Kinetics of sickle hemoglobin polymerization. II. A double nucleation mechanism

A double nucleation mechanism for the polymerization of sickle hemoglobin is described. The mechanism accounts for all of the major kinetic observations: the appearance of a delay, the high concentration dependence of the delay time, and the stochastic behavior of slowly polymerizing samples in small volumes. The mechanism postulates that there are two pathways for polymer formation: polymerization is initiated by homogeneous nucleation in the solution phase, followed by nucleation of additional polymers on the surface of existing ones. This second pathway is called heterogeneous nucleation. Since the surface of polymers is continuously increasing with time, heterogeneous nucleation provides a mechanism for the extreme autocatalysis that is manifested as an apparent delay in the kinetic progress curves. In this mechanism, each spherulitic domain of polymers is considered to be initiated by a single homogeneous nucleation event. The mechanism explains the irreproducibility of the delay time for single domain formation as arising from stochastic fluctuations in the time at which the homogeneous nucleus for the first polymer is formed. Integration of the linearized rate equations that describe this model results in a simple kinetic form: A[cosh(Bt)-1] (Bishop & Ferrone, 1984). In the accompanying paper (Ferrone et al., 1985) it was shown that the initial 10 to 15% of progress curves, with delay times varying from a few milliseconds to over 10(5) seconds, is well fit by this equation. In this paper, we present an approximate statistical thermodynamic treatment of the equilibrium nucleation processes that shows how the nucleus sizes and nucleation equilibrium constants depend on monomer concentration. The equilibrium model results in expressions for B and B2A as a function of monomer concentration in terms of five adjustable parameters: the bimolecular addition rate of a monomer to the growing aggregate, the fraction of polymerized monomers that serve as heterogeneous nucleation sites, the free energy of intermolecular bonding within the polymer, and two parameters that describe the free energy change as a function of size for the bonding of the heterogeneous nucleus to a polymer surface. This model provides an excellent fit to the data for B and B2A as a function of concentration using physically reasonable parameters. The model also correctly predicts the time regime in which stochastic behavior is observed for polymerization in small volumes.     

Non-equilibrium freezing behaviour of aqueous systems.

The tendencies to non-equilibrium freezing behaviour commonly noted in representative aqueous systems derive from bulk and surface properties according to the circumstances. Supercooling and supersaturation are limited by heterogeneous nucleation in the presence of solid impurities. Homogeneous nucleation has been observed in aqueous systems freed from interfering solids. Once initiated, crystal growth is ofter slowed and, very frequently, terminated with increasing viscosity. Nor does ice first formed always succeed in assuming its most stable crystalline form. Many of the more significant measurements on a given systeatter permitting the simultaneous representation of thermodynamic and non-equilibrium properties. The diagram incorporated equilibrium melting points, heterogeneous nucleation temperatures, homogeneous nucleation temperatures, glass transition and devitrification temperatures, recrystallization temperatures, and, where appropriate, solute solubilities and eutectic temperatures. Taken together, the findings on modle systems aid the identification of the kinetic and thermodynamic factors responsible for the freezing-thawing survival of living cells.     

Kinetic studies on photolysis-induced gelation of sickle cell hemoglobin suggest a new mechanism.

The kinetics of deoxyhemoglobin S gelation have been investigated using photolytic dissociation of the carbon monoxide complex to initiate the process. Measurements over a wide range of times, 10(-3)-10(4) show that both the concentration dependence of the tenth-time (i.e., the time required to complete one-tenth the reaction) and the time dependence of the process decrease as gelation speeds up. In slowly gelling samples, where single domains of polymers are formed in the small sample volumes employed with this technique (1-2 x 10(-9) cm3), there is a marked increase in the variability of the tenth-times. These results are explained by a mechanism in which gelation is initiated by homogeneous nucleation of polymers in the bulk solution phase, followed by heterogeneous nucleation on the surface of existing polymers. At the lowest concentrations, homogeneous nucleation is so improbable that stochastic behavior is observed in the small sample volumes, and heterogeneous nucleation is the dominant pathway for polymer formation, thereby accounting for the high time dependence. At the highest concentrations homogeneous nucleation becomes much more probable, and the time dependence decreases. The decrease in concentration dependence of the tenth-time with increasing concentration results from a decrease in size of both the homogeneous and heterogeneous critical nuclei. The model rationalizes the major observations on the kinetics of gelation of deoxyhemoglobin S, and is readily testable by further experiments.     

