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.     

Solution nonideality related to solute molecular characteristics of amino acids.

By measuring the freezing-point depression for dilute, aqueous solutions of all water-soluble amino acids, we test the hypothesis that nonideality in aqueous solutions is due to solute-induced water structuring near hydrophobic surfaces and solute-induced water destructuring in the dipolar electric fields generated by the solute. Nonideality is expressed with a single solute/solvent interaction parameter I, calculated from experimental measure of delta T. A related parameter, I(n), gives a method of directly relating solute characteristics to solute-induced water structuring or destructuring. I(n)-values correlate directly with hydrophobic surface area and inversely with dipolar strength. By comparing the nonideality of amino acids with progressively larger hydrophobic side chains, structuring is shown to increase with hydrophobic surface area at a rate of one perturbed water molecule per 8.8 square angstroms, implying monolayer coverage. Destructuring is attributed to dielectric realignment as described by the Debye-Hückel theory, but with a constant separation of charges in the amino-carboxyl dipole. By using dimers and trimers of glycine and alanine, this destructuring is shown to increase with increasing dipole strength using increased separation of fixed dipolar charges. The capacity to predict nonideal solution behavior on the basis of amino acid characteristics will permit prediction of free energy of transfer to water, which may help predict the energetics of folding and unfolding of proteins based on the characteristics of constituent amino acids.     

Osmotically unresponsive water fraction on proteins: non-ideal osmotic pressure of bovine serum albumin as a function of pH and salt concentration

How much does protein-associated water differ in colligative properties (freezing point, boiling point, vapor pressure and osmotic behavior) from pure bulk water? This question was approached by studying the globular protein bovine serum albumin (BSA), using changes in pH and salt concentration to alter its native structural conformation and state of aggregation. BSA osmotic pressure was investigated experimentally and analyzed using the molecular model of Fullerton et al. [Biochem Cell Biol 1992;70(12):1325]. Analysis yielded both the extent of osmotically unresponsive water (OUW) and the effective molecular weight values of the membrane-impermeable BSA solute. Manipulation of BSA conformation and aggregation by membrane-penetrating cosolutes show that alterations in pH and salt concentration change the amount of bulk water that escapes into BSA from a minimum of 1.4 to a maximum of 11.7 g water per g dry mass BSA.     

Effective interactions between chaotropic agents and proteins

Chaotropic agents are cosolutes that can disrupt the hydrogen bonding network between water molecules and reduce the stability of the native state of proteins by weakening the hydrophobic effect. In this work, we represent the chaotropic agent as a factor that reduces the amount of order in the structures formed by water molecules, both in the bulk and the hydration shells around hydrophobic amino acids. In this framework we show that low chaotrope concentrations lead to a destabilization of the native state of proteins, and that high concentrations induce complete denaturation. We also find that the reduction of the number of bulk ordered states of water molecules can give origin to an effective interaction between chaotropic molecules and proteins.     

Thermodynamics of some nucleic acid bases and nucleosides in water, and their transfer to aqueous glucose and sucrose solutions at 298.15 K

The partial molar heat capacities and volumes of some of the constituents of nucleic acids have been determined in water and 1 molal aqueous glucose and sucrose solutions in order to elucidate the nature of interactions occurring between various nucleic acid bases, nucleosides and the sugar (glucose and sucrose) molecules. The results have been explained in terms of the contributions from hydrophobic interactions, hydrophilic interactions and the hydrogen bonding between the solute and solvent molecules. The results have also been compared with those of amino acids and peptides in aqueous glucose and sucrose solutions.     

On the osmotically unresponsive water compartment in cells

Differences in colligative properties (freezing point, boiling point, vapor pressure and osmotic behavior) between water in living cells and pure bulk water were investigated by re-evaluating reports of the osmotic behavior of mammalian cells. In five different animal cells, osmotically unresponsive water (OUW) values ranged from 1.1 to 2.2 g per g dry mass. Detailed analysis of human red blood cell (RBC) data indicates a major role for hemoglobin OUW-values, aggregation and packing in cell volume regulation that can be explained for the first time in relevant molecular terms.     

