Characterization and comparison of protein structures. Part I - Characterization

Journal of Theoretical Biology

Volumn 198, Issue 2, 1999, Pages 197-218

  Chechetkin, V R ^a   Lobzin, V V ^a  

^a TROITSK INSTITUTE FOR INNOVATION AND FUSION RESEARCH   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; ENTROPY; FOURIER ANALYSIS; HYDROPHOBICITY; PERIODICITY; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; SPECTROSCOPY;

EID: 0033591305     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1006/jtbi.1999.0910     Document Type: Article

References (59)

1. Anderson, T. W. (1958). An Introduction to Multivariate Statistical Analysis. New York: Wiley.
2. Benson, D. C. (1990). Fourier method for biosequence analysis. Nucl. Acids Res. 18, 6305-6310.
3. Black, S. D. & Mould, D. R. (1991). Development of hydrophobicity parameters to analyze proteins which bear post or cotranslational modifications. Analyt. Biochem. 193, 72-82.
4. Chan, H. S. (1995). Kinetics of protein folding. Nature, Lond. 373, 664-665.
5. Chechetkin, V. R. & Lobzin, V. V. (1996). Levels of ordering in coding and noncoding regions of DNA sequences. Phys. Lett. A 222, 354-360.
6. Chechetkin, V. R. & Lobzin, V. V. (1998a). Study of correlations in segmented DNA sequences: Application to structural coupling between exons and introns. J. Theor. Biol. 190, 69-83.
7. Chechetkin, V. R. & Lobzin, V. V. (1998b). Nucleosome units and hidden periodicities in DNA sequences. J. Biomol. Struct. Dyn. 15, 937-947.
8. Chechetkin, V. R. & Lobzin, V. V. (1998c). Topology of protein folding. Phys. Lett. A 250, 443-448.
9. Chechetkin, V. R. & Turygin, A. Y. (1994). On the spectral criteria of disorder in non-periodic sequences: Application to inflation models, symbolic dynamics, and DNA sequences. J. Phys. A: Math. Gen. 27, 4875-4898.
10. Chechetkin, V. R. & Turygin, A. Y. (1995). Search of hidden periodicities in DNA sequences. J. Theor. Biol. 175, 477-494.
11. Chechetkin, V. R. & Turygin, A. Y. (1996). Study of correlations in DNA sequences. J. Theor. Biol. 178, 205-217.
12. Chechetkin, V. R., Knizhnikova, L. A. & Turygin, A. Y. (1994). Three-quasiperiodicity, mutual correlations, ordering, and long-range modulations in genomic nucleotide sequences for viruses. J. Biomol. Struct. Dyn. 12, 271-299.
13. Cheever, E. A., Overton, G. C. & Searls, D. B. (1991). Fast fourier-transform-based correlation of DNA sequences using complex plane encoding. CABIOS 7, 143-154.
14. Chen, S.-J. & Dill, K. A. (1996). Symmetries in proteins: A knot theory approach. J. Chem. Phys. 104, 5964-5973.
15. Chou, P. Y. & Fasman, U. D. (1978). Prediction of the secondary structure of proteins from their amino acid sequence. In: Advances in Enzymology (Meister, A., ed.) pp. 45-147. New York: Interscience.
16. Creighton, T. (1993). Proteins: Structures and Molecular Properties. New York: Freeman.
17. De Gennes, P.-G. (1979). Scaling Concepts in Polymer Physics. Ithaca: Cornell University Press.
18. Dill, K. A. (1990). Dominant forces in protein folding. Biochemistry 29, 7133-7155.
19. Donnelly, D., Johnson, M. S., Blundell, T. L. & SaunDers, J. (1989). An analysis of the periodicity of conserved residues in sequence alignments of g-protein coupled receptors - Implications for the three-dimensional structure. FEBS Lett. 251, 109-116.
20. Donnelly, D., Overington, J. P. & Blundell, T. L. (1994). The prediction and orientation of α-helices from sequence alignments: The combined use of environment-dependent substitution tables, Fourier transform methods and helix capping rules. Prot. Engin. 7, 645-653.
21. Eisenberg, D., Schwartz, E., Komaromy, M. & Wall, R. (1984). Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J. Mol. Biol. 179, 125-142.
22. Feller, W. (1970). An Introduction to Probability Theory and Its Applications. New York: Wiley.
23. Flory, P. J. (1969). Statistical Mechanics of Chain Molecules. New York: Interscience.
24. Flurry, P. L. (Jr.) (1980). Symmetry Groups: Theory and Chemical Applications. Englewood Cliffs, NJ: Prentice-Hall.
25. Grindley, H. M., Artymiuk, P. J., Rice, D. W. & Willett, P. (1993). Identification of tertiary structure resemblance in proteins using a maximal common subgrath isomorphism algorithm. J. Mol. Biol. 229, 707-721.
26. Hamermesh, M. (1964). Group Theory and Its Applications to Physical Problems. Reading, MA: Addison-Wesley.
27. Holm, L. & Sander, C. (1993). Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138.
28. Holm, L. & Sander, C. (1994). Searching protein structure databases has come of age. Proteins: Struct., Funct. Genet. 19, 165-173.
