Analytic Markovian Rates for Generalized Protein Structure Evolution

Autor(en)

Ivan Coluzza, James T. MacDonald, Michael I. Sadowski, William R. Taylor, Richard A. Goldstein

Abstrakt

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.

Organisation(en)

Computergestützte Physik und Physik der Weichen Materie

Externe Organisation(en)

Imperial College London, National Institute for Medical Research

Journal

PLoS ONE

Band

7

Anzahl der Seiten

9

ISSN

1932-6203

DOI

https://doi.org/10.1371/journal.pone.0034228

Publikationsdatum

2012

Peer-reviewed

Ja

ÖFOS 2012

1070 Andere Naturwissenschaften, 103002 Akustik

Link zum Portal

https://ucrisportal.univie.ac.at/de/publications/c19b719e-5a6c-4e99-807b-b96b32a722be