Skip to main content
PMC home page
Protein Science : A Publication of the Protein Society logoLink to Protein Science : A Publication of the Protein Society
. 1999 Apr;8(4):897–904. doi: 10.1110/ps.8.4.897

Protein structural topology: Automated analysis and diagrammatic representation.

D R Westhead 1, T W Slidel 1, T P Flores 1, J M Thornton 1
PMCID: PMC2144300  PMID: 10211836

Abstract

The topology of a protein structure is a highly simplified description of its fold including only the sequence of secondary structure elements, and their relative spatial positions and approximate orientations. This information can be embodied in a two-dimensional diagram of protein topology, called a TOPS cartoon. These cartoons are useful for the understanding of particular folds and making comparisons between folds. Here we describe a new algorithm for the production of TOPS cartoons, which is more robust than those previously available, and has a much higher success rate. This algorithm has been used to produce a database of protein topology cartoons that covers most of the data bank of known protein structures.

Full Text

The Full Text of this article is available as a PDF (359.9 KB).

Selected References

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

  1. Bennett M. J., Choe S., Eisenberg D. Refined structure of dimeric diphtheria toxin at 2.0 A resolution. Protein Sci. 1994 Sep;3(9):1444–1463. doi: 10.1002/pro.5560030911. [DOI] [PMC free article] [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. Duquerroy S., Camus C., Janin J. X-ray structure and catalytic mechanism of lobster enolase. Biochemistry. 1995 Oct 3;34(39):12513–12523. [PubMed] [Google Scholar]
  4. Eck M. J., Sprang S. R. The structure of tumor necrosis factor-alpha at 2.6 A resolution. Implications for receptor binding. J Biol Chem. 1989 Oct 15;264(29):17595–17605. doi: 10.2210/pdb1tnf/pdb. [DOI] [PubMed] [Google Scholar]
  5. Flores T. P., Moss D. S., Thornton J. M. An algorithm for automatically generating protein topology cartoons. Protein Eng. 1994 Jan;7(1):31–37. doi: 10.1093/protein/7.1.31. [DOI] [PubMed] [Google Scholar]
  6. Flower D. R. Automating the identification and analysis of protein beta-barrels. Protein Eng. 1994 Nov;7(11):1305–1310. doi: 10.1093/protein/7.11.1305. [DOI] [PubMed] [Google Scholar]
  7. Flower D. R. Beta-sheet topology. A new system of nomenclature. FEBS Lett. 1994 May 16;344(2-3):247–250. doi: 10.1016/0014-5793(94)00393-9. [DOI] [PubMed] [Google Scholar]
  8. Frishman D., Argos P. Knowledge-based protein secondary structure assignment. Proteins. 1995 Dec;23(4):566–579. doi: 10.1002/prot.340230412. [DOI] [PubMed] [Google Scholar]
  9. Grigoriev I. V., Mironov A. A., Rakhmaninova A. B. Interhelical contacts determining the architecture of alpha-helical globular proteins. J Biomol Struct Dyn. 1994 Dec;12(3):559–572. doi: 10.1080/07391102.1994.10508759. [DOI] [PubMed] [Google Scholar]
  10. Jones T. A., Liljas L. Structure of satellite tobacco necrosis virus after crystallographic refinement at 2.5 A resolution. J Mol Biol. 1984 Aug 25;177(4):735–767. doi: 10.1016/0022-2836(84)90047-0. [DOI] [PubMed] [Google Scholar]
  11. Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983 Dec;22(12):2577–2637. doi: 10.1002/bip.360221211. [DOI] [PubMed] [Google Scholar]
  12. Kirkpatrick S., Gelatt C. D., Jr, Vecchi M. P. Optimization by simulated annealing. Science. 1983 May 13;220(4598):671–680. doi: 10.1126/science.220.4598.671. [DOI] [PubMed] [Google Scholar]
  13. Ko T. P., Ng J. D., McPherson A. The three-dimensional structure of canavalin from jack bean (Canavalia ensiformis). Plant Physiol. 1993 Mar;101(3):729–744. doi: 10.1104/pp.101.3.729. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Koch I., Kaden F., Selbig J. Analysis of protein sheet topologies by graph theoretical methods. Proteins. 1992 Apr;12(4):314–323. doi: 10.1002/prot.340120403. [DOI] [PubMed] [Google Scholar]
  15. Levitt M., Chothia C. Structural patterns in globular proteins. Nature. 1976 Jun 17;261(5561):552–558. doi: 10.1038/261552a0. [DOI] [PubMed] [Google Scholar]
  16. Li J. D., Carroll J., Ellar D. J. Crystal structure of insecticidal delta-endotoxin from Bacillus thuringiensis at 2.5 A resolution. Nature. 1991 Oct 31;353(6347):815–821. doi: 10.1038/353815a0. [DOI] [PubMed] [Google Scholar]
  17. Murzin A. G., Lesk A. M., Chothia C. beta-Trefoil fold. Patterns of structure and sequence in the Kunitz inhibitors interleukins-1 beta and 1 alpha and fibroblast growth factors. J Mol Biol. 1992 Jan 20;223(2):531–543. doi: 10.1016/0022-2836(92)90668-a. [DOI] [PubMed] [Google Scholar]
  18. Nagano K. Logical analysis of the mechanism of protein folding. IV. Super-secondary structures. J Mol Biol. 1977 Jan 15;109(2):235–250. doi: 10.1016/s0022-2836(77)80032-6. [DOI] [PubMed] [Google Scholar]
  19. Orengo C. A., Michie A. D., Jones S., Jones D. T., Swindells M. B., Thornton J. M. CATH--a hierarchic classification of protein domain structures. Structure. 1997 Aug 15;5(8):1093–1108. doi: 10.1016/s0969-2126(97)00260-8. [DOI] [PubMed] [Google Scholar]
  20. 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]
  21. 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]
  22. Richardson J. S. beta-Sheet topology and the relatedness of proteins. Nature. 1977 Aug 11;268(5620):495–500. doi: 10.1038/268495a0. [DOI] [PubMed] [Google Scholar]
  23. Sayle R. A., Milner-White E. J. RASMOL: biomolecular graphics for all. Trends Biochem Sci. 1995 Sep;20(9):374–374. doi: 10.1016/s0968-0004(00)89080-5. [DOI] [PubMed] [Google Scholar]
  24. Sternberg M. J., Thornton J. M. On the conformation of proteins: the handedness of the connection between parallel beta-strands. J Mol Biol. 1977 Feb 25;110(2):269–283. doi: 10.1016/s0022-2836(77)80072-7. [DOI] [PubMed] [Google Scholar]
  25. Stirk H. J., Woolfson D. N., Hutchinson E. G., Thornton J. M. Depicting topology and handedness in jellyroll structures. FEBS Lett. 1992 Aug 10;308(1):1–3. doi: 10.1016/0014-5793(92)81036-l. [DOI] [PubMed] [Google Scholar]
  26. Westhead D. R., Hatton D. C., Thornton J. M. An atlas of protein topology cartoons available on the World-Wide Web. Trends Biochem Sci. 1998 Jan;23(1):35–36. doi: 10.1016/s0968-0004(97)01161-4. [DOI] [PubMed] [Google Scholar]

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

RESOURCES