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http://dx.doi.org/10.5012/bkcs.2012.33.3.963

Nonclassical Chemical Kinetics for Description of Chemical Fluctuation in a Dynamically Heterogeneous Biological System  

Lim, Yu-Rim (Department of Chemistry, Chung-Ang University)
Park, Seong-Jun (Department of Chemistry, Chung-Ang University)
Lee, Sang-Youb (Department of Chemistry, Seoul National University)
Sung, Jae-Young (Department of Chemistry, Chung-Ang University)
Publication Information
Bulletin of the Korean Chemical Society / v.33, no.3, 2012 , pp. 963-970 More about this Journal
Abstract
We review novel chemical kinetics proposed for quantitative description of fluctuations in reaction times and in the number of product molecules in a heterogeneous biological system, and discuss quantitative interpretation of randomness parameter data in enzymatic turnover times of ${\beta}$-galactosidase. We discuss generalization of renewal theory for description of chemical fluctuation in product level in a multistep biopolymer reaction occurring in a dynamically heterogeneous environment. New stochastic simulation results are presented for the chemical fluctuation of a dynamically heterogeneous reaction system, which clearly show the effects of the initial state distribution on the chemical fluctuation. Our stochastic simulation results are found to be in good agreement with predictions of the analytic results obtained from the generalized master equation.
Keywords
Chemical fluctuation; Nonclassical kinetics; Single enzyme kinetics; Reaction event counting;
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1 Asbury, C. L.; Fehr, A. N.; Block, S. M. Science 2003, 302, 2130.   DOI
2 Eid, J.; Fehr, A.; Gray, J.; Luong, K.; Lyle, J.; Otto, G.; Peluso, P.; Rank, D.; Baybayan, P.; Bettman, B.; Bibillo, A.; Bjornson, K.; Chaudhuri, B.; Christians, F.; Cicero, R.; Clark, S.; Dalal, R.; de Winter, A.; Dixon, J. Science 2009, 323, 133.   DOI
3 Clarke, J.; Wu, H.-C.; Jayasinghe, L.; Patel, A.; Reid, S.; Bayley, H. Nature Nanotechnology 2009, 4, 265.   DOI
4 Visscher, K.; Schnitzer, M. J.; Block, S. M. Nature 1999, 400, 184.   DOI
5 Min, W.; Gopich, I. V.; English, B. P.; Kou, S. C.; Xie, X. S.; Szabo, A. J. Phys. Chem. B 2006, 110, 20093.   DOI
6 Cao, J.; Silbey, R. J. J. Phys. Chem. B 2008, 112, 12867.   DOI
7 Jung, W.; Yang, S.; Sung, J. J. Phys. Chem. B 2010, 114, 9840.
8 Cao, J. J. Phys. Chem. B 2011, 115, 5493   DOI
9 Fisher, M. E.; Kolomeisky, A. B. Proc. Natl. Acc. Sci. 2001, 98, 7748.
10 Yang, S.; Cao, J.; Silbey, R. J.; Sung, J. Biophys J. 2011, 101, 519   DOI
11 Balazsi, G.; Oudenaarden, A. V.; Collins, J. J. Cell 2011, 144, 910.   DOI
12 Raj, A.; Oudenaarden, A. V. Cell 2008, 135, 216.   DOI   ScienceOn
13 Maamar, H.; Raj, A.; Dubnau, D. Science 2007, 317, 526.   DOI
14 Maheshri, N.; O'Shea, E. K. Ann. Rev. Biophys. Biomol. Struct. 2007, 36, 413.   DOI
15 Rao, C. V.; Wolf, D. M.; Arkin, A. P. Nature 2002, 420, 231.   DOI
16 Sung, J.; Silbey, R. J. Phys. Rev. Lett. 2003, 91, 160601.   DOI
17 Zwanzig, R. Acc. Chem. Res. 1990, 23, 148.   DOI
18 Sung, J.; Silbey, R. J. Chem. Phys. Lett. 2005, 415, 10.   DOI
19 Cao, J. J. Phy. Chem. B 2006, 110, 19040   DOI
20 Gopich, I. V.; Szabo, A. J. Chem. Phys. 2006, 124, 154712.   DOI
21 Montroll, E. W.; Weiss, J. J. Math. Phys. 1965, 167.
22 Barkai, E.; Jung, Y.; Silbey, R. J. Ann. Rev. Phys. Chem. 2004, 55, 457.   DOI
23 Lim, Y. R.; Park, S. J.; Park, B. J.; Cao, J.; Silbey, R. J.; Sung, J. J. Chem. Theor. Comp. 2012, 8, in press.
24 Gillespie, D. T. J. Phys. Chem. 1977, 81, 2340.   DOI
25 Mandel, L.; Wolf, E. Optical Coherence and Quantum Optics; Cambridge University Press: New York, 1995.
26 Yang, S.; Cao, J. J. Chem. Phys. 2002, 117, 10996.   DOI
27 Kampen, N. G. V. Stochastic Processes in Physics and Chemistry; North Holland: Amsterdam, 2007
28 Velonia, K.; Flomenbom, O.; Loos, D.; Masuo, S.; Cotlet, M.; Engelborghs, Y.; Hofkens, J.; Rowan, A. E.; Klafter, J.; Nolte, R. J. M.; de Schryver, F. C. Angew. Chem. Int. Ed. 2005, 44, 560.   DOI
29 English, B. P.; Min, W.; van Oijen, A. M.; Lee, K. T.; Luo, G.; Sun, H.; Cherayil, B. J.; Xie, X. S. Nat. Chem. Biol. 2006, 2, 87.   DOI
30 Elowitz, M. B.; Levine, A. J.; Siggia, E. D.; Swain, P. S. Science 2002, 297, 1183.   DOI   ScienceOn