Hidden Thermodynamic Information in Protein Amino Acid Mutation Tables

TL;DR

This paper investigates how amino acid mutation tables encode thermodynamic information by combining substitution matrices with hydropathicity scales, revealing underlying binary properties and subgroup structures that influence mutation rates.

Contribution

It introduces a novel analysis linking mutation matrices with thermodynamic scales, uncovering binary amino acid properties and subgroup structures that improve mutation prediction.

Findings

MZ hydropathicity scale yields better mutation rate predictions.

Mutation rates reflect binary amino acid properties related to thermodynamics.

Identification of quaternary 4x5 subgroups called mutons (Mu5).

Abstract

We combine the standard 1992 20x20 substitution matrix based on block alignment, BLOSUM62, with the standard 1982 amino acid hydropathicity scale KD as well as the modern 2007 hydropathicity scale MZ, and compare the results. The 20-parameter KD and MZ hydropathicity scales have different thermodynamic character, corresponding to first and second order transitions. The KD and MZ comparisons show that the mutation rates reflect quantitative iteration of qualitative amino acid phobic and philic binary 2x10 properties that define quaternary 4x5 subgroups (but not quinary 5x4 subgroups), with the modern MZ bioinformatic scale giving much better results. The quaternary 5 mer MZ 4x5 subgroups are called mutons (Mu5).