Crowding and hydration effects on protein conformation: a study with sol-gel encapsulated proteins.

We are developing an experimental system for testing the effects of macromolecular crowding and molecular confinement on protein structure. In the present study, solvent effects on the secondary structure of two proteins were examined by circular dichroism following encapsulation in the hydrated pores of a silica glass matrix by the sol-gel method. Changes in the unfolded conformations of encapsulated apomyoglobin and reduced serum albumin were analyzed after equilibration with aqueous solutions of natural osmolytes, short-chain alcohols, polyethylene glycol, and a complete series of Hofmeister cations. In many instances, the alpha-helical content of the encapsulated protein was increased by addition of solutes at concentrations that have no effect on the protein in the absence of the glass. The results are discussed from the perspective of water structure. We argue that perturbed water at the silica interface causes an increase in the average free energy of the bulk water phase which, consequently, diminishes the strength of the hydrophobic effect inside the glass matrix and destabilizes the conformation of encapsulated proteins. We propose that solutes can increase the strength of the hydrophobic effect and influence folding equilibria without directly interacting with the protein. A hypothesis is provided for the apparent paradox that kosmotropic (strongly water binding) anions favor native protein structure, whereas chaotropic (weakly water binding) cations enhance native protein structure. The encapsulation results suggest that macromolecular crowding and molecular confinement are accompanied by hydration effects that may oppose or potentiate the stabilizing effects of excluded volume on protein structure, depending on the surface chemistry of the crowding agent and its influence on bulk water structure. In the crowded environment of a living cell, excluded volume effects, surface-induced water structure, and compatible solutes are expected to complement the dominant forces in protein folding.     

Cell volumes and water contents of frog muscles in solutions of permeant sugars and sugar alcohols

1. Previous work has suggested that living cells may acquire and then maintain different water contents and hence volume, in solutions containing different concentrations of solutes that are permeant to the cell membrane. Toward better understanding of this phenomenon, two hypotheses were introduced: one hypothesis is based on the membrane-pump theory; another represents an extension of the polarized multilayer theory of cell water, a part of the association-induction (AI) hypothesis. To test the different predictions of these hypotheses, the water contents of frog muscle equilibrated at 25 degrees C in solutions of different concentrations of seven pentoses, seven hexoses, seven dissacharides, two trisaccharides, and six sugar alcohols were determined. 2. The earlier finding of sustained shrinkage of muscle cells in concentrated solutions of permeant solutes was confirmed once more. 3. In equimolal solutions of sugars and sugar alcohols with different steric conformations but the same or closely similar molecular weight(s), muscles had the same or closely similar water content(s). 4. In equimolal solutions of different sugars and sugar alcohols, the equilibrium water contents of the muscles increased with decreasing molecular weights of these solutes. 5. The water contents of muscles, equilibrated in 0.4 M solutions of different sugars and sugar alcohols, are positively correlated with the equilibrium distribution coefficients (or q-values) of the sugar and sugar alcohols in the muscle cell water with a linear correlation coefficient of +0.973. 6. The relationships between the equilibrium water contents of muscles (in solutions containing different concentrations of different sugars and sugar alcohols) and the concentrations of these sugars and sugar alcohols agree in general contours with that predicted by an equation derived on the basis of the polarized multilayer theory of cell water. 7. The experimental findings described above do not agree with the prediction based on the membrane-pump hypothesis; they do agree with all four predictions of the hypothesis based on the polarized multilayer theory of cell water.     

Studies on the physical state of water in living cells and model systems. III. The high osmotic activities of aqueous solutions of gelatin, polyvinylpyrrolidone and poly (ethylene oxide) and their relation to the reduced solubility for NA+, sugars, and free amino acids

Very high osmotic activities of concentrated aqueous solutions of gelatin, polyvinylpyrrolidone, and poly(ethylene oxide) were recorded. These observed values are far above those predictable from the molar concentrations of these polymers or those of aqueous solutions of native hemoglobin of equal concentrations. It was shown that these high osmotic activities are closely associated with the ability of the gelatin- or polymer-dominated water to exclude Na+ salts, sucrose, and glycine. Both phenomena are interpreted as reflecting the polarization of multilayers of water by the polymers enhancing the H2O to H2O interaction and also reducing the translational and rotational motional freedom of the water.     