Conformational changes of peptides at solid/liquid interfaces: a Monte Carlo study

Monte Carlo simulations were performed to study the conformational changes of negatively charged model peptides dissolved in water adsorbed onto charged surfaces. 8-, 16-, and 20-residues peptides were used, each of them consisted of repeating diblock units of aspartic acid (ASP, polar amino acid) and isoleucine (ILE, nonpolar amino acid) residues. We found that a water patch was retained at the charged surface, separating the peptide from it. We believed that these water molecules were primarily responsible for giving a particular orientation to the peptide at the surface. Water did play a role to some extent in the structural stability of the 8-residues peptide. However, for higher chain lengths (16-residues and 20-residues), the intrinsic hydrogen-bonding network (or intrinsic structural stability) showed a predominant effect over hydrophobic dehydration for the stability of the peptide at the surface.     

Molecular dynamics simulations of water within models of ion channels.

The transbilayer pores formed by ion channel proteins contain extended columns of water molecules. The dynamic properties of such waters have been suggested to differ from those of water in its bulk state. Molecular dynamics simulations of ion channel models solvated within and at the mouths of their pores are used to investigate the dynamics and structure of intra-pore water. Three classes of channel model are investigated: a) parallel bundles of hydrophobic (Ala20) alpha-helices; b) eight-stranded hydrophobic (Ala10) antiparallel beta-barrels; and c) parallel bundles of amphipathic alpha-helices (namely, delta-toxin, alamethicin, and nicotinic acetylcholine receptor M2 helix). The self-diffusion coefficients of water molecules within the pores are reduced significantly relative to bulk water in all of the models. Water rotational reorientation rates are also reduced within the pores, particularly in those pores formed by alpha-helix bundles. In the narrowest pore (that of the Ala20 pentameric helix bundle) self-diffusion coefficients and reorientation rates of intra-pore waters are reduced by approximately an order of magnitude relative to bulk solvent. In Ala20 helix bundles the water dipoles orient antiparallel to the helix dipoles. Such dipole/dipole interaction between water and pore may explain how water-filled ion channels may be formed by hydrophobic helices. In the bundles of amphipathic helices the orientation of water dipoles is modulated by the presence of charged side chains. No preferential orientation of water dipoles relative to the pore axis is observed in the hydrophobic beta-barrel models.     

Picosecond-resolved solvent reorganization and energy transfer in biological and model cavities

Water molecules in hydrophobic biological cleft/cavities are of contemporary interest for the biomolecular structure and molecular recognition of hydrophobic ligands/drugs. Here, we have explored picosecond-resolved solvation dynamics of water molecules and associated polar amino acids in the hydrophobic cleft around Cys-34 position of Endogenous Serum Albumin (ESA). While site selective acrylodan labeling to Cys-34 allows us to probe solvation in the cleft, Förster resonance energy transfer (FRET) from intrinsic fluorescent amino acid Trp 214 to the extrinsic acrylodan probes structural integrity of the protein in our experimental condition. Temperature dependent solvation in the cleft clearly shows that the dynamics follows Arrhenius type behavior up to 60 °C, after which a major structural perturbation of the protein is evident. We have also monitored polarization gated dynamics of the acrylodan probe and FRET from Trp 214 to acrylodan at various temperatures. The dynamical behavior of the immediate environments around the probe acrylodan in the cleft has been compared with a model biomimetic cavity of a reverse micelle (w₀ = 5). Using same fluorescent probe of acrylodan, we have checked the structural integrity of the model cavity at various temperatures using picosecond-resolved FRET from Trp to acrylodan in the cavity. We have also estimated possible distribution of donor-acceptor distances in the protein and reverse micelles. Our studies reveal that the energetics of the water molecules in the biological cleft is comparable to that in the model cavity indicating a transition from bound state to quasibound state, closely consistent with a recent MD simulation study.     

