)A, beta (deg) = 90.0. The crystal structures of both complexes were refined from diffractometer data to conventional R values of 0.073 for the 5'GMP compound (5,284 observed reflections, 1,322 variables) and 0.030 for the 5'-IMP compound (1,529 observed reflections, 296 variables). In both structures, the Ni(II) is surrounded by two water molecules, one chelate ethylenediamine, and two nucleotide molecules. The synthesis was carried out from Ni(en)2Cl2.0.5H2O and the nucleotide in water medium. The dimer structure of the initial complex is broken, and one ethylenediamine is substituted by two molecules of the nucleotide with the N(7) of the purine ring in cis-position. Differences between both structures are largely due to retention in the structure or loss of the en molecule substituted and to the intermolecular hydrogen bonds of the en molecule coordinated. A third complex of composition [Ni(en)(5'IMPH)2(H2O)2] (en).6H2O similar to the 5'GMP complex has been obtained in the form of blue crystals, but unfortunately its crystal structure failed to be refined. This complex is isostructural with the monoclinic one.