Sequence variability of proteins evolutionarily constrained by solution-thermodynamic function

Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics

Volumn 69, Issue 1, 2004, Pages 8-

  Braun, F N ^a  

^a STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

FIBROIN; HEMOGLOBIN; INSECT PROTEIN; PROTEIN; PROTEIN BINDING; SILK; SOLUTION AND SOLUBILITY;

AMINO ACID SEQUENCE; BIOLOGICAL MODEL; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; DIMERIZATION; GENETIC VARIABILITY; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY; PROCEDURES; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SOLUTION AND SOLUBILITY; STRUCTURE ACTIVITY RELATION; THERMODYNAMICS;

AMINO ACID SEQUENCE; COMPUTER SIMULATION; DIMERIZATION; EVOLUTION, MOLECULAR; FIBROINS; GENETIC VARIATION; HEMOGLOBINS; INSECT PROTEINS; MODELS, CHEMICAL; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN BINDING; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; SILK; SOLUTIONS; STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS;

AMINO ACIDS; CONFORMATIONS; GELATION; GENETIC ENGINEERING; GIBBS FREE ENERGY; HYDROPHOBICITY; MUTAGENESIS; PHASE DIAGRAMS; PHASE SEPARATION; SELF ASSEMBLY; THERMAL EFFECTS; THERMODYNAMICS;

FIBRILLIZATIONS; MUTATION; SIMPLE EXACT MODEL (SEM);

PROTEINS;

EID: 85036389111     PISSN: 1063651X     EISSN: None     Source Type: Journal    
DOI: 10.1103/PhysRevE.69.011903     Document Type: Article

References (43)

