The simplicity of completion time distributions for common complex biochemical processes

Physical Biology

Volumn 7, Issue 1, 2010, Pages

  Bel, Golan ^a   Munsky, Brian ^a   Nemenman, Ilya ^b  

^a CENTER FOR NONLINEAR STUDIES   (United States)

^b EMORY UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BIOCHEMISTRY; COMPUTER SIMULATION; STATISTICAL DISTRIBUTION; STATISTICAL MODEL; TIME;

ALGORITHMS; BIOCHEMICAL PROCESSES; COMPUTER SIMULATION; MODELS, STATISTICAL; STATISTICAL DISTRIBUTIONS; TIME; TIME FACTORS;

EID: 75449108347     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/7/1/016003     Document Type: Article

References (26)

1. Faeder J, Hlavacek W, Reischl I, Blinov M, Metzger H, Redondo A, Wofsy C and Goldstein B 2003 Investigation of early events in FceRI-mediated signaling using a detailed mathematical model J. Immunol. 170 3769-81
2. Hopfield J 1974 Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity Proc. Natl Acad. Sci. USA 71 4135-9
3. Yan J, Magnasco M and Marko J 1999 A kinetic proofreading mechanism for disentanglement of DNA by topoisomerases Nature 401 932-5
4. Sancar A, Unsal-Kacmaz L L-B amd K and Linn S 2004 Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints Annu. Rev. Biochem. 73 39-85
5. Blanchard S, Gonzalez J R, Kim H, ChUSAnd Puglist J 2004 tRNA selection and kinetic proofreading in translation Nat. Struct. Mol. Biol. 11 1008-14
6. Jovanovic-Talisman T, Tetenbaum-Novatt J, McKenney A, Zilman A, Peters R, Rout M and Chait B 2008 Artificial nanopores that mimic the transport selectivity of the nuclear pore complex Nature 457 1023
7. McKeithan T 1995 Kinetic proofreading in T-cell receptor signal transduction Proc. Natl Acad. Sci. USA 92 5042-6
8. Rabinowitz J, Beeson C, Lyons D, Davis M and McConnell H 1996 Kinetic discrimination in T-cell activation Proc. Natl Acad. Sci. USA 93 1401-5
9. Rosette C et al 2001 The impact of duration versus extent of TCR occupancy of T cell activation: a revision of the kinetic proofreading model Immunity 15 59-70
10. Liu Z, Haleem-Smith H, Chen H and Metzger H 2001 Unexpected signals in a system subject to kinetic proofreading Proc. Natl Acad. Sci. USA 98 7289-94
11. Goldstein B, Faeder J and Hlavacek W 2004 Mathematical and computational models of immune-receptor signalling Nat. Rev. Immunol. 4 445-56
12. Hlavacek W, Redondo A, Wofsy C and Goldstein B 2002 Kinetic proofreading in receptor-mediated transduction of cellular signals: receptor aggregation partially activated receptors, and cytosolic messengers Bull. Math. Biol. 64 887-911
13. Redner S 2001 A Guide To First-Passage Processes (Cambridge: Cambridge University Press)
14. D'Orsogna M and Chou T 2005 First passage and cooperativity of queuing kinetics Phys. Rev. Lett. 95 170603
15. Shaevitz J, Block S and Schnitzer M 2005 Statistical kinetics of macromolecular dynamics Biophys. J. 89 2277-85
16. Lee C L, Stell G and Wang J 2003 First passage time distribution and non-makovian dynamics of protein folding J. Chem. Phys. 118 959
17. Leite V B P, Alonso L C P, Newton M and Wang J 2005 Single molecule electron transfer dynamics in complex environments Phys. Rev. Lett. 95 118301
18. Lu T, Shen T, Zong C, Hasty J and Wolynes P 2006 Statistic of cellular signal transduction as a race to the nucleus by multiple random walkers in compartment/phosphorylation space Proc. Natl Acad. Sci. USA 103 16752-7
19. Xu W L, Xue K and Wang E K 2008 Exploring the origin of power law distribution in single-molecule conformation dynamics: energy landscape perspectives Chem. Phys. Lett. 463 405-9
20. Ninio J 1987 Alternative to the steady-state method: derivation of reaction rates from first-passage times and pathway probabilities Proc. Natl Acad. Sci. USA 84 663-7
21. Bel G and Barkai E 2006 Random walk to a nonergodic equilibrium concept Phys. Rev. E 73 016125
22. Doan T, Mendez A, Detwiler P, Chen J and Rieke F 2006 Multiple phosphorylation sites confer reproducibility of the rod's single-photon responses Science 313 530
23. Munsky B and Khammash M 2008 Transient analysis of stochastic switches and trajectories with applications to gene regulatory networks IET Syst. Biol. 2 323-33
24. Stern S, Dror T, Stolovicki E, Brenner N and Braun E 2007 Genome-wide transcriptional plasticity underlies cellular adaptation to novel challenge Mol. Syst. Biol. 3 106
25. Ziv E, Nemenman I and Wiggins C 2007 Optimal information processing in small stochastic biochemical networks PLoS ONE 2 e1077
26. Gutenkunst R, Waterfall J, Casey F, Brown K, Myers C and Sethna J 2007 Universally sloppy parameter sensitivities in systems biology PLoS Comput. Biol. 3 e189