Concentration of specific amino acids at the catalytic/active centers of highly-conserved "housekeeping" enzymes of central metabolism in archaea, bacteria and Eukaryota: is there a widely conserved chemical signal of prebiotic assembly?

From the RNA world to the RNA/protein world: contribution of some riboswitch-binding species?

Some amino acids and their formal derivatives, currently riboswitch-binding species, could have interacted with polyribonucletides in prebiotic environments, leading to the peptide formation. If the resulting compounds had led to a sustainable polymerization of amino acids and the new structures had catalytic activity, such would have been an important contribution to the transition from the RNA world to the RNA/Protein world.

Uniquely localized intra-molecular amino acid concentrations at the glycolytic enzyme catalytic/active centers of Archaea, Bacteria and Eukaryota are associated with their proposed temporal appearances on earth

The distributions of amino acids at most-conserved sites nearest catalytic/active centers (C/AC) in 4,645 sequences of ten enzymes of the glycolytic Embden-Meyerhof-Parnas pathway in Archaea, Bacteria and Eukaryota are similar to the proposed temporal order of their appearance on Earth. Glycine, isoleucine, leucine, valine, glutamic acid and possibly lysine often described as prebiotic, i.e., existing or occurring before the emergence of life, were localized in positional and conservational defined aggregations in all enzymes of all Domains. The distributions of all 20 biologic amino acids in most-conserved sites nearest their C/ACs were quite different either from distributions in sites less-conserved and further from their C/ACs or from all amino acids regardless of their position or conservation. The major concentrations of glycine, e.g., perhaps the earliest prebiotic amino acid, occupies ≈ 16 % of all the most-conserved sites within a volume of ≈ 7-8 Å radius from their C/ACs and decreases linearly towards the molecule's peripheries. Spatially localized major concentrations of isoleucine, leucine and valine are in the mid-conserved and mid-distant sites from their C/ACs in protein interiors. Lysine and glutamic acid comprise ≈ 25-30 % of all amino acids within an irregular volume bounded by ≈ 24-28 Å radii from their C/ACs at the most-distant least-conserved sites. The unreported characteristics of these amino acids: their spatially and conservationally identified concentrations in Archaea, Bacteria and Eukaryota, suggest some common structural organization of glycolytic enzymes that may be relevant to their evolution and that of other proteins. We discuss our data in relation to enzyme evolution, their reported prebiotic putative temporal appearances on Earth, abundances, biological "cost", neighbor-sequence preferences or "ordering" and some thermodynamic parameters.

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.