Origin of Homochirality of Amino Acids in the Biosphere

Why Were [GADV]-amino Acids and GNC Codons Selected and How Was GNC Primeval Genetic Code Established?

Correspondence relations between codons and amino acids are determined by genetic code. Therefore, genetic code holds a key of the life system composed of genes and protein. According to the GNC-SNS primitive genetic code hypothesis, which I have proposed, it is assumed that the genetic code originated from GNC code. In this article, first, it is discussed from a standpoint of primeval protein synthesis, why four [GADV]-amino acids were selected and used in the first GNC code. Next, it is explained from another standpoint of the most primitive anticodon-stem loop tRNAs (AntiC-SL tRNAs), how four GNCs were selected for the first codons. Furthermore, in the last section of this article, I will explain my idea of how the correspondence relations between four [GADV]-amino acids and four GNC codons were established. Namely, the origin and evolution of the genetic code was discussed comprehensively from several aspects of [GADV]-proteins, [GADV]-amino acids, GNC codons, and anticodon stem-loop tRNAs (AntiC-SL tRNAs), which relate each other to the origin of the genetic code, as integrating GNC code frozen-accident theory, coevolution theory, and adaptive theory on the origin of the genetic code.

DStabilize: A Web Resource to Generate Mirror Images of Biomolecules

Peptides comprising D-amino acids have been shown to be resistant to proteolysis. This makes them potential candidates as probes of cellular interactions, notably protein-biomolecule interactions. However, the empirical conversion of the amino acids that constitute a peptide from L-forms to D-forms will result in abrogation of the normal interactions made by the L-amino acids due to side-chain orientation changes that are associated with the changes in chirality. These interactions can be preserved by reversing the sequence of the D-peptide. We present a web server (http://dstabilize.bii.a-star.edu.sg/) that allows users to convert between L-proteins and D-proteins and for sequence reversal of D-peptides, along with the capability of performing other empirical geometric transforms. This resource allows the user to generate structures of interest easily for subsequent in silico processing.

Explaining the Variations in Isotopic Ratios in Meteoritic Amino Acids

Measurements of the isotopic abundances in meteoritic amino acids have found enhancements of ²H/H, ¹⁵N/¹⁴N, and ¹³C/¹²C in the amino acids in the meteorites studied. We show that they are consistent with the processing of the constituents of the meteorites by electron antineutrinos that would be expected from a core-collapse supernova or neutron-star merger. Using theoretical electron antineutrino cross-sections, we are able to predict these isotopic ratio variations depending on the time-integrated antineutrino flux at the site where the amino acids were processed.

Connections Between Nuclear Physics and the Origin of Life - Examining the Origin of Biomolecular Chirality

The discovery of bio-molecules in meteorites with an excess of one chiral state has created one of the biggest questions in astrobiology today. That is, what is the origin of bio-molecular homochirality? Studies of this question are highly interdisciplinary, and while several phenomenological models exist, we examine the relationship between fundamental symmetries at the particle level and the macroscopic formation of bio-molecules. A model has been developed which couples fundamental interactions with the formation of molecular chirality. In this magneto-chiral model atomic nuclei bound in amino acids interact via the weak interaction in stellar environments. Nuclei are coupled to the molecular geometry (chirality) via the shielding tensor, the same interaction responsible for NMR identification. Associated with this is the fact that isotopic abundances vary from solar system values. Interactions with leptons can selectively destroy one chiral state over the other while changing isotopic values. Possible sites are proposed in which this model may exist.

The self-disproportionation of enantiomers (SDE) of amino acids and their derivatives

This review covers the phenomenon of the self-disproportionation of enantiomers (SDE) of amino acids and their derivatives in all its guises from phase transformations (recrystallization, sublimation, and distillation), to the application of force fields, through to chromatography including HPLC, MPLC, gravity-driven column chromatography, and SEC. The relevance of the SDE phenomenon to amino acid research and to marketed pharmaceuticals is clear given the potential for alteration of the enantiomeric excess of a portion of a scalemic sample. In addition, the possible contribution of the SDE phenomenon to the genesis of prebiotic homochirality is considered.

