Clays and other minerals in prebiotic processes

Clays and other minerals have been investigated in context with prebiotic processes, mainly in polymerization of amino acids. It was found that peptides adsorbed on the clay, prior to polymerization, influence the reaction. The ratio between the amount of the peptides adsorbed and that of the clay is important for the yield as well as for the degrees of polymerization obtained. Adsorption prior to reaction produces a certain order in the aggregates of the clay particles which might induce better reaction results. Excess of added peptides disturbs this order and causes lesser degrees of polymerization. In addition to adsorption, clays are also able to occlude between their layers substances out of the environment, up to very high concentrations.     

Clays and other minerals in prebiotic processes

Clays and other minerals have been investigated in context with prebiotic processes, mainly in polymerization of amino acids. It was found that peptides adsorbed on the clay, prior to polymerization, influence the reaction. The ratio between the amount of peptides adsorbed and that of the clay is important for the yield as well as for the degrees of polymerization obtained. Adsorption prior to reaction produces a certain order in the aggregates of the clay particles which might induce better reaction results. Excess of added peptides disturbs this order and causes lesser degrees of polymerization. In addition to adsorption, clays are also able to occlude between their layers substances out of the environment, up to very high concentrations.     

Clays as possible catalysts for peptide formation in the prebiotic era

From the point of view of prebiotic synthesis, clays might have performed functions of concentration, catalysis, and protection of molecules.The degrees of polymerization obtained, when amino acid adenylates are added to montmorillonite suspensions in water, are much higher than those obtained by polymerization in the absence of such a clay. In addition, they are of a discrete spectrum, usually multiplies of 6 or 7, and reach values of up to 40 mers. In the absence of clay a continuous spectrum of degrees of polymerization is obtained, and usually up to 4–6 mers only. Copolymerization in the absence of clays yields mostly random copolymers, in their presence mostly block copolymers are obtained.Optical density measurements show that after adsorption has taken place on the clay, stacking of its layers occurs. Polymerization starts only after these stacked layers have been formed. The distances between the layers — as measured by X-rays — increase during polymerization, probably because the resulting polymers settle in their interspace, while the adsorption site of the active monomers is at the edges of the clay.     

Clays as possible catalysts for peptide formation in the prebiotic era.

From the point of view of prebiotic synthesis, clays might have performed functions of concentration, catalysis, and protection of molecules. The degree of polymerization obtained when amino acid adenylates are added to montmorillonite suspensions in water, are much iigher than those obtained by polymerization in the absence of such a clay. In addition, they are of a discrete spectrum, usually multiplies of 6 or 7, and reach values of up to 40 mers. In the absence of clay a continuous spectrum of degrees of polymerization is obtained, and usually up to 4-6 mers only. Copolymerization in the absence of clays yields mostly random copolymers in their presence mostly block copolymers are obtained. Optical density measurements show that after adsorption has taken place on the clay, stacking of its layers occurs. Polymerization starts only after these stacked layers have been formed. The distance between the layers - as measured by X-rays - increase during polymerization, probably because the resulting polymers settle in their interspace, while the adsorption site of the active monomers is at the edges of the clay.     

The mechanism of clay catalyzed polymerization of amino acid adenylates.

Amino acid adenylates were adsorbed on montmorillonite when either the interspatial faces or the edges of the latter were blocked. By this method it could be observed that adsorption of the amino acid adenylates takes place mostly on the planes of the clay. However, for polymerization to take place, the edges of the clay have to be free as well and apparently only these molecules polymerize which are attached to the planes of the clay by their amino groups and to the edges of the clay by their phosphate group. Thus all the charges of the molecules which might produce their repulsion from each other would be neutralized. As a consequence of these attachments polymerization on the clay would take place on its planar sites, but only on those neighboring its edges. The question whether neutralization of charges is also the reason why biochemical substrates have to attach themselves by several points to enzymes and thus make biochemistry fit into the framework of general chemistry, is raised.     

