PROMOTIF--a program to identify and analyze structural motifs in proteins (original) (raw)

Abstract

We describe a suite of programs, PROMOTIF, that analyzes a protein coordinate file and provides details about the structural motifs in the protein. The program currently analyzes the following structural features: secondary structure; beta-and gamma-turns; helical geometry and interactions; beta-strands and beta-sheet topology; beta-bulges; beta-hairpins; beta-alpha-beta units and psi-loops; disulphide bridges; and main-chain hydrogen bonding patterns. PROMOTIF creates postscript files showing the examples of each type of motif in the protein, and a summary page. The program can also be used to compare motifs in a group of related structures, such as an ensemble of NMR structures.

Full Text

The Full Text of this article is available as a PDF (7.1 MB).

Selected References

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

  1. Chan A. W., Hutchinson E. G., Harris D., Thornton J. M. Identification, classification, and analysis of beta-bulges in proteins. Protein Sci. 1993 Oct;2(10):1574–1590. doi: 10.1002/pro.5560021004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Chothia C. Proteins. One thousand families for the molecular biologist. Nature. 1992 Jun 18;357(6379):543–544. doi: 10.1038/357543a0. [DOI] [PubMed] [Google Scholar]
  3. Efimov A. V. Structure of alpha-alpha-hairpins with short connections. Protein Eng. 1991 Feb;4(3):245–250. doi: 10.1093/protein/4.3.245. [DOI] [PubMed] [Google Scholar]
  4. Hutchinson E. G., Thornton J. M. A revised set of potentials for beta-turn formation in proteins. Protein Sci. 1994 Dec;3(12):2207–2216. doi: 10.1002/pro.5560031206. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Hutchinson E. G., Thornton J. M. HERA--a program to draw schematic diagrams of protein secondary structures. Proteins. 1990;8(3):203–212. doi: 10.1002/prot.340080303. [DOI] [PubMed] [Google Scholar]
  6. 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]
  7. Lewis P. N., Momany F. A., Scheraga H. A. Chain reversals in proteins. Biochim Biophys Acta. 1973 Apr 20;303(2):211–229. doi: 10.1016/0005-2795(73)90350-4. [DOI] [PubMed] [Google Scholar]
  8. Milner-White E., Ross B. M., Ismail R., Belhadj-Mostefa K., Poet R. One type of gamma-turn, rather than the other gives rise to chain-reversal in proteins. J Mol Biol. 1988 Dec 5;204(3):777–782. doi: 10.1016/0022-2836(88)90368-3. [DOI] [PubMed] [Google Scholar]
  9. Oefner C., Suck D. Crystallographic refinement and structure of DNase I at 2 A resolution. J Mol Biol. 1986 Dec 5;192(3):605–632. doi: 10.1016/0022-2836(86)90280-9. [DOI] [PubMed] [Google Scholar]
  10. 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]
  11. Tang J., James M. N., Hsu I. N., Jenkins J. A., Blundell T. L. Structural evidence for gene duplication in the evolution of the acid proteases. Nature. 1978 Feb 16;271(5646):618–621. doi: 10.1038/271618a0. [DOI] [PubMed] [Google Scholar]
  12. Wilmot C. M., Thornton J. M. Analysis and prediction of the different types of beta-turn in proteins. J Mol Biol. 1988 Sep 5;203(1):221–232. doi: 10.1016/0022-2836(88)90103-9. [DOI] [PubMed] [Google Scholar]