Path-based approach to random walks on networks characterizes how proteins evolve new functions

Physical Review Letters

Volumn 111, Issue 8, 2013, Pages

  Manhart, Michael ^a   Morozov, Alexandre V ^a,b  

^a RUTGERS UNIVERSITY   (United States)

^b RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOPHYSICAL MODEL; CONTINUOUS-TIME RANDOM WALK; DIRECTED EVOLUTION; EVOLUTIONARY ADAPTATION; KEY FEATURE; NEW FUNCTIONS; NUMERICAL ALGORITHMS; STATISTICAL PROPERTIES;

ALGORITHMS; RANDOM PROCESSES;

PROTEINS;

PROTEIN;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; CHEMICAL MODEL; CHEMISTRY; PHYSIOLOGY; STATISTICS; THERMODYNAMICS;

ALGORITHMS; MODELS, BIOLOGICAL; MODELS, CHEMICAL; PROTEINS; STOCHASTIC PROCESSES; THERMODYNAMICS;

EID: 84883140639     PISSN: 00319007     EISSN: 10797114     Source Type: Journal    
DOI: 10.1103/PhysRevLett.111.088102     Document Type: Article

References (45)

1. D. M. Weinreich, N. F. Delaney, M. A. DePristo, and D. L. Hartl, Science 312, 111 (2006). SCIEAS 0036-8075 10.1126/science.1123539
2. F. J. Poelwijk, D. J. Kiviet, D. M. Weinreich, and S. J. Tans, Nature (London) 445, 383 (2007). NATUAS 0028-0836 10.1038/nature05451
3. M. Carneiro and D. L. Hartl, Proc. Natl. Acad. Sci. U.S.A. 107, 1747 (2010). PNASA6 0027-8424 10.1073/pnas.0906192106
4. F. Noé, C. Schütte, E. Vanden-Eijnden, L. Reich, and T. R. Weikl, Proc. Natl. Acad. Sci. U.S.A. 106, 19 011 (2009). PNASA6 0027-8424 10.1073/pnas.0905466106
5. P. G. Bolhuis, D. Chandler, C. Dellago, and P. L. Geissler, Annu. Rev. Phys. Chem. 53, 291 (2002). ARPLAP 0066-426X 10.1146/annurev.physchem.53.082301. 113146
6. D. ben-Avraham and S. Havlin, Diffusion and Reactions in Fractals and Disordered Systems (Cambridge University Press, Cambridge, England, 2000).
7. S. Condamin, O. Bénichou, V. Tejedor, R. Voituriez, and J. Klafter, Nature (London) 450, 77 (2007). NATUAS 0028-0836 10.1038/nature06201
8. D. M. Roma, R. A. O'Flanagan, A. E. Ruckenstein, A. M. Sengupta, and R. Mukhopadhyay, Phys. Rev. E 71, 011902 (2005). PLEEE8 1539-3755 10.1103/PhysRevE.71.011902
9. C. H. Waddington, The Strategy of the Genes. A Discussion of Some Aspects of Theoretical Biology (Allen and Unwin, London, 1957).
10. S. Kauffman, The Origins of Order: Self-Organization and Selection in Evolution (Oxford University Press, New York, 1993).
11. T. Enver, M. Pera, C. Peterson, and P. W. Andrews, Cell Stem Cell 4, 387 (2009). CSCEC4 1875-9777 10.1016/j.stem.2009.04.011
12. J. T. Bridgham, E. A. Ortlund, and J. W. Thornton, Nature (London) 461, 515 (2009). NATUAS 0028-0836 10.1038/nature08249
13. A. E. Lobkovsky, Y. I. Wolf, and E. V. Koonin, PLoS Comput. Biol. 7, e1002302 (2011). PCBLBG 1553-7358 10.1371/journal.pcbi.1002302
14. J. D. Noh and H. Rieger, Phys. Rev. Lett. 92, 118701 (2004). PRLTAO 0031-9007 10.1103/PhysRevLett.92.118701
15. E. M. Bollt and D. ben-Avraham, New J. Phys. 7, 26 (2005). NJOPFM 1367-2630 10.1088/1367-2630/7/1/026
16. C. Dellago, P. G. Bolhuis, F. S. Csajka, and D. Chandler, J. Chem. Phys. 108, 1964 (1998). JCPSA6 0021-9606 10.1063/1.475562
17. C. Dellago, P. G. Bolhuis, and P. L. Geissler, Adv. Chem. Phys. 123, 1 (2003). ADCPAA 0065-2385 10.1002/0471231509
18. G. Hummer, J. Chem. Phys. 120, 516 (2004). JCPSA6 0021-9606 10.1063/1.1630572