Role of transition metal ferrocyanides (II) in chemical evolution

Due to ease of formation of cyanide under prebiotic conditions, cyanide ion might have formed stable complexes with transition metal ions on the primitive earth. In the course of chemical evolution insoluble metal cyano complexes, which settled at the bottom of primeval sea could have formed peptide and metal amino acid complexes through adsorption processes of amino acids onto these metal cyano complexes.Adsorption of amino acids such as glycine, aspartic acid, and histidine on copper ferrocyanide and zinc ferrocyanide have been studied over a wide pH range of 3.6 – 8.5. Amino acids were adsorbed on the metal ferrocyanide complexes for different time periods. The progress of the adsorption was followed spectro-photometrically using ninhydrin reagent. Histidine was found to show maximum adsorption on both the adsorbents at neutral pH. Zinc ferrocyanide exhibits good sorption behaviour for all the three amino acids used in these investigations.     

Sequential adsorption of F(ab')(2) and BSA on negatively and positively charged polystyrene latexes

The aim of the present work is to study the sequential adsorption of F(ab')(2) and bovine serum albumin (BSA) molecules adsorbed onto positively and negatively charged polystyrene latexes. Cationic and anionic latexes were prepared by emulsifier-free emulsion polymerization. Adsorptions of F(ab')(2) on both latexes at a low ionic strength and different pHs were performed. The cationic latex showed a higher adsorption of F (ab')(2) molecules over a range of pH, which could be due to the formation of multilayers. Sequential adsorption of anti-CRP F(ab')(2) and monomeric BSA were performed at two different pre-adsorbed F(ab')(2) amounts on both types of latex. Displacement of F(ab')(2) occurred only when the preadsorbed amounts were larger than a certain critical value, which depends on the adsorption pH. A greater displacement of larger preadsorbed amounts might be the result of a weaker contact between the protein molecules and the polystyrene surface. The displacement of F(ab')(2) previously adsorbed onto both latexes occurred due to pH changes, an increase of ionic strength and the presence of BSA molecules. The effect caused by these three factors was studied independently. The main factors in the desorption of F(ab')(2) on the anionic latex are the changes in pH and ionic strength, whereas on the cationic latex the desorption is mainly caused by the increase of the ionic strength and the presence of BSA. The colloidal stability of the immunotatex was improved by BSA adsorption, especially on cationic latex. (c) 1995 John Wiley & Sons, Inc.     

Electrostatic effects upon adsorption and desorption of polylysines on the surface of lipid membranes of different composition

Electrokinetic measurements are carried out in suspensions of liposomes made from mixtures of charged (cardiolipin, CL) and neutral (phosphatidylcholine, PC) lipids in the presence of lysine and lysine-based polypeptides. Neither monolysine nor polylysines adsorbed on neutral (PC) membranes. In the case of negatively charged membranes (CL/PC) all polypeptides showed a sharp dependence of liposome electrophoretic mobility on the amount of polymer added to the cell. In suspension of cardiolipin liposomes the position of zero charge point coincided for all high-molecular polylysines; thus, pentalysine neutralizes the membrane surface, whereas polycations with a higher polymerization degree change a sign of the surface charge. Electrophoretic mobility of liposomes in plateau range depended on the molecular weight of polylysines and composition of liposomes; for large macromolecules the absolute value came close to its value for the initial liposomes. Adsorption of polycations on planar bilayer lipid membranes (BLM) resulted in alteration of the boundary potential measured by the method of intramembranous field compensation (IFC). The electrokinetic measurements and IFC method gave close results in the case of lysine monomers; their surface concentration could be fitted by an isotherm of the molecule distribution between the membrane surface and solution. Considerable differences of the surface and boundary potentials found in the case of pentalysine, correspond to changes in the dipole component of boundary potential induced by the adsorbed molecules. Using the IFC method, the kinetics of the adsorption process before saturation was studied. The adsorption of polylysines was markedly slower (more than hour) than that of pentalysine (tens of min) or monolysine (minutes). Washout experiments showed that adsorption of penta-and monolysine on planar BLM was reversible, while that of high-molecular polylysines was practically irreversible.     

