Structural diversity of protein segments follows a power-law distribution

Biophysical Journal

Volumn 91, Issue 4, 2006, Pages 1213-1223

  Sawada, Yoshito ^a   Honda, Shinya ^a  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONFORMATIONAL TRANSITION; ENTROPY; FRACTAL ANALYSIS; PROTEIN CONFORMATION; PROTEIN STRUCTURE;

EID: 33746837770     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.076661     Document Type: Article

References (49)

1. Privalov, P. L. 1979. Stability of proteins: small globular proteins. Adv. Protein Chem. 33:167-241.
2. Murzin, A. G., S. E. Brenner, T. Hubbard, and C. Chothia. 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:536-540.
3. Orengo, C. A., A. D. Michie, S. Jones, D. T. Jones, M. B. Swindells, and J. M. Thornton. 1997. CATH: a hierarchic classification of protein domain structures. Structure. 5:1093-1108.
4. Holm, L., and C. Sander. 1993. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:123-138.
5. Madej, T., J. F. Gibrat, and S. H. Bryant. 1995. Threading a database of protein cores. Proteins. 23:356-369.
6. Shindyalov, I. N., and P. E. Bourne. 1998. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. 11:739-747.
7. Hou, J., G. E. Sims, C. Zhang, and S. H. Kim. 2003. A global representation of the protein fold space. Proc. Natl. Acad. Sci. USA. 100:2386-2390.
8. Liu, X., K. Fan, and W. Wang. 2004. The number of protein folds and their distribution over families in nature. Proteins. 54:491-499.
9. Taylor, W. R. 2002. A 'periodic table' for protein structures. Nature. 416:657-660.
10. Jaenicke, R. 1999. Stability and folding of domain proteins. Prog. Biophys. Mol. Biol. 71:155-241.
11. Gilbert, W. 1978. Why genes in pieces? Nature. 271:501.
12. Blake, C. C. 1978. Do genes-in-pieces imply proteins-in-pieces? Nature. 273:267.
13. Go, M. 1981. Correlation of DNA exonic regions with protein structural units in haemoglobin. Nature. 291:90-92.
14. Seidel, H. M., D. L. Pompliano, and J. R. Knowles. 1992. Exons as microgenes? Science. 257:1489-1490.
15. Karplus, M., and D. L. Weaver. 1976. Protein-folding dynamics. Nature. 260:404-406.
16. Baldwin, R. L., and G. D. Rose. 1999. Is protein folding hierarchic? I. Local structure and peptide folding. Trends Biochem. Sci. 24:26-33.
17. Iwakura, M., T. Nakamura, C. Yamane, and K. Maki. 2000. Systematic circular permutation of an entire protein reveals essential folding elements. Nat. Struct. Biol. 7:580-585.
18. Lupas, A. N., C. P. Ponting, and R. B. Russell. 2001. On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world? J. Struct. Biol. 134:191-203.
19. Rost, B. 2002. Did evolution leap to create the protein universe? Curr. Opin. Struct. Biol. 12:409-416.
20. Richards, J. A., and X. Jia. 1999. Remote sensing digital image analysis. Springer-Verlag, New York.
21. Hobohm, U., M. Scharf, R. Schneider, and C. Sander. 1992. Selection of representative protein data sets. Protein Sci. 1:409-417.
22. Wang, G., and R. L. Dunbrack, Jr. 2003. PISCES: a protein sequence culling server. Bioinformatics. 19:1589-1591.
23. Shannon, C. E. 1951. Prediction and entropy of printed English. Bell Syst. Tech. J. 30:51-64.
24. Kabsch, W., and C. Sander. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:2577-2637.
25. Kullback, S., and R. A. Leibler. 1951. On information and sufficiency. Ann. Math. Stat. 22:79-86.
26. Witten, I. H., and T. C. Bell. 1991. The zero-frequency problem: estimating the probabilities of novel events in adaptive text compression. IEEE Trans. Inf. Theory. 37:1085-1094.
27. Zipf, G. K. 1949. Human behavior and the principle of least effort. Addison-Wesley, Cambridge, MA.
28. Mandelbrot, B. 1953. An information theory of the statistical structure of language. In Communication Theory. W. Jackson, editor. Academic Press, New York. 486-502.
29. Dill, K. A. 1985. Theory for the folding and stability of globular proteins. Biochemistry. 24:1501-1509.
30. Dokholyan, N. V., B. Shakhnovich, and E. I. Shakhnovich. 2002. Expanding protein universe and its origin from the biological Big Bang. Proc. Natl. Acad. Sci. USA. 99:14132-14136.
31. Aurora, R., and G. D. Rose. 1998. Helix capping. Protein Sci. 7:21-38.
32. Sibanda, B. L., and J. M. Thornton. 1985. Beta-hairpin families in globular proteins. Nature. 316:170-174.
33. Li, H., R. Helling, C. Tang, and N. Wingreen. 1996. Emergence of preferred structures in a simple model of protein folding. Science. 273:666-669.
34. Strait, B. J., and T. G. Dewey. 1996. The Shannon information entropy of protein sequences. Biophys. J. 71:148-155.
35. Luscombe, N. M., J. Qian, Z. Zhang, T. Johnson, and M. Gerstein. 2002. The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties. Genome Biol. 3:R00401-R00407.
36. Wuchty, S. 2001. Scale-free behavior in protein domain networks. Mol. Biol. Evol. 18:1694-1702.
37. Barabasi, A.-L. 2002. Linked: the new science of networks. Perseus Books, Cambridge, MA.
38. Czirok, A., R. N. Mantegna, S. Havlin, and H. E. Stanley. 1995. Correlations in binary sequences and a generalized Zipf analysis. Phys. Rev. E. 52:446-452.
39. Bornberg-Bauer, E. 1997. How are model protein structures distributed in sequence space? Biophys. J. 73:2393-2403.
40. Pierce, J. R. 1980. An introduction to information theory: symbols, signals and noise. Dover, New York.
41. 2002. Folding as grammar. Nat. Struct. Biol. 9:713.
42. Sims, G. E., I. G. Choi, and S. H. Kim. 2005. Protein conformational space in higher order φ-ψ maps. Proc. Natl. Acad. Sci. USA. 102:618-621.
43. Simons, K. T., C. Kooperberg, E. Huang, and D. Baker. 1997. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol. 268:209-225.
44. Kinch, L. N., J. O. Wrabl, S. S. Krishna, I. Majumdar, R. I. Sadreyev, Y. Qi, J. Pei, H. Cheng, and N. V. Grishin. 2003. CASP5 assessment of fold recognition target predictions. Proteins. 53(Suppl. 6):395-409.
45. Koonin, E. V., Y. I. Wolf, and G. P. Karev. 2002. The structure of the protein universe and genome evolution. Nature. 420:218-223.
46. Allen, J. P., J. T. Colvin, D. G. Stinson, C. P. Flynn, and H. J. Stapleton. 1982. Protein comformation from electron spin relaxation data. Biophys. J. 38:299-310.
47. Isogai, Y., and T. Itoh. 1984. Fractal analysis of tertiary structure of protein molecules. J. Phys. Soc. Japan. 53:2162-2171.
48. Ikeda, K., K. Tomii, T. Yokomizo, D. Mitomo, K. Maruyama, S. Suzuki, and J. Higo. 2005. Visualization of conformational distribution of short to medium size segments in globular proteins and identification of local structural motifs. Protein Sci. 14:1253-1265.
49. Honda, S., K. Yamasaki, Y. Sawada, and H. Morii. 2004. 10 residue folded peptide designed by segment statistics. Structure. 12:1507-1518.