A MECHANISTIC VIEW OF THE NON-IDEAL OSMOTIC AND MOTIONAL BEHAVIOR OF INTRACELLULAR WATER

It is commonly assumed that essentially all of the water in cells has the same ideal motional and colligative properties as does water in bulk liquid state. This assumption is used in studies of volume regulation, transmembrane movement of solutes and electrical potentials, solute and solution motion, solute solubility and other phenomena. To get at the extent and the source of non-ideally behaved water (an operational term dependent on the measurement method), we studied the motional and colligative properties of water in cells, in solutions of amino acids and glycine peptides whose surface characteristics are known, and in solution of bovine serum albumin, hemoglobin and some synthetic polypeptides. Solutions of individual amino acids with progressively larger hydrophobic side chains showed one perturbed water molecule (structured-slowed in motion) per nine square angstroms of hydrophobic surface area. Water molecules adjacent to hydrophobic surfaces form pentagonal structural arrays, as shown by X-ray diffraction studies, that are reported to be disrupted by heat, electric field, hydrostatic pressure and phosphorylation state. Hydrophilic amino acids demonstrated water destructuring (increased motion) that was attributed to dielectric realignment of dipolar water molecules in the electric field between charge groups. In solutions of proteins, several methods indicate the equivalent of 2–8 layers of structured water molecules extending beyond the protein surface, and we have recently demonstrated that induced protein conformational change modifies the extent of non-ideally behaved water. Water self-diffusion rate as measured in three different cell types was about half that of bulk water, indicating that most of the water in these cells was slower in motion than bulk water. In different cell types the extent of osmotically perturbed water ranged from less than half to almost all of the intracellular water. The assumption that essentially all intracellular water has ideal osmotic and motional behavior is not supported by the experimental findings. The non-ideality of cell water is an operational term. Therefore, the amount of non-ideally behaving water is dependent on the characteristics of water targeted, i.e. the measurement method, and a large fraction of it is explainable in mechanistic terms at a molecular level based on solute—solvent interactions.     

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.     

Amino acid/water interactions study: a new amino acid scale

Partition ratios of 8 free l-amino acids (Gln, Glu, His, Lys, Met, Ser, Thr, and Tyr) were measured in 10 different polymer/polymer aqueous two-phase systems containing 0.15?M NaCl in 0.01?M phosphate buffer, pH 7.4. The solute-specific coefficients representing the solute dipole/dipole, hydrogen-bonding and electrostatic interactions with the aqueous environment of the amino acids were determined by multiple linear regression analysis using a modified linear solvation energy relationship. The solute-specific coefficients determined in this study together with the solute-specific coefficients reported previously for amino acids with non-polar side-chains where used in a Quantitative Structure/Property Relationship analysis. It is shown that linear combinations of these solute-specific coefficients are correlated well with various physicochemical, structural, and biological properties of amino acids.     

Separation of amino acids and peptides by temperature induced phase partitioning. Theoretical model for partitioning and experimental data

There is a strong interest in use of ‘smart polymers’ in separation systems. These are polymers which can react on external influence, such as temperature or pH change. With such polymers it is possible from the outside to affect the properties of a separation system. Amphiphilic copolymers show drastic changes in solubility properties, such as self-association and phase separation, at e.g. temperature increase. The random copolymers of ethylene oxide and propylene oxide units (EOPO-polymers) can form aqueous two-phase systems above the copolymer cloud point temperature. Two phases are formed, one consisting of 40–60% polymer in water and the other of almost 100% water. Amino acids and peptides can be partitioned in the thermoseparating systems. The partitioning strongly depends on the solute hydrophobicity, where aromatic amino acids and peptides are partitioned to the polymer phase and hydrophilic to the water phase. Salt effects can be used to enhance the partitioning of charged molecules. The thermodynamic driving forces which govern the partitioning of molecules in a thermoseparated aqueous phase system is described with use of the Flory-Huggins theory for polymer solutions. Expressions are derived which show the entropic and enthalpic effects on solute partitioning. This revised version was published online in July 2006 with corrections to the Cover Date.     

