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...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3367531?pdf=render |
| _version_ | 1818899884059656192 |
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| author | Ivan Coluzza James T MacDonald Michael I Sadowski William R Taylor Richard A Goldstein |
| author_facet | Ivan Coluzza James T MacDonald Michael I Sadowski William R Taylor Richard A Goldstein |
| author_sort | Ivan Coluzza |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-19T19:55:03Z |
| format | Article |
| id | doaj.art-578e1daafbae4d8aad11bbe51451c7b6 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-19T19:55:03Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-578e1daafbae4d8aad11bbe51451c7b62022-12-21T20:07:50ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-0175e3422810.1371/journal.pone.0034228Analytic markovian rates for generalized protein structure evolution.Ivan ColuzzaJames T MacDonaldMichael I SadowskiWilliam R TaylorRichard A GoldsteinA 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.http://europepmc.org/articles/PMC3367531?pdf=render |
| spellingShingle | Ivan Coluzza James T MacDonald Michael I Sadowski William R Taylor Richard A Goldstein Analytic markovian rates for generalized protein structure evolution. PLoS ONE |
| 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 |
| url | http://europepmc.org/articles/PMC3367531?pdf=render |
| work_keys_str_mv | AT ivancoluzza analyticmarkovianratesforgeneralizedproteinstructureevolution AT jamestmacdonald analyticmarkovianratesforgeneralizedproteinstructureevolution AT michaelisadowski analyticmarkovianratesforgeneralizedproteinstructureevolution AT williamrtaylor analyticmarkovianratesforgeneralizedproteinstructureevolution AT richardagoldstein analyticmarkovianratesforgeneralizedproteinstructureevolution |