Anticooperative Binding Governs the Mechanics of Ethidium-Complexed DNA

DNA intercalators bind nucleic acids by stacking between adjacent basepairs. This causes a considerable elongation of the DNA backbone as well as untwisting of the double helix. In the past few years, single-molecule mechanical experiments have become a common tool to characterize these deformations and to quantify important parameters of the intercalation process. Parameter extraction typically relies on the neighbor-exclusion model, in which a bound intercalator prevents intercalation into adjacent sites. Here, we challenge the neighbor-exclusion model by carefully quantifying and modeling the force-extension and twisting behavior of single ethidium-complexed DNA molecules. We show that only an anticooperative ethidium binding that allows for a disfavored but nonetheless possible intercalation into nearest-neighbor sites can consistently describe the mechanical behavior of intercalator-bound DNA. At high ethidium concentrations and elevated mechanical stress, this causes an almost complete occupation of nearest-neighbor sites and almost a doubling of the DNA contour length. We furthermore show that intercalation into nearest-neighbor sites needs to be considered when estimating intercalator parameters from zero-stress elongation and twisting data. We think that the proposed anticooperative binding mechanism may also be applicable to other intercalating molecules.     

Antibacterial nitroacridine, Nitroakridin 3582: binding to nucleic acids in vitro and effects on selected cell-free model systems of macromolecular biosynthesis

Nitroakridin 3582 (NA) formed complexes with native deoxyribonucleic acid (DNA) and with transfer ribonucleic acid (tRNA) species from Escherichia coli. Spectrophotometric titrations of NA with these nucleic acids produced numerical results from which nonlinear adsorption isotherms were derived. These curves indicated the existence of more than one class of binding sites on the polymers to which NA was bound by more than one process. The stoichiometry of strong binding of NA to double helical DNA was in agreement with a conventional value (1 ligand molecule per 4.2 component nucleotides) for complete intercalation binding. NA inhibited the DNA-dependent DNA polymerase I and RNA polymerase reactions, the first strongly and the second appreciably. These inhibitions corresponded to the extents to which NA inhibits DNA and RNA biosyntheses in vivo. Evidently, NA interferes with the template function of DNA. The drug also inhibited the polymerization of phenylalanine in a cell-free E. coli ribosome-polyuridylic acid [poly (U)] system. The effect paralleled an inhibition of the poly (U)-directed binding of phenylalanyl tRNA to ribosomes. Ethidium bromide acted similarly. The antimalarial drug, chloroquine, stimulated polyphenylalanine synthesis, apparently as a result of stimulating the poly (U)-directed binding of phenylalanyl tRNA to ribosomes.     

Polymerization on the Rocks: Theoretical Introduction

It is difficult if not impossible to synthesize long polymers of amino acids, nucleotides, etc., in homogeneous aqueous solution. We suggest that long polymers were synthesized on the surface of minerals in a prebiotic process analogous to solid-phase synthesis. Provided that the affinity of a mineral for an oligomer increases with the length of the oligomer, adsorption must become essentially irreversible for sufficiently long oligomers. Irreversibly adsorbed oligomers may be elongated indefinitely by repeated cycles in which the mineral with its adsorbed oligomers is first incubated with activated monomers and then washed free of deactivated monomer and side-products. We discuss in some detail the formation of oligomers of negatively-charged amino acids such as glutamic acid on anion-exchange minerals such as hydroxylapatite or illite. We show that the average length of adsorbed oligomers at steady state, n, depends on the balance between the rate of chain elongation and the rate of hydrolysis, and we derive a very approximate formula for n.     

Adsorption, desorption, and activity of glucose oxidase on selected clay species.

The adsorption of the enzyme glucose oxidase (EC 1.1.3.4) to clays followed the pattern described for other proteins as being pH dependent. Maximum adsorption occurred at or below the isoelectric point of the enzyme. The amount of enzyme adsorbed to clay was influenced by the type of clay used, and also the saturating cations. Initially adsorbed enzyme showed low specific activities, and as amounts of enzyme adsorbed approached maximum stauration of clay, specific activities increased approaching that determined for free enzyme. The adsorption of glucose oxidase involved a temperature-independent cation-exchange mechanism, and enzyme adsorbed to surfaces of clay could be desorbed in active form by elevation of pH of suspending solution. This was followed by a slower temperature-dependent fixation, probably by hydrogen bonding, which resulted in protein being irreversibly adsorbed to clay surfaces. It is proposed that on adsorption of glucose oxidase to clay surfaces unravelling of the protein structure occurred, which allowed penetration of protein into the interlamellar spaces of montmorillonite. This proposal was based on the observed expansion of montmorillonite to 23 A, and the decreases in amount of a second-protein lysozyme adsorbed with extended incubation times of glucose oxidase - clay complexes at pH 4.5.     

