Stability of the genetic code and optimal parameters of amino acids

TL;DR

This paper investigates how the structure of the genetic code influences the optimal physico-chemical parameters of amino acids, revealing a co-evolutionary relationship that enhances code stability against errors.

Contribution

It demonstrates that the genetic code structure strictly determines the optimal amino acid parameters, linking code stability with amino acid properties through inverse problem analysis.

Findings

Optimal amino acid parameters are unambiguously determined by code structure.

Hydrophobicity values correlate with natural scales, indicating co-evolution.

The genetic code's structure constrains amino acid properties to maximize stability.

Abstract

The standard genetic code is known to be much more efficient in minimizing adverse effects of misreading errors and one-point mutations in comparison with a random code having the same structure, i.e. the same number of codons coding for each particular amino acid. We study the inverse problem, how the code structure affects the optimal physico-chemical parameters of amino acids ensuring the highest stability of the genetic code. It is shown that the choice of two or more amino acids with given properties determines unambiguously all the others. In this sense the code structure determines strictly the optimal parameters of amino acids. In the code with the structure of the standard genetic code the resulting values for hydrophobicity obtained in the scheme leave one out and in the scheme with fixed maximum and minimum parameters correlate significantly with the natural scale. This indicates the co-evolution of the genetic code and physico-chemical properties of amino acids.