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Hidden thermodynamic information in protein amino acid mutation tables

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  • Phillips, J.C.

Abstract

We combine the standard 1992 20×20 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 2×10 properties that define quaternary 4×5 subgroups (but not quinary 5×4 subgroups), with the modern MZ bioinformatic scale giving much better results. The quaternary 5-mer MZ 4×5 subgroups are called mutons (Mu5). Among all hydropathicity scales, the MZ scale uniquely exhibits a smooth, deep mutational minimum at its center associated with alanine, glycine, the smallest amino acid, and histidine.

Suggested Citation

  • Phillips, J.C., 2017. "Hidden thermodynamic information in protein amino acid mutation tables," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 469(C), pages 676-680.
    • Handle: RePEc:eee:phsmap:v:469:y:2017:i:c:p:676-680
    DOI: 10.1016/j.physa.2016.11.074
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    References listed on IDEAS

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    1. Phillips, J.C., 2016. "Autoantibody recognition mechanisms of p53 epitopes," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 451(C), pages 162-170.
    2. Phillips, J.C., 2014. "Fractals and self-organized criticality in proteins," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 415(C), pages 440-448.
    3. Phillips, J.C., 2015. "Phase transitions in the web of science," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 428(C), pages 173-177.
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    Cited by:

    1. Moret, M.A. & Zebende, G.F. & Phillips, J.C., 2019. "Hydropathic wave ordering of alpha crystallin—Membrane interactions enhances human lens transparency and resists cataracts," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 514(C), pages 573-579.

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