Optimization of a stochastically simulated gene network model via simulated annealing

Biophysical Journal

Volumn 91, Issue 9, 2006, Pages 3196-3205

  Tomshine, Jonathan ^a   Kaznessis, Yiannis N ^a  

^a University of Minnesota   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; DIMERIZATION; DISSOCIATION CONSTANT; GENE EXPRESSION; GENETIC ANALYSIS; PROTEIN DEGRADATION; PROTEIN DNA BINDING; PROTEIN DOMAIN; SIMULATION; STOCHASTIC MODEL;

EID: 33751204469     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.083485     Document Type: Article

References (40)

1. Goldbeter, A. 2002. Computational approaches to cellular rhythms. Nature. 420:238-245.
2. Stelling, J., U. Sauer, Z. Szallasi, F. J. Doyle 3rd, and J. Doyle. 2004. Robustness of cellular functions. Cell. 118:675-685.
3. Kaern, M., W. J. Blake, and J. J. Collins. 2003. The engineering of gene regulatory networks. Annu. Rev. Biomed. Eng. 5:179-206.
4. Guet, C. C., M. B. Elowitz, W. Hsing, and S. Leibler. 2002. Combinatorial synthesis of genetic networks. Science. 296:1466-1470.
5. Gardner, T. S., C. R. Cantor, and J. J. Collins. 2000. Construction of a genetic toggle switch in Escherichia coli. Nature. 403:339-342.
6. Atkinson, M. R., M. A. Savageau, J. T. Myers, and A. J. Ninfa. 2003. Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell. 113:597-607.
7. Elowitz, M. B., and S. Leibler. 2000. A synthetic oscillatory network of transcriptional regulators. Nature. 403:335-338.
8. Tuttle, L., H. Salis, J. Tomshine, and Y. N. Kaznessis. 2005. Model-driven designs of an oscillating gene network. Biophys. J. 89:3873-3883.
9. Smolen, P., D. A. Baxter, and J. H. Byrne. 2002. A reduced model clarifies the role of feedback loops and time delays in the Drosophila circadian oscillator. Biophys. J. 83:2349-2359.
10. Vilar, J. M., H. Y. Kueh, N. Barkai, and S. Leibler. 2002. Mechanisms of noise-resistance in genetic oscillators. Proc. Natl. Acad. Sci. USA. 99:5988-5992.
11. Barkai, N., and S. Leibler. 2000. Circadian clocks limited by noise. Nature. 403:267-268.
12. Hasty, J., M. Dolnik, V. Rottschafer, and J. J. Collins. 2002. Synthetic gene network for entraining and amplifying cellular oscillations. Phys. Rev. Lett. 88:148101.
13. Shea, M. A., and G. K. Ackers. 1985. The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation. J. Mol. Biol. 181:211-230.
14. Arkin, A., J. Ross, and H. H. McAdams. 1998. Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected Escherichia coli cells. Genetics. 149:1633-1648.
15. McAdams, H. H., and A. Arkin. 1997. Stochastic mechanisms in gene expression. Proc. Natl. Acad. Sci. USA. 94:814-819.
16. Mendes, P., and D. Kell. 1998. Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics. 14:869-883.
17. Francois, P., and V. Hakim. 2004. Design of genetic networks with specified functions by evolution in silico. Proc. Natl. Acad. Sci. USA. 101:580-585.
18. Gillespie, D. T. 2000. The chemical Langevin equation. J. Chem. Phys. 113:297-306.
19. Elowitz, M. B., A. J. Levine, E. D. Siggia, and P. S. Swain. 2002. Stochastic gene expression in a single cell. Science. 297:1183-1186.
20. Kirkpatrick, S., J. C. D. Gelatt, and M. P. Vecchi. 1983. Optimization by simulated annealing. Science. 220:671-680.
21. Liu, J. S. 2001. Monte Carlo Strategies in Scientific Computing. Springer-Verlag, New York, NY.
