Protein Evolution within a Structural Space

Eric J. Deeds, Nikolay V. Dokholyan, Eugene I. Shakhnovich

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Abstract

Understanding of the evolutionary origins of protein structures represents a key component of the understanding of molecular evolution as a whole. Here we seek to elucidate how the features of an underlying protein structural "space" might impact protein structural evolution. We approach this question using lattice polymers as a completely characterized model of this space. We develop a measure of structural comparison of lattice structures that is analogous to the one used to understand structural similarities between real proteins. We use this measure of structural relatedness to create a graph of lattice structures and compare this graph (in which nodes are lattice structures and edges are defined using structural similarity) to the graph obtained for real protein structures. We find that the graph obtained from all compact lattice structures exhibits a distribution of structural neighbors per node consistent with a random graph. We also find that subgraphs of 3500 nodes chosen either at random or according to physical constraints also represent random graphs. We develop a divergent evolution model based on the lattice space which produces graphs that, within certain parameter regimes, recapitulate the scale-free behavior observed in similar graphs of real protein structures.

Original languageEnglish (US)
Pages (from-to)2962-2972
Number of pages11
JournalBiophysical journal
Volume85
Issue number5
DOIs
Publication statusPublished - Nov 2003

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All Science Journal Classification (ASJC) codes

  • Biophysics

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