29. Honig, B. & Cohen, F. E. (1996). Adding backbone to protein folding: Why proteins are polypeptides. Folding & Design 1, R17-R20.
30. Hopp, T. P. & Woods, K. R. (1981). Prediction of protein antigenic determinants from amino acid sequences. Proc. Nat. Acad. Sci. U.S.A. 78, 3824-3828.
31. Hubbard, T. J. P., Murzin, A. G., Brenner, S. E. & Chothia, C. (1997). SCOP: A structure classification of protein database. Nucl. Acids Res. 25, 236-239.
32. Kolmogorov, A. N. (1986). On the empirical determination of distribution law. In: Probability Theory and Mathematical Statistics. Collected Papers by A. N. Kolmogorov, pp. 134-141. Moscow: Nauka (in Russian).
33. Kraulis, P. (1991). MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946-950.
34. Kyte, J. & Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132.
35. Lee, W. J. & Luo, L. F. (1997). Periodicity of base correlation in nucleotide sequence. Phys. Rev. E 56, 848-851.
36. Liu, G., Olson, W. K. & Schlick, T. (1995). Application of Fourier analysis to computer simulation of supercoiled DNA. Comp. Polymer Sci. 5, 7-27.
37. Luo, L. F. (1997). Collected Works on Theoretical Biophysics. Hohhot: Inner Mongolia University Press.
38. Luo, L. F. & Li, X. Q. (1997). Prediction of topological structure of protein from its secondary structure sequence. In: Proc. of International Symposium on Theoretical Biophysics and Biomathematics (Luo, L. F., Li, Q. Z. & Lee, W. J., eds) pp. 71-76. Hohhot: Inner Mongolia University Press.
39. Makeev, V. J. & Tumanyan, V. G. (1996). Search of periodicities in primary structure of biopolymers: A general fourier approach. CABIOS 12, 49-54.
40. McLachlan, A. D. (1993). Multichannel fourier analysis of patterns in protein sequences. J. Phys. Chem. 97, 3000-3006.
41. McLachlan, A. D. & Stewart, M. (1976). The 14-fold periodicity in α-tropomyosine and the interaction with actin. J. Mol. Biol. 235, 1278-1290.
42. Mitchell, E. M., Artymiuk, P. J., Rice, D. W. & Willett, P. (1989). Use of techniques derived from graph theory to compare secondary structure motifs in proteins. J. Mol. Biol. 212, 151-166.
43. Murzin, A. G., Brenner, S. E., Hubbard, T. & Chothia, C. (1995). SCOP: A structural classification of protein database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
44. Orengo, C. A., Jones, D. T. & Thornton, J. M. (1994). Protein superfamilies and domain superfolds. Nature, Lond. 372, 631-634.
45. Privalov, P. L. & Gill, S. J. (1988). Stability of protein structure and hydrophobic interaction. Adv. Prot. Chem. 39, 191-234.
46. Richards, F. M. (1977). Areas, volumes, packing, and protein structure. Annu. Rev. Biophys. Bioeng. 6, 151-176.
47. Rose, G. D. (1988). Hydrophobicity profiles. In: CompuTational Molecular Biology: Sources and Methods for Sequence Analysis (Lesk, A. M., ed.) pp. 198-204. Oxford: Oxford University Press.
48. Sali, A. & Blundell, T. L. (1989). Definition of general topological equivalence in protein structures. J. Mol. Biol. 212, 403-428.
49. Schneider, G., Röhlk, S. & Wrede, P. (1993). Analysis of cleavage-site patterns in protein precursor sequences with a perceptron-type neural network. Biochem. Biophys. Res. Commun. 194, 951-959.
50. Silverman, B. D. & Linsker, R. (1986). A measure of DNA periodicity. J. Theor. Biol. 118, 295-300.
51. Socci, N. D., Bialek, W. S. & Onuchic, J. N. (1994). Properties and origins of protein secondary structure. Phys. Rev. E 49, 3440-3443.
52. Stepanov, V. M. (1996). Molecular Biology. Structure and Functions of Proteins. Moscow: Vysshaya Shkola (in Russian).
53. Subbarao, N. & Haneef, I. (1991). Defining topological equivalences in macromolecules. Protein Engin. 4, 877-884.
54. Tavare, S. & Giddings, B. W. (1989). Some statistical aspects of the primary structure of nucleotide sequences. In: Mathematical Methods for DNA Sequences (Waterman, M. S., ed.) pp. 116-132. Boca Raton: CRC Press.
55. Trifonov, E. N. (1989). The multiple codes of nucleotide sequences. Bull. Math. Biol. 51, 417-432.
56. Turygin, A. Y. & Chechetkin, V. R. (1994). Criteria for disorder in non-periodic sequences. Zhur. eksp. tear. Fiz. 106, 335-354 (English translation: JETP 79, 186-196).
57. Weiss, O. & Herzel, H. (1998). Measuring correlations in protein sequences. Zs. Phys. Chemie 204, 183-197.
58. Zhang, P., Tobias, I. & Olson, W. K. (1994). Computer simulations of protein-induced structural changes in closed circular DNA. J. Mol. Biol. 242, 271-290.
59. Zwanzig, R., Szabo, A. & Bagchi, B. (1992). Levinthal's paradox. Proc. Nat. Acad. Sci. U.S.A. 89, 20-22.