Transformational homologies in amino acid sequences suggest memberships in protein families

Journal of Statistical Physics

Volumn 93, Issue 3-4, 1998, Pages 673-697

  Mandell, Arnold J ^a,b   Selz, Karen A ^a,b   Shlesinger, Michael F ^c  

^a EMORY UNIVERSITY   (United States)

^b FLORIDA ATLANTIC UNIVERSITY   (United States)

^c OFFICE OF NAVAL RESEARCH   (United States)

Author keywords

Hydrophbic free energy eigenfunctions; Maximum entropy power spectra; Protein physics; Wavelets

Indexed keywords

EID: 0040585188     PISSN: 00224715     EISSN: None     Source Type: Journal    
DOI: 10.1023/b:joss.0000033248.97129.3f     Document Type: Article

References (65)

1. L. P. Kadanoff, From Order to Chaos; Essays: Critical, Chaotic and Otherwise (World Scientific Press, Singapore, 1993).
2. D. Gershon, Nature 389:418 (1997).
3. A. M. Lesk and C. Chothía, J. Mol. Biol. 136:225 (1980).
4. C. Branden and J. Tooze, Introduction to Protein Structure (Garland, N.Y., 1991).
5. D. Searls, Nature 389:417 (1997).
6. A. J. Mandell, K. A. Selz, and M. F. Shlesinger, Physica A 244:254 (1997).
7. A. J. Mandell, K. A. Selz, and M. F. Shlesinger, Proc. International School of Physics; Enrico Fermi Course. CXXXIV, F. Mallamace and H. E. Stanley, ed. (I.O.S. Press, Amsterdam, 1997), pp. 175-192.
8. A. J. Mandell, K. A. Selz, and M. F. Shlesinger, Proc. Natl. Acad. Sci. 94:13576 (1997).
9. A. J. Mandell, Michael J. Owens, Karen A. Selz, W. Neal Morgan, Michael F. Shlesinger, and Charles B. Nemeroff, Biopolymers 46:89 (1998).
10. E. A. Di Marzio and A. J. Mandell, J. Chem. Physics 107:5510 (1997).
11. T. E. Creighton, Proteins, Structures and Molecular Properties (Freeman, N.Y., 1984).
12. A. A. Zamyatnin, Prog. Biopliys. Mol. Biol. 24:109 (1972).
13. W. Kauzmann, Adv. Prot. Chem. 14:1 (1959).
14. C. Tanford, Proc. Natl. Acad. Sci. 76:4175 (1979).
15. F. H. Stillinger, Science 209:451 (1980).
16. W. Blokzijl and J. B. Engberts, Angew. Chem. Int. Edn. Engl. 32:1545 (1993).
17. C. Y. Lee, J. A. McCammon, and P. J. Rossky, J. Chem. Phys 80:4448 (1984).
18. J. T. Edsall, J. Am. Chem. Soc. 57:1506 (1935).
19. J. M. Sturtevant. Proc. Natl. Acad. Sci. 74:2236 (1977).
20. P. L. Privalov and N. N. Khechinashvili, J. Mol. Biol. 86:665 (1974).
21. J. A. Reynolds, D. B. Gilbert, and C. Tanford, Proc. Natl. Acad. Sci. 71:2925 (1974).
22. B. K. Lee and F. M. Richards, J. Mol. Biol. 55:379 (1971).
23. R. Lumry and S. Rajender, Biopolymers 9:1125 (1970).
24. Y. Nozaki and C. Tanford, J. Biol. Chem. 246:2211 (1971).
25. P. Manavalen and P. K. Ponnuswamy, Nature 275:673 (1978).
26. J. Kyte and R. F. Doolittle, J. Mol. Biol. 157:105 (1982).
27. S. H. White and R. E. Jacobs, Biophys. J. 57:911 (1990).
