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.     

The polymerization of amino acid adenylates on sodium-montmorillonite with preadsorbed polypeptides

We studied the spontaneous polymerization of amino acid adenylates on Na-montmorillonite in dilute, neutral suspension, after polypeptides were adsorbed on the clay. This led to the unexpected finding that the degrees of polymerization (DP's) of the oligo- and poly-peptides obtained depended on the amounts of polypeptides that were preadsorbed. Plotting average molecular weights obtained against c-spacings of the clay platelet aggregates which widened as a result of polypeptide addition and adsorption before the polymerization, does not permit an obvious explanation of these observations. The best correlation assigns a role to the fractional occupation of the individual intercalation layers of the polypeptides, as the adsorption increases towards a first complete mono-interlayer, then to an incipient and eventually to a complete double layer on to a third interlayer, after which the clay stacking breaks up. Spacings which correspond to an intermediate occupation of any of the three successive interlayers favor amino acids self-addition to polymers. The opposite is true for nearly empty or filled intercalation layers. We hypothesize and describe, how a catalytic activity may derive from c-spacings that offer adsorption sites for the reagent amino acid adenylate within the peripheral recesses of irregularly stacked clay platelets by bringing the anhydride bonds and neutral amino groups into favorable reaction distances. Moderately filled intercalation spaces may also act as sinks for the newly formed oligomers and facilitate the freeing of reaction sites for the occupation by fresh reagent. The c-spacings required for these mechanisms are the result of the intercalation of the preadsorbed polymer, but similar conditions prevail when polymers are adsorbed as they are generated during polymerization.     

Peptide Formation Mechanism on Montmorillonite Under Thermal Conditions

The oligomerization of amino acids is an essential process in the chemical evolution of proteins, which are precursors to life on Earth. Although some researchers have observed peptide formation on clay mineral surfaces, the mechanism of peptide bond formation on the clay mineral surface has not been clarified. In this study, the thermal behavior of glycine (Gly) adsorbed on montmorillonite was observed during heating experiments conducted at 150 °C for 336 h under dry, wet, and dry–wet conditions to clarify the mechanism. Approximately 13.9 % of the Gly monomers became peptides on montmorillonite under dry conditions, with diketopiperazine (cyclic dimer) being the main product. On the other hand, peptides were not synthesized in the absence of montmorillonite. Results of IR analysis showed that the Gly monomer was mainly adsorbed via hydrogen bonding between the positively charged amino groups and negatively charged surface sites (i.e., Lewis base sites) on the montmorillonite surface, indicating that the Lewis base site acts as a catalyst for peptide formation. In contrast, peptides were not detected on montmorillonite heated under wet conditions, since excess water shifted the equilibrium towards hydrolysis of the peptides. The presence of water is likely to control thermodynamic peptide production, and clay minerals, especially those with electrophilic defect sites, seem to act as a kinetic catalyst for the peptide formation reaction.     

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.     

Membrane perturbation induced by interfacially adsorbed peptides

The structural and energetic characteristics of the interaction between interfacially adsorbed (partially inserted) alpha-helical, amphipathic peptides and the lipid bilayer substrate are studied using a molecular level theory of lipid chain packing in membranes. The peptides are modeled as "amphipathic cylinders" characterized by a well-defined polar angle. Assuming two-dimensional nematic order of the adsorbed peptides, the membrane perturbation free energy is evaluated using a cell-like model; the peptide axes are parallel to the membrane plane. The elastic and interfacial contributions to the perturbation free energy of the "peptide-dressed" membrane are evaluated as a function of: the peptide penetration depth into the bilayer's hydrophobic core, the membrane thickness, the polar angle, and the lipid/peptide ratio. The structural properties calculated include the shape and extent of the distorted (stretched and bent) lipid chains surrounding the adsorbed peptide, and their orientational (C-H) bond order parameter profiles. The changes in bond order parameters attendant upon peptide adsorption are in good agreement with magnetic resonance measurements. Also consistent with experiment, our model predicts that peptide adsorption results in membrane thinning. Our calculations reveal pronounced, membrane-mediated, attractive interactions between the adsorbed peptides, suggesting a possible mechanism for lateral aggregation of membrane-bound peptides. As a special case of interest, we have also investigated completely hydrophobic peptides, for which we find a strong energetic preference for the transmembrane (inserted) orientation over the horizontal (adsorbed) orientation.     

The possible role of clays in prebiotic peptide synthesis

Hypotheses of macromolecule formations during the prebiotic era are described. The presumed role of minerals and clays in these reactions are: concentration of monomers, proton release by ion exchange whenever the reaction demands it, scattering of the charges of the interacting substances, thus allowing such substances to interact, which in the absence of clays repel each other due to their charges. Because of these reasons the polymerization mechanism in the presence of clays is different from that in their absence. While in the absence of clays only free amino acids or peptides can interact with active amino acid anhydrides, giving thus peptides increased by only one unit, in the presence of clays two molecules of amino acid anhydrides can interact, giving a still active peptide anhydride which can interact with another active peptide. Clays catalyze polymerization only in these cases where the amino acid is small enough to enter between the sheets of the clay. Apparently most of the reactions also occur there and not on the surface of the clay. Copolymerization of different pairs of amino acids proceeds selectively in the presence of clay. The relationship between this selecitvity and prebiotic parent proteins is discussed.     

