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Structural Variations in Protein Superfamilies: Actin and Tubulin

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Abstract

Structures of homologous proteins are usually conserved during evolution, as are critical active site residues. This is the case for actin and tubulin, the two most important cytoskeleton proteins in eukaryotes. Actins and their related proteins (Arps) constitute a large superfamily whereas the tubulin family has fewer members. Unaligned sequences of these two protein families were analysed by searching for short groups of family-specific amino acid residues, that we call motifs, and by counting the number of residues from one motif to the next. For each sequence, the set of motif-to-motif residue counts forms a subfamily-specific pattern (landmark pattern) allowing actin and tubulin superfamily members to be identified and sorted into subfamilies. The differences between patterns of individual subfamilies are due to inserts and deletions (indels). Inserts appear to have arisen at an early stage in eukaryote evolution as suggested by the small but consistent kingdom-dependent differences found within many Arp subfamilies and in γ-tubulins. Inserts tend to be in surface loops where they can influence subfamily-specific function without disturbing the core structure of the protein. The relatively few indels found for tubulins have similar positions to established results, whereas we find many previously unreported indel positions and lengths for the metazoan Arps.

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Acknowledgements

We thank F. Metoz for an introduction to PERL and programming advice. We are grateful for financial support from the Association pour la Recherche sur le Cancer (ARC), Grant number 3973.

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Authors and Affiliations

  1. Institut de Biologie Structurale, 41 rue Jules Horowitz, 38027, Grenoble Cedex 1, France

    Richard H. Wade & Isabel Garcia-Saez

  2. The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow, G61 1BD, Scotland, UK

    Frank Kozielski

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  1. Richard H. Wade
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Correspondence to Richard H. Wade.

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Wade, R.H., Garcia-Saez, I. & Kozielski, F. Structural Variations in Protein Superfamilies: Actin and Tubulin. Mol Biotechnol 42, 49–60 (2009). https://doi.org/10.1007/s12033-008-9128-6

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