Nucleation of calcium oxalate crystals on an imprinted polymer surface from pure aqueous solution and urine

Calcium oxalate (CaOx) is the most common component of human kidney stones. Heterogeneous nucleation is regarded as the key mechanism in this process. In this study, we have used an imprinted 6-methacrylamidohexanoic acid/divinylbenzene co-polymer as a biomimetic surface to nucleate CaOx crystal formation. The polymer was imprinted with either calcium oxalate monohydrate (COM) or dihydrate (COD) template crystals. These were washed out of the polymer, which was then immersed in various test solutions. The test solutions were an aqueous solution of calcium chloride and sodium oxalate, artificial urine and a sample of real urine. Crystals that formed on the polymer surface were characterized by X-ray powder diffraction, Fourier transform infrared spectroscopy, atomic absorption spectroscopy and scanning electron microscopy. Results showed that in the aqueous solution the COM-imprinted polymer induced the nucleation of COM. The COD-imprinted polymer induced only trace amounts of COD crystallization, together with larger quantities of COM. In artificial and real urines, COM also specifically precipitated on the COM-imprinted surface. The results show that, at least to some extent, the imprinted polymers direct formation of their morphologically matched crystals. In the case of COD, however, it appears that either rapid hydrate transformation of COD to COM occurs, or the more stable COM polymorph is directly co-precipitated by the polymer. Our results support the hypothesis that heterogeneous nucleation plays a key role in CaOx stone formation and that the imprinted polymer model could provide an additional and superior diagnostic tool for stone researchers to assess stone-risk in urine.Abbreviations COD calcium oxalate dihydrate - COM calcium oxalate monohydrate - COT calcium oxalate trihydrate - dvb divinylbenzene - 6-maaha 6-methylacrylamidohexanoic acid     

Heterogeneous nucleation in sickle hemoglobin: experimental validation of a structural mechanism

Sickle hemoglobin polymerizes by two types of nucleation: homogeneous nucleation of aggregates in solution, and heterogeneous nucleation on preexisting polymers. It has been proposed that the same contact that is made in the interior of the polymer between the mutant site beta6 and its receptor pocket on an adjacent molecule is the primary contact site for the heterogeneous nucleus. We have constructed cross-linked hybrid molecules in which one beta-subunit is from HbA with Glu at beta6, and the other is from HbS with a Val at beta6. We measured solubility (using sedimentation) and polymerization kinetics (using laser photolysis) on cross-linked hybrids, and cross-linked HbS as controls. We find approximately 4000 times less heterogeneous nucleation in the cross-linked AS molecules than in cross-linked HbS, in strong confirmation of the proposal. In addition, changes in stability of the nucleus support a further proposal that more than one beta6 contact is involved in the homogeneous nucleus.     

Zero-sized effect of nano-particles and inverse homogeneous nucleation. Principles of freezing and antifreeze

It was found that freezing of water in terms of homogeneous nucleation of ice never occurs even in ultra-clean micro-sized water droplets under normal conditions. More surprisingly, at sufficiently low supercoolings, foreign nano-particles exert no effect on the nucleation barrier of ice; it is as if they physically "vanished." This effect, called hereafter the "zero-sized" effect of foreign particles (or nucleators), leads to the entry of a so-called inverse homogeneous-like nucleation domain, in which nucleation is effectively suppressed. The freezing temperature of water corresponds to the transition temperature from the inverse homogeneous-like nucleation regime to foreign particle-mediated heterogeneous nucleation. The freezing temperature of water is mainly determined by (i) the surface roughness of nucleators at large supercoolings, (ii) the interaction and structural match between nucleating ice and the substrate, and (iii) the size of the effective surface of nucleators at low supercoolings. Our experiments showed that the temperature of -40 degrees C, commonly regarded as the temperature of homogeneous nucleation-mediated freezing, is actually the transition temperature from the inverse homogeneous-like nucleation regime to foreign particle-mediated heterogeneous nucleation in ultra-clean water. Taking advantage of inverse homogeneous-like nucleation, the interfacial tensions between water and ice in very pure water and antifreeze aqueous solutions were measured at a very high precision for the first time. The principles of freezing promotion and antifreeze and the selection for the biological ice nucleation and antifreeze proteins are obtained. The results provide completely new insights into freezing and antifreeze phenomena and bear generic implications for all crystallization systems.     

Ice nucleation in solutions and freeze-avoiding insects-homogeneous or heterogeneous?