Water and the cytoskeleton.

The diffusion of intracellular fluid and solutes is mainly limited by the density and the geometry of crossbridges between cytoskeletal polymers mediating the formation of an integrated cytoplasmic scaffold. Evidence for specific relationships between water and cytoskeletal polymers arises from the effect of heavy water on their polymerization process in vitro and on the cytoskeleton of living cells. The hydration of cytoskeletal subunits is modified through polymerization, a mechanism which may be involved in the direct contribution of the cytoskeleton to the osmotic properties of cells together with changes of hydration of polymers within networks. The dynamic properties of the hydration layer of cytoskeletal polymers may reflect the repetitive distribution of the surface charges of subunits within the polymer lattice, thus inducing a local and long range ordering of the diffusion flows of water and solutes inside polymer networks. The interactions between subunits in protofilaments and between protofilaments determine the specific viscoelastic properties of each type of polymer, regulated by associated proteins, and the mechanical properties of the cell through the formation of bundles and gels. Individual polymers are interconnected into dynamic networks through crossbridging by structural associated proteins and molecular motors, the activity of which involves cooperative interactions with the polymer lattice and likely the occurence of coordinated modifications of the hydration layer of the polymer surface. The cytoskeletal polymers are polyelectrolytes which constitute a large intracellular surface of condensed anionic charges and form a buffering structure for the sequestration of cations involved in the regulation of intracellular events. This property allows also the association of cytoplasmic enzymes and multimolecular complexes with the cytoskeleton, facilitating metabolic channelling and the localization of these complexes in specific subdomains of the cytoplasm. The consequences of interactions between membranes and the cytoskeleton in all cellular compartments range from the local immobilization and clustering of lipids and membrane proteins to the regulation of water and ion flows by the association of cytoskeletal subunits or polymers with transmembrane channels. The possibility that the polyelectrolyte properties of the cytoskeletal polymers contribute to the modulation of membrane potentials supports the hypothesis of a direct involvement of the cytoskeleton in intercellular communications.     

Origins of protein denatured state compactness and hydrophobic clustering in aqueous urea: inferences from nonpolar potentials of mean force

Free energies of pairwise hydrophobic association are simulated in aqueous solutions of urea at concentrations ranging from 0-8 M. Consistent with the expectation that hydrophobic interactions are weakened by urea, the association of relatively large nonpolar solutes is destabilized by urea. However, the association of two small methane-sized nonpolar solutes in water has the opposite tendency of being slightly strengthened by the addition of urea. Such size effects and the dependence of urea-induced stability changes on the configuration of nonpolar solutes are not predicted by solvent accessible surface area approaches based on energetic parameters derived from bulk-phase solubilities of model compounds. Thus, to understand hydrophobic interactions in proteins, it is not sufficient to rely solely on transfer experiment data that effectively characterize a single nonpolar solute in an aqueous environment but not the solvent-mediated interactions among two or more nonpolar solutes. We find that the m-values for the rate of change of two-methane association free energy with respect to urea concentration is a dramatically nonmonotonic function of the spatial separation between the two methanes, with a distance-dependent profile similar to the corresponding two-methane heat capacity of association in pure water. Our results rationalize the persistence of residual hydrophobic contacts in some proteins at high urea concentrations and explain why the heat capacity signature (DeltaC(P)) of a compact denatured state can be similar to DeltaC(P) values calculated by assuming an open random-coil-like unfolded state.     

Studies on the physical state of water in living cells and model systems. X. The dependence of the equilibrium distribution coefficient of a solute in polarized water on the molecular weights of the solute: experimental confirmation of the "size rule" in model studies

The equilibrium distribution of 14 sugars, sugar alcohols, and other nonelectrolytes in solutions of polyethylene oxide (PEO) and of native and alkali-denatured bovine hemoglobin were studied over wide concentration ranges. The results show that the equilibrium concentrations of all the solutes studies are rectilinearly related to their external concentrations. This straight-line relationship demonstrates the existence of these solutes entirely or almost entirely in the aqueous phase of these systems. Therefore the slope of each of these straight lines equals the equilibrium distribution coefficient or q-value of the solute involved. In general, the q-values decrease with increasing molecule weights (M.W.) of the solutes in 15% solutions of PEO, 20% solutions of alkali-denatured hemoglobin (and in 18% gelatin) but not in 39% solution of native hemoglobin. In solutions of PEO, of alkali-denatured hemoglobin studied (and of gelatin) a fraction of the water (20% to 30%) appears to have solvency similar to that of normal liquid water. The experimental findings of M.W.-dependent solute exclusion were discussed in the light of four alternative theories that have been offered to explain this type of phenomena. Among these four theories only the polarized multilayer theory agrees with most, if not all the facts known.     

