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A protein taxonomy based on secondary structure

Nature Structural Biology volume 6, pages 672–682 (1999)Cite this article

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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Figure 1: Similarity tree for the 183 proteins in our data set, generated automatically as described in the Methods.
Figure 2: The tree obtained using VAST11.
Figure 3: Primary sequence tree, constructed using the neighbor-joining (NJ) method34.

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Acknowledgements

We thank R. Srinivasan, V. Murthy and P. Thiessen for helpful suggestions, and J. Cohen for providing access to his tree-construction program, Tande. We are particularly indebted to an anonymous referee for assistance in bringing this paper to fruition. Supported by the Sloan Foundation (T.P.) andthe NIH (G.D.R.).

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Author notes

  1. Rajeev Aurora

    Present address: Monsanto, Mail Zone AA3G, St. Louis, 700 Chesterfield Parkway, Missouri, 63198, USA

Authors and Affiliations

  1. Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, 21205, Maryland, USA

    Teresa Przytycka, Rajeev Aurora & George D. Rose

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  1. Teresa Przytycka
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Correspondence to George D. Rose.

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Przytycka, T., Aurora, R. & Rose, G. A protein taxonomy based on secondary structure. Nat Struct Mol Biol 6, 672–682 (1999). https://doi.org/10.1038/10728

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