This article challenges the common view that solutions and cold-hardy freeze-avoiding insects always freeze by heterogeneous nucleation. Data are presented to show that the nucleation temperatures of a variety of solutions and freeze-avoiding insects are a function of the water volume as described by the data previously published by Bigg in 1953. The article also points out that the relationships between melting point depression and depression of nucleation temperature are different for samples undergoing homogeneous nucleation and those undergoing heterogeneous nucleation. Aqueous solutions and freeze-avoiding insects display a relationship like that of homogeneously nucleated samples. It is also argued that the identity of the "impurities" assumed to cause heterogeneous nucleation in aqueous solutions and insects is obscure and that the "impurities" have features which make their existence rather unlikely.     

Effects of confinement on insulin amyloid fibrils formation

Insulin, a 51-residue protein universally used in diabetes treatment, is known to produce amyloid fibrils at high temperature and acidic conditions. As for other amyloidogenic proteins, the mechanisms leading to nucleation and growth of insulin fibrils are still poorly understood. We here report a study of the fibrillation process for insulin confined in a suitable polymeric hydrogel, with the aim of ascertain the effects of a reduced protein mobility on the various phases of the process. The results indicate that, with respect to standard aqueous solutions, the fibrillation process is considerably slowed down at moderately high concentrations and entirely suppressed at low concentration. Moreover, the analysis of the initial stages of the fibrillation process in aqueous solutions revealed a large spatial heterogeneity, which is completely absent when the fibrillation is carried out in the hydrogel. We attribute this heterogeneity to the diffusion in solution of large amyloidal aggregates, which must be formed very fast compared to the average times for the whole sample. These findings are interpreted in the framework of recently suggested heterogeneous nucleation mechanisms. Moreover, they may be useful for the development of new insulin pharmaceutical formulations, more stable against adverse conditions.     

Ice nucleation in nature: supercooling point (SCP) measurements and the role of heterogeneous nucleation

In biological systems, nucleation of ice from a supercooled aqueous solution is a stochastic process and always heterogeneous. The average time any solution may remain supercooled is determined only by the degree of supercooling and heterogeneous nucleation sites it encounters. Here we summarize the many and varied definitions of the so-called "supercooling point," also called the "temperature of crystallization" and the "nucleation temperature," and exhibit the natural, inherent width associated with this quantity. We describe a new method for accurate determination of the supercooling point, which takes into account the inherent statistical fluctuations of the value. We show further that many measurements on a single unchanging sample are required to make a statistically valid measure of the supercooling point. This raises an interesting difference in circumstances where such repeat measurements are inconvenient, or impossible, for example for live organism experiments. We also discuss the effect of solutes on this temperature of nucleation. Existing data appear to show that various solute species decrease the nucleation temperature somewhat more than the equivalent melting point depression. For non-ionic solutes the species appears not to be a significant factor whereas for ions the species does affect the level of decrease of the nucleation temperature.     

An Investigation of Freezing of Supercooled Water on Anti-Freeze Protein Modified Surfaces

This work investigates how functionalization of aluminium surfaces with natural type III Anti-Freeze Protein (AFP) affects the mechanism of heterogeneous ice nucleation. First the bulk ice nucleation properties of distilled water and aqueous solution of AFP were evaluated by differential scanning calorimetry. Then the modified surface was characterized by Secondary Ions Mass Spectroscopy (SIMS), Fourier Transform InfraRed (FTIR) spectroscopy and contact angle measurement. Freezing experiments were then conducted in which water droplets underwent a slow controlled cooling. This study shows that compared to uncoated aluminium, the anti-freeze proteins functionalized surfaces exhibit a higher and narrower range of freezing temperature. It was found that these proteins that keep living organisms from freezing in cold environment act in the opposite way once immobilized on surfaces by promoting ice nucleation. Some suggestions regarding the mechanism of action of the observed phenomena were proposed based on the Classical Nucleation Theory (CNT).     

Heterogeneous nucleation of protein crystals on fluorinated layered silicate

Here, we describe an improved system for protein crystallization based on heterogeneous nucleation using fluorinated layered silicate. In addition, we also investigated the mechanism of nucleation on the silicate surface. Crystallization of lysozyme using silicates with different chemical compositions indicated that fluorosilicates promoted nucleation whereas the silicates without fluorine did not. The use of synthesized saponites for lysozyme crystallization confirmed that the substitution of hydroxyl groups contained in the lamellae structure for fluorine atoms is responsible for the nucleation-inducing property of the nucleant. Crystallization of twelve proteins with a wide range of pI values revealed that the nucleation promoting effect of the saponites tended to increase with increased substitution rate. Furthermore, the saponite with the highest fluorine content promoted nucleation in all the test proteins regardless of their overall net charge. Adsorption experiments of proteins on the saponites confirmed that the density of adsorbed molecules increased according to the substitution rate, thereby explaining the heterogeneous nucleation on the silicate surface.     

