Protein Families: Evolution

Abstract

Analysis of protein sequence and structure shows that proteins can be grouped into evolutionarily related families. These families can be used to understand protein function and aspects of genome evolution.

Keywords: protein families; evolution; homology; sequence; structure; genomes

Figure 1.

Domain architecture of proteins. The top panel shows the amino acid sequence of hematopoietic cell kinase. Comparison of this sequence with other proteins reveals three distinct conserved regions, termed SH3, SH2 and tyrosine kinase (TyrKc) domains. These are shown schematically in the middle panel. Each of these domains corresponds to a distinct entity in the three‐dimensional structure (lower panel). These regions can be recombined and found with other combinations of domains in other proteins.

Figure 2.

Example of protein repeats: (a) the quinoprotein ethanol dehydrogenase contains a repeating ‘PQQ’ region. These do not correspond to stable structures in their own right, but come together to form a compact 3D structure, as shown in (b). Additional insertions in each repeat disrupt the overall symmetry of the molecule.

Figure 3.

Trees and function as part of phylogenetic analysis. Functional features common to ‘A’ and ‘C’ are also likely to be shared by ‘B’, whereas they will not be shared by ‘D’ if they have arisen at the point indicated by the circle.

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Further Reading

Branden C and Tooze J (1998) Introduction to Protein Structure. New York, NY: Garland Science Publishing.

Durbin R, Eddy SR, Krogh A and Mitchison G (1998) Biological Sequence Analysis. Cambridge, UK: Cambridge University Press.

Chothia C (1992) Proteins. One thousand families for the molecular biologist. Nature 357: 543–544.

International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409: 860–921.

Lespinet O, Wolf YI, Koonin EV and Aravind L (2002) The role of lineage specific gene family expansion in the evolution of eukaryotes. Genome Research 12: 1048–1059.

Nishikimi M, Fukuyama R, Minoshima S, Shimizu N and Yagi K (1994) Cloning and chromosomal mapping of the human nonfunctional gene for L‐gulono‐gamma‐lactone oxidase, the enzyme for L‐ascorbic acid biosynthesis missing in man. Journal of Biological Chemistry 269: 13685–13688.

Tatusov RL, Koonin EV and Lipman DJ (1997) A genomic perspective on protein families. Science 278: 631–637.

Todd AE, Orengo CA and Thornton JM (2002) Evolution of function in protein superfamilies, from a structural perspective. Journal of Molecular Biology 307: 1113–1143.

Web Links

Pfam (Protein Families' Database of Alignments and HMMs) http://www.sanger.ac.uk/Software/Pfam/

SCOP (Structural Classification of Proteins) http://scop.mrc‐lmb.cam.ac.uk/scop

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How to Cite close
Copley, Richard R(Sep 2006) Protein Families: Evolution. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0006003]