19. B. Harland and S. X. Sun, J. Chem. Phys. 127, 104103 (2007). JCPSA6 0021-9606 10.1063/1.2775439
20. W. E and E. Vanden-Eijnden, J. Stat. Phys. 123, 503 (2006). JSTPBS 0022-4715 10.1007/s10955-005-9003-9
21. P. Metzner, C. Schütte, and E. Vanden-Eijnden, Multiscale Model. Simul. 7, 1192 (2009). MMSUBT 1540-3459 10.1137/070699500
22. G. H. Weiss, Aspects and Applications of the Random Walk (North Holland, Amsterdam, 1994).
23. K. B. Zeldovich, P. Chen, and E. I. Shakhnovich, Proc. Natl. Acad. Sci. U.S.A. 104, 16 152 (2007). PNASA6 0027-8424 10.1073/pnas.0705366104
24. N. Tokuriki, F. Stricher, L. Serrano, and D. S. Tawfik, PLoS Comput. Biol. 4, e1000002 (2008). PCBLBG 1553-7358 10.1371/journal.pcbi.1000002
25. N. Tokuriki and D. S. Tawfik, Curr. Opin. Struct. Biol. 19, 596 (2009). COSBEF 0959-440X 10.1016/j.sbi.2009.08.003
26. J. D. Bloom and F. H. Arnold, Proc. Natl. Acad. Sci. U.S.A. 106, 9995 (2009). PNASA6 0027-8424 10.1073/pnas.0901522106
27. T. A. Whitehead, A. Chevalier, Y. Song, C. Dreyfus, S. J. Fleishman, C. De Mattos, C. A. Myers, H. Kamisetty, P. Blair, I. A. Wilson, and D. Baker, Nat. Biotechnol. 30, 543 (2012). NABIF9 1087-0156 10.1038/nbt.2214
28. P. Hänggi, P. Talkner, and M. Borkovec, Rev. Mod. Phys. 62, 251 (1990). RMPHAT 0034-6861 10.1103/RevModPhys.62.251
29. See Supplemental Material at http://link.aps.org/supplemental/10.1103/ PhysRevLett.111.088102 for details of reaction rate results.
30. P. Metzner, C. Schütte, and E. Vanden-Eijnden, J. Chem. Phys. 125, 084110 (2006). JCPSA6 0021-9606 10.1063/1.2335447
31. S. Mayer, S. Rüdiger, H. C. Ang, A. C. Joerger, and A. R. Fersht, J. Mol. Biol. 372, 268 (2007). JMOBAK 0022-2836 10.1016/j.jmb.2007.06.044
32. T. Clackson and J. A. Wells, Science 267, 383 (1995). SCIEAS 0036-8075 10.1126/science.7529940
33. L. Serrano, A. G. Day, and A. R. Fersht, J. Mol. Biol. 233, 305 (1993). JMOBAK 0022-2836 10.1006/jmbi.1993.1508
34. N. Tokuriki, F. Stricher, J. Schymkowitz, L. Serrano, and D. S. Tawfik, J. Mol. Biol. 369, 1318 (2007). JMOBAK 0022-2836 10.1016/j.jmb.2007.03.069
35. A. A. Bogan and K. S. Thorn, J. Mol. Biol. 280, 1 (1998). JMOBAK 0022-2836 10.1006/jmbi.1998.1843
36. K. S. Thorn and A. A. Bogan, Bioinformatics 17, 284 (2001). BOINFP 1367-4803 10.1093/bioinformatics/17.3.284
37. L. D. Bogarad and M. W. Deem, Proc. Natl. Acad. Sci. U.S.A. 96, 2591 (1999). PNASA6 0027-8424 10.1073/pnas.96.6.2591
38. X. Wang, G. Minasov, and B. K. Shoichet, J. Mol. Biol. 320, 85 (2002). JMOBAK 0022-2836 10.1016/S0022-2836(02)00400-X
39. M. Manhart, A. Haldane, and A. V. Morozov, Theor. Popul. Biol. 82, 66 (2012). TLPBAQ 0040-5809 10.1016/j.tpb.2012.03.007
40. J. H. Gillespie, Evolution (Lawrence, Kans.) 38, 1116 (1984). EVOLAO 0014-3820 10.2307/2408444
41. M. A. DePristo, D. M. Weinreich, and D. L. Hartl, Nat. Rev. Genet. 6, 678 (2005). 1471-0056 10.1038/nrg1672
42. S. Bershtein, K. Goldin, and D. S. Tawfik, J. Mol. Biol. 379, 1029 (2008). JMOBAK 0022-2836 10.1016/j.jmb.2008.04.024
43. C. J. Brown, A. K. Johnson, A. K. Dunker, and G. W. Daughdrill, Curr. Opin. Struct. Biol. 21, 441 (2011). COSBEF 0959-440X 10.1016/j.sbi.2011.02.005
44. S. L. Rutherford, Nat. Rev. Genet. 4, 263 (2003). 1471-0056 10.1038/nrg1041
45. J. F. Crow and M. Kimura, An Introduction to Population Genetics Theory (Harper and Row, New York, 1970).