Synthesis of oligonucleotides by proteinoid microspheres acting on ATP

Enhanced catalytic activity from proteinoid microspheres

Creating materials that are capable of catalyzing enzymatic reactions could be important to the treatment of both acute and chronic wounds, as well as other topical diseases. As a first step in the design of catalytic biomaterials, a new class of proteinoid microsphere (PM), that includes amino acids found in phosphatase enzyme active sites, has been constructed. This material can significantly enhance catalytic activity for phosphoester hydrolysis, with observed specific activity increases between 35- and 55-fold. Further specific activity increases occur when metal cations, notably iron or zinc, are added to the PMs. Specific activity increases between 140- and 300-fold for these metal modified systems are measured. The phosphatase activity increase is demonstrated for both aromatic phosphate esters as well as the high-energy phosphate bond of adenosine triphosphate. PMs bind substrate heterogeneously on their surfaces in an enthalpically driven reaction that is defined by an overall favorable free energy, but unfavorable entropy. The catalytic PMs have been successfully blended with polyolefin foam and extruded with PLA. These materials remain fully active.

Triggered release from peptide-proteinoid microspheres

Proteinoid microspheres (PM) are unusual polymers formed by the thermal condensation of amino acids. Although they have been studied for over 60 years, they are only now beginning to garner interest as controlled release agents. Although they are very biocompatible, it has been problematic to design useful triggers that release small molecules from PM interiors. This has severely limited their usefulness. In the present study, short peptides have been successfully incorporated into PMs during their formation. The resulting hybrid peptide-PMs can release their interior content when hydrolyzed by a proteinase. Specifically, if a matrix metalloproteinase (MMP) cleavage site peptide is incorporated into a PM, the peptide-PM will release interior contents only in the presence of the MMP recognizing the cleavage peptide. The release rate can be determined by the concentration of the peptide in the PM synthesis mixture. This potentially makes peptide-PMs useful for delivering inhibitors or drugs into acute and chronic wounds, periodontal disease sites, and other disease states involving the fine-tuned regulation of proteinases.

Triggered release of small molecules from proteinoid microspheres

Proteinoid microspheres (PM) are formed by the thermal condensation of amino acids. They have been useful to further evolutionary theory, as catalysts for some biochemical reactions, but they have not been overly useful as controlled delivery agents. It is possible however to construct PMs that contain organic small molecules in the interior space. This means that a PM could be used as a delivery agent, if a suitable method could be discovered to cause the release of the internal material. This report describes the formation of a PM that includes a molecular bridging agent that can be removed in a reducing environment. Removal of the bridge opens a hole or window in the PM that allows the interior material to escape. The rate at which the interior material is released from the PM can be controlled by the size of the window or by the reduction potential in the environment. These PMs can be used to temporally treat a variety of complications including wounds (chronic or acute) by delivering a sequestered reagent in a controlled manner and are advantageous in that amino acids are the primary delivery vehicle breakdown product.

Chemical evolution of RNA under hydrothermal conditions and the role of thermal copolymers of amino acids for the prebiotic degradation and formation of RNA

The roles of thermal copolymers of amino acids (TCAA) were studied for the prebiotic degradation of RNA. A weak catalytic ability of TCAA consisted of Glu, L-Ala, L-Val, L-Glu, L-Asp, and optionally L-His was detected for the cleavage of the ribose phosphodiester bond of a tetranucleotide (5'-dCrCdGdG) in aqueous solution at 80 degees C. The rate constants of the disappearance of 5'-dCrCdGdG were determined in aqueous solutions using different pH buffer and TCAA. The degradation rates were enhanced 1.3-3.0 times in the presence of TCAA at pH 7.5 and 8.0 at 80 degrees C, while the hydrolysis of oligoguanylate (oligo(G)) was accelerated about 1.6 times at pH 8.0. A weak inhibitory activity for the cleavage of oligo(G) was detected in the presence of 0.055 M TCAA-Std. On the other hand, our recent study on the influences of TCAA for the template-directed reaction of oligo(G) on a polycytidylic acid template showed that TCAA has an acceleration activity for the degradation of the activated nucleotide monomer and an acceleration activity for the formation of G5' ppG capped oligo(G). This series of studies suggest that efficient and selective catalytic or inhibitory activities for either the degradation or formation of RNA under hydrothermal conditions could have hardly emerged from the simple thermal condensation products of amino acids. A scenario is going to be deduced on the chemical evolution of enzymatic activities and RNA molecules concerning hydrothermal earth conditions.

