Cargando…
Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements
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 s...
Autores principales: | , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2017
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5552740/ https://www.ncbi.nlm.nih.gov/pubmed/28798365 http://dx.doi.org/10.1038/s41598-017-08041-7 |
_version_ | 1783256506884423680 |
---|---|
author | Bohórquez, Hugo J. Suárez, Carlos F. Patarroyo, Manuel E. |
author_facet | Bohórquez, Hugo J. Suárez, Carlos F. Patarroyo, Manuel E. |
author_sort | Bohórquez, Hugo J. |
collection | PubMed |
description | 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 ([Formula: see text] = 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 | Online Article Text |
id | pubmed-5552740 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-55527402017-08-14 Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements Bohórquez, Hugo J. Suárez, Carlos F. Patarroyo, Manuel E. Sci Rep Article 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 ([Formula: see text] = 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. Nature Publishing Group UK 2017-08-10 /pmc/articles/PMC5552740/ /pubmed/28798365 http://dx.doi.org/10.1038/s41598-017-08041-7 Text en © The Author(s) 2017 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Bohórquez, Hugo J. Suárez, Carlos F. Patarroyo, Manuel E. Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements |
title | 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_short | 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 |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5552740/ https://www.ncbi.nlm.nih.gov/pubmed/28798365 http://dx.doi.org/10.1038/s41598-017-08041-7 |
work_keys_str_mv | AT bohorquezhugoj masssecondarystructurepropensityofaminoacidsexplaintheirmutabilityandevolutionaryreplacements AT suarezcarlosf masssecondarystructurepropensityofaminoacidsexplaintheirmutabilityandevolutionaryreplacements AT patarroyomanuele masssecondarystructurepropensityofaminoacidsexplaintheirmutabilityandevolutionaryreplacements |