Quantification of Peptide Bond Types in Human Proteome Indicates How DNA Codons were Assembled at Prebiotic Conditions

Jozef Nahalka

doi:10.4172/jpb.1000184

Abstract

[GADV]-protein world hypothesis [1] leaded me to quantification of decapeptides assembled from G, A, V, D in human proteome. The G, A, V, and D amino acids were related to the nucleotides Guanine (g), Cystosine (c), Uracil (u), and Adenine (a). The search revealed agreement with the genetic code. The types of prebiotic peptide bonds represent probably the first selection power that established the base order in the codons. The genetic code underwent three phases of formation, which explain why modern codons have their particular order of nucleotides: the monobase, dibase and the modern phase (tribase). Sequence alignments and 3D structures of aminoacyl-tRNA synthetases confirm the depicted picture of “relatedness” and the picture indicates how “relatedness” is used by aminoacyl-tRNA synthetases for navigation into and within of the C-terminal anticodon-binding domain. The findings presented here illustrate the novel concept of possible translation of the amino acid sequence into a nucleotide sequence that can be in interactive or contrary mode regarding to desired protein-RNA interactions. Hopefully, it could be used in synthetic biology.

Highlights

It seems that determining the origin of the genetic code is a much more challenging issue deciphering the code
The final phase was illustrated analogically, for example, the highest number among GXGXGXGXGX (X=all 20AA) peptides was obtained for GGGGGGGGGG, so glycine connected to di-guanine nucleic acid preferentially reacted with other glycine connected to mono or diguanine nucleotide - “tribase codon-amino acid” phase of creation
These three phases were named according to Crick [21] who postulated that the evolution of the genetic code involved three phases: of which a molecule is capable

Summary

Introduction

It seems that determining the origin of the genetic code is a much more challenging issue deciphering the code. The final phase was illustrated analogically, for example, the highest number among GXGXGXGXGX (X=all 20AA) peptides was obtained for GGGGGGGGGG, so glycine connected to di-guanine nucleic acid preferentially reacted with other glycine connected to mono or diguanine nucleotide (gg-G + g-G = ggg-GG) - “tribase codon-amino acid” phase of creation. These three phases were named according to Crick [21] who postulated that the evolution of the genetic code involved three phases: of which a molecule is capable (i.e., van der Waals repulsion). “Relatedness” should be defined in terms of a composite of all the interactions of which a molecule is capable and these in a proportion defined by the context in question.” [16]

A BLAST search of human taxid

Materials and Methods

Results and Discussion

Summary