From non-random molecular structure to life and mind

The evolutionary hierarchy molecular structure-->macromolecular structure-->protobiological structure-->biological structure-->biological functions has been traced by experiments. The sequence always moves through protein. Extension of the experiments traces the formation of nucleic acids instructed by proteins. The proteins themselves were, in this picture, instructed by the self-sequencing of precursor amino acids. While the sequence indicated explains the thread of the emergence of life, protein in cellular membrane also provides the only known material basis for the emergence of mind in the context of emergence of life.

Metabolism of proteinoid microspheres

The literature of metabolism in proteinoids and proteinoid microspheres is reviewed and criticized from a biochemical and experimental point of view. Closely related literature is also reviewed in order to understand the function of proteinoids and proteinoid microspheres. Proteinoids or proteinoid microspheres have many activities. Esterolysis, decarboxylation, amination, deamination, and oxidoreduction are catabolic enzyme activities. The formation of ATP, peptides or oligonucleotides is synthetic enzyme activities. Additional activities are hormonal and inhibitory. Selective formation of peptides is an activity of nucleoproteinoid microspheres; these are a model for ribosomes. Mechanisms of peptide and oligonucleotide syntheses from amino acids and nucleotide triphosphate by proteinoid microspheres are tentatively proposed as an integrative consequence of reviewing the literature.

Vestiges of early molecular processes leading to the genetic code

We compare predictions from a proposed model for the origin of the genetic code (J. Theor. Biol (1993) 164, 291-305) with existing information on the base content of codons and abundance of amino acid in different organisms. A comparison is also made between the three groups of amino acids suggested by the model and the two classes of aminoacetyl-tRNA synthetases. The observed agreements tend to support the model.

Thermal synthesis of amino acids and the origin of life

The recent review by Marshall (1994) of the production of amino acids from the interstellar components, formaldehyde and ammonia, is placed in the larger context of the origin of life. Thermal energy, being ubiquitous in the Earth, emerges as the sole necessary form of energy. To appreciate the overview of the natural evolutionary sequence it is necessary to recognize stepwiseness in evolution, a principle that has however been often ignored. Since self organization of thermal protein to cells is instantaneous, but only one step in a geochemical ladder, individual steps may be regarded as instantaneous, while the sequence requires measurable time. Two steps indicated are extrusion of a hot, dry organic magma of amino acids --> peptides into an aqueous environment in which occurs a second step of self organization. In this paper, spinoffs of the defensible theory for the origin of life have been briefly reviewed as a fundamental consequence of nonrandom thermal copolymerization of amino acids.