Spontaneous formation and amplification of an enantioenriched α-amino nitrile: a chiral precursor for Strecker amino acid synthesis

Without the addition of any chiral substances, the spontaneous formation of an enantioenriched α-amino nitrile (up to 96% ee), which is a chiral precursor for Strecker amino acid synthesis, has been achieved in combination with conglomerate formation. The frequency of the formation of enantiomorphs exhibits an approximate stochastic distribution, i.e., L-form occurred 21 times and D-form occurred 22 times, which fulfils the conditions necessary for spontaneous absolute asymmetric synthesis.

S-Isovaline Contained in Meteorites, Induces Enantiomeric Excess in D,L-glutamic Acid During Recrystallization

S-Isovaline (S-Iva: 6.7 mmol) and D,L-glutamic acid (Glu: 2 mmol) were dissolved in 10 ml of hot water, and the resulting solution was divided in 5 vessels. After recrystallization, the crystals were collected from each vessel, and the enantiomeric excess (ee) of Glu was determined with chemical derivatization using 1-fluoro-2,4-dinitrophenyl- 5-L-leucinamide followed by high-performance liquid chromatography. Ten crystallizations provided all D-rich Glu with ee values of 2.69 % ± 0.81% (mean ± standard deviation), and those using R-Iva provided all L-rich Glu with ee values of 6.24 % ± 2.20%. Five recrystallizations of D,L-Glu alone provided ee values of 0.474 % ± 0.33%. The differences among these three ee values were statistically significant, showing that S-Iva, which was present in meteorites caused a significant induction of ee in this physiological amino acid. This is the first outcome that S-Iva induced ee changes in a physiological amino acid. S-Iva did not induce any ee changes in D,L-asparagine, leucine, valine, methionine, phenylalanine, tryptophan, glutamine, tyrosine, aspartic acid, or histidine under similar recrystallizations.

Dynamic induction of enantiomeric excess from a prochiral azobenzene dimer under circularly polarized light

The ability to photoinduce enantiomeric excess from the chirality of circularly polarized light (CPL) is pertinent to the study of the origin of homochirality in biomolecules. Such CPL-induced reactions, including both chirality generation and formation of partial enantiomeric imbalance, from nonchiral starting compounds have been known, however, only for the conversion of diarylolefins into chiral helicenes. In this study we synthesized three different prochiral molecules, each featuring a pair of photoisomerizable phenylazo moieties arranged symmetrically upon the phenyl rings of an sp3-hybridized carbon atom (1), the phenyl rings of [2.2]paracyclophane (2), and the ortho positions of a phenyl ring bearing a naphthyl unit (3), and then investigated the possibility of photoinducing enantiomeric excess under CPL. Irradiation of 1-3 with light induced E ↔ Z photoisomerizations of their azobenzene moieties, giving mixtures of their EE, EZ, and ZZ isomers in the photostationary state (PSS). Among these regioisomers, the EZ forms are chiral and existed as racemic mixtures of R and S stereoisomers. Upon CPL irradiation of 3, circular dichroism (CD) revealed enantiomeric enrichment of one of the EZ stereoisomers; furthermore, irradiation with r- or l-CPL gave CD signals opposite in sign, but with equal intensity, in the PSS. In contrast, 1 and 2 did not give any detectable induced CD upon CPL irradiation. These experimental results can be explained by considering the different Kuhn anisotropy factors (g) of the (R)-EZ and (S)-EZ stereoisomers of 1-3, assuming that the origin of the enantiomeric excess is the enantio-differentiating photoisomerization from EZ stereoisomers to nonchiral EE or ZZ regioisomers by r- or l-CPL. In short, we demonstrate the simultaneous induction of chirality and enantiomeric excess from a prochiral azobenzene dimer via a chiral regioisomer formed in situ upon CPL irradiation.

Deracemization of amino acids by partial sublimation and via homochiral self-organization

Deracemization of a 50/50 mixture of enantiomers of aliphatic amino acids (Ala, Leu, Pro, Val) can be achieved by a simple sublimation of a pre-solubilized solid mixture of the racemates with a huge amount of a less-volatile optically active amino acid (Asn, Asp, Glu, Ser, Thr). The choice of chirality correlates with the handedness of the enantiopure amino acids--Asn, Asp, Glu, Ser, and Thr. The deracemization, enantioenrichment and enantiodepletion observed in these experiments clearly demonstrate the preferential homochiral interactions and a tendency of natural amino acids to homochiral self-organization. These data may contribute toward an ultimate understanding of the pathways by which prebiological homochirality might have emerged.