Strategies for the recovery of chemicals from fermentation: a review of the use of polymeric adsorbents.

Many different compounds can be produced by using microorganisms or enzymes. An important element in the design of a viable biotechnological process is the selection of an economical and efficient separations train. Production of chemicals via biotechnology generally requires isolation and purification from dilute, aqueous solution. A general framework for separation process design relies on exploiting a unique molecular physicochemical property (or properties) for separating the molecule of interest from water and the other species in solution. Important properties that can be utilized for the recovery of low molecular weight polar compounds are molecular charge, hydrophobicity, Lewis acidity or basicity, volatility, and limited solubility. In turn, it can be useful to characterize molecular properties by using separation processes, such as, for example, hydrophobicity by measuring octanol/water partition coefficients. This paper reviews the use of adsorption onto hydrophobic, nonpolar macroreticular polymers and Lewis acid-base complexation by using functionalized polymers for the recovery of amino acids, carboxylic acids, alcohols, and ketones from dilute aqueous solution. The focus will be on utilizing physical and chemical properties to predict uptake capacity. This information will be relevant to separation process development and will help to characterize molecular properties in aqueous solution.     

Effect of the concentration of DODMAC and 1-decanol on the behavior of reverse micelles in the extraction of amino acids

The concentrations of dioctyldimethyl ammonium chloride (DODMAC) and 1-decanol in isooctane needed to form reverse micelles by phase contact have been determined. The behavior of these reverse micelles in the extraction of aspartic acid, glutamic acid, and threonine was studied by analyzing all of the ionic species in the aqueous phase. The amino acid is extracted from the aqueous phase by exchanging with the Cl(-) counterions of DODMAC in the reverse micelles. The ionic species in the reverse micelles tend toward their undissociated states as the water uptake by the reverse micelles decreases. The effect of 1-decanol on the extraction of the amino acids with two negative charges is due to the change in the water uptake of the reverse micelles. The concentration of DODMAC has no effect on the ion exchange of the amino acid with one negative charge with the Cl(-) counterions of DODMAC in the reverse micelles. Higher molar ratios of decanol to DODMAC favor the selective separation of amino acids with different charge numbers. (c) 1995 John Wiley & Sons, Inc.     

High-performance liquid chromatography of platinum complexes on solvent generated anion exchangers : III. Application to the analysis of cisplatin in urine using automated column switching

Platinum complexes are retained on solvent generated anion exchangers, prepared by coating reversed-phase (C-18) supports with a monolayer of hexadecyltrimethylammonium bromide. The retention mechanism is described in terms of ion—dipole interactions in the stationary phase, reinforced by a hydrophobic effect. The high degree of ligand selectivity exhibited by these systems arises from the use of purely aqueous mobile phases which maximize the differences in solute dipole and hydrophobic surface area. By using stationary phases of different surface characteristics and the application of automated column switching, the technique is applicable to the clinical analysis of cisplatin in urine. After chromatography, the purified cisplatin fractions are determined by atomic absorption spectrophotometry. The recovery of cisplatin from urine is 101.1% with a relative standard deviation of 3.6% and the limit of detection is 2 μg/ml.     

New expressions to describe solution nonideal osmotic pressure, freezing point depression, and vapor pressure.

New empirical expressions for osmotic pressure, freezing point depression, and vapor pressure are proposed based on the concepts of volume occupancy and (or) hydration force. These expressions are in general inverse relationships in comparison to the standard ideal expressions for the same properties. The slopes of the new equations are determined by the molecular weight of the solute and known constants. The accuracy and precision of the molecular weights calculated from the slope are identical and approximately 1% for the experiments reported here. The nonideality of all three colligative expressions is described by a dimensionless constant called the solute-solvent interaction parameter I. The results on sucrose have the same I = 0.26 for all three solution properties. The nonideality parameter I increased from 0.26 on sucrose to 1.7 on hemoglobin to successfully describe the well-known nonideal response of macromolecules.     

