Comparison of Monte Carlo Simulations of Cytochrome b 6f with Experiment Using Latin Hypercube Sampling

Bulletin of Mathematical Biology

Volumn 73, Issue 9, 2011, Pages 2152-2174

  Schumaker, Mark F ^a   Kramer, David M ^a,b  

^a WASHINGTON STATE UNIVERSITY   (United States)

^b Michigan State University   (United States)

Author keywords

Cytochrome b 6f; Latin hypercube sampling; Monte Carlo; Photosynthesis; Q cycle

Indexed keywords

CYTOCHROME B6F;

ARTICLE; BIOLOGICAL MODEL; COMPARATIVE STUDY; COMPUTER SIMULATION; ELECTRON TRANSPORT; MONTE CARLO METHOD; PHOTOSYNTHESIS; PHYSIOLOGY;

COMPUTER SIMULATION; CYTOCHROME B6F COMPLEX; ELECTRON TRANSPORT; MODELS, BIOLOGICAL; MONTE CARLO METHOD; PHOTOSYNTHESIS;

EID: 79961022056     PISSN: 00928240     EISSN: 15229602     Source Type: Journal    
DOI: 10.1007/s11538-010-9616-2     Document Type: Article

References (36)

1. Alric, J., Pierre, Y., Picot, D., Lavergne, J., & Rappaport, F., (2005). Spectral and redox characterization of the heme ci of the cytochrome b6f complex. Proc. Natl. Acad. Sci. USA, 102(44), 15860-15865.
2. Blythe, R. A., & Evans, M. R. (2007). Nonequilibrium steady states of matrix-product form: a solver's guide. J. Phys. A, Math. Theor., 40, R333-R441.
3. Cape, J. L., Bowman, M. K., & Kramer, D. M. (2006). Understanding the cytochrome bc complexes by what they don't do. The Q-cycle at 30. Trends Plant Sci., 11, 46-55.
4. Cape, J. L., Bowman, M. K., & Kramer, D. M. (2007). A semiquinone intermediate generated at the Qo site of the cytochrome bc1 complex. Importance for the Q-cycle and superoxide production. Proc. Natl. Acad. Sci. USA, 104, 7887-7892.
5. 1 and related bc complexes, the Rieske/cytochrome b complex as the functional core of a central electron/proton transfer complex. In C. N. Hunter, F. Daldal, M. C. Thurnauer, & J. T. Beatty (Eds.), The purple photosynthetic bacteria (pp. 451-473). Dordrecht: Springer.
6. Cramer, W. A., Zhang, H., Yan, J., Kurisu, G., & Smith, J. L. (2006). Transmembrane traffic in the cytochrome b6f complex. Annu. Rev. Biochem., 75, 769-790.
7. Davey, K. R. (2008). Latin hypercube sampling and pattern search in magnetic field optimization problems. IEEE Trans. Magn., 44(6), 974-977.
8. Dekker, J. P., & Boekema, E. J. (2005). Supramolecular organization of thylakoid membranes in green plants. Biochim. Biophys. Acta, 1706, 12-39.
9. 6f complex dependent on the occupation and structure of the qi site and vice versa? J. Biol. Chem., 284(31), 20822-20829.
10. Derrida, B. (2007). Non-equilibrium steady states: fluctuations and large deviations of the density and current. J. Stat. Mech., P07023.
11. Frenklach, M., Packard, A., Seiler, P., & Feeley, R. (2004). Collaborative data processing in developing predictive models of complex reaction systems. Int. J. Chem. Kinet., 36(1), 57-66.
12. Fu, M. C. (2002). Optimization for simulation: theory vs. practice. INFORMS J. Comput., 14, 192-215.
13. Gillespie, D. T. (1976). A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comput. Phys., 22, 403-434.
14. Gillespie, D. T. (1977). Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem., 81, 2340-2361.
15. Helton, J. C., & Davis, F. J. (2003). Latin hypercube sampling and the propagation of uncertainty in analysis of complex systems. Reliab. Eng. Syst. Saf., 81, 23-69.
16. Helton, J. C., Johnson, J. D., Sallaberry, C. J., & Storlie, C. B. (2006). Survey of sampling-based methods for uncertainty and sensitivity analysis. Reliab. Eng. Syst. Saf., 91, 1175-1209.