1. S. Wright, in Proceedings of the Sixth International Congress on Genetics, edited by D. F. Jones (Brooklyn Botanic Gardens, New York, 1932), Vol. 1.
2. B. Drossel, Adv. Phys. 50, 209 (2001).
3. H.S. Chan and E. Bornberg-Bauer, Appl. Bioinform.1, 121 (2002).
4. E. Bornberg-Bauer and H.S. Chan, Proc. Natl. Acad. Sci. U.S.A. 96, 10689 (1999).
5. D. M. Taverna and R. A. Goldstein, in Proceedings of the 2000 Pacific Symposium on Biocomputing 2000, Honolulu, edited by R. B. Altman, A. K. Dunker, L. Hunter, and T. E. Klein (World Scientific, Singapore, 2000).
6. B.P. Blackburne and J. Hirst, J. Chem. Phys. 115, 1935 (2001).
7. F. N. Braun and D. A. Liberles, Intl. J. Biol. Macromol. 33, 19 (2003).
8. O. Annunziata, O. Ogun, and G.B. Benedek, Proc. Natl. Acad. Sci. U.S.A. 100, 970 (2003).
9. O. Galkin, K. Chen, R.L. Nagel, R.E. Hirsch, and P.G. Vekilov, Proc. Natl. Acad. Sci. U.S.A. 99, 8479 (2002).
10. M. Muschol and F. Rosenberger, J. Chem. Phys. 107, 1953 (1997).
11. F.N. Braun, J. Chem. Phys. 116, 6826 (2002).
12. W.A. Eaton and J. Hofrichter, Adv Protein Chem 40, 63 (1990).
13. A. Coniglio, J. Phys.: Condens. Matter 13, 9039 (2001).
14. J. Bergenholtz, M. Fuchs, and T. Voigtmann, J. Phys.: Condens. Matter 12, 6575 (2000).
15. We neglect diploidy, linkage effects, malarial resistance etc.
16. F.N. Braun and C. Viney, Int. J. Biol. Macromol. 32, 59 (2003).
17. Related experimental observations concerning the relation between sequence hydrophobicity and the physical chemistry of silk glands have been presented by H.J. Jin and D.L. Kaplan, Nature (London) 424, 1057 (2003).
18. F. Vollrath and D.P. Knight, Nature (London) 410, 541 (2001).
19. B. Vallone, A.E. Miele, P. Vecchini, E. Chaincone, and M. Brunori, Proc. Natl. Acad. Sci. U.S.A. 95, 6103 (1998).
20. K.A. Dill, Biochemistry 24, 1501 (1985).
21. R.J. Baxter, J. Chem. Phys. 49, 2770 (1968)
22. C. Regnaut and J.C. Ravey, J. Chem. Phys. 91, 1211 (1989).
23. Y.C. Chiew and E.D. Glandt, J. Phys. A 16, 2599 (1983).
24. L. Onsager, Ann. N.Y. Acad. Sci. 51, 627 (1949).
25. In constructing the secondary plateau of Fig. 44, we subsume the nematic-isotropic biphasic region for convenience into the liquid-dispersed phase.
26. K.A. Dill, D.O.V. Alonso, and K. Hutchinson, Biochemistry 28, 5439 (1989).
27. F. Jacob and J. Monod, J. Mol. Biol. 3, 318 (1961).
28. G.A. Wray, Mol. Biol. Evol. 20, 1377 (2003).
29. Physiological concentrations lie in the range (Formula presented) 10–30 g/dl 9. The corresponding volume fraction can be estimated according to (Formula presented) substituting (Formula presented)kDa for the molecular weight of the tetramer (Formula presented) is Avogadro’s number).
30. The exact position of the HbS substitution in the surface of the native tertiary structure is a classic result of x-ray crystallography. That this presents a rather well-defined hydrophobic sticky patch is of course captured only very crudely by the low-resolution of the present approach.
31. For an overview of the distinction between negative and positive selection, see D.A. Liberles and M. L Wayne, Genome Biology 3, 1018 (2002).
32. X. Gu, Mol. Biol. Evol. 16, 1664 (1999).
33. The number of hydrophobic residues in the tetramer n is inferred by counting over the separately archived α and β subunits, then doubling. Our dataset comprises 20 hemoglobin-sequenced primates listed by G.J.P. Naylor and M. Gerstein, J. Mol. Evol. 51, 223 (2000). Ruffed lemur, brown lemur, galago, slender loris, slow loris, tarsier, spider monkey, capuchin, marmoset, tamarin, gorilla, human, colobus, langur, green monkey, macaque, mandril, mangabey, yellow baboon, gelada.
34. K. Kerkam, C. Viney, D. Kaplan, and S. Lombardi, Nature (London) 349, 596 (1991).
35. Nephila dragline silk comprises two fibroins, spidroin I and spidroin II. According to the theory of Ref. 16, liquid crystalline mesogens in the gland are assembled exclusively from spidroin II. The Swiss-prot data presented in Fig. 55 is extrapolated from available spidroin II sequence fragments, N.clavipes, N.madagascariensis, and N.senegalensis. See J. Gatesy, C. Hayashi, D. Motriuk, J. Woods, and R. Lewis, Science 291, 2603 (2001).
36. Assuming 1 generation ∼1 yr, and a per-site HP flipping rate of 1 pauling, i.e., (Formula presented) site (Formula presented) 37, we estimate (Formula presented) for (Formula presented) fibroins. Hence, positive selection for liquid crystallinity in the Nephila silk gland confers a fitness advantage at least of the order of (Formula presented)
37. M. Kimura, The Neutral Theory of Molecular Evolution (Cambridge University Press, Cambridge, 1983).
38. D.M. Taverna and R.A. Goldstein, Proteins 46, 105 (2002).
39. S.A. Benner, G. Cannarozzi, D. Gerloff D, M. Turcotte, and G. Chelvanayagam, Chem. Rev. (Washington, D.C.) 97, 2725 (1997).
40. A. Irbaeck and E. Sandelin, Biophys. J. 79, 2252 (2000);E. Sandelin, Biophys. J. (to be published).
41. S. Ohno, Evolution by Gene Duplication (Springer, Berlin, 1970).
42. R. A. Raff, The Shape of Life (University of Chicago Press, Chicago, 1996).
43. J. D. Bryngelson and E. M. Billings, in Physics of Biological Systems, edited by H. Flybjerg et al. (Springer, Berlin, 1997).