The molecular stoichiometric hydration model (SHM) as applied to tendon/collagen, globular proteins and cells

This report describes and documents the presence of multiple water-of-hydration fractions on proteins and in cells. Initial studies of hydration fractions in g of water/g of DM (dry mass) for tendon/collagen led to the development of the molecular SHM (stoichiometric hydration model) and the development of methods for calculating the size of hydration fractions on a number of different proteins of known amino acid composition. The water fractions have differences in molecular motion and other physical properties due to electrostatic interactions of polar water molecules with electric fields generated by covalently bound pairs of opposite partial charge on the protein backbone. The methods allow calculation of the size of four hydration fractions: single water bridges, double water bridges, dielectric water clusters over polar-hydrophilic surfaces and water clusters over hydrophobic surfaces. These four fractions provide monolayer water coverage. The predicted SHM hydration fractions match closely measured hydration fraction values for collagen and for globular proteins. This report also presents water sorption findings that support the SHM. The SHM is applicable for cell systems where it has been studied. In seven cell systems studied, more than half of all of the cell water had properties unlike those of bulk water. The SHM predicts and explains the commonly cited and measured bound water fraction of 0.2-0.4 g of water/g of DM on proteins. The commonly accepted concept that water beyond this bound water fraction can be considered bulk-like water in its physical properties is unwarranted.     

Prebiotic phosphate: a problem insoluble in water ? ]

It is well-known that in water phosphate readily reacts with calcium, precipitating as insoluble apatite. How phosphorus could have been available for prebiotic reactions is still an open problem. We suggest that phosphorus-containing compounds might have accumulated in a hydrophobic medium, since the absence of calcium ions would have prevented them from precipitating as apatite. Hydrophobic compounds may have been synthesized on the early Earth through the polymerization of methane or through Fischer-Tropsch-type reactions. Moreover, hydrophobic compounds would have been delivered to the early Earth by extraterrestrial infall. In previous articles (Morchio and Traverso [1999], Morchio et al. [2001]) we suggested that such hydrophobic material would have formed a hydrophobic layer on the surface of the sea, which would have provided an environment thermodynamically more suitable than water for the concentration and polymerization of organic molecules fundamental to life, particularly amino acids and (pyrimidine) bases. It may be hypothesized that elemental phosphorus or phosphorus-containing compounds (such as phosphite) deriving from volcanic eruptions would have ended up raining down into the hydrophobic layer, accumulating due to the absence of calcium ions, in an environment protected against hydrolysis. Phosphorus-containing compounds might have interacted with hydrophobic molecules in the layer giving rise to polymers. In particular, phosphite might have reacted with the hydrophobic amino acids, giving rise to phosphoamino acids, which, in turn, might have interacted with pyrimidine bases (relatively abundant in the layer) giving rise to peptides and oligonucleotide-like polymers. Indeed, it has been experimentally shown (Zhou et al. [1996]) that, in an anhydrous organic medium (pyridine), dialkilphosphite reacts with amino acids to form phosphoamino acids, which interact with pyrimidine nucleosides to give nucleotides, short oligonucleotides and phosphoryl peptides.     

Hydration enthalpy characteristics of amino acids in solutions

The enthalpies of solvation of 17 amino acids were evaluated by using the sublimation enthalpies of amino acids and the standard enthalpies of their solution in water. An equation was derived, which relates the volume-specific enthalpy of sublimation (deltaH(subl)/V(w)) to the sum of the common bond lengths in molecules (sigman(i)l(i)) of substances examined. The results obtained are interpreted in terms of the effect of hydrophobic and hydrophilic side chain on the interactions between the zwitterions of amino acids and water molecules.     

Computer simulation of hydration networks around amino acids

The networks of solvent hydrogen bonds around polar and apolar amino acids have been studied by computer simulation techniques using a non-pair additive model for the water molecules interactions. Analysis of the simulated aqueous solutions has shown the presence of water molecules which (a) form a bridge around individual polar solute atoms (self-bridging loops) and (b) form chains between different polar solute atoms (polar bridging chains). Some of these networks associated with polar solute atoms from pentagons but 4, 6 and 7 sided polygons are also seen. The water molecule close to apolar solute atoms (<4.0 Å) also form irregular networks with polygons of 4, 5, 6 and 7 sides. These networks are compared with those found experimentally in ice, clathrates and crystal hydrates of macromolecules.     

