POLYPEPTIDES. IX. THE KINETICS OF STRONG-BASE INITIATED POLYMERIZATIONS OF AMINO ACID-N-CARBOXYANHYDRIDES

From helix-coil transitions to protein folding

An evolution of procedures to simulate protein structure and folding pathways is described. From an initial focus on the helix-coil transition and on hydrogen-bonding and hydrophobic interactions, our original attempts to determine protein structure and folding pathways were based on an experimental approach. Experiments on the oxidative folding of reduced bovine pancreatic ribonuclease A (RNase A) led to a mechanism by which the molecule folded to the native structure by a minimum of four different pathways. The experiments with RNase A were followed by development of a molecular mechanics approach, first, making use of global optimization procedures and then with molecular dynamics (MD), evolving from an all-atom to a united-residue model. This hierarchical MD approach facilitated probing of the folding trajectory to longer time scales than with all-atom MD, and hence led to the determination of complete folding trajectories, thus far for a protein containing as many as 75 amino acid residues. With increasing refinement of the computational procedures, the computed results are coming closer to experimental observations, providing an understanding as to how physics directs the folding process.

Chirality and life

The crucial role of homochirality and chiral homogeneity in the self-replication of contemporary biopolymers is emphasized, and the experimentally demonstrated advantages of these chirality attributes in simpler polymeric systems are summarized. The implausibility of life without chirality and hence of a biogenic scenario for the origin of chiral molecules is stressed, and chance and determinate abiotic mechanisms for the origin of chirality are reviewed briefly in the context of their potential viability on the primitive Earth. It is concluded that all such mechanisms would be nonviable, and that the turbulent prebiotic environment would require an ongoing extraterrestrial source for the accumulation of chiral molecules on the primitive Earth. A scenario is described wherein the circularly polarized ultraviolet synchrotron radiation from the neutron star remnants of supernovae engenders asymmetric photolysis of the racemic constituents in the organic mantles on interstellar dust grains, whereupon these chiral constituents are transported repetitively to the primitive Earth by direct accretion of the interstellar dust or through impacts of comets and asteroids.

Computer experiment for selection of optical isomer during prebiotic polymerization

Computer experiments simulating prebiotic polymerization were carried out using the Monte Carlo method. A high degree of single optical isomers from racemic monomers occurred by assuming a small asymmetry in their chemical natures, which was included to investigate an amplification of the asymmetry due to parity non-conservation. The asymmetry developed much more slowly than the growth of polymers, and the degree of asymmetry in the polymers increased with the degree of polymerization. Competition between the preferential selection and the disturbance by the statistical fluctuation are discussed.

Experiments on the amplification of optical activity

By way of investigating possible mechanisms for the abiotic amplification of small enantiomeric excesses (e.e.'s) in almost racemic mixtures of amino acid enantiomers, we have undertaken a quantitative study of the base-initiated partial polymerization of leucine and valine N-carboxy-anhydride (NCA) enantiomer mixtures containing known excesses of both the R- and S-forms. Polymerization to the extent of ca. 50% of leucine NCA having an 8-70% e.e. of either the R- or S-enantiomer led to an e.e. enhancement in the polymer, which contained a 12-84% e.e. of that enantiomer which predominated in the original monomer NCA. A corresponding decrease in the e.e. of the initially predominant enantiomer was noted in the unpolymerized residue from each reaction. Polymerization to the extent of 25-50% of mixtures of valine NCA enantiomers containing a 12-13% e.e. of either R- or S-isomer led to polymers showing a 7-8% decrease in the e.e. of the initially predominant enantiomer, and to an increase of its e.e. in the unpolymerized residue. these divergent results, the latter of which is quite novel, are compared with earlier qualitative results in the literature and are discussed briefly from the viewpoint of both mechanism and the amplification of optical activity.

The asymmetry of life

Stereoselective physical phenomena and their possible importance for the prevalence of D-sugars and L-aminoacids in living matter are reviewed. A classification is presented according to which a selective force provides a microscopic or macroscopic selection depending on its generality when taken over a macrosystem (a 'unitary biosphere' such as the Earth). The microscopic 'selections' are not genuine selections because the final sense of asymmetry is here determined by chance, in other words the initial choice is 'random', while it is 'directed' in the macroscopic selection. Two macroscopic selections appear possible: 1. selection due to an intrinsic energy difference between enantiomorph configurations, 2. selection accomplished by elliptically polarised radiation.