Synthesis of amino acyl-adenylates under prebiotic conditions

Summary In a system containing zeolites, ATP and amino acids, amino acid-ADP anhydrides are able to form in an aqueous medium at neutral pH and room temperature. When montmorillonite, a clay possessing swelling properties, is added, polypeptides are formed. It is suggested that this may be the mechanism whereby prebiotic synthesis of peptides took place.Killed on May 30, 1972, at the Lydda Airport massacre.     

Molecular Modelling of The Mechanism of Action of Organic Clay-Swelling Inhibitors

Abstract

It is well known that the sodium smectite class of clays swells macroscopically in contact with water, whereas under normal conditions the potassium form does not. In recent work using molecular simulation methods, we have provided a quantitative explanation both for the swelling behaviour of sodium smectite clays and the lack of swelling of potassium smectites [1]. In the present paper, we apply similar modelling methods to study the mechanism of inhibition of clay-swelling by a range of organic molecules.

Experimentally, it is known that polyalkylene glycols (polyethers) of intermediate to high relative molecular mass are effective inhibitors of smectite clay swelling. We use a range of atomistic simulation techniques, including Monte Carlo and molecular dynamics, to investigate the interactions between a selection of these compounds, water, and a model smectite clay mineral. These interactions occur by means of organised intercalation of water and organic molecules within the galleries between individual clay layers.

The atomic interaction potentials deployed in this work are not as highly optimised as those used in our clay-cation-water work [1]. Nevertheless, our simulations yield trends and results that are in qualitative and sometimes semi-quantitative agreement with experimental findings on similiar (but not identical) systems. The internal energy of adsorption of simple polyethers per unit mass on the model clay is not significantly different from that for water adsorption; our Monte Carlo studies indicate that entropy is the driving force for the sorption of the simpler organic molecules inside the clay layers: a single long chain polyethylene glycol can displace a large number of water molecules, each of whose translational entropy is greatly enhanced when outside the clay. Hydrophobically modified polyalkylene glycols also enjoy significant van der Waals interactions within the layers which they form within the clay galleries.

In conjunction with experimental studies, our work furnishes valuable insights into the relative effectiveness of the compounds considered and reveals the generic features that high performance clay-swelling inhibitors should possess. For optimal inhibitory activity, these compounds should be reasonably long chain linear organic molecules with localised hydrophobic and hydrophilic regions along the chain. On intercalation of these molecules within the clay layers, the hydrophobic regions provide an effective seal against ingress of water, while the hydrophilic ones enhance the binding of the sodium cations to the clay surface, preventing their hydration and the ensuing clay swelling.     

Adsorption of lecithin liposomes to acid clay

The interaction between lecithin liposomes and acid clay was investigated to clarify the mechanism for liposome adsorption to the clay. It was found that the multilamellar vesicular structure of the liposomes was broken as a result of primary adsorption. The acid clay particles aggregated and were eventually covered by the lecithin layer structure. In the case of kaolin, on the other hand, the liposomes were weakly adsorbed to the clay and maintained the vesicular structure. The amount of primary adsorption to the clay surface, which was estimated from the adsorption isotherm, was more for acid clay than for kaolin, and the total amount adsorbed to the acid clay was also more than to kaolin. This result can be explained by the much higher density of the negative charge on the acid clay surface than that for kaolin. The liposomes are therefore considered to be adsorbed to the acid clay mainly by the choline positive charge residing at the end of the lecithin molecule, although this is of no net charge as a whole.     

Structure of thermal polymers of amino acids

When glutamic acid is a predominant amino acid in a thermally polymerized mixture of amino acids, pyro Glu is exclusively found at the N-terminal end of the poly-amino acid polymer. It probably initiates the polymerization process. Lysine-containing polymers will probably contain epsilon N-(glutamyl)L-lysine cross links which may account for the higher molecular weights observed in these polymers (100-200 000). Incorporation of some amino acids facilitates the incorporation of others. When utilizing mixtures of three to eight amino acids with glutamic acid as one of the amino acids, some fractions are obtained which include all the amino acids in the polymerization mixture. The biosynthesis of glutathione, gramicidin, tyrocidine and cell-wall polypeptides has demonstrated that non-random amino acid sequence peptides can be biologically synthesized without the direct participation of nucleic acids. That is, the enzymes appear to provide adequate chemical specificity to form non-random amino acid sequence peptides. The properties and replication of the scrapie agent may provide us with more profound insight as to the evolution of purely physical-chemical systems into biological systems.     