Effect of salts on the properties of aqueous sugar systems, in relation to biomaterial stabilization. 1. Water sorption behavior and ice crystallization/melting

Trehalose and sucrose, two sugars that are involved in the protection of living organisms under extreme conditions, and their mixtures with salts were employed to prepare supercooled or freeze-dried glassy systems. The objective of the present work was to explore the effects of different salts on water sorption, glass transition temperature (T(g)), and formation and melting of ice in aqueous sugar systems. In the sugar-salt mixtures, water adsorption was higher than expected on the basis of the water uptake by each pure component. In systems with a reduced mass fraction of water (w less-than-or-equal 0.4), salts delayed water crystallization, probably due to ion-water interactions. In systems where > 0.6, water crystallization could be explained by the known colligative properties of the solutes. The glass transition temperature of the maximally concentrated matrix (T(g)') was decreased by the presence of salts. However, the actual T(g) values of the systems were not modified. Thus, the effect of salts on sorption behavior and formation of ice may reflect dynamic water-salt-sugar interactions which take place at a molecular level and are related to the charge/mass ratio of the cation present without affecting supramolecular or macroscopic properties.     

Basic biological research with the striated muscle by using cryotechniques and electron microscopy.

Several basic mechanisms underlying living phenomena are not really understood. Unequivocal interpretations of data concerning the following phenomena--to name but a few--are missing: cellular accumulation of potassium; cellular exclusion of sodium, cell volume regulation, shape change of cells (e.g. of muscle cells during contraction), electrical potential differences between inside and outside of living cells. The theoretical treatment of these phenomena as found in all current textbooks is based on the membrane-pump theory (MPT) with the following essential features. The bulk of the main cellular cation K+ is freely dissolved in free cellular water and membrane-situated pumps are responsible for the high level of K+ and the low level of Na+ found in virtually all living cells. On the other hand, the above mentioned phenomena are explained by the association-induction hypothesis (AIH) without the proposal of membrane-situated pumps and with the postulations of selective K+ adsorption to cellular proteins and of a specific cell water structure which has a low solvency for Na+ and other solutes. Experimental findings are reviewed which contradict the MPT and support the AIH. In addition, electron microscopic experiments with cryoprocessed striated muscle are reviewed which establish cellular K+ binding (adsorption) and a cellular water structure which is different from that of normal free water. Cryoexperiments with the striated muscle and model systems are proposed which may help to obtain further information on the specific interactions between proteins, ions, and water in living cells.     

Free Radical Formation by Ultrasound in Aqueous Solutions. A Spin Trapping Study

Our recent spin trapping studies of free radical generation by ultrasound in aqueous solutions are reviewed. The very high temperatures and pressures induced by acoustic cavitation in collapsing gas bubbles in aqueous solutions exposed to ultrasound lead to the thermal dissociation of water vapor into H atoms and OH radicals. Their formation has been confirmed by spin trapping. Sonochemical reactions occur in the gas phase (pyrolysis reactions), in the gas-liquid interfacial region, and in the bulk of the solution (radiation-chemistry reactions). The high temperature gradients in the interfacial regions lead to pyrolysis products from non-volatile solutes present at sufficiently high concentrations. The sonochemically generated radicals from carboxylic acids, amino acids, dipeptides. sugars, pyrimidine bases. nucleosides and nucleo-tides were identified by spin trapping with the non-volatile spin trap 3.5-dibromo-2.6-dideuterio-4-nitrosobenzenesulfonate. At low concentrations of the non-volatile solutes. the spin-trapped radicals produced by sonolysis are due to H atom and OH radical reactions. At higher concentrations of these non-volatile solutes, sonolysis leads to the formation of additional radicals due to pyrolysis processes (typically methyl radicals). A preferred localization of non-volatile surfactants (compared to analogous non-surfactant solutes) was demonstrated by the detection of pyrolysis radicals at 500-fold lower concentrations. Pyrolysis radicals were also found in the sonolysis of aqueous solutions containing only certain nitrone spin traps. The more hydrophobic the spin trap, the lower the concentration at which the pyrolysis radicals can be observed. The effect of varying the temperature of collapsing transient cavities in aqueous solutions of different rare gases and of N₂O on radical yields and on cell lysis of mammalian cells was investigated.     

