The emergence of scaling in sequence-based physical models of protein evolution

Biophysical Journal

Volumn 88, Issue 6, 2005, Pages 3905-3911

  Deeds, Eric J ^a   Shakhnovich, Eugene I ^b  

^a HARVARD UNIVERSITY   (United States)

^b HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; MEASUREMENT; MORPHOGENESIS; PHYSICAL MODEL; PROTEIN DOMAIN; PROTEIN EVOLUTION; PROTEIN STRUCTURE; SCALE FREE SYSTEM; SCALING; STATISTICAL ANALYSIS; SYSTEM ANALYSIS;

EID: 22244441443     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.104.051433     Document Type: Article

References (27)

1. Albert, R., and A.-L. Barabasi. 2002. Statistical mechanics of complex networks. Rev. Mod. Phys. 74:47-97.
2. Barabasi, A. L., and R. Albert. 1999. Emergence of scaling in random networks. Science. 286:509-512.
3. Chan, H. S., and E. Bornberg-Bauer. 2002. Perspectives on protein evolution from simple exact models. Appl Bioinformatics. 1:121-144.
4. Chan, H. S., and K. A. Dill. 1990. The effects of internal constraints on the configurations of chain molecules. J. Chem. Phys. 92:3118-3135.
5. Chiu, T. L., and R. A. Goldstein. 2000. How to generate improved potentials for protein tertiary structure prediction: a lattice model study. Proteins. 41:157-163.
6. Deeds, E. J., N. V. Dokholyan, and E. I. Shakhnovich. 2003. Protein evolution within a structural space. Biophys. J. 85:2962-2972.
7. Deeds, E. J., B. Shakhnovich, and E. I. Shakhnovich. 2004. Proteomic traces of speciation. J. Mol. Biol. 336:695-706.
8. Dinner, A. R., V. Abkevich, E. Shakhnovich, and M. Karplus. 1999. Factors that affect the folding ability of proteins. Proteins. 35:34-40.
9. 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.
10. England, J. L., and E. I. Shakhnovich. 2003. Structural determinant of protein designability. Phys. Rev. Lett. 90:218101.
11. Goldstein, R. A., Z. A. Luthey-Schulten, and P. G. Wolynes. 1992. Optimal protein-folding codes from spin-glass theory. Proc. Natl. Acad. Sci. USA. 89:4918-4922.
12. Kim, J., P. L. Krapivsky, B. Kahng, and S. Redner. 2002. Infinite-order percolation and giant fluctuations in a protein interaction network. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 66:055101.
13. Koonin, E. V., Y. I. Wolf, and G. P. Karev. 2002. The structure of the protein universe and genome evolution. Nature. 420:218-223.
14. Lesk, A. M., L. Lo Conte, and T. J. Hubbard. 2001. Assessment of novel fold targets in CASP4: predictions of three-dimensional structures, secondary structures, and interresidue contacts. Proteins Suppl. 5:98-118.
15. 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.
16. Li, J., J. Wang, J. Zhang, and W. Wang. 2004. Thermodynamic and kinetic foldability of a lattice protein model. J. Chem. Phys. 120:6274-6287.
17. Maslov, S., and K. Sneppen. 2002. Specificity and stability in topology of protein networks. Science. 296:910-913.
18. Mirny, L. A., and E. I. Shakhnovich. 1996. How to derive a protein folding potential? A new approach to an old problem. J. Mol. Biol. 264:1164-1179.
19. Miyazawa, S., and R. L. Jernigan. 1985. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules. 18:534-552.
20. Miyazawa, S., and R. L. Jernigan. 1996. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J. Mol. Biol. 256:623-644.
21. Qian, J., N. M. Luscombe, and M. Gerstein. 2001. Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model. J. Mol. Biol. 313:673-681.
22. Shakhnovich, E. I., and A. Gutin. 1990. Enumeration of all compact conformations of copolymers with random sequence links. J. Chem. Phys. 93:5967-5971.
23. Thomas, P. D., and K. A. Dill. 1996. Statistical potentials extracted from protein structures: how accurate are they? J. Mol. Biol. 257:457-469.
24. Tiana, G., R. A. Broglia, and E. I. Shakhnovich. 2000. Hiking in the energy landscape in sequence space: a bumpy road to good folders. Proteins. 39:244-251.
25. Tiana, G., B. E. Shakhnovich, N. V. Dokholyan, and E. I. Shakhnovich. 2004. Imprint of evolution on protein structures. Proc. Natl. Acad. Sci. USA. 101:2846-2851.
26. Xia, Y., and M. Levitt. 2004. Simulating protein evolution in sequence and structure space. Curr. Opin. Struct. Biol. 14:202-207.
27. Zhang, L., and J. Skolnick. 1998. How do potentials derived from structural databases relate to "true" potentials? Protein Sci. 7:112-122.