The influence of hydrophobic ions and dipolar molecules on the electrostatic barrier in biomembranes

To calculate the electric field inside a membrane the aqueous phase can be approximated by a conductor since the dielectric constant of water is much larger than that of the membrane. Then, using the method of image charges, ions adsorbed inside the membrane can be considered as dipoles and dipolar molecules adsorbed inside the membrane may similarly be regarded as sets of two similarly oriented dipoles. The microscopic interactions and, therefore, the spatial correlations of the adsorbed species can then be obtained. Together with the Gouy theory for the diffuse double layer these results allow the determination of the adsorbed phase—aqueous phase equilibrium. From the densities and spatial correlations of the adsorbed ions and dipolar species, their influence upon the electrostatic barrier as experienced by an ion translocating the membrane can be calculated. Changes observed in the relaxation time and initial conductance of translocating hydrophobic ions in voltage-pulse experiments on bilayer membranes are predicted using this model of the electrostatic barrier. In addition, an equation giving the surface tension as a function of the (non-ideal) adsorption of hydrophobic ions and dipoles is derived.     

Integral equation theories for predicting water structure around molecules

Water plays a crucial role in the structure and function of proteins and other biological macromolecules; thus, theories of aqueous solvation for these molecules are of great importance. However, water is a complex solvent whose properties are still not completely understood. Statistical mechanical integral equation theories predict the density distribution of water molecules around a solute so that all particles are fully represented and thus potentially both molecular and macroscopic properties are included. Here we discuss how several theoretical tools we have developed have been integrated into an integral equation theory designed for globular macromolecular solutes such as proteins. Our approach predicts the three-dimensional spatial and orientational distribution of water molecules around a solute. Beginning with a three-dimensional Ornstein-Zernike equation, a separation is made between a reference part dependent only on the spatial distribution of solvent and a perturbation part dependent also on the orientational distribution of solvent. The spatial part is treated at a molecular level by a modified hypernetted chain closure whereas the orientational part is treated as a Boltzmann prefactor using a quasi-continuum theory we developed for solvation of simple ions. A potential energy function for water molecules is also needed and the sticky dipole models of water, such as our recently developed soft-sticky dipole (SSD) model, are ideal for the proposed separation. Moreover, SSD water is as good as or better than three point models typically used for simulations of biological macromolecules in structural, dielectric and dynamics properties and yet is seven times faster in Monte Carlo and four times faster in molecular dynamics simulations. Since our integral equation theory accurately predicts results from Monte Carlo simulations for solvation of a variety of test cases from a single water or ion to ice-like clusters and ion pairs, the application of this theory to biological macromolecules is promising.     

Thermodynamic elucidation of solute-induced lipid interdigitation phase: lipid interactions with hydrophobic versus amphipathic species.

Comparative thermodynamic studies on the interactions of aqueous dispersions of dipalmitoyl phosphatidylcholine (DPPC) bilayer vesicles with hydrophobic and amphipathic species were conducted to elucidate the nature of the solute-induced interdigitated lipid phase. Cyclohexanol, a strong hydrophobic species, lowers the temperature (tm) of the lipid main phase transition from the gel to the liquid-crystalline phase. Unlike ethanol (an amphipathic species), as reported previously, cyclohexanol does not exert a biphasic effect on tm (lowering tm at lower concentrations and raising tm at higher concentrations). At cyclohexanol greater than or equal to 15.4 mg/ml or 0.154 M, the thermogram of DPPC vesicles exhibits a small transition adjacent to the main phase transition but at a lower temperature. In contrast, ethanol does not promote such a small transition. Furthermore, the enthalpy (delta H) of the transition is increased in the presence of cyclohexanol. The sign of the enthalpy change (delta H-delta Ho) is positive and that of the free energy change (delta G-delta Go) is negative, a characteristic of solute-solute hydrophobic interaction. In contrast, DPPC bilayer vesicles exhibit both (delta H-delta Ho) and (delta G-delta Go) greater than 0 in the presence of ethanol in a concentration range where lipid vesicles exist in an interdigitated phase. To support the above distinct thermodynamic observations, fluorescence steady-state polarization (P) measurements were also performed. At the temperature below tm, the value of P decreases as cyclohexanol concentration increases, while a biphasic effect on P was found in the presence of ethanol. These findings support the postulation that the solute-induced interdigitated lipid phase requires the solute molecule to be amphipathic in nature.     

