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

J Mol Evol. 1990 Jan;30(1):43-59. doi: 10.1007/BF02102452.

Abstract

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, cytochromes c, serine proteinases, eye-lens gamma crystallins, and dinucleotide-binding domains.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Crystallins / genetics
  • Crystallins / ultrastructure
  • Globins / genetics
  • Globins / ultrastructure
  • Humans
  • Immunoglobulins / genetics
  • Immunoglobulins / ultrastructure
  • Molecular Sequence Data
  • Molecular Structure
  • Nucleotides / metabolism
  • Phylogeny*
  • Protein Conformation
  • Proteins / genetics*
  • Proteins / metabolism
  • Proteins / ultrastructure
  • Sequence Homology, Nucleic Acid
  • Serine Endopeptidases / genetics

Substances

  • Crystallins
  • Immunoglobulins
  • Nucleotides
  • Proteins
  • Globins
  • Serine Endopeptidases