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.     

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.     

Enzyme immobilization on ultrafine cellulose fibers via poly(acrylic acid) electrolyte grafts

Ultrafine cellulose fiber (diameter 200-400 nm) surfaces were grafted with polyacrylic acid (PAA) via either ceric ion initiated polymerization or methacrylation of cellulose with methacrylate chloride (MACl) and subsequent free-radical polymerization of acrylic acid. PAA grafts by ceric ion initiated polymerization increased with increasing reaction time (2-24 h), monomer (0.3-2.4 M), and initiator (1-10 mM) concentrations, and spanned a broad range from 5.5-850%. PAA grafts on the methacrylated cellulose fibers also increased with increasing molar ratios of MACl to cellulosic hydroxyl groups (MACl/OH, 2-6.4) and monomer acrylic acid (AA) to initiator potassium persulfate (KPS) ratios ([AA]/[KPS], 1.5-6), and were in a much narrower range between 12.8% and 29.4%. The adsorption of lipase (at 1 mg/ml lipase and pH 7) and the activity of adsorbed lipase (pH 8.5, 30 degrees C), in both cases decreased with increasing PAA grafts. The highest adsorption and activity of the lipase on the ceric ion initiated grafted fibers were 1.28 g/g PAA and 4.3 U/mg lipase, respectively, at the lowest grafting level of 5.5% PAA, whereas they were 0.33 g/g PAA and 7.1 U/mg lipase, respectively, at 12.8% PAA grafts on the methacrylated and grafted fibers. The properties of the grafted fibers and the absorption behavior and activity of lipase suggest that the PAA grafts are gel-like by ceric-initiated reaction and brush-like by methacrylation and polymerization. The adsorbed lipase on the ceric ion-initiated grafted surface possessed greatly improved organic solvent stability over the crude lipase. The adsorbed lipases exhibited 0.5 and 0.3 of the initial activity in the second and third assay cycles, respectively.     

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.     

Lipid domain boundaries as prebiotic catalysts of peptide bond formation

To address central problems in the origin of life such as the formation of linear polymers composed of only a small number of types of molecules, we have modeled the distribution of peptides in lipid monolayers. We show that short peptides and amino acids accumulate at the boundary between lipid domains, and that the concentration towards the boundary is higher the longer the peptide. We invoke a constraint on diffusion to one dimension as well as on orientation to suggest that polymerization of peptides is more likely to occur at the domain boundary than within domains or in the bulk phase. In a simple model, in which polymerization is taken to occur only at the boundary, we show that the equilibrium distribution of polymer lengths is shifted towards longer peptides. Since the reaction is occurring in a partially non-aqueous environment, hydrolysis is reduced and condensation increased to yield a significant polymerization. We show also that the free energy change from the redistribution of peptides within domains is sufficient to drive the formation of the peptide bond.     

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.     

Plant prolyl hydroxylase recognizes poly(L-proline) II helix

Substrate specificity of a prolyl hydroxylase from Vinca rosea suspension-cultured cells was studied using synthetic oligo(L-proline)s and their t-butyloxycarbonyl derivatives (Pron and Boc-Pron; n = 2-8) as peptidyl substrates. All peptides with a residual number of 5 or greater served as substrates in the enzyme reaction at 30 degrees C, after the preincubation of the enzyme and peptides at 0 degrees C prior to addition of cofactors and cosubstrate. Under the same conditions, the hydroxylation of Pro5 reached a plateau within 10 min, but that of Boc-Pro8 and poly(L-proline) increased linearly up to 40 min. If the preincubation temperature was raised to 30 degrees C, only Pro5 among the peptides was unable to serve as a substrate. The optimum temperature of the enzyme was 30 degrees C toward Boc-Pro8 and poly(L-proline) but it decreased to 15 degrees C using Pro5. These data suggest that the enzyme can bind Pro5 only at low temperature. Poly(L-proline) and Boc-Pron (n greater than or equal to 5) in aqueous solution are known to have a left-handed helical structure (poly(L-proline) II helix). Moreover, Pro5 was indicated as forming this helix below 10 degrees C. Accordingly, the enzyme recognizes the poly(L-proline) II helix, that is, the secondary structure of a substrate rather than the primary structure.     

Angiotensin I-converting enzyme inhibitory oligo-tyrosine peptides synthesized by α-chymotrypsin

Oligo-tyrosine peptides with degrees of polymerization ranging from 2 to 5 could be synthesized by α-chymotrypsin-catalyzed reaction with l-tyrosine ethyl ester in aqueous media, although the peptide yield was low due to a preferential hydrolysis of the substrate. It was also confirmed that α-chymotrypsin efficiently converted tyrosine tetramer to the dimer which was resistant to the digestion. Both Tyr-Tyr and Tyr-Tyr-Tyr showed high inhibitory activity for angiotensin I-converting enzyme from rabbit lung, and their IC₅₀ values were 34 μM and 51 μM, respectively. These two peptides exhibited a mix of competitive and noncompetitive inhibitions. Tyr-Tyr-Tyr was first recognized as an ACE inhibitor, suggesting that α-chymotrypsin could be applied to synthesis of novel potential materials for antihypertensive medicines.     