Autocatalytic sets of proteins

This article investigates the possibility that the emergence of reflexively autocatalytic sets of peptides and polypeptides may be an essentially inevitable collective property of any sufficiently complex set of polypeptides. The central idea is based on the connectivity properties of random directed graphs. In the set of amino acid monomer and polymer species up to some maximum length, M, the number of possible polypeptides is large, but, for specifiable "legitimate" end condensation, cleavage and transpeptidation exchange reactions, the number of potential reactions by which the possible polypeptides can interconvert is very much larger. A directed graph in which arrows from smaller fragments to larger condensation products depict potential synthesis reactions, while arrows from the larger peptide to the smaller fragments depict the reverse cleavage reactions, comprises the reaction graph for such a system. Polypeptide protoenzymes are able to catalyze such reactions. The distribution of catalytic capacities in peptide space is a fundamental problem in its own right, and in its bearing on the existence of autocatalytic sets of proteins. Using an initial idealized hypothesis that an arbitrary polypeptide has a fixed a priori probability of catalyzing any arbitrary legitimate reaction to assign to each polypeptide those reactions, if any, which it catalyzes, the probability that the set of polypeptides up to length M contains a reflexively autocatalytic subset can be calculated and is a percolation problem on such reaction graphs. Because, as M increases, the ratio of reactions among the possible polypeptides to polypeptides rises rapidly, the existence of such autocatalytic subsets is assured for any fixed probability of catalysis. The main conclusions of this analysis appear independent of the idealizations of the initial model, introduce a novel kind of parallel selection for peptides catalyzing connected sequences of reactions, depend upon a new kind of minimal critical complexity whose properties are definable, and suggest that the emergence of self replicating systems may be a self organizing collective property of critically complex protein systems in prebiotic evolution. Similar principles may apply to the emergence of a primitive connected metabolism. Recombinant DNA procedures, cloning random DNA coding sequences into expression vectors, afford a direct avenue to test the distribution of catalytic capacities in peptide space, may provide a new means to select or screen for peptides with useful properties, and may ultimately lead toward the actual construction of autocatalytic peptide sets.

An organismic critique of molecular darwinism

The molecular darwinian approach to the emergence of life treats the competition between RNA sequences for nucleotide resources as the primordial selective process in prebiotic evolution, which prescribes possible pathways for the subsequent elaboration of organizational relationships. Since success in this competition is determined by the "phenotypic" properties of RNA strands in the absence of organizational context, the genesis of biotic organization is dependent upon the establishment of co-operative, hypercyclic interactions between competing RNA sequences. The thesis of this paper is that hypercycle theory is based on unwarranted assumptions about the conditions of prebiotic evolution, and that the implications of these assumptions run counter to both empirical evidence and to the rational by which natural selection operates in evolution generally. An organismic alternative to hypercycle theory is suggested, based on the catalytic microsphere and the thermodynamics of selection.

The evolution of prebiological self-organization: probable colloid-chemical evolution of first prokaryotic cells

This is an attempt to analyse the mechanisms of self-assembly in the course of the origin and early evolution of life on the Earth. A special attention is paid to the investigation of transient stages between the physico-chemical and biological bases of self-assembly, including experimental models and paleontological results. The theory of coacervate-in-coacervate is discussed from the point of view of evolution of first procaryotic cells. Many of the high developed structures of the contemporary cells, such as ribosomes, chromosomes, lipid membranes, some other organelles etc., are claimed to posses a rudimentary polyionic coacervate character.

Self-instructed condensation of amino acids into polymers

In contemporary cells biological information is largely stored in nucleic acids. Therefore, a prerequisite in many theories on the origin of cellular life is the pre-existence of self-replicating polynucleotides that had to be formed by abiotic processes on the prebiotic Earth. It is usually assumed that the spontaneous synthesis of a self-replicating polynucleotide could take place readily. However, serious stereochemical obstacles exist which make Such a synthesis extremely improbable. Amino acids on the other hand, which are abundantly formed in prebiotic simulation experiments, are relatively easily polymerized to macromolecules (protoproteins) that share with modern proteins many properties: e.g., definable non-random structure, selected amino acid sequences, enzyme-like activities and self-assembly into supramolecular structures. Prebiotic polyamino acids are therefore regarded by some scientists, including the present author, as the first informational macromolecules. The origin of this information is the chemical reactivity of the various prebiotic amino acids and their chemical response to their environment. The first informational polynucleotides were likely formed by a polynucleotide polymerase activity of prebiotic protoproteins. A contemporary model for this process is seen, e.g., in the activity of template-free Q beta-replicase.