22. Salis, H., and Y. Kaznessis. 2005. Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions. J. Chem. Phys. 122:54103-1-54103-13.
23. Wang, R., Z. Jing, and L. Chen. 2005. Modelling periodic oscillation in gene regulatory networks by cyclic feedback systems. Bull. Math. Biol. 67:339-367.
24. Riggs, A. D., S. Bourgeois, and M. Cohn. 1970. The lac repressor-operator interaction. 3. Kinetic studies. J. Mol. Biol. 53:401-417.
25. Fickert, R., and B. Muller-Hill. 1992. How Lac repressor finds lac operator in vitro. J. Mol. Biol. 226:59-68.
26. Levandoski, M. M., O. V. Tsodikov, D. E. Frank, S. E. Melcher, R. M. Saecker, and M. T. Record, Jr. 1996. Cooperative and anticooperative effects in binding of the first and second plasmid Osym operators to a LacI tetramer: evidence for contributions of non-operator DNA binding by wrapping and looping. J. Mol. Biol. 260:697-717.
27. Beckwith, J. R., and D. Zipser, editors. 1970. The Lactose Operon. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
28. McKnight, S. L., and K. R. Yamamoto, editors. 1992. Transcriptional Regulation. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
29. Zhang, X., T. Reeder, and R. Schleif. 1996. Transcription activation parameters at ara pBAD. J. Mol. Biol. 258:14-24.
30. Hendrickson, W., and R. F. Schleif. 1984. Regulation of the Escherichia coli L-arabinose operon studied by gel electrophoresis DNA binding assay. J. Mol. Biol. 178:611-628.
31. Martin, K. J., and R. F. Schleif. 1987. Equilibrium DNA-binding of AraC protein. Compensation for displaced ions. J. Mol. Biol. 195:741-744.
32. Kleinschmidt, C., K. Tovar, W. Hillen, and D. Porschke. 1988. Dynamics of repressor-operator recognition: the Tn10-encoded tetracycline resistance control. Biochemistry. 27:1094-1104.
33. Bertrand-Burggraf, E., J. F. Lefevre, and M. Daune. 1984. A new experimental approach for studying the association between RNA polymerase and the tet promoter of pBR322. Nucleic Acids Res. 12:1697-1706.
34. Halford, S. E., and J. F. Marko. 2004. How do site-specific DNA-binding proteins find their targets? Nucleic Acids Res. 32:3040-3052.
35. Madisetti, V. K., and D. B. Williams. 1998. Signals and systems. In The Digital Signal Processing Handbook. V. K. Madisetti and D. B. Williams, editors. CRC Press, Boca Raton, FL.
36. Frigo, M., and S. G. Johnson. 1998. FFTW: an adaptive software architecture for the FFT. In Proceedings of the 1998 IEEE International Conference on Acoustics, Speech and Signal Processing, New York, NY. 1381-1384.
37. Stickle, D. F., K. M. Vossen, D. A. Riley, and M. G. Fried. 1994. Free DNA concentration in E. coli estimated by an analysis of competition for DNA binding proteins. J. Theor. Biol. 168:1-12.
38. Frank, D. E., R. M. Saecker, J. P. Bond, M. W. Capp, O. V. Tsodikov, S. E. Melcher, M. M. Levandoski, and M. T. Record, Jr. 1997. Thermodynamics of the interactions of lac repressor with variants of the symmetric lac operator: effects of converting a consensus site to a non-specific site. J. Mol. Biol. 267:1186-1206.
39. Wissmann, A., R. Baumeister, G. Muller, B. Hecht, V. Helbl, K. Pfleiderer, and W. Hillen. 1991. Amino acids determining operator binding specificity in the helix-turn-helix motif of Tn10 Tet repressor. EMBO J. 10:4145-4152.
40. Salis, H., V. Sotiropoulos, and Y. N. Kaznessis. 2006. Multiscale Hy3S: hybrid stochastic simulation for supercomputers. BMC Bioinformatics. 7:93.