Skip to main content
NCBI home page
Protein Science : A Publication of the Protein Society logoLink to Protein Science : A Publication of the Protein Society
. 1995 Jan;4(1):103–112. doi: 10.1002/pro.5560040113

A procedure for detecting structural domains in proteins.

M B Swindells 1
PMCID: PMC2142966  PMID: 7773168

Abstract

A procedure is described for detecting domains in proteins of known structure. The method is based on the intuitively simple idea that each domain should contain an identifiable hydrophobic core. By applying the algorithm described in the companion paper (Swindells MB, 1995, Protein Sci 4:93-102) to identify distinct cores in multi-domain proteins, one can use this information to determine both the number and the location of the constituent domains. Tests have shown the procedure to be effective on a number of examples, even when the domains are discontinuous along the sequence. However, deficiencies also occur when hydrophobic cores from different domains continue through the interface region and join one another.

Full Text

The Full Text of this article is available as a PDF (5.8 MB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Abad-Zapatero C., Griffith J. P., Sussman J. L., Rossmann M. G. Refined crystal structure of dogfish M4 apo-lactate dehydrogenase. J Mol Biol. 1987 Dec 5;198(3):445–467. doi: 10.1016/0022-2836(87)90293-2. [DOI] [PubMed] [Google Scholar]
  2. Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  3. Busetta B., Barrans Y. The prediction of protein domains. Biochim Biophys Acta. 1984 Oct 23;790(2):117–124. doi: 10.1016/0167-4838(84)90214-0. [DOI] [PubMed] [Google Scholar]
  4. Colonna-Cesari F., Perahia D., Karplus M., Eklund H., Brädén C. I., Tapia O. Interdomain motion in liver alcohol dehydrogenase. Structural and energetic analysis of the hinge bending mode. J Biol Chem. 1986 Nov 15;261(32):15273–15280. [PubMed] [Google Scholar]
  5. Cooper J. B., Khan G., Taylor G., Tickle I. J., Blundell T. L. X-ray analyses of aspartic proteinases. II. Three-dimensional structure of the hexagonal crystal form of porcine pepsin at 2.3 A resolution. J Mol Biol. 1990 Jul 5;214(1):199–222. doi: 10.1016/0022-2836(90)90156-G. [DOI] [PubMed] [Google Scholar]
  6. Crippen G. M. The tree structural organization of proteins. J Mol Biol. 1978 Dec 15;126(3):315–332. doi: 10.1016/0022-2836(78)90043-8. [DOI] [PubMed] [Google Scholar]
  7. Holm L., Sander C. Parser for protein folding units. Proteins. 1994 Jul;19(3):256–268. doi: 10.1002/prot.340190309. [DOI] [PubMed] [Google Scholar]
  8. Holm L., Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol. 1993 Sep 5;233(1):123–138. doi: 10.1006/jmbi.1993.1489. [DOI] [PubMed] [Google Scholar]
  9. Holmes M. A., Matthews B. W. Structure of thermolysin refined at 1.6 A resolution. J Mol Biol. 1982 Oct 5;160(4):623–639. doi: 10.1016/0022-2836(82)90319-9. [DOI] [PubMed] [Google Scholar]
  10. Kamphuis I. G., Kalk K. H., Swarte M. B., Drenth J. Structure of papain refined at 1.65 A resolution. J Mol Biol. 1984 Oct 25;179(2):233–256. doi: 10.1016/0022-2836(84)90467-4. [DOI] [PubMed] [Google Scholar]
  11. Lapatto R., Blundell T., Hemmings A., Overington J., Wilderspin A., Wood S., Merson J. R., Whittle P. J., Danley D. E., Geoghegan K. F. X-ray analysis of HIV-1 proteinase at 2.7 A resolution confirms structural homology among retroviral enzymes. Nature. 1989 Nov 16;342(6247):299–302. doi: 10.1038/342299a0. [DOI] [PubMed] [Google Scholar]
  12. Orengo C. A., Flores T. P., Taylor W. R., Thornton J. M. Identification and classification of protein fold families. Protein Eng. 1993 Jul;6(5):485–500. doi: 10.1093/protein/6.5.485. [DOI] [PubMed] [Google Scholar]
  13. Ploegman J. H., Drent G., Kalk K. H., Hol W. G. Structure of bovine liver rhodanese. I. Structure determination at 2.5 A resolution and a comparison of the conformation and sequence of its two domains. J Mol Biol. 1978 Aug 25;123(4):557–594. [PubMed] [Google Scholar]
  14. Quiocho F. A., Vyas N. K. Novel stereospecificity of the L-arabinose-binding protein. Nature. 1984 Aug 2;310(5976):381–386. doi: 10.1038/310381a0. [DOI] [PubMed] [Google Scholar]
  15. Richardson J. S. The anatomy and taxonomy of protein structure. Adv Protein Chem. 1981;34:167–339. doi: 10.1016/s0065-3233(08)60520-3. [DOI] [PubMed] [Google Scholar]
  16. Robbins A. H., Stout C. D. The structure of aconitase. Proteins. 1989;5(4):289–312. doi: 10.1002/prot.340050406. [DOI] [PubMed] [Google Scholar]
  17. Rose G. D. Automatic recognition of domains in globular proteins. Methods Enzymol. 1985;115:430–440. doi: 10.1016/0076-6879(85)15031-7. [DOI] [PubMed] [Google Scholar]
  18. Swindells M. B. A procedure for the automatic determination of hydrophobic cores in protein structures. Protein Sci. 1995 Jan;4(1):93–102. doi: 10.1002/pro.5560040112. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Taylor W. R., Orengo C. A. Protein structure alignment. J Mol Biol. 1989 Jul 5;208(1):1–22. doi: 10.1016/0022-2836(89)90084-3. [DOI] [PubMed] [Google Scholar]
  20. Wodak S. J., Janin J. Location of structural domains in protein. Biochemistry. 1981 Nov 10;20(23):6544–6552. doi: 10.1021/bi00526a005. [DOI] [PubMed] [Google Scholar]
  21. Zehfus M. H. Binary discontinuous compact protein domains. Protein Eng. 1994 Mar;7(3):335–340. doi: 10.1093/protein/7.3.335. [DOI] [PubMed] [Google Scholar]

Articles from Protein Science : A Publication of the Protein Society are provided here courtesy of The Protein Society

RESOURCES