Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements

Abstract Why is an amino acid replacement in a protein accepted during evolution? The answer given by bioinformatics relies on the frequency of change of each amino acid by another one and the propensity of each to remain unchanged. We propose that these replacement rules are recoverable from the se...

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Autores principales:	Hugo J. Bohórquez, Carlos F. Suárez, Manuel E. Patarroyo
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/cb76b1d6138444888f1136d1f6f0f2f2
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spelling	oai:doaj.org-article:cb76b1d6138444888f1136d1f6f0f2f22021-12-02T15:06:04ZMass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements10.1038/s41598-017-08041-72045-2322https://doaj.org/article/cb76b1d6138444888f1136d1f6f0f2f22017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-08041-7https://doaj.org/toc/2045-2322Abstract Why is an amino acid replacement in a protein accepted during evolution? The answer given by bioinformatics relies on the frequency of change of each amino acid by another one and the propensity of each to remain unchanged. We propose that these replacement rules are recoverable from the secondary structural trends of amino acids. A distance measure between high-resolution Ramachandran distributions reveals that structurally similar residues coincide with those found in substitution matrices such as BLOSUM: Asn ↔ Asp, Phe ↔ Tyr, Lys ↔ Arg, Gln ↔ Glu, Ile ↔ Val, Met → Leu; with Ala, Cys, His, Gly, Ser, Pro, and Thr, as structurally idiosyncratic residues. We also found a high average correlation ($$\overline{R}$$ R¯ = 0.85) between thirty amino acid mutability scales and the mutational inertia (I X ), which measures the energetic cost weighted by the number of observations at the most probable amino acid conformation. These results indicate that amino acid substitutions follow two optimally-efficient principles: (a) amino acids interchangeability privileges their secondary structural similarity, and (b) the amino acid mutability depends directly on its biosynthetic energy cost, and inversely with its frequency. These two principles are the underlying rules governing the observed amino acid substitutions.Hugo J. BohórquezCarlos F. SuárezManuel E. PatarroyoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-12 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Hugo J. Bohórquez Carlos F. Suárez Manuel E. Patarroyo Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements
description	Abstract Why is an amino acid replacement in a protein accepted during evolution? The answer given by bioinformatics relies on the frequency of change of each amino acid by another one and the propensity of each to remain unchanged. We propose that these replacement rules are recoverable from the secondary structural trends of amino acids. A distance measure between high-resolution Ramachandran distributions reveals that structurally similar residues coincide with those found in substitution matrices such as BLOSUM: Asn ↔ Asp, Phe ↔ Tyr, Lys ↔ Arg, Gln ↔ Glu, Ile ↔ Val, Met → Leu; with Ala, Cys, His, Gly, Ser, Pro, and Thr, as structurally idiosyncratic residues. We also found a high average correlation ($$\overline{R}$$ R¯ = 0.85) between thirty amino acid mutability scales and the mutational inertia (I X ), which measures the energetic cost weighted by the number of observations at the most probable amino acid conformation. These results indicate that amino acid substitutions follow two optimally-efficient principles: (a) amino acids interchangeability privileges their secondary structural similarity, and (b) the amino acid mutability depends directly on its biosynthetic energy cost, and inversely with its frequency. These two principles are the underlying rules governing the observed amino acid substitutions.
format	article
author	Hugo J. Bohórquez Carlos F. Suárez Manuel E. Patarroyo
author_facet	Hugo J. Bohórquez Carlos F. Suárez Manuel E. Patarroyo
author_sort	Hugo J. Bohórquez
title	Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements
title_short	Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements
title_full	Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements
title_fullStr	Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements
title_full_unstemmed	Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements
title_sort	mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/cb76b1d6138444888f1136d1f6f0f2f2
work_keys_str_mv	AT hugojbohorquez masssecondarystructurepropensityofaminoacidsexplaintheirmutabilityandevolutionaryreplacements AT carlosfsuarez masssecondarystructurepropensityofaminoacidsexplaintheirmutabilityandevolutionaryreplacements AT manuelepatarroyo masssecondarystructurepropensityofaminoacidsexplaintheirmutabilityandevolutionaryreplacements
_version_	1718388610213871616

Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements

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