28. M. Degli Esposti, M. Crimi, and G. Venturoh, Eur. J. Biochem. 190:207 (1990).
29. K. A. Sharp, A. Nicholls, R. F. Fine, and B. Honig, Science 252:106, 1991.
30. J. M. Sanches-Ruiz, Eur. Biophys. J. 24:261 (1996).
31. J. Janin, Prog. Biophys. Molec. Biol. 64:145 (1995).
32. C. Chothia, Nature 254:304 (1975).
33. K. W. Plaxco, K. T. Simons, and D. Baker, J. Mol. Biol. 277:985 (1998).
34. H. S. Chan, Nature 392:761 (1998).
35. A. M. Gronenborn and G. M. Clore, Science 263:536 (1994).
36. K. A. Dill, K. M. Fiebig, and H. S. Chan, Proc. Natl. Acad. Sci. 90:1942 (1993).
37. R. M. Pashley, P. M. McGuiggan, B. W. Ninham, and D. F. Evans, Science 229:1088 (1985).
38. J. Israelachvili and H. Wennerstrom, Nature 379:219 (1996).
39. C. Chothia, Ann. Rev. Biochem. 53:537 (1984).
40. G. D. Rose, Nature 272:586 (1978).
41. A. J. Mandell, Ann. Rev. Pharmacol. Toxicol. 24:237 (1984).
42. A. J. Mandell, P. V. Russo, and B. Blomgren, Ann. Rev. N. Y. Acad. Sci. 504:88 (1987).
43. I. Daubechies, A. Grossman, and Y. Meyer, J. Math. Phys. 27:1271 (1986).
44. A. Grossmann and J. Morlet, SIAM J. Math. Anal. 15:723 (1984).
45. D. S. Broomhcad and G. P. King, Physica D 20:217 (1986).
46. D. S. Broomhead, R. Jones, and G. P. King, J. Phys. A 20:L563 (1987).
47. R. N. Madan, Maximum Entropy and Bayesian Methods (Kluwer Academic, Netherlands, 1993).
48. K. Linderstrøm-Lang and J. Schellman, Enzymes 1:443 (1959).
49. A. Arneodo, G. Grasseau, and M. Holschneider, Phys. Rev. Lett. 61:2281 (1988).
50. M. V. Wickerhauser, Adapted Wavelet Analysis from Theory to Software (A. K. Peters, Wellesley, MA, 1994), pp. 103-150.
51. M. Farge, Ann. Rev. Fl. Mech. 24:395 (1992).
52. J. P. Burg, Geophysics 37:375 (1972).
53. L. L. Gatlin, Information Theory and the Living System (Columbia University Press, New York, 1972).
54. A. M. Yaglom, Correlation Theory of Stationary and Related Random Functions (Springer-Verlag, New York, 1986).
55. G. C. Wagner, J. T. Colvin, J. P. Allen, and H. J. Stapleton, J. Am. Chem. Soc. 107:5591 (1985).
56. S. Alexander, J. Bernasconi, W. Schneider, and R. Orbach, Rev. Mod. Physics 53:175 (1981).
57. S. G. Mallat, IEEE Trans. on Pattern Anal. Machine Intell. PAMI-II:674 (1989).
58. A. Fournier, D. Fussell, and L. Carpenter, Commun. ACM 25:371 (1982).
59. R. F. Voss, NATO ASI Series F17, R. A. Earnshaw, ed. (Springer-Verlag, New York, 1985).
60. J. C. Yoccoz, Ann. Sci. de l'ENS 17:333 (1984).
61. M. R. Herman, Asterisque 1:103 (1983).
62. G. H. Hardy and E. M. Wright, Introduction to the Theory of Numbers, 5th ed. (Clarendon, London, 1979).
63. J. S. Richardson, Adv. Prot. Chem. 34:167 (1981).
64. J. Janin, Bull. Inst. Pasteur 77:337 (1979).
65. J. Douglass, O. Civelli, and E. Herbert, Annu. Rev. Biochem. 53:698 (1984).