Journal of Molecular Evolution

, Volume 30, Issue 1, pp 43–59 | Cite as

Molecular anatomy: Phyletic relationships derived from three-dimensional structures of proteins

  • Mark S. Johnson
  • Michael J. Sutcliffe
  • Tom L. Blundell
Article

Summary

A distance measure that reflects the dissimilarity among structures has been developed on the basis of the three-dimensional structures of similar proteins, this being totally independent of sequence in the sense that only the relative spatial positions of mainchain alpha-carbon atoms need be known. This procedure leads to phyletic relationships that are in general correlated with the sequence phylogenies based on residue type. Such relationships among known protein three-dimensional structures are also a useful aid to their classification and selection in knowledge-based modeling using homologous structures. We have applied this approach to six homologous sets of proteins: immunoglobulin fragments, globins, cytochromesc, serine proteinases, eye-lens gamma crystallins, and dinucleotide-binding domains.

Key words

Phyletic trees from x-ray crystal structures Sequences Globins Cytochromes Immunoglobulins Serine proteinases Eye-lens gamma crystallins Dinucleotide-binding proteins 

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Copyright information

© Springer-Verlag New York Inc 1990

Authors and Affiliations

  • Mark S. Johnson
    • 1
  • Michael J. Sutcliffe
    • 1
  • Tom L. Blundell
    • 1
  1. 1.Laboratory of Molecular Biology, Department of Crystallography, Birkbeck CollegeUniversity of LondonLondonUK

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