A protein taxonomy based on secondary structure. |
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Authors: | T Przytycka R Aurora G D Rose |
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Affiliation: | Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA. |
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Abstract: | Does a protein's secondary structure determine its three-dimensional fold? This question is tested directly by analyzing proteins of known structure and constructing a taxonomy based solely on secondary structure. The taxonomy is generated automatically, and it takes the form of a tree in which proteins with similar secondary structure occupy neighboring leaves. Our tree is largely in agreement with results from the structural classification of proteins (SCOP), a multidimensional classification based on homologous sequences, full three-dimensional structure, information about chemistry and evolution, and human judgment. Our findings suggest a simple mechanism of protein evolution. |
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