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Analytic Markovian Rates for Generalized Protein Structure Evolution

Coluzza, I; MacDonald, JT; Sadowski, MI; Taylor, WR; Goldstein, RA; (2012) Analytic Markovian Rates for Generalized Protein Structure Evolution. PLoS ONE , 7 (5) , Article e34228. 10.1371/journal.pone.0034228. Green open access

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Abstract

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.

Type: Article
Title: Analytic Markovian Rates for Generalized Protein Structure Evolution
Open access status: An open access version is available from UCL Discovery
DOI: 10.1371/journal.pone.0034228
Publisher version: http://dx.doi.org/10.1371/journal.pone.0034228
Language: English
Additional information: © 2012 Coluzza et al. 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 credited.
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Infection and Immunity
URI: https://discovery.ucl.ac.uk/id/eprint/1403673
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