On the 20 canonical amino acids by a cooperative vector-addition principle based on the quasi-28-gon symmetry of the genetic code

The 20 standard amino acids together with 64 tri-nucleotide codons selected in the genetic code constitute a paradigm of complexity in Nature. Atomic rationals for the choice of nucleobases by Nature have recently received much attention. For the importance of stereoelectronic effect in noncovalent intermolecular interaction and biomolecular recognition, the nitrogen atoms of sp hybrid in nucleobases are often the major binding sites for protons and metal ions. Upon a systematic analysis of the structural regularity of nucleobases, we used covalent bonding hybrid of nitrogen atoms, the sp nitrogen atom hybrids (Scheme 1a), as a determinative measure for their empirical stereoelectronic property, the resulted genetic code in UCGA succession shows an almost linear correlation between amino acid property and sp N-numbers. We suggested a possible primordial core in the genetic code on the basis of two pieces of evidence. First, accompanied with a linear correlation between the hydropathy of amino acids and the sp nitrogen-atom numbers of nucleobases in a rearranged genetic code, codons for A, V, T, G and P form a crossed-intersection core (Fig. 1a); second, a stereostructural re-classification of the 20 amino acids lead to five distinct groups of amino acids (Scheme 1b), which precisely overlap the above five groups of codons. Subsequently, a physical organic chemistry principle was employed together with geometrical approaches to analyzing a rearranged code, quasi-28-gon symmetries with two presumed evolutionary axes were revealed from the code, displayed in the Yang’s model for the genetic code (Fig. 1c). The full details of the elucidation and representation of a quasi-28-gon symmetry are given in several previous papers. The purpose of this communication is to describe a newly identified vector-in-space addition principle within the 20 canonical amino acids at their atomic level, which is consistent with the coevolution postulate and further shows that the atomic contents in amino acids may play a role in the origin and evolution of the genetic code.