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Analytic Markovian Rates for Generalized Protein Structure Evolution
A general understanding of the complex phenomenon of protein evolution requires the accurate description of the constraints that define the sub-space of proteins with mutations that do not appreciably reduce the fitness of the organism. Such constraints can have multiple origins, in this work we pre...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367531/ https://www.ncbi.nlm.nih.gov/pubmed/22693543 http://dx.doi.org/10.1371/journal.pone.0034228 |
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author | Coluzza, Ivan MacDonald, James T. Sadowski, Michael I. Taylor, William R. Goldstein, Richard A. |
author_facet | Coluzza, Ivan MacDonald, James T. Sadowski, Michael I. Taylor, William R. Goldstein, Richard A. |
author_sort | Coluzza, Ivan |
collection | PubMed |
description | A general understanding of the complex phenomenon of protein evolution requires the accurate description of the constraints that define the sub-space of proteins with mutations that do not appreciably reduce the fitness of the organism. Such constraints can have multiple origins, in this work we present a model for constrained evolutionary trajectories represented by a Markovian process throughout a set of protein-like structures artificially constructed to be topological intermediates between the structure of two natural occurring proteins. The number and type of intermediate steps defines how constrained the total evolutionary process is. By using a coarse-grained representation for the protein structures, we derive an analytic formulation of the transition rates between each of the intermediate structures. The results indicate that compact structures with a high number of hydrogen bonds are more probable and have a higher likelihood to arise during evolution. Knowledge of the transition rates allows for the study of complex evolutionary pathways represented by trajectories through a set of intermediate structures. |
format | Online Article Text |
id | pubmed-3367531 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-33675312012-06-12 Analytic Markovian Rates for Generalized Protein Structure Evolution Coluzza, Ivan MacDonald, James T. Sadowski, Michael I. Taylor, William R. Goldstein, Richard A. PLoS One Research Article A general understanding of the complex phenomenon of protein evolution requires the accurate description of the constraints that define the sub-space of proteins with mutations that do not appreciably reduce the fitness of the organism. Such constraints can have multiple origins, in this work we present a model for constrained evolutionary trajectories represented by a Markovian process throughout a set of protein-like structures artificially constructed to be topological intermediates between the structure of two natural occurring proteins. The number and type of intermediate steps defines how constrained the total evolutionary process is. By using a coarse-grained representation for the protein structures, we derive an analytic formulation of the transition rates between each of the intermediate structures. The results indicate that compact structures with a high number of hydrogen bonds are more probable and have a higher likelihood to arise during evolution. Knowledge of the transition rates allows for the study of complex evolutionary pathways represented by trajectories through a set of intermediate structures. Public Library of Science 2012-05-23 /pmc/articles/PMC3367531/ /pubmed/22693543 http://dx.doi.org/10.1371/journal.pone.0034228 Text en Coluzza et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Coluzza, Ivan MacDonald, James T. Sadowski, Michael I. Taylor, William R. Goldstein, Richard A. Analytic Markovian Rates for Generalized Protein Structure Evolution |
title | Analytic Markovian Rates for Generalized Protein Structure Evolution |
title_full | Analytic Markovian Rates for Generalized Protein Structure Evolution |
title_fullStr | Analytic Markovian Rates for Generalized Protein Structure Evolution |
title_full_unstemmed | Analytic Markovian Rates for Generalized Protein Structure Evolution |
title_short | Analytic Markovian Rates for Generalized Protein Structure Evolution |
title_sort | analytic markovian rates for generalized protein structure evolution |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367531/ https://www.ncbi.nlm.nih.gov/pubmed/22693543 http://dx.doi.org/10.1371/journal.pone.0034228 |
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