Evolutionary changes in the information content of polypeptides

Thermal proteins arising from the self-sequencing of amino acids satisfy the necessary conditions required for them to become a candidate of the evolutionary precursors of contemporary proteins. The source matrix of information or, equivalently, the statistical ensemble of polypeptides, in reference to which the information content of each amino acid residue can be defined and determined, changes with time endogenously through the production of and the change in the mechanism of production of polypeptides. The change proceeds in the direction along which the order of autocatalysis, the number of autocatalytic polymers needed for synthesizing one such polymer, increases. The underlying dynamics is material flow equilibration working in any material aggregate open to material flow, saying that any open system changes its interaction with the exterior endogenously and successively so as to maintain the continuity of material flow there. The self-sequencing and the autocatalytic polymerization of amino acids are the forms of producing polypeptides. The change in the mechanism of producing polypeptides results from the incorporation of polynucleotides into the polypeptide synthesis. The earlier polymeric information translation proceeds from polypeptide to polynucleotide. The direction of translation is reversed at a later stage of evolution. All these evolutionary events are consistent with viewing thermal proteins produced by self-sequencing of amino acids as an evolutionary precursor of contemporary proteins.

Prebiotic oligodeoxynucleotide synthesis in a cyclic evaporating system at low temperatures

Deoxynucleoside 5'-monophosphates were condensed by cyanamide or by l-ethyl-3-(3-dimethylaminopropyl) carbodiimide in the presence of ammonium chloride at 0 degree, 37 degrees or 60 degrees C through several cycles of evaporation to dryness with replenishment of all reactants at each cycle. We found that at 37 degrees or 60 degrees cyanamide gives distinctly more high molecular weight material than does carbodiimide. Indeed, the yield of condensed products for the cyanamide reaction (dimers and higher oligomers) was found to be between 60 percent and 80 percent. The molecular weight distribution of the product shifts to higher molecular weights as cycling continues at 37 degrees or 60 degrees for both condensing agents. The water soluble carbodiimide gives higher yields of low molecular weight product but much lower yields of the higher molecular weight products. At 0 degree yields of high molecular weight product were low for both condensing agents. Results of characterization of the products demonstrate the synthesis of oligodeoxynucleotides including tetramers, with 3'-5' phosphodiester linkages.

Natural self-organization of polynucleotides and polypeptides in protobiogenesis: appearance of a protohypercycle

Basic thermal polyamino acids or proteinoids have been reported to be catalytic for both self-instructing polymerization of amino acids and internucleotide synthesis. We show theoretically that a complex suspension of thermal proteinoids, free amino acids, nucleotides and ATP as an energy source can exhibit an evolutionary character. The suspension can produce a prototype of Eigen's hypercycle, or protohypercycle, for which translation proceeds from amino acid to nucleotide. The protohypercycle is suggested to be an evolutionary precursor of the hypercycle, in which translation is from nucleotide to amino acid. The possibility that the Fox-Nakashima microsphere containing both lysine-rich and acidic proteinoids may work as a model of a protohypercycle is considered.

Models for protocellular photophosphorylation

Several photoreactions for transducing light energy have been analyzed for their relevance as models for protocellular photophosphorylation. Inorganic ions and compounds could have played a role in protocellular photophosphorylation. Organic catalysts may have been the next significant agents used by protocells for photophosphorylation. Membranous photophosphorylation probably became the most recent type of photoenergy transduction to be acquired by protocells; it is still used by modern cells although components of the other types of phosphorylation are found in present day cells. Recorded yields of energy-rich phosphates from the model reactions discussed are small. Arguments are advanced that such yields could have been sufficient to have fueled protocellular metabolism which was probably very slow compared to modern cellular metabolism. Future prospects for research in this area are discussed.