Alternating current studies of charge carrier transport in lipid bilayers. Pentachlorophenol in lecithin-cholesterol membranes.

Surface and interior electrical properties of lecithin-cholesterol bilayer membranes treated with the uncoupler pentachlorophenol have been determined on the basis of a.c. measurements over a wide range of frequencies (0.02 to 1000 kHZ). The method used depends on accurately determining the resistance of the aqueous solution in series with each individual membrane by extrapolating admittance data into infinite frequency. Loss tangent vs. frequency curves are corrected by subtracting out a loss contribution which is present in untreated membranes and is due, presumably, to dielectric relaxation. The results, which are useful below 100 kHZ, can be fitted to loss tangent curves computed for a three-element equivalent circuit consisting of frequency independent conductance-capacitance pairs, arranged in series to represent surface and interior properties of membranes. Interior conductances agree with net conductances obtained from d.c. measurements. The pH and concentration dependence of surface conductance is consistent with a scheme of transport in which a fixed number of surface binding sites are filled preferentially with neutral pentachlorophenol molecules, which in turn dissociate to supply protons to the aqueous phase. Surface capacitances range from 15 to 90 times that of interior capacitance and show a systematic increase with pentachlorophenol concentration at high pH, and a decrease with concentration at low pH.     

物理环境影响蛋白质晶体形核的研究进展

物理环境是影响蛋白质晶体形核的重要因素。文中回顾了各种物理环境如光、电场、超声波、磁场、微重力、温度、机械振动、异相形核界面对蛋白质晶体形核的影响,并对各物理环境下蛋白质晶体形核的可能机制进行探讨,展望了利用物理环境影响蛋白质晶体形核的研究前景。     

Kinetics and template nucleation of self-assembled hydroxyapatite nanocrystallites by chondroitin sulfate

Biomineralization is an important process, which is often assisted by biomolecules. In this paper, the effect of chondroitin sulfate on the crystallization of hydroxyapatite was examined quantitatively based on a generic heterogeneous nucleation model. It is found that chondroitin sulfate can suppress the supersaturation-driven interfacial structure mismatch between the hydroxyapatite crystal and the substrate and promote the formation of ordered hydroxyapatite nanocrystallite assemblies. The nucleation mechanism of self-aligned hydroxyapatite nanocrystallites was examined from the viewpoints of kinetics and interfacial structure and properties, which contributes to an understanding of the fundamentals of biomineralization of self-assembled structures. The results obtained from this study will provide a basic principle to design and fabricate highly orderly organic-inorganic hybrid materials.     

Role of Nonspecific Interactions in Molecular Chaperones through Model-Based Bioinformatics

Molecular chaperones are large proteins or protein complexes from which many proteins require assistance in order to fold. One unique property of molecular chaperones is the cavity they provide in which proteins fold. The interior surface residues which make up the cavities of molecular chaperone complexes from different organisms has recently been identified, including the well-studied GroEL-GroES chaperonin complex found in Escherichia coli. It was found that the interior of these protein complexes is significantly different than other protein surfaces and that the residues found on the protein surface are able to resist protein adsorption when immobilized on a surface. Yet it remains unknown if these residues passively resist protein binding inside GroEL-GroEs (as demonstrated by experiments that created synthetic mimics of the interior cavity) or if the interior also actively stabilizes protein folding. To answer this question, we have extended entropic models of substrate protein folding inside GroEL-GroES to include interaction energies between substrate proteins and the GroEL-GroES chaperone complex. This model was tested on a set of 528 proteins and the results qualitatively match experimental observations. The interior residues were found to strongly discourage the exposure of any hydrophobic residues, providing an enhanced hydrophobic effect inside the cavity that actively influences protein folding. This work provides both a mechanism for active protein stabilization in GroEL-GroES and a model that matches contemporary understanding of the chaperone protein.     

