Intrinsic noise analysis and stochastic simulation on transforming growth factor beta signal pathway

doi:10.1088/1674-1056/19/10/108202

中国物理B ›› 2010, Vol. 19 ›› Issue (10): 108202-108202.doi: 10.1088/1674-1056/19/10/108202

Intrinsic noise analysis and stochastic simulation on transforming growth factor beta signal pathway

王路, 欧阳颀

The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China; Center for Theoretical Biology, Peking University, Beijing 100871, China

收稿日期:2010-04-21 修回日期:2010-06-10 出版日期:2010-10-15 发布日期:2010-10-15
基金资助:
Project supported by the National Natural Science Foundation of China (Grant No. 10721403), and the National Basic Research Program of China (Grant No. 2009CB918500).

Intrinsic noise analysis and stochastic simulation on transforming growth factor beta signal pathway

Wang Lu(王路)^a)b) and Ouyang Qi(欧阳颀)^a)b)†

^aThe State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China; ^b Center for Theoretical Biology, Peking University, Beijing 100871, China

Received:2010-04-21 Revised:2010-06-10 Online:2010-10-15 Published:2010-10-15
Supported by:
Project supported by the National Natural Science Foundation of China (Grant No. 10721403), and the National Basic Research Program of China (Grant No. 2009CB918500).

摘要/Abstract

摘要： A typical biological cell lives in a small volume at room temperature; the noise effect on the cell signal transduction pathway may play an important role in its dynamics. Here, using the transforming growth factor-β signal transduction pathway as an example, we report our stochastic simulations of the dynamics of the pathway and introduce a linear noise approximation method to calculate the transient intrinsic noise of pathway components. We compare the numerical solutions of the linear noise approximation with the statistic results of chemical Langevin equations, and find that they are quantitatively in agreement with the other. When transforming growth factor-β dose decreases to a low level, the time evolution of noise fluctuation of nuclear Smad2--Smad4 complex indicates the abnormal enhancement in the transient signal activation process.

Abstract: A typical biological cell lives in a small volume at room temperature; the noise effect on the cell signal transduction pathway may play an important role in its dynamics. Here, using the transforming growth factor-β signal transduction pathway as an example, we report our stochastic simulations of the dynamics of the pathway and introduce a linear noise approximation method to calculate the transient intrinsic noise of pathway components. We compare the numerical solutions of the linear noise approximation with the statistic results of chemical Langevin equations, and find that they are quantitatively in agreement with the other. When transforming growth factor-β dose decreases to a low level, the time evolution of noise fluctuation of nuclear Smad2–Smad4 complex indicates the abnormal enhancement in the transient signal activation process.

Key words: transforming growth factor-β, noise, chemical Langevin equation, linear noise approximation

中图分类号: (Stochastic processes)

02.50.Ey

87.15.N- (Properties of solutions of macromolecules) 87.15.Ya (Fluctuations) 87.16.A- (Theory, modeling, and simulations) 87.16.Xa (Signal transduction and intracellular signaling)

王路, 欧阳颀. Intrinsic noise analysis and stochastic simulation on transforming growth factor beta signal pathway[J]. 中国物理B, 2010, 19(10): 108202-108202.

Wang Lu(王路) and Ouyang Qi(欧阳颀). Intrinsic noise analysis and stochastic simulation on transforming growth factor beta signal pathway[J]. Chin. Phys. B, 2010, 19(10): 108202-108202.

参考文献 30

[1]	Wang H L, Fu Z P, Xu X H and Ouyang Q 2009 Chin. Phys. B 18 2082
[2]	Bezrukov S M and Vodyanoy I 1995 Nature 378 362
[3]	Elowitz M B, Levine A J, Siggia E D and Swain P S 2002 Science 297 1183
[4]	Scott M, Ingalls B and Kaern M 2006 Chaos 16 026107
[5]	Li Z Y, Xie Z W, Chen T and Ouyang Q 2009 Chin. Phys. B 18 5544
[6]	Heinrich R, Neel B G and Rapoport T A 2002 Mol. Cell 9 957
[7]	Raser J M and O'Shea E K 2005 Science 309 2010
[8]	Eissing T, Allgower F and Bullinger E 2005 Syst. Biol. (Stevenage) 152 221
[9]	Massague J 2008 Cell 134 215
[10]	Shi Y and Massague J 2003 Cell 113 685
[11]	Clarke D C and Liu X 2008 Trends Cell Biol. 18 430
[12]	Hill C S 2009 Cell Res. 19 36
[13]	Schmierer B and Hill C S 2005 Mol. Cell. Biol. 25 9845
[14]	Howell J E and McAnulty R J 2006 Curr. Drug. Targets 7 547
[15]	Schiller M, Javelaud D and Mauviel A 2004 J. Dermatol. Sci. 35 83
[16]	Chung S W, Miles F L, Sikes R A, Cooper C R, Farach-Carson M C and Ogunnaike B A 2009 Biophys. J. 96 1733
[17]	Nakabayashi J and Sasaki A 2009 J. Theor. Biol. 259 389
[18]	Schmierer B, Tournier A L, Bates P A and Hill C S 2008 Proc. Nat. Acad. Sci. USA 105 6608
[19]	Gillespie D T 1977 J. Phys. Chem. 81 2340
[20]	Rathinam M, Petzold L R, Cao Y and Gillespie D T 2003 J. Chem. Phys. 119 12784
[21]	Gardiner C W 1985 Handbook of Stochastic Methods for Physics, Chemistry, and the Natural Sciences (Berlin, New York: Springer-Verlag) Chap. 7
[22]	Elf J and Ehrenberg M 2003 Genome Res. 13 2475
[23]	Gillespie D T 2000 J. Chem. Phys. 113 297
[24]	Kampen N G V 1992 Stochastic Processes in Physics and Chemistry (Amsterdam, New York: North-Holland) Chap. 10
[25]	Ullah M and Wolkenhauer O 2007 IET Syst. Biol. 1 247
[26]	Chen A M, Zhang J J, Yuan Z J and Zhou T S 2009 Acta Phys. Sin. 58 2804 (in Chinese)
[27]	Elf J, Paulsson J, Berg O G and Ehrenberg M 2003 Biophys. J. 84 154
[28]	Yan L, Wang H L and Ouyang Q 2010 Chin. Phys. Lett. 27 010501
[29]	Ullah M and Wolkenhauer O 2010 Wiley Interdisciplinary Reviews: Systems Biology and Medicine Advance access published on December 10, 2009; doi:10.1002/wsbm.078.
[30]	Thattai M and van Oudenaarden A 2001 Proc. Nat. Acad. Sci. USA 98 8614 endfootnotesize

Intrinsic noise analysis and stochastic simulation on transforming growth factor beta signal pathway

Intrinsic noise analysis and stochastic simulation on transforming growth factor beta signal pathway

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