The Production ofde novo Folded Proteins by a Stepwise Chain Elongation: A Model for Prebiotic Chemical Evolution of Macromolecular Sequences

Abstract

We describe an experimental procedure to mimic the formation of long (over 40 residues) co-oligopetide sequences in many identical copies which may have occurred in the prebiotic molecular evolution. The basic hypothesis is that chain formation is based on the stepwise fragment condensation of randomly generated short oligopeptides, whereby the elongation takes place under the contingent environmental constraints (solubility, pH, salinity), which eliminate most of the products, and thus determine the selection towards one particular small set of chains. The present work aims at verifying the validity of this scheme. In order to do so, we utilize a classic synthetic procedure based on the Merrifield solid-phase synthesis of peptides for the synthesis of randomly produced peptides as well as for their stepwise fragment condensation. Thus, starting from a library of peptides with n=10, the first condensation step produces a library of 16 peptides with 20 residues each (n=20), of which only four remain water-soluble and, therefore, capable to undergo the next fragment condensation step. This gives rise to 16 peptides with n=30, out of which twelve precipitate out under the chosen pH and buffer conditions and are eliminated. Finally, a 44-residue-long water-soluble de novo protein is obtained. This has no homologies or similarities with extant proteins, and, based on circular dichroism (CD), it assumes a stable three-dimensional folding. In agreement with CD data, molecular-modelling simulations suggest an helical fold for the protein with poor, if any, structural homology with known proteins. The implication of this procedure as a general mechanism for the etiology of de novo macromolecular sequences and globular proteins in the origin of life is briefly discussed.

Chemistry Constraints on the Origin of Life

“…[22] Focusing on prebiotic kinetic control should encourage the study of simple peptidesa sc atalysts for the synthesis of peptide and nucleic acid bonds.I nt his context, we have even formulated an alternative (the evolutiono fp roteases) to the notion of self-reproduction. In other words,a ll this might be enough to propose alternative routes to move out of the impasse of the present situation on the origin of life.…”

“…In particular,t he actiono fc atalytic prebiotic peptides for the synthesis of protein-likes tructures has never been properly investigated and is one of these open questions that somehow do not attract interest in the literature on the origino fl ife.T here is one paper on the condensation of random co-oligopeptidesw ith ten residues each;aproof of concept that this kind of condensation can give rise to proteins. [22] In fact, one ex novo foldable protein with over 40 residues was obtained;however, in this case,the condensation of the decapeptides was carried out by the Merrifield methodb ecause at that time the actiono fp eptides such as SerÀHis was not yet known.…”

“…One might assume that, in analogy to pbz formation, an entire family of proteolytic polypeptidesc ould have been formed, which byt heir proper evolution -m utual proteolytic cleavage and fragment condensation-may have given rise to enzymes capable of catalyzing other complexr eactions,i ncludingt he synthesis of oligonucleotides.I tw ould be ak ind of "proteases-first" hypothesis.I t is as cenario that has the same validity as the prebiotic RNAh ypothesis.I tc an be tested experimentally to ac ertain extent because we know,i np rinciple,h ow to make prebiotic polypeptides and proteins [7,20,22] much more than we know how to make as r-RNAm olecule.…”

Question 1: Origin of Life and the Living State

“…Here, my student, Thomas LaBean showed some years ago that stochastic polypeptides biased to the known ratio of amino acids in evolved proteins form helix and beta sheet structures and molten globules or even better folded structures, (LaBean 1993). Luisi and colleagues have recently extended this to fully random polypeptides (Chessari et al 2006). Thus, in so far as folding modestly well is required for catalytic activity, this property seems abundant among polymers of the standard twenty amino acids.…”

Catalysis in the Primordial World

“…32,33 Firstly, two small families (A and B) of four decapeptides each were synthesized, and by their combinations (A•B), 16 oligopeptides of length 20 were prepared. However, only four of them were soluble in water.…”