Specific assay for endotoxin using immobilized histidine and Limulus amebocyte lysate.

The LAL test is inhibited or enhanced by many substances. To overcome these problems, we have developed a specific endotoxin assay method using an ultrafiltration unit, a fluorometric LAL reagent, and immobilized histidine (which is a specific adsorbent for endotoxins). This method is composed of two steps. The first step is the adsorption of endotoxins. Using immobilized histidine, endotoxins are quantitatively adsorbed on the adsorbent, and the adsorbed endotoxins are separated from LAL-inhibiting or -enhancing substances by the ultrafiltration unit. The second step is the reaction of adsorbed endotoxins with the LAL reagent. The endotoxins adsorbed on immobilized histidine are directly reacted with the LAL reagent in a filter cup and show enough activity for assay. The reproducibility and the accuracy of this method are high, and the recovery of endotoxins from a sample solution is more than 95%. The new endotoxin assay method using immobilized histidine can be utilized for the determination of endotoxins in a solution containing LAL-inhibiting or -enhancing substances such as amino acids and antibiotics instead of requiring employment of the more common gel-clot technique.     

Interaction of basic polypeptides with phospholipid monolayers

Adsorption of the polylysine and of the copolypeptides: L-lysine/L-serine and L-lysine/L-phenylalanine on phospholipid monolayers has been investigated. The charge density of the monolayers was varied by using the negatively charged phosphatidyl serine and the neutral phosphatidyl choline at different ratios. The surface concentrations of the adsorbed polypeptides was determined by measuring the surface radiation of their radioactive label.The adsorbing capacity of the monolayer surfaces increases with their negative charge, however with respect to polypeptides the surface activity sequence is pL < pLS < pLφ. From the dependence of adsorption on the ionic strength it was concluded that it is controlled by three types of interaction: (1) electrostatic attraction to the negatively charged surface; (2) electrostatic repulsion between adsorbed polybases; (3) hydrophobic interactions involving specific structural arrangements. This is true even of the apparently neutral PC monolayer where the fixed phosphate groups form an electrical double layer with the more mobile choline groups which can be interpenetrated by the charged groups of the basic polypeptides.     

Mechanical properties of the sodium montmorillonite interlayer intercalated with amino acids

Nanosized montmorillonite clay dispersed in small amounts in polymer results in polymer nanocomposites having superior engineering properties compared to those of the native polymer. These nanoinclusions are created by treating clay with an organic modifier which makes clay organophilic and results in intercalation or exfoliation of the montmorillonite. The modifiers used are usually long carbon chains with alkylammonium or alkylphosphonium cations. In this work, we have investigated the use of some alternative molecules which can act as modifiers for clay composites using clay for reinforcing a matrix of biopeptides or proteins. Such composites have potential applications in the fields of biomedical engineering and pharmaceutical science. In this work, the amino acids arginine and lysine are used as modifiers. The intercalation and mechanical behavior of the interlayer spacing with these amino acids as inclusions under compression and tension are studied using molecular dynamics simulations. Significant differences in the responses are observed. This work also provides an insight into the orientation and interaction of amino acids in the interlayer under different stress paths.     

Amino acid- -naphthylamide hydrolysis by Pseudomonas aeruginosa arylamidase

The intracellular and constitutive arylamidase from Pseudomonas aeruginosa was purified 528-fold by salt fractionation, ion-exchange chromatography, gel filtration, and adsorption chromatography. This enzyme hydrolyzed basic and neutral N-terminal amino acid residues from amino-beta-naphthylamides, dipeptide-beta-naphthylamides, and a variety of polypeptides. Only those substrates having an l-amino acid with an unsubstituted alpha-amino group as the N-terminal residue were susceptible to enzymatic hydrolysis. The molecular weight was estimated to be 71,000 daltons. The lowest K(m) values were associated with substrates having neutral or basic amino acid residues with large side chains with no substitution or branching on the beta carbon atom.