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. 1978 May;75(5):2180–2184. doi: 10.1073/pnas.75.5.2180

A general method to assess similarity of protein structures, with applications to T4 bacteriophage lysozyme.

S J Remington, B W Matthews
PMCID: PMC392515  PMID: 276859

Abstract

A method is proposed that permits the structural similarity between any pair of proteins to be analyzed in a completely general manner. In the proposed procedure, all possible structural segments of a given length from one protein are compared with all possible segments from the other protein. This set of comparisons reveals any structural similarities between the two proteins being compared, and also provides a basis for estimating the probability that a particular degree of structural homology could have occurred by chance. Application of the method to the comparison of T4 bacteriophage lysozyme and carp calcium-binding protein suggests that the previously reported structural similarity between parts of these two proteins [Tufty, R. M.& Kretsinger, R. H. (1975) Science 187, 167-169] is no better than would be expected by chance. On the other hand, the structural correspondence between phage lysozyme and hen egg-white lysozyme [Rossman, M.G. & Argos, P. (1976) J. Mol. Biol. 105, 75-96] does appear to be significant.

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Selected References

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

  1. 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]
  2. Diamond R. Real-space refinement of the structure of hen egg-white lysozyme. J Mol Biol. 1974 Jan 25;82(3):371–391. doi: 10.1016/0022-2836(74)90598-1. [DOI] [PubMed] [Google Scholar]
  3. Fermi G. Three-dimensional fourier synthesis of human deoxyhaemoglobin at 2-5 A resolution: refinement of the atomic model. J Mol Biol. 1975 Sep 15;97(2):237–256. doi: 10.1016/s0022-2836(75)80037-4. [DOI] [PubMed] [Google Scholar]
  4. Fitch W. M. An improved method of testing for evolutionary homology. J Mol Biol. 1966 Mar;16(1):9–16. doi: 10.1016/s0022-2836(66)80258-9. [DOI] [PubMed] [Google Scholar]
  5. Fitch W. M. Further improvements in the method of testing for evolutionary homology among proteins. J Mol Biol. 1970 Apr 14;49(1):1–14. doi: 10.1016/0022-2836(70)90372-4. [DOI] [PubMed] [Google Scholar]
  6. Freer S. T., Kraut J., Robertus J. D., Wright H. T., Xuong N. H. Chymotrypsinogen: 2.5-angstrom crystal structure, comparison with alpha-chymotrypsin, and implications for zymogen activation. Biochemistry. 1970 Apr 28;9(9):1997–2009. doi: 10.1021/bi00811a022. [DOI] [PubMed] [Google Scholar]
  7. Huber R., Epp O., Steigemann W., Formanek H. The atomic structure of erythrocruorin in the light of the chemical sequence and its comparison with myoglobin. Eur J Biochem. 1971 Mar 1;19(1):42–50. doi: 10.1111/j.1432-1033.1971.tb01285.x. [DOI] [PubMed] [Google Scholar]
  8. Kretsinger R. H. Gene triplication deduced from the tertiary structure of a muscle calcium binding protein. Nat New Biol. 1972 Nov 15;240(98):85–88. doi: 10.1038/newbio240085a0. [DOI] [PubMed] [Google Scholar]
  9. 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]
  10. Matthews B. W., Remington S. J. The three dimensional structure of the lysozyme from bacteriophage T4. Proc Natl Acad Sci U S A. 1974 Oct;71(10):4178–4182. doi: 10.1073/pnas.71.10.4178. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Moews P. C., Kretsinger R. H. Refinement of the structure of carp muscle calcium-binding parvalbumin by model building and difference Fourier analysis. J Mol Biol. 1975 Jan 15;91(2):201–225. doi: 10.1016/0022-2836(75)90160-6. [DOI] [PubMed] [Google Scholar]
  12. Rao S. T., Rossmann M. G. Comparison of super-secondary structures in proteins. J Mol Biol. 1973 May 15;76(2):241–256. doi: 10.1016/0022-2836(73)90388-4. [DOI] [PubMed] [Google Scholar]
  13. Remington S. J., Eyck L. F., Matthews B. W. Atomic coordinates for T4 phage lysozyme. Biochem Biophys Res Commun. 1977 Mar 21;75(2):265–270. doi: 10.1016/0006-291x(77)91038-5. [DOI] [PubMed] [Google Scholar]
  14. 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]
  15. Rossmann M. G., Argos P. Exploring structural homology of proteins. J Mol Biol. 1976 Jul 25;105(1):75–95. doi: 10.1016/0022-2836(76)90195-9. [DOI] [PubMed] [Google Scholar]
  16. Rossmann M. G., Argos P. The taxonomy of protein structure. J Mol Biol. 1977 Jan 5;109(1):99–129. doi: 10.1016/s0022-2836(77)80048-x. [DOI] [PubMed] [Google Scholar]
  17. Schulz G. E., Schirmer R. H. Topological comparison of adenyl kinase with other proteins. Nature. 1974 Jul 12;250(462):142–144. doi: 10.1038/250142a0. [DOI] [PubMed] [Google Scholar]
  18. 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]
  19. Tufty R. M., Kretsinger R. H. Troponin and parvalbumin calcium binding regions predicted in myosin light chain and T4 lysozyme. Science. 1975 Jan 17;187(4172):167–169. doi: 10.1126/science.1111094. [DOI] [PubMed] [Google Scholar]

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