Measuring evolutionary rates of proteins in a structural context

We describe how to measure site-specific rates of evolution in protein-coding genes and how to correlate these rates with structural features of the expressed protein, such as relative solvent accessibility, secondary structure, or weighted contact number. We present two alternative approaches to ra...

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Detalles Bibliográficos
Autores principales: Sydykova, Dariya K., Jack, Benjamin R., Spielman, Stephanie J., Wilke, Claus O.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000 Research Limited 2018
Materias:
Method Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5676193/
https://www.ncbi.nlm.nih.gov/pubmed/29167739
http://dx.doi.org/10.12688/f1000research.12874.2
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author Sydykova, Dariya K.
Jack, Benjamin R.
Spielman, Stephanie J.
Wilke, Claus O.
author_facet Sydykova, Dariya K.
Jack, Benjamin R.
Spielman, Stephanie J.
Wilke, Claus O.
author_sort Sydykova, Dariya K.
collection PubMed
description We describe how to measure site-specific rates of evolution in protein-coding genes and how to correlate these rates with structural features of the expressed protein, such as relative solvent accessibility, secondary structure, or weighted contact number. We present two alternative approaches to rate calculations: One based on relative amino-acid rates, and the other based on site-specific codon rates measured as dN/ dS. We additionally provide a code repository containing scripts to facilitate the specific analysis protocols we recommend.
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spelling pubmed-56761932017-11-21 Measuring evolutionary rates of proteins in a structural context Sydykova, Dariya K. Jack, Benjamin R. Spielman, Stephanie J. Wilke, Claus O. F1000Res Method Article We describe how to measure site-specific rates of evolution in protein-coding genes and how to correlate these rates with structural features of the expressed protein, such as relative solvent accessibility, secondary structure, or weighted contact number. We present two alternative approaches to rate calculations: One based on relative amino-acid rates, and the other based on site-specific codon rates measured as dN/ dS. We additionally provide a code repository containing scripts to facilitate the specific analysis protocols we recommend. F1000 Research Limited 2018-02-09 /pmc/articles/PMC5676193/ /pubmed/29167739 http://dx.doi.org/10.12688/f1000research.12874.2 Text en Copyright: © 2018 Sydykova DK et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Method Article
Sydykova, Dariya K.
Jack, Benjamin R.
Spielman, Stephanie J.
Wilke, Claus O.
Measuring evolutionary rates of proteins in a structural context
title Measuring evolutionary rates of proteins in a structural context
title_full Measuring evolutionary rates of proteins in a structural context
title_fullStr Measuring evolutionary rates of proteins in a structural context
title_full_unstemmed Measuring evolutionary rates of proteins in a structural context
title_short Measuring evolutionary rates of proteins in a structural context
title_sort measuring evolutionary rates of proteins in a structural context
topic Method Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5676193/
https://www.ncbi.nlm.nih.gov/pubmed/29167739
http://dx.doi.org/10.12688/f1000research.12874.2
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