Water transport in a cluster of closely packed erythrocytes at subzero temperatures

A one-dimensional model has been developed to describe the kinetics of water transport in a cluster of closely packed cells. For the case of human red blood cells, the intracellular medium has been treated as an ideal, hydrated, nondilute multicomponent electrolyte solution. Results show that the volume flux of water out of the interior cells of the cluster lags behind that of the exterior cells. At any given temperature (or time), the amount of water retained within a cluster of closely packed cells of a given type exceeds (on an overall percentage basis) the amount of water retained within a single isolated cell of the same type. For a given cooling rate the probability of intracellular ice nucleation at any given temperature will therefore be greater for cells in the interior of a cluster, and the survival signature for a cell cluster should peak at a cooling rate which is less than the corresponding optimal value for a single, isolated cell. These results are consistent with experimental observations.     

Separation of DNA fragments and single strand conformation polymorphism analysis in bare capillaries using poly(acrylamide–dimethylacrylamide) as a separation medium

A short chain poly(acrylamide–dimethylacrylamide) (PADMA) was synthesized in aqueous phase using isopropanol as a chain transfer agent, and was characterized according to the chemical composition and molecular mass. This polymer can form a stable dynamic coating on the inner surface of the capillary, thereby suppressing the electroosmotic flow and DNA–capillary wall interaction. The sieving medium has low viscosity and capillary filling with this medium and medium replacement were conveniently carried out by commercial capillary electrophoresis instruments. The effects of components and concentration of copolymers on the separation of DNA fragments were investigated. Highly efficient separation of DNA fragments, successful single strand conformation polymorphism (SSCP) analysis and good reproducibility of the migration time were obtained in bare capillaries using these copolymers as sieving media. Our preliminary results demonstrate that PADMA will become an alternative matrix for DNA separation by capillary electrophoresis.     

Plant size,flowering synchrony and edge effects: What,how and where they affect the reproductive success of a Neotropical tree species

Plant reproductive success is supposedly influenced by phenology and individual size, which may be modified under edge effects. We tested if reproductive success, estimated by fruit set, in Senefeldera verticillata (Euphorbiaceae) is related to flowering synchrony and tree size, including plant height and circumference at breast height. The study was carried out in the interior and in edges of clearings for gas pipelines and electric lines of a lowland rainforest in south‐eastern Brazil. Monthly observations were performed during one reproductive season, of 19 individuals that grew at edges of electric lines and gas pipelines and at forest interior. Reproductive success was significantly higher at forest interior than at gas pipeline area; there was no significant difference between gas pipeline and electric line areas or between forest interior and electric line area. In the forest edges, only plant height was positively related to plant reproductive success. This is probably related to crown exposure to sunlight, which enhances flower production. At forest interior, reproductive success was positively influenced by the synchrony of flowering activity among neighbouring individuals. In contrast, flowering synchrony based on phenophase intensity negatively impacted reproductive success. Senefeldera verticillata shows temporal dioecy and is mainly pollinated by small social bees, and the high degree of flowering synchrony at low intensity may increase the number of mating partners and therefore enhance its reproductive success. Inside the forest fragments, individuals with thicker trunks showed lower reproductive success, which may be related to a loss of reproductive capacity of older individuals. Our results evidenced the complexity of responses experienced by tropical plants subjected to forest fragmentation because of linear clearings.     

Critical Role of Silicon in Directing the Bio-inspired Mineralization of Gelatin in the Presence of Hydroxyapatite

Significant progress has been made on understanding the critical role of organic components in directing the collagen mineralization.We hypothesize that the inorganic trace elements might also play important role in the mineralization of collagenous matrix.To this aim,we systematically compared the in-vitro biomineralization behaviors of gelatin,gelatin-HA and gelatin-SiHA electrospun membranes.The results indicated that the presence of Si ions played a striking influence on the nucleation behaviors and mineralized structures.The gelatin-SiHA samples demonstrated more homogeneous nucleation within the gelatin fiber and growth along the fiber direction,in comparison with the heterogeneous nucleation and growth of spherulitic clusters on top of the nanofiber surface,i.e.extrafibrillar mineralization.The likely shift of the nucleation mode to the intrafibrillar mineralization in the presence of Si ions led to good alignment of apatite c-axis with the long axis of the nanofiber,resulting in a mineralization process and microstructure that were closer to those in natural bone.Cellular response analysis indicated that Si incorporation improved the MSC attachment and cytoskeleton organization.Such findings might have important implication in both understanding the complex mechanisms involved in collagen mineralization and optimal designing of advanced bio-inspired materials with potential superior mechanical and biological properties.