Isolation and purification of serum and interfacial peptides of a trypsinolyzed β-lactoglobulin oil-in-water emulsion

Information on the conformation of proteins adsorbed to an oil–water interface is usually determined by following the time course of enzymatic hydrolysis of the protein in an oil-in-water emulsion. Unlike previous works reported in the literature, the research presented in this paper provides information on which peptides are actually in contact with the lipid bilayer (interfacial peptides) and those segments that project into the aqueous phase (serum peptides). In order to achieve this classification of peptides, we present a method to separate serum peptides from interfacial peptides by initial centrifugation steps followed by reversed-phase high-performance liquid chromatography. The effectiveness of the method was ascertained by performing proteolysis on β-lactoglobulin adsorbed to an oil-water interface in a soybean oil-water emulsion. It was found that more peptides are qualitatively and quantitatively found adsorbed to the oil–water interface as compared to peptides released into the serum.     

温度对不同粘粒含量稻田土壤有机碳矿化的影响

模拟了亚热带地区3种不同粘粒含量的水稻土(砂壤土、壤粘土、粉粘土)在5种温度(10、15、20、25和30℃)下的有机碳(SOC)矿化特征,分析SOC矿化对温度变化的响应.结果表明:在160d的培养期内,温度对3种水稻土SOC矿化量的影响有一定差异,30℃时砂壤土、壤粘土和粉粘土SOC矿化量分别是10℃时的3.5、5.2和4.7倍.在较低温度(≤20℃)下,SOC矿化速度较低且相对稳定;在较高温度(≥25℃)下,前期SOC矿化速度较高,随着培养时间的延长逐渐降低,并趋于稳定.3种水稻土SOC矿化的温度系数(Q10)随培养时间出现波动,砂壤土的Q10平均值最低,为1.92,壤粘土和粉粘土的Q10平均值较接近,分别为2.37和2.32;3种土壤矿化速率常数(k)与温度呈极显著的指数相关(P<0.01).3种水稻土有机碳矿化对温度变化的响应敏感度依次为壤粘土>粉粘土>砂壤土.     

Potential Pitfalls in MALDI-TOF MS Analysis of Abiotically Synthesized RNA Oligonucleotides

Demonstration of the abiotic polymerization of ribonucleotides under conditions consistent with conditions that may have existed on the prebiotic Earth is an important goal in “RNA world” research. Recent reports of abiotic RNA polymerization with and without catalysis rely on techniques such as HPLC, gel electrophoresis, and MALDI-TOF MS to analyze the reaction products. It is essential to understand the limitations of these techniques in order to accurately interpret the results of these analyses. In particular, techniques that rely on mass for peak identification may not be able to distinguish between a single, linear RNA oligomer and stable aggregates of smaller linear and/or cyclic RNA molecules. In the case of MALDI-TOF MS, additional complications may arise from formation of salt adducts and MALDI matrix complexes. This is especially true for abiotic RNA polymerization reactions because the concentration of longer RNA chains can be quite low and RNA, as a polyelectrolyte, is highly susceptible to adduct formation and aggregation. Here we focus on MALDI-TOF MS analysis of abiotic polymerization products of imidazole-activated AMP in the presence and absence of montmorillonite clay as a catalyst. A low molecular weight oligonucleotide standard designed for use in MALDI-TOF MS and a 3′-5′ polyadenosine monophosphate reference standard were also run for comparison and calibration. Clay-catalyzed reaction products of activated GMP and UMP were also examined. The results illustrate the ambiguities associated with assignment of m/z values in MALDI mass spectra and the need for accurate calibration of mass spectra and careful sample preparation to minimize the formation of adducts and other complications arising from the MALDI process.     

Reactions of nitroimidazoles with free radicals--enhancement of reaction by u.v. irradiation

The free-radical reactivity of the nitroimidazole derivatives metronidazole, misonidazole, benznidazole and ornidazole was investigated by observing their effect on the polymerization of acrylamide in aqueous solution. Free-radical polymerization was initiated by the thermal decomposition of potassium peroxydisulphate at 50 degrees C. Measurement of the polymerization rate showed an inhibitory effect of the nitroimidazoles which was greatly enhanced when the system was irradiated with u.v. light near their absorption maximum of 320-325 nm. Analysis of the competitive kinetics of the system enabled calculation of the rate constant for reaction of the ground state and photoexcited nitroimidazole with the polyacrylamide free radicals. No significant difference between the various nitroimidazoles could be found in the dark reaction, but in the u.v.-irradiated system the order of reactivity (misonidazole greater than benznidazole greater than metronidazole approximately equal to ornidazole) was the same as the reported relative mutagenic, cytotoxic and radiosensitizing potency of the compounds. These results imply that the excited states of the nitroimidazoles are important to their activity in radical-radical reactions.