Preferential interaction of pentagastrin with the gel state of dimyristoyl glycerophosphocholine

Fluorescence and circular dichroism spectra indicate that pentagestrin interacts with dimyristoyl glycerophosphocholine more strongly below the phase transition temperature of the lipid than above it. Studies on the interaction of several peptides with dimyristoyl glycerophosphocholine suggest that this property may be related to the ability of these peptides to form amphipathic structures containing two hydrophobic amino acids separated by two other amino acids. Pentagastrin has a marked effect on the proton magnetic resonance spectra of dipalmitoyl glycerophosphocholine below the phase transition temperature indicating that the peptide decreases the motional freedom of the lipid.     

Cyclo-hexa-peptides at the water/cyclohexane interface: a molecular dynamics simulation

Molecular dynamic (MD) simulations have been performed to study the behaviors of ten kinds of cyclo-hexa-peptides (CHPs) composed of amino acids with the diverse hydrophilic/hydrophobic side chains at the water/cyclohexane interface. All the CHPs take the “horse-saddle” conformations at the interface and the hydrophilicity/hydrophobicity of the side chains influences the backbones’ structural deformations. The orientations and distributions of the CHPs at the interface and the differences of interaction energies (ΔΔE) between the CHPs and the two liquid phases have been determined. RDF analysis shows that the H-bonds were formed between the O_C atoms of the CHPs’ backbones and H_w atoms of water molecules. N atoms of the CHPs’ backbones formed the H-bonds or van der Waals interactions with the water solvent. It was found that there is a parallel relationship between ΔΔE and the lateral diffusion coefficients (D _xy ) of the CHPs at the interface. The movements of water molecules close to the interface are confined to some extent, indicating that the dynamics of the CHPs and interfacial water molecules are strongly coupled.

Evaluation of selectivity changes in HIC systems using a preferential interaction based analysis

It is well established that salt enhances the interaction between solutes (e.g., proteins, displacers) and the weak hydrophobic ligands in hydrophobic interaction chromatography (HIC) and that various salts (e.g., kosmotropes, chaotropes, and neutral) have different effects on protein retention. In this article, the solute affinity in kosmotropic, chaotropic, and neutral mobile phases are compared and the selectivity of solutes in the presence of these salts is examined. Since solute binding in HIC systems is driven by the release of water molecules, the total number of released water molecules in the presence of various types of salts was calculated using the preferential interaction theory. Chromatographic retention times and selectivity reversals of both proteins and displacers were found to be consistent with the total number of released water molecules. Finally, the solute surface hydrophobicity was also found to have a significant effect on its retention in HIC systems.     

Distribution of amino acids in a lipid bilayer from computer simulations

We have calculated the distribution in a lipid bilayer of small molecules mimicking 17 natural amino acids in atomistic detail by molecular dynamics simulation. We considered both charged and uncharged forms for Lys, Arg, Glu, and Asp. The results give detailed insight in the molecular basis of the preferred location and orientation of each side chain as well the preferred charge state for ionizable residues. Partitioning of charged and polar side chains is accompanied by water defects connecting the side chains to bulk water. These water defects dominate the energetic of partitioning, rather than simple partitioning between water and a hydrophobic phase. Lys, Glu, and Asp become uncharged well before reaching the center of the membrane, but Arg may be either charged or uncharged at the center of the membrane. Phe has a broad distribution in the membrane but Trp and Tyr localize strongly to the interfacial region. The distributions are useful for the development of coarse-grained and implicit membrane potentials for simulation and structure prediction. We discuss the relationship between the distribution in membranes, bulk partitioning to cyclohexane, and several amino acid hydrophobicity scales.     