Cell surface charge. Correlation of partition with electrophoresis

Critical mixtures of aqueous solutions os polymers separate into two or more immiscible phases. Particulate materials distribute in such phase systems generally between one bulk phase and the interface between bulk phases. The distribution is described by a simple partition law, and is qunatitatively determined by, inter alia, the nature of the particle surface, particularly net electrical charge. The partition behaviour of various cells, native or modified by treatment with trypsin, neurominidase or maleic anhydride, correlate strongly with electrophoretic mobility. Partition behaviour and electrophoretic mobility are both dependent upon cell surface charge. Thus, in appropriate conditions, changes in surface charge may be registered as changes in partition.     

Solute excluded-volume effects on the stability of globular proteins: A statistical thermodynamic theory

A statistical thermodynamic theory is developed to investigate the effects of solute excluded volume on the stability of globular proteins. Proteins are modeled as two states in chemical equilibrium: the denatured state is modeled as a flexible chain of tangent hard spheres (pearl-necklace chain) while the native state is modeled as a single hard sphere. Study of model proteins bovine pancreatic trypsin inhibitor and lysozyme in a McMillan-Mayer model solution of hard spheres indicates that the excluded volume of solutes has three distinct types of effects on protein stability: (1) small-size solutes strongly denature proteins, (2) medium-size solutes stabilize proteins at low solute concentrations and destabilize them at high concentrations, and (3) large-size solutes stabilize native-state proteins across the whole liquid region. The study also finds that increasing the chain length of hard-chain polymer solutes has an effect on protein stability that is similar to increasing the diameter of spherical solutes. This work qualitatively explains why stabilizers tend to be large size molecules such as sugars, polymers, polynols, nonionic, and anionic surfactants while denaturants tend to be small size molecules such as alcohols, glycols, amides, formamides, ureas, and guanidium salts. Quantitative comparison between theoretical predictions and experimental results for folding free energy changes shows that the excluded-volume effect is at least as important as the binding and/or electrostatic effects on solute-assisted protein-denaturation processes. Our theory may also be able to explain the effect of excluded volume on the Φ condensation of DNA. © 1996 John Wiley & Sons, Inc.     

Application of a thermodynamic model to the prediction of phase separations in freeze-concentrated formulations for protein lyophilization

Many of the compounds considered for use in pharmaceutical formulations demonstrate incompatibilities with other components at high enough concentrations, including pairs of polymers, polymers and salts, or even proteins in combination with polymers, salts, or other proteins. Freeze concentration can force solutions into a region where incompatibilities between solutes will manifest as the formation of multiple phases. Such phase separation complicates questions of the stability of the formulation as well as labile components, such as proteins. Yet, phase separation events are difficult to identify by common formulation screening methods. In this report, we use the osmotic virial expansion model of Edmond and Ogston (1) to describe phase-separating behavior of ternary aqueous polymer solutions. Second osmotic virial coefficients of polyethylene glycol 3350 (PEG) and dextran T500 were measured by light scattering. Assuming an equilibrium between ice and water in the freeze-concentrated solution, a degree of freeze concentration can be estimated, which, when combined with the phase separation spinodal, describes a "phase separation envelope" in which phase separation tendencies can be expected in the frozen solution. The phase separation envelope is bounded at low temperatures by the glass transition temperature of the freeze-concentrated solution. Scanning electron microscopic images and infrared spectroscopy of protein structure are provided as experimental evidence of the phase separation envelope in a freeze-dried system of PEG, dextran, and hemoglobin.     

