analytic markovian rates for generalized protein structure evolution进化分析广义马尔可夫过程的利率的蛋白质结构.pdfVIP

Analytic Markovian Rates for Generalized Protein Structure Evolution 1 2 3 3 3 Ivan Coluzza *, James T. MacDonald , Michael I. Sadowski , William R. Taylor , Richard A. Goldstein 1 Department of Physics, University of Vienna, Vienna, Austria, 2 Division of Molecular Biosciences, Imperial College London, London, United Kingdom and Centre for Synthetic Biology and Innovation, Imperial College London, London, United Kingdom, 3 National Institute for Medical Research, The Ridgeway, London, United Kingdom 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. Citation: Coluzza I, MacDonald JT, Sadowski MI, Ta