A Hierarchical Approach to Protein Molecular Evolution
arXiv:cond-mat/9903310 · doi:10.1073/pnas.96.6.2591
Abstract
Biological diversity has evolved despite the essentially infinite complexity of protein sequence space. We present a hierarchical approach to the efficient searching of this space and quantify the evolutionary potential of our approach with Monte Carlo simulations. These simulations demonstrate that non-homologous juxtaposition of encoded structure is the rate-limiting step in the production of new tertiary protein folds. Non-homologous ``swapping'' of low energy secondary structures increased the binding constant of a simulated protein by relative to base substitution alone. Applications of our approach include the generation of new protein folds and modeling the molecular evolution of disease.
15 pages. 2 figures. LaTeX style
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