The role of catalysis on the formation of an active proto-enzyme in the prebiotic aqueous environment

Carlo Canepa

doi:10.4236/ns.2013.55069

Abstract

A model detailing the conditions for the formation of active enzymes from amino acid monomers in the pre-biotic aqueous environment is proposed, making use of only a minimal number of parameters: the intensity of the amino acid source and the experimental rate coefficient for polypeptide hydrolysis. In a closed system with fixed total amino acid concentration, the formation of polypeptides of significant length is precluded by hydrolysis. In the presence of an amino acid source, the behavior of the steady state solutions is dependent on the efficiency of the catalytic activity in the environment. In absence of catalysis the formation of long amino acid chains shows a remarkable similarity to the equilibrium problem, i.e. it is equally unlikely that an active protein forms. In the presence of catalysis the concentration of polypeptides of significant length increases dramatically to about the same order of magnitude as the steady state concentration of the monomers. Besides the important notion of the proto-enzyme concentration, the model offers a link between the given environmental conditions (flux of monomers, rates of the peptide bond formation and hydrolysis, size of the amino acid set) and properties of the polypeptide relevant to its catalytic properties, such as its length and conserved number of residues.

Highlights

This work aims to discuss, on the basis of known chemistry, if the prebiotic conditions on Earth could allow for the spontaneous formation of catalytic polypeptides without any prior complex RNA-based chemistry that could code for enzymes with specific amino acid sequences
An evolutionary process able to build an active enzyme with n amino acid residues from its monomeric components must have produced most the possible polypeptides of length n
It has been determined experimentally that, in order to retain the catalytic activity of an enzyme, a fraction between 0.1 and 0.2 of its amino acid sequence is constrained [13]

Summary

Introduction

This work aims to discuss, on the basis of known chemistry, if the prebiotic conditions on Earth could allow for the spontaneous formation of catalytic polypeptides without any prior complex RNA-based chemistry that could code for enzymes with specific amino acid sequences. We assume a source of amino acids sustained by processes driven by an energy source acting on simple organic compounds and focus on the formation of peptide bonds among amino acid units until the critical length that allows for catalytic properties is attained. There are a number of simulations of the processes taking place in interstellar ices showing how many amino acids may form from simple organic molecules. A similar approach was undertaken by Chen and Nowak [6] that investigated the equilibrium configuration of RNA polymers formed from activated monomers and exhibiting self-replication and selection

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