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

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.

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.

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.

Thermosynthesis by biomembranes: energy gain from cyclic temperature changes

A theoretical mechanism is described allowing biomembranes to convert heat into electrical energy during temperature cycling (thermosynthesis). Necessary conditions for thermosynthesis are a temperature dependent electrical capacity and a conductivity as low as that of artificial lipid bilayers. Temperature cycling, and consequently thermosynthesis, can take place in leaves during cyclic transpiration and in organisms in natural waters that are carried along by convection currents. Electrogenic ATPases can convert the electrical energy gained by thermosynthesis into ATP if their activity and stoichiometry are properly regulated. The power of thermosynthesis is discussed and its possible value compared with the power of respiration. Environments where thermosynthesis may occur are listed. Thermosynthesis is a plausible energy source for the first living organisms.

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.

Factors controlling the size of proteinoid microspheres

Proteinoid microspheres were prepared from aqueous solutions containing various metal halides under different pH values and ionic strengths. The effects of pH and ionic strength on the diameter of the microspheres and also the solubility of the proteinoid in hot solution (100 degrees C) were investigated by means of different physiochemical measurements. It is found that, under high ionic strength, the diameter of the microsphere is mainly affected by the salt concentration, while the pH of the system is the main factor when the ionic strength is low. Moreover, the change in the solubility with ionic strength and pH is found to show a striking resemblance to that in the diameter with both factors. On the basis of these results, the external and internal factors controlling the size of proteinoid microspheres are clarified, and a plausible mechanism of the proteinoid microsphere formation under prebiotic conditions is also discussed.

Formation of specific amino acid sequences during carbodiimide-mediated condensation of amino acids in aqueous solution

Carbodiimide-mediated peptide synthesis in aqueous solution at room temperature has been studied with respect to self-ordering of amino acids. Inasmuch as glutamic acid is readily converted into pyroglutamic acid, the peptides formed by copolymerization of glutamic acid with other amino acids are preferentially pyroglutamyl-peptides. Competition experiments were carried out to determine the influence of the amino acid side chains on the reactivity of amino acids and peptides during the dehydration condensation. The results show that the self-ordering process is controlled by both the activated carboxyl component (amino acid or growing peptide) and the incoming amino acid. A condensation of pyroglutamic acid, alanine and another amino acid component Xxx (Xxx = Gly, Val, Leu or Gly-Tyr) preferentially yielded the dipeptide pyroGlu-Ala, but the formation of the tripeptide pyroGlu-Ala-Ala became strongly reduced because of competing reactions. A simple explanation for the observed selectivities is not at hand. Polypeptides were so far only obtained when they were allowed to precipitate in the reaction system. Evidence for the non-random copolymerization of larger peptides is presented as well.

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.