The apolar surface area of amino acids and its empirical correlation with hydrophobic free energy

A linear equation is presented which accounts quantitatively for the free energy of transfer of amino acids from water to apolar solvent as a function of accessible surface area and partial charges of the constituents of amino acids. Starting from these parameters the apolar surface area is defined and correlated with the measured free transfer energy. The resulting linear correlation makes it possible to calculate more precisely the "hydrophobic" contribution of both apolar and polar groups including uncharged side chains of arginine, lysine, glutamic and aspartic acids, and histidine, respectively, to protein stabilization.     

Hybridization-displaced charges for amino-acids: a new model using two point charges per atom along with bond-center charges

A new charge distribution is proposed for the amino acids where each atom is associated with two point charges while each bond center is associated with one point charge. Centroids of charges arising due to atomic orbital hybridization called hybridization-displaced charges (HDC) and those located at the atomic sites and bond centers obtained by a modified form of the Mulliken scheme were combined. The density matrix calculations required for this analysis were performed at the B3LYP/6-31G** level of density functional theory. The combination of HDC centroids with the modified Mulliken charges was found to yield dipole moments and surface molecular electrostatic potentials (MEP) of the amino acids in good agreement with those obtained by rigorous DFT calculations or those obtained using the MEP-fitted CHelpG charges. This study shows that the combination of HDC centroids with the modified Mulliken charges is significantly superior to the conventional Mulliken charges.     

Compartmentalization of amino acids in surfactant aggregates

Cationic amino acids, arginine and lysine partition differentially from water into aqueous micellar sodium dodecanoate. Conversely, partitioning of serine, glycine, aspartic acid, glutamic acid, threonine, alanine, proline, valine, leucine, phenylalanine and isoleucine do not vary appreciably. Partitioning from neat hexane into dodecylammonium propionate trapped water in hexane is, however, dependent upon both electrostatic and hydrophobic interactions. These results imply that the interior of dedecylammonium propionate aggregates is negatively charged and is capable of hydrogen bonding in addition to providing a hydrophobic enviroment. The solubilities of amino acids in neat hexane substantiate the previously derived amino acid hydrophobicity scale. Relevance of partitioning in these systems to the postulated selective amino acid compartmentalization is discussed.     

Peptide synthesis catalyzed by polyethylene glycol-modified chymotrypsin in organic solvents

Chymotrypsin modified with polyethylene glycol was successfully used for peptide synthesis in organic solvents. The benzene-soluble modified enzyme readily catalyzed both aminolysis of N-benzoyl-L-tyrosine p-nitroanilide and synthesis of N-benzoyl-L-tyrosine butylamide in the presence of trace amounts of water. A quantitative reaction was obtained when either hydrophobic or bulky amides of L- as well as D-amino acids were used as acceptor nucleophiles, while almost no reaction occurred with free amino acids or ester derivatives. The acceptor nucleophile specificity of modified chymotrypsin as a catalyst in the formation of both amide and peptide bonds in organic solvents was quite comparable to that in aqueous solution as well as to that of the leaving group in hydrolysis reactions. By contrast, the substrate specificity of modified chymotrypsin in organic solvents was different from that in water since arginine and lysine esters were found to be as effective as aromatic amino acids to form the acyl-enzyme with subsequent synthesis of a peptide bond.     