History of the membrane (pump) theory of the living cell from its beginning in mid-19th century to its disproof 45 years ago--though still taught worldwide today as established truth

The concept that the basic unit of all life, the cell, is a membrane-enclosed soup of (free) water, (free) K+ (and native) proteins is called the membrane theory. A careful examination of past records shows that this theory has no author in the true sense of the word. Rather, it grew mostly out of some mistaken ideas made by Theodor Schwann in his Cell Theory. (This is not to deny that there is a membrane theory with an authentic author but this authored membrane theory came later and is much more narrowly focussed and accordingly can at best be regarded as an offshoot of the broader and older membrane theory without an author.) However, there is no ambiguity on the demise of the membrane theory, which occurred more than 60 years ago, when a flood of converging evidence showed that the asymmetrical distribution of K+ and Na+ observed in virtually all living cells is not the result of the presence of a membrane barrier that permits some solutes like water and K+ to move in and out of the cell, while barring--absolutely and permanently--the passage of other solutes like Na+. To keep the membrane theory afloat, submicroscopic pumps were installed across the cell membrane to maintain, for example, the level of Na+ in the cell low and the level of K+ high by the ceaseless pumping activities at the expense of metabolic energy. Forty-five year ago this version of the membrane theory was also experimentally disproved. In spite of all these overwhelming evidence against the membrane-pump theory, it still is being taught as verified truth in all high-school and biology textbooks known to us today. Meanwhile, almost unnoticed, a new unifying theory of the living cell, called the association-induction hypothesis came into being some 40 years ago. Also little noticed was the fact that it has received extensive confirmation worldwide and has shown an ability to provide self-consistent interpretations of most if not all known experimental observations that are contradicting the membrane-pump theory as well as other observations that seem to support the membrane pump theory.     

Aggregation and conformational studies on a pentapeptide derivative

Most of the disease causing proteins such as beta amyloid, amylin, and huntingtin protein, which are natively disordered, readily form fibrils consisting of beta-sheet polymers. Though all amyloid fibrils are made up of beta-sheet polymers, not all peptides with predominant beta-sheet content in the native state develop into amyloid fibrils. We hypothesize that stable amyloid like fibril formation may require mixture of different conformational states in the peptide. We have tested this hypothesis on amyloid forming peptide namely HCl(Ile)(5)NH(CH(2)CH(2)O)(3)CH(3) (I). We show peptide I, has propensity to form self-assembled structures of beta-sheets in aqueous solutions. When incubated over a period of time in aqueous buffer, I self assembled into beta sheet like structures with diameters ranging from 30 to 60 A that bind with amyloidophilic dyes like Congo red and Thioflavin T. Interestingly peptide I developed into unstable fibrils after prolonged aging at higher concentration in contrast with the general mature fibril-forming propensity of various amyloid petides known to date.     

Equilibrium centrifugation of proteins in acidic solutions. Beta-lactoglobulin A in aqueous acetic, propionic, and butyric acids.

Short chain aliphatic acids are almost neutrally buoyant in aqueous solutions, and preferential interaction of macromolecules with these solvent components should not greatly affect apparent molecular weights determined by equilibrium ultracentrifugation. The feasibility of molecular weight estimations using native, neutral pH values of partial specific volume has been tested: equilibrium ultracentrifugation of β-lactoglobulin A (β-LgA) has been carried out in aqueous acetic, propionic, and butyric acids in the absence of any other added electrolyte. These solutions are highly nonideal because of the extreme Donnan effect. Apparent molecular weights estimated at infinite dilution using the native neutral pH value of the partial specific volume, $\text{v}{}_{\mathrm{p}}$, differed by less than 5% from the monomer formula weight. The 10 m acids appear to be least effective as dissociating agents for β-LgA, with a weak reversible monomer-dimer association suggested in 10 m acetic acid, with significant heterogeneity apparent in 10 m propionic acid, and with a lack of direct solubility in 10 m butyric acid. All the 0.1 m acids and all the 1 m acids were essentially equally effective as dissociating agents, with the exception of 1 m butyric acid which dissolved β-LgA only slowly to give significantly heterogeneous solutions. From these results and from our previous experiments with aldolase (6), it appears feasible to use the native values of $\text{v}{}_{\mathrm{p}}$ to obtain estimates of molecular weights of proteins in aqueous organic acids as dissociating agents.     