17. Hill, T. L. (1977). Free energy transduction in biology (p. 6). New York: Academic Press.
18. 6f complex. In D. A. Bryant (Ed.), The molecular biology of cyanobacteria (pp. 259-317). Dordrecht: Kluwer Academic.
19. Kirchhoff, H. (2008). Molecular crowding and order in photosynthetic membranes. Trends Plant Sci., 13, 201-207.
20. Kirchhoff, H., Horstmann, S., & Weiss, E. (2000). Control of the photosynthetic electron transport by PQ diffusion microdomains in thylakoids of higher plants. Biochim. Biophys. Acta, 1459, 148-168.
21. Kleijnen, J. P. C., Sanchez, S. M., Lucas, T. W., & Cioppa, T. M. (2005). A user's guide to the brave new world of designing simulation experiments. INFORMS J. Comput., 17, 263-289.
22. Kramer, D. M., & Crofts, A. J. (1993). The concerted reduction of high and low potential chains of the bf complex by plastoquinol. Biochim. Biophys. Acta, 1183, 72-84.
23. Kurisu, G., Zhang, H., Smith, J. L., & Cramer, W. A. (2003). Structure of the cytochrome b6f complex of oxygenic photosynthesis: tuning the cavity. Science, 302, 1009-1014.
24. McKay, M. D., Beckman, R. J., & Conover, W. J. (1979). A comparison of three methods for selecting values of input variables in the analysis of output from a computer code. Technometrics, 21(2), 239-245.
25. Minasny, B. (2004). Latin hypercube sampling. Matlab Central, www. mathworks. com/matlabcentral/fileexchange/authors/11803.
26. Muller, F., Crofts, A. R., & Kramer, D. M. (2002). Multiple Q-cycle bypass reactions at the Qo site of the cytochrome bc1 complex. Biochemistry, 41, 7866-7874.
27. Ort, D. R., & Kramer, D. (2009). Photosynthesis: the light reactions. Encycl. Life Sci. doi: 10. 1002/9780470015902. a0001309. pub2.
28. Press, W. H., Teukolsky, S. A., Vetterling, W. T., & Flannery, B. P. (1992). Numerical recipes in Fortran (2nd ed., pp. 402-406). Cambridge: Cambridge Univ. Press.
29. Rich, P., Heathcote, P., & Moss, D. A. (1987). Kinetic Studies of Electron Transfer in a hybrid system constructed from the cytochrome bf complex and photosystem I. Biochim. Biophys. Acta, 892(1), 138-151.
30. Saltelli, A., Ratto, M., Tarantola, S., & Campolongo, F. (2006). Sensitivity analysis practices: strategies for model-based inference. Reliab. Eng. Syst. Saf., 91, 1109-1125.
31. Shinkarev, V. P., & Wraight, C. A. (2007). Intermonomer electron transfer in the bc(1) complex dimer is controlled by the energized state and by impaired electron transfer between low and high potential hemes. FEBS Lett, 581, 1535-1541.
32. Smith, J. L., Zhang, H., Yan, J., Kurisu, G., & Cramer, W. A. (2004). Cytochrome bc complexes: a common core of structure and function surrounded by diversity in the outlying provinces. Curr. Opin. Struct. Biol., 14, 432-439.
33. 6f complex: De plus ca change de plus c'est la meme chose. J. Bioenerg. Biomembr., 31, 201-213.
34. Spear, R. C. (1997). Large simulation models: calibration, uniqueness and goodness of fit. Environ. Model. Softw., 12, 219-228.
35. Tremmel, I. G., Kirchhoff, H., Weis, E., & Farquhar, G. D. (2003). Dependence of plastoquinol diffusion on the shape, size, and density of integral thylakoid proteins. Biochim. Biophys. Acta, 1607, 97-109.
36. Tremmel, I. G., Weis, E., & Farquhar, G. D. (2007). Macromolecular crowding and its influence on possible reaction mechanisms in photosynthetic electron flow. Biochim. Biophys. Acta, 1767, 353-361.