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. 1992 Mar;1(3):401–408. doi: 10.1002/pro.5560010312

An optimization approach to predicting protein structural class from amino acid composition.

C T Zhang 1, K C Chou 1
PMCID: PMC2142205  PMID: 1304347

Abstract

Proteins are generally classified into four structural classes: all-alpha proteins, all-beta proteins, alpha + beta proteins, and alpha/beta proteins. In this article, a protein is expressed as a vector of 20-dimensional space, in which its 20 components are defined by the composition of its 20 amino acids. Based on this, a new method, the so-called maximum component coefficient method, is proposed for predicting the structural class of a protein according to its amino acid composition. In comparison with the existing methods, the new method yields a higher general accuracy of prediction. Especially for the all-alpha proteins, the rate of correct prediction obtained by the new method is much higher than that by any of the existing methods. For instance, for the 19 all-alpha proteins investigated previously by P.Y. Chou, the rate of correct prediction by means of his method was 84.2%, but the correct rate when predicted with the new method would be 100%! Furthermore, the new method is characterized by an explicable physical picture. This is reflected by the process in which the vector representing a protein to be predicted is decomposed into four component vectors, each of which corresponds to one of the norms of the four protein structural classes.

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Selected References

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  1. Adams M. J., Levy H. R., Moffat K. Crystallization and preliminary x-ray data for glucose-6-phosphate dehydrogenase from Leuconostoc mesenteroides. J Biol Chem. 1983 May 10;258(9):5867–5868. [PubMed] [Google Scholar]
  2. Barnell W. O., Yi K. C., Conway T. Sequence and genetic organization of a Zymomonas mobilis gene cluster that encodes several enzymes of glucose metabolism. J Bacteriol. 1990 Dec;172(12):7227–7240. doi: 10.1128/jb.172.12.7227-7240.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Carlacci L., Chou K. C., Maggiora G. M. A heuristic approach to predicting the tertiary structure of bovine somatotropin. Biochemistry. 1991 May 7;30(18):4389–4398. doi: 10.1021/bi00232a004. [DOI] [PubMed] [Google Scholar]
  4. Chou K. C., Carlacci L. Energetic approach to the folding of alpha/beta barrels. Proteins. 1991;9(4):280–295. doi: 10.1002/prot.340090406. [DOI] [PubMed] [Google Scholar]
  5. Chou K. C., Carlacci L. Simulated annealing approach to the study of protein structures. Protein Eng. 1991 Aug;4(6):661–667. doi: 10.1093/protein/4.6.661. [DOI] [PubMed] [Google Scholar]
  6. Chou K. C. Energy-optimized structure of antifreeze protein and its binding mechanism. J Mol Biol. 1992 Jan 20;223(2):509–517. doi: 10.1016/0022-2836(92)90666-8. [DOI] [PubMed] [Google Scholar]
  7. Chou K. C., Némethy G., Pottle M., Scheraga H. A. Energy of stabilization of the right-handed beta alpha beta crossover in proteins. J Mol Biol. 1989 Jan 5;205(1):241–249. doi: 10.1016/0022-2836(89)90378-1. [DOI] [PubMed] [Google Scholar]
  8. Chou P. Y., Fasman G. D. Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Biochemistry. 1974 Jan 15;13(2):211–222. doi: 10.1021/bi00699a001. [DOI] [PubMed] [Google Scholar]
  9. Cleland W. W. Statistical analysis of enzyme kinetic data. Methods Enzymol. 1979;63:103–138. doi: 10.1016/0076-6879(79)63008-2. [DOI] [PubMed] [Google Scholar]
  10. Fersht A. R. Conformational equilibria in -and -chymotrypsin. The energetics and importance of the salt bridge. J Mol Biol. 1972 Mar 14;64(2):497–509. doi: 10.1016/0022-2836(72)90513-x. [DOI] [PubMed] [Google Scholar]
  11. Fouts D., Ganguly R., Gutierrez A. G., Lucchesi J. C., Manning J. E. Nucleotide sequence of the Drosophila glucose-6-phosphate dehydrogenase gene and comparison with the homologous human gene. Gene. 1988 Mar 31;63(2):261–275. doi: 10.1016/0378-1119(88)90530-6. [DOI] [PubMed] [Google Scholar]
  12. Garnier J., Osguthorpe D. J., Robson B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol. 1978 Mar 25;120(1):97–120. doi: 10.1016/0022-2836(78)90297-8. [DOI] [PubMed] [Google Scholar]
  13. Haghighi B., Levy H. R. Glucose-6-phosphate dehydrogenase from Leuconostoc mesenteroides. Conformational transitions induced by nicotinamide adenine dinucleotide, nicotinamide adenine dinucleotide phosphate, and glucose 6-phosphate monitored by fluorescent probes. Biochemistry. 1982 Dec 7;21(25):6421–6428. doi: 10.1021/bi00268a016. [DOI] [PubMed] [Google Scholar]
