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Protein domains

Part 4. Bioinformatics

4.6. Methods for Structure Analysis and Prediction

Specialist Review

  1. Jaap Heringa

Published Online: 15 APR 2005

DOI: 10.1002/047001153X.g406204

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Heringa, J. 2005. Protein domains. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 4:4.6:68.

Author Information

  1. Vrije Universiteit, Centre for Integrative Bioinformatics VU, Amsterdam, The Netherlands

Publication History

  1. Published Online: 15 APR 2005


Many cellular processes involve proteins composed of multiple domains. The modular nature afforded by breaking up a protein's three-dimensional structure into discrete domains has many evolutionary advantages. First, it allows proteins to evolve to complex cooperative functions that require elaborate, large, and stable structural scaffolds, which would be impossible to form otherwise within the structural constraints associated with the protein-folding process. Second, it can bring active sites in proximity in a fixed stoichiometric ratio. Third, otherwise unstable intermediates can be accommodated within interdomain clefts. Fourth, the flexibility afforded by protein domain linker regions, for example, hinge regions, can greatly aid the activity of the cooperative catalytic process carried out by a multidomain enzyme. Fifth, the repeated and combinatorial use of domains in multidomain proteins has provided nature both an evolutionary economic and versatile system to maintain and enhance cellular activity.


  • protein;
  • domain;
  • domain structure;
  • protein module;
  • domain motion;
  • domain linker;
  • domain prediction;
  • domain database