CHANGES OF AMINO ACID COMPOSITION OF CHLORELLA CELLS DURING THEIR LIFE CYCLE

The cells of Chlorella ellipsoidea were grown synchronously,and at different stages of their life cycle, the cells wereanalysed for their contents in amino acids existing in freeforms as well as in the fractions of bulk protein and peptides.Throughout the algal life cycle, the content of bulk protein(per unit dry weight of cells) remained relatively constant,being about 20 to 40 times those of peptides and free aminoacids. The amino acid composition of the protein fraction alsoremained fairly constant, the predominant amino acids beingalanine, glutamic acid, glycine and leucine. The contents inthe bulk peptides increased appreciably during the periods ofgrowth and "ripening" (light period), and decreased markedlyduring the periods of "post-ripening" and cellular division(dark period). Similar modes of change in content were alsoobserved in most of the individual amino acids contained inthe peptide fraction. The most abundant component in the peptidefraction was arginine followed by glutamic acid, glycine andcyst(e)ine. Rather irregular was the mode of change of the levelsof individual free amino acids, although, as a whole, theirbehavior was similar to that of bulk peptides, increasing duringthe light period and decreasing during the dark period. Themost predominant free amino acids were glutamic acid and alaninefollowed by proline. Experimental evidence showed that the processes of formationof free amino acids and peptides are for the most part lightdependent, while the synthesis of protein, which is thoughtto be effected using as building blocks mostly free amino acids—formeddirectly or indirectly from early photosynthates or derivedfrom pre-formed peptides—is essentially a light-independentprocess. Peptides, as a whole, seem to have significance asreservoirs of building blocks for the syntheses in the darkof protein and other nitrogenous cellular substances. The synthesisof protein in the dark takes place not only by consuming thefree amino acids and peptides that have been accumulated duringthe light period, but also by assimilating the exogenous nitrogensource (nitrate). The distribution of individual amino acidsin the three main fractions mentioned above as it changed duringthe course of algal cell cycle was followed in detail, and theresults obtained were discussed in relation to various relevantdata reported by other workers. (Received June 29, 1964; )     

Spin-label studies on the aqueous regions of phospholipid multilayers.

Water-soluble spin labels were used to study dimyristoyllecithin (DML) phospholipid multilayers. Previous studies report that there is a "bound" water region associated with dimyristoyllecithin containing about 10 molecules of water per phospholipid, a "trapped" water region located between the lamellae containing approximately 11 molecules per phospholipid, and a "ftion show that certain water-soluble spin-label mol-cules have their motional properties differentially modified by these three water environements. Furthermore, the labels also reveal the onset of lipid-phase transitions even though they have high water solubility. A phosphate-containing spin label demonstrated strong an isotropic motion in the lipid-water system above the phase transition but not below. The addition of cholesterol to the DML-water system removed the anisotropic motion of 2,2,6,6-tetramehtyl-4-phosphopiperidine-N-oxyl (Tempophosphate) and obscured the detection bound, trapped, and free water. In addition to the change-charge interactions between Tempophosphate and DML, two other spin labels were used both in the charged and uncharged states. 2,2,6,6-Tetramethyl-4-aminopiperidine-N-oxyl (Tempamine) in the charged state showed extremely strong anisotropic motion, presumably due to the interaction between the charged amine and the phosphate group of DML. When only partially charged, Tempamine showed much less anisotropic motion. PCA was analyzed at pH values where the carboxyl group was protonated and unprotonated. The resulting interaction was different at the two pH values. These water-soluble spin labels mimic ionic or nonionic solutes. Upon freezing, the spin labels are shown to be expelled from the ice regions into the remaining aqueous regions. The usefulness of this approach in studying solute behavior when freezing occurs and potential studies involving aqueous regions of cytoplasm are considered.     

Electron spin-echo studies of spin-labelled lipid membranes and free fatty acids interacting with human serum albumin

Human serum albumin (HSA) is an abundant plasma protein that transports fatty acids and also binds a wide variety of hydrophobic pharmacores. Echo-detected (ED) EPR spectra and D₂O-electron spin echo envelope modulation (ESEEM) Fourier-transform spectra of spin-labelled free fatty acids and phospholipids were used jointly to investigate the binding of stearic acid to HSA and the adsorption of the protein on dipalmitoyl phosphatidylcholine (DPPC) membranes. In membranes, torsional librations are detected in the ED-spectra, the intensity of which depends on chain position at low temperature. Water penetration into the membrane is seen in the D₂O-ESEEM spectra, the intensity of which decreases greatly at the middle of the membrane. Both the chain librational motion and the water penetration are only little affected by adsorption of serum albumin at the DPPC membrane surface. In contrast, both the librational motion and the accessibility of the chains to water are very different in the hydrophobic fatty acid binding sites of HSA from those in membranes. Indeed, the librational motion of bound fatty acids is suppressed at low temperature, and is similar for the different chain positions, at all temperatures. Correspondingly, all segments of the bound chains are accessible to water, to rather similar extents.