  14. Hanukoglu I., Gutfinger T. cDNA sequence of adrenodoxin reductase. Identification of NADP-binding sites in oxidoreductases. Eur J Biochem. 1989 Mar 15;180(2):479–484. doi: 10.1111/j.1432-1033.1989.tb14671.x. [DOI] [PubMed] [Google Scholar]
  15. Ho Y. S., Howard A. J., Crapo J. D. Cloning and sequence of a cDNA encoding rat glucose-6-phosphate dehydrogenase. Nucleic Acids Res. 1988 Aug 11;16(15):7746–7746. doi: 10.1093/nar/16.15.7746. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Kawai H., Kikuchi T., Okamoto Y. A prediction of tertiary structures of peptide by the Monte Carlo simulated annealing method. Protein Eng. 1989 Nov;3(2):85–94. doi: 10.1093/protein/3.2.85. [DOI] [PubMed] [Google Scholar]
  17. Klein P., Delisi C. Prediction of protein structural class from the amino acid sequence. Biopolymers. 1986 Sep;25(9):1659–1672. doi: 10.1002/bip.360250909. [DOI] [PubMed] [Google Scholar]
  18. Klein P. Prediction of protein structural class by discriminant analysis. Biochim Biophys Acta. 1986 Nov 21;874(2):205–215. doi: 10.1016/0167-4838(86)90119-6. [DOI] [PubMed] [Google Scholar]
  19. LaDine J. R., Carlow D., Lee W. T., Cross R. L., Flynn T. G., Levy H. R. Interaction of Leuconostoc mesenteroides glucose-6-phosphate dehydrogenase with pyridoxal 5'-diphospho-5'-adenosine. Affinity labeling of Lys-21 and Lys-343. J Biol Chem. 1991 Mar 25;266(9):5558–5562. [PubMed] [Google Scholar]
  20. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  21. 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]
  22. Levy H. R., Christoff M., Ingulli J., Ho E. M. Glucose-6-phosphate dehydrogenase from Leuconostoc mesenteroides: revised kinetic mechanism and kinetics of ATP inhibition. Arch Biochem Biophys. 1983 Apr 15;222(2):473–488. doi: 10.1016/0003-9861(83)90546-5. [DOI] [PubMed] [Google Scholar]
  23. Levy H. R., Daouk G. H. Simultaneous analysis of NAD- and NADP-linked activities of dual nucleotide-specific dehydrogenases. Application to Leuconostoc mesenteroides glucose-6-phosphate dehydrogenase. J Biol Chem. 1979 Jun 10;254(11):4843–4847. [PubMed] [Google Scholar]
  24. Lim V. I. Structural principles of the globular organization of protein chains. A stereochemical theory of globular protein secondary structure. J Mol Biol. 1974 Oct 5;88(4):857–872. doi: 10.1016/0022-2836(74)90404-5. [DOI] [PubMed] [Google Scholar]
  25. Merril C. R. Gel-staining techniques. Methods Enzymol. 1990;182:477–488. doi: 10.1016/0076-6879(90)82038-4. [DOI] [PubMed] [Google Scholar]
  26. Nogae I., Johnston M. Isolation and characterization of the ZWF1 gene of Saccharomyces cerevisiae, encoding glucose-6-phosphate dehydrogenase. Gene. 1990 Dec 15;96(2):161–169. doi: 10.1016/0378-1119(90)90248-p. [DOI] [PubMed] [Google Scholar]
  27. Olive C., Geroch M. E., Levy H. R. Glucose 6-phosphate dehydrogenase from Leuconostoc mesenteroides. Kinetic studies. J Biol Chem. 1971 Apr 10;246(7):2047–2057. [PubMed] [Google Scholar]
  28. Persico M. G., Viglietto G., Martini G., Toniolo D., Paonessa G., Moscatelli C., Dono R., Vulliamy T., Luzzatto L., D'Urso M. Isolation of human glucose-6-phosphate dehydrogenase (G6PD) cDNA clones: primary structure of the protein and unusual 5' non-coding region. Nucleic Acids Res. 1986 Mar 25;14(6):2511–2522. doi: 10.1093/nar/14.6.2511. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Poteete A. R., Sun D. P., Nicholson H., Matthews B. W. Second-site revertants of an inactive T4 lysozyme mutant restore activity by restructuring the active site cleft. Biochemistry. 1991 Feb 5;30(5):1425–1432. doi: 10.1021/bi00219a037. [DOI] [PubMed] [Google Scholar]
  30. Rowley D. L., Wolf R. E., Jr Molecular characterization of the Escherichia coli K-12 zwf gene encoding glucose 6-phosphate dehydrogenase. J Bacteriol. 1991 Feb;173(3):968–977. doi: 10.1128/jb.173.3.968-977.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Wada K., Aota S., Tsuchiya R., Ishibashi F., Gojobori T., Ikemura T. Codon usage tabulated from the GenBank genetic sequence data. Nucleic Acids Res. 1990 Apr 25;18 (Suppl):2367–2411. doi: 10.1093/nar/18.suppl.2367. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Wilkinson A. J., Fersht A. R., Blow D. M., Winter G. Site-directed mutagenesis as a probe of enzyme structure and catalysis: tyrosyl-tRNA synthetase cysteine-35 to glycine-35 mutation. Biochemistry. 1983 Jul 19;22(15):3581–3586. doi: 10.1021/bi00284a007. [DOI] [PubMed] [Google Scholar]
  33. Wilson S. R., Cui W. L. Applications of simulated annealing to peptides. Biopolymers. 1990 Jan;29(1):225–235. doi: 10.1002/bip.360290127. [DOI] [PubMed] [Google Scholar]

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