Studies on the physical state of water in living cells and model systems. II. NMR relaxation times of water protons in aqueous solutions of gelatin and oxygen-containing polymers which reduce the solvency of water for NA+, sugars, and free amino acids

This communication reports our study of the NMR relaxation times, T1 and T2 of water protons in aqueous solutions of bovine serum albumin, gelatin, polyvinylpyrrolidone, poly(ethylene oxide), and polyvinylmethylether over a wide concentration range. In contrast to solutions of gelatin and bovine serum albumin, the T1/T2 ratio of the three synthetic polymers are close to unity over the entire range studied. When combined with earlier-reported data of water made "non-solvent" to Na salts, the present data provided the basis for calculating the T1 and T2 as well as the rotational correlation time tau c of the "non-solvent" water. It was shown that only a modest increase by a factor of about 3 of tau c is enough to produce water that is "non-solvent" for Na citrate and sulfate. The new data reconciles NMR data of living cells with the theory of the cell water given in the association-induction hypothesis. The variability of tau c of "non-solvent" water also offers explanations of apparently conflicting conclusions on the physical state of cell water from dielectric measurements.     

Effect of the compatible solute ectoine on the stability of the membrane proteins

Mechanical single molecule techniques offer exciting possibilities for investigating protein folding and stability in native environments at sub-nanometer resolutions. Compatible solutes show osmotic activity which even at molar concentrations do not interfere with cell metabolism. They are known to protect proteins against external stress like temperature, high salt concentrations and dehydrating conditions. We studied the impact of the compatible solute ectoine (1M) on membrane proteins by analyzing the mechanical properties of Bacteriorhodopsin (BR) in its presence and absence by single molecule force spectroscopy. The unfolding experiments on BR revealed that ectoine decreases the persistence length of its polypeptide chain thereby increasing its tendency to coil up. In addition, we found higher unfolding forces indicating strengthening of those intra molecular interactions which are crucial for stability. This shows that force spectroscopy is well suited to study the effect of compatible solutes to stabilize membrane proteins against unfolding. In addition, it may lead to a better understanding of their detailed mechanism of action.     

The zebrafish genome encodes the largest vertebrate repertoire of functional aquaporins with dual paralogy and substrate specificities similar to mammals

Background  

Aquaporins are integral membrane proteins that facilitate the transport of water and small solutes across cell membranes. These proteins are vital for maintaining water homeostasis in living organisms. In mammals, thirteen aquaporins (AQP0-12) have been characterized, but in lower vertebrates, such as fish, the diversity, structure and substrate specificity of these membrane channel proteins are largely unknown.     

Electrolyte and non-electrolyte distribution in the ehrlich ascites tumor cells during the cell cycle

In a previous study, evidence was presented for changes in the state of water and osmotically active solutes during the cell cycle. Total water was constant at 82% (w/w), while the fraction of water that was osmotically active decreased from a maximum during S to a minimum at mitosis. Total Na⁺, K⁺, and C1^? in milliequivalents per liter of cell water remained constant. Therefore, electrolytes are sequestered in the osmotically inactive water. Evidence is now presented that Na⁺ exists primarily as one compartment, with a second, slower compartment appearing during S and disappearing during G2. Na⁺ is completely exchangeable during the entire cell cycle. The distribution of other penetrating solutes was also investigated. When placed in hyperosmotic ethylene glycol solutions, cells first shrink, then swell to their original volumes. ¹⁴C-ethylene glycol distributes in 89% of cell water throughout the cell cycle. However, ¹⁴C-urea distributes in anywhere from 86–100% of the cell water, depending on the stage in the cell cycle. Both solutes are at chemical equilibrium in water in which they are distributed, but they differ in their effects on cell volume. The final volume at which cells equilibrate in urea varies with the concentration of urea in the environment and with time into the cell cycle. Results suggest a loss of osmotically active particles or decreased osmotic activity of urea.     

中度嗜盐菌相容性溶质机制的研究进展

生活在高盐环境中的中度嗜盐菌不仅能抗衡外界的高渗透压胁迫,而且还能迅速适应短时间内的渗透冲击。为适应该环境,中度嗜盐菌依赖于一种被称为相容性溶质的物质,以执行渗透保护功能。这类物质属于极性的、易溶的和低分子量的有机化合物,其中包括糖类、氨基酸类、甜菜碱类和四氢嘧啶类等。中度嗜盐菌主要采用相容性溶质机制来适应盐环境。在此,就中度嗜盐菌的盐适应机理、相容性溶质的种类和特点,以及其作用的分子机制进行了阐述和讨论。