Exploring the role of hydrophilic amino acids in unfolding of protein in aqueous ethanol solution

Hydrophobic association is the key contributor behind the formation of well packed core of a protein which is often believed to be an important step for folding from an unfolded chain to its compact functional form. While most of the protein folding/unfolding studies have evaluated the changes in the hydrophobic interactions during chemical denaturation, the role of hydrophilic amino acids in such processes are not discussed in detail. Here we report the role of the hydrophilic amino acids behind ethanol induced unfolding of protein. Using free energy simulations, we show that chicken villin head piece (HP‐36) protein unfolds gradually in presence of water‐ethanol binary mixture with increasing composition of ethanol. However, upon mutation of hydrophilic amino acids by glycine while keeping the hydrophobic amino acids intact, the compact state of the protein is found to be stable at all compositions with gradual flattening of the free energy landscape upon increasing compositions. The local environment around the protein in terms of ethanol/water number significantly differs in wild type protein compared to the mutated protein. The calculated Wyman‐Tanford preferential binding coefficient of ethanol for wild type protein reveals that a greater number of cosolutes (here ethanol) bind to the unfolded state compared to its folded state. However, no significant increase in binding coefficient of ethanol at the unfolded state is found for mutated protein. Local‐bulk partition coefficient calculation also suggests similar scenarios. Our results reveal that the weakening of hydrophobic interactions in aqueous ethanol solution along with larger preferential binding of ethanol to the unfolded state mediated by hydrophilic amino acids combinedly helps unfolding of protein in aqueous ethanol solution.     

Effects of protein perturbants on phospholipid bilayers

Series of alcohols, amides, ureas, and sulfoxides with increasingly longer hydrocarbon chains have been shown to lower progressively the thermal denaturation temperature of proteins. This effect is presumably due to a hydrophobic interaction between the solute and nonpolar domains of the protein. Theoretically, these interactions should occur between the solute and any macromolecular structure having a nonpolar region to which the solute has access. A recent review by Arakawa et al. has summarized evidence for such an interaction between organic solutes and proteins and suggested that these interactions are favored at higher temperatures. The present study investigates the effects of several classes of compounds on the stability of phospholipid vesicles. The results show that many compounds that are known to perturb protein function also destabilize phospholipid bilayers as reflected by solute-induced loss of vesicle contents.     

氨基酸的表面特性和溶剂化自由能

我们计算了氨基酸的溶剂可接近面积,局域偶极矩及表面电场.结果显示了亲、疏水基团与水相互作用具有不同的微观本质,由此提出了新的估计氨基酸溶剂化能的方法.     

Self-association of the histidine kinase CheA as studied by pulsed dipolar ESR spectroscopy

Biologically important protein complexes often involve molecular interactions that are low affinity or transient. We apply pulsed dipolar electron spin resonance spectroscopy and site-directed spin labeling in what to our knowledge is a new approach to study aggregation and to identify regions on protein surfaces that participate in weak, but specific molecular interactions. As a test case, we have probed the self-association of the chemotaxis kinase CheA, which forms signaling clusters with chemoreceptors and the coupling protein CheW at the poles of bacterial cells. By measuring the intermolecular dipolar interactions sensed by spin-labels distributed over the protein surface, we show that the soluble CheA kinase aggregates to a small extent through interactions mediated by its regulatory (P5) domain. Direct dipolar distance measurements confirm that a hydrophobic surface at the periphery of P5 subdomain 2 associates CheA dimers in solution. This result is further supported by differential disulfide cross-linking from engineered cysteine reporter sites. We suggest that the periphery of P5 is an interaction site on CheA for other similar hydrophobic surfaces and plays an important role in structuring the signaling particle.