Formation of peptides from amino acids by single or multiple additions of ATP to suspensions of nucleoproteinoid microparticles

When lysine-rich proteinoid, which catalyzes the formation of peptides from amino acids and ATP, is complexed with acidic proteinoid to form microspheres of mixed constitution, the normal synthesis by basic proteinoid alone is multiplied several-fold. The product consists not only of small peptides but also of a high-molecular-weight fraction of substituted proteinoid. Suspensions of particles of lysine-rich proteinoid complexed with polyadenylic acid catalyze the synthesis of peptides from each of the amino acids tested with ATP. When equimolar solutions of mixtures of glycine and phenylalanine with ATP are tested in suspensions of complexes of lysine-rich proteinoid and each of various polyribonucleotides, both homopeptides and heteropeptides are produced. Glycylphenylalanine or phenylalanylglycine is the principal product; the preference is related to which polyribonucleotide is in the complex. The rate of conversion of amino acid to peptide is a function of whether ATP is added in a single batch or in repeated amounts adding to the same amount as in the single batch. Related experiments indicate a relatively rapid initial rate of decay of ATP in the system. These results are discussed relative to the mechanisms for continuous generation in modern organisms, as are the results in peptide formation.

Life from an orderly cosmos

Recent astrophysical studies suggest a high degree of order in the inanimate universe, stemming from cosmic beginnings. This state is consistent with the nonrandomness observed experimentally in the thermal polymers of amino acids that figure as an early inanimate stage in organic evolution. The various stages in inanimate matter, protocells, and evolved cells and the degree of order that they represent comport with the second law of thermodynamics on a cosmic scale.

Catalysis of peptide bond formation by histidyl-histidine in a fluctuating clay environment

The condensation of glycine to form oligoglycines during wet-dry fluctuations on clay surfaces was enhanced up to threefold or greater by small amounts of histidyl-histidine. In addition, higher relative yields of the longer oligomers were produced. Other specific dipeptides tested gave no enhancement, and imidazole, histidine, and N-acetylhistidine gave only slight enhancements. Histidyl-histidine apparently acts as a true catalyst (in the sense of repeatedly catalyzing the reaction), since up to 52 nmol of additional glycine were incorporated into oligoglycine for each nmol of catalyst added. This is the first known instance of a peptide or similar molecule demonstrating a catalytic turnover number greater than unity in a prebiotic oligomer synthesis reaction, and suggests that histidyl-histidine is a model for a primitive prebiotic protoenzyme. Catalysis of peptide bond synthesis by a molecule which is itself a peptide implies that related systems may be capable of exhibiting autocatalytic growth.

Metabolic microspheres: origins and evolution

A systematic review of catalytic activities in thermal proteinoids and microspheres aggregated therefrom yields some new inferences on the origins and evolution of metabolism. Experiments suggest that, instead of being inert, protocells were already biochemically and cytophysically competent. The emergence and refinement of metabolism ab initio is thus partly traced conceptually. When the principle of molecular self-instruction, as of amino acids in peptide synthesis, is taken into account as a concomitant of natural selection, an expanded theory of organismic evolution, including saltations, emerges.

Synthesis of peptides from amino acids and ATP with lysine-rich proteinoid

Lysine-rich proteinoids in aqueous solution catalyze the formation of peptides from free amino acids and ATP. This catalytic activity is not found in acidic proteinoids, even though the latter contain some basic amino acid. The pH optimum for the synthesis is about 11, but is appreciable below 8 and above 13. Temperature data indicate an optimum at 20 degrees C or above, with little increase in rate to 60 degrees C. Pyrophosphate can be used instead of ATP, with lesser yields resulting. The ATP-aided syntheses of peptides in aqueous solution occur with several types of proteinous amino acid.

The evolutionary significance of phase-separated microsystems

The source, preparation, and properties of phase-separated systems such as lipid layers, coacervate droplets, sulphobes, and proteinoid microspheres are reviewed. These microsystems are of interest as partial models for the cell and as partial or total models for the protocell. Conceptual benefits from study of such models are: clues to experiments on origins, insights into principles of action and, in some instances, presumable models of the origin of the protocell. The benefits to evolution of organized chemical units are many, and can in part be analyzed. Ease of formation suggests that such units would have arisen early in primondiae organic evolution. Integration of these various concepts and the results of consequent experiments have contributed to the developing theory of the origins of primordial and of contemporary life.