Dynamics and Sensitivity of Signaling Pathways

Yi TM, Huang Y, Simon MI, Doyle J. Robust perfect adaptation in bacterial chemotaxis through integral feedback control. Proceedings of the National Academy of Sciences. 2000;97(9):4649–53.

CAS  Article  Google Scholar 

Ferrell JE Jr, Ha SH. Ultrasensitivity part iii: cascades, bistable switches, and oscillators. Trends in Biochemical Sciences. 2014;39(12):612–8.

CAS  PubMed  PubMed Central  Article  Google Scholar 

Behar M, Hao N, Dohlman HG, Elston TC. Dose-to-duration encoding and signaling beyond saturation in intracellular signaling networks. PLoS Comput Biol. 2008;4(10):e1000197.

PubMed  PubMed Central  Article  CAS  Google Scholar 

Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S, et al. Oncogenic signaling pathways in the cancer genome atlas. Cell. 2018;173(2):321–37.

CAS  PubMed  PubMed Central  Article  Google Scholar 

Aggarwal BB, Sethi G, Baladandayuthapani V, Krishnan S, Shishodia S. Targeting cell signaling pathways for drug discovery: an old lock needs a new key. Journal of Cellular Biochemistry. 2007;102(3):580–92.

CAS  PubMed  Article  Google Scholar 

Walsh CT, Wencewicz TA. Prospects for new antibiotics: a molecule-centered perspective. The Journal of Antibiotics. 2014;67(1):7–22.

CAS  PubMed  Article  Google Scholar 

Emiola A, George J, Andrews SS. A complete pathway model for lipid a biosynthesis in escherichia coli. PloS One. 2015;10(4):e0121216.

PubMed  PubMed Central  Article  CAS  Google Scholar 

Gomez-Uribe C, Verghese GC, Mirny LA. Operating regimes of signaling cycles: statics, dynamics, and noise filtering. PLoS Comput Biol. 2007;3(12):e246.

PubMed  PubMed Central  Article  CAS  Google Scholar 

Stadtman E, Chock P. Superiority of interconvertible enzyme cascades in metabolic regulation: analysis of monocyclic systems. Proceedings of the National Academy of Sciences. 1977;74(7):2761–5.

CAS  Article  Google Scholar 

Fell DA. Metabolic control analysis: a survey of its theoretical and experimental development. Biochemical Journal. 1992;286(2):313–30.

CAS  PubMed  PubMed Central  Article  Google Scholar 

Kholodenko BN, Hoek JB, Westerhoff HV, Brown GC. Quantification of information transfer via cellular signal transduction pathways. FEBS Letters. 1997;414(2):430–4.

CAS  PubMed  Article  Google Scholar 

Sauro HM, Kholodenko BN. Quantitative analysis of signaling networks. Progress in Biophysics and Molecular Biology. 2004;86(1):5–43.

CAS  PubMed  Article  Google Scholar 

Small JR, Fell DA. Covalent modification and metabolic control analysis: Modification to the theorems and their application to metabolic systems containing covalently modifiable enzymes. European Journal of Biochemistry. 1990;191(2):405–11.

CAS  PubMed  Article  Google Scholar 

Goldbeter A, Koshland DE. An amplified sensitivity arising from covalent modification in biological systems. Proceedings of the National Academy of Sciences. 1981;78(11):6840–4.

CAS  Article  Google Scholar 

Huang CY, Ferrell JE. Ultrasensitivity in the mitogen-activated protein kinase cascade. Proceedings of the National Academy of Sciences. 1996;93(19):10078–83.

CAS  Article  Google Scholar 

Brown GC, Hoek JB, Kholodenko BN. Why do protein kinase cascades have more than one level? Trends in Biochemical Sciences. 1997;22(8):288–288.

CAS  PubMed  Article  Google Scholar 

• Blüthgen, N., Bruggeman, F.J., Legewie, S., Herzel, H., Westerhoff, H.V., Kholodenko, B.N.: Effects of sequestration on signal transduction cascades. The FEBS Journal 273(5), 895–906 (2006). This paper demonstrates the effects of increasing enzyme concentration, and subsequent substrate sequestration, on zero-order ultrasensitivity.

Gunawardena J. Multisite protein phosphorylation makes a good threshold but can be a poor switch. Proceedings of the National Academy of Sciences. 2005;102(41):14617–22.

CAS  Article  Google Scholar 

• Markevich, N.I., Hoek, J.B., Kholodenko, B.N.: Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades. The Journal of Cell Biology 164(3), 353–359 (2004). This paper was the first to show that sequestration could have major implications on the qualitative behaviour of signaling networks.

Sauro HM. Moiety-conserved cycles and metabolic control analysis: problems in sequestration and metabolic channelling. BioSystems. 1994;33(1):55–67.

CAS  PubMed  Article  Google Scholar 

Sauro, H.M.: Systems biology: an introduction to metabolic control analysis. Ambrosius Publishing (2018)

Lustig B, Jerchow B, Sachs M, Weiler S, Pietsch T, Karsten U, van de Wetering M, Clevers H, Schlag PM, Birchmeier W, et al. Negative feedback loop of wnt signaling through upregulation of conductin/axin2 in colorectal and liver tumors. Molecular and Cellular Biology. 2002;22(4):1184–93.

CAS  PubMed  PubMed Central  Article  Google Scholar 

Sturm OE, Orton R, Grindlay J, Birtwistle M, Vyshemirsky V, Gilbert D, Calder M, Pitt A, Kholodenko B, Kolch W. The mammalian mapk/erk pathway exhibits properties of a negative feedback amplifier. Science Signaling. 2010;3(153):ra90–ra90.

CAS  PubMed  Article  Google Scholar 

Miyazono K. Positive and negative regulation of tgf-beta signaling. Journal of Cell Science. 2000;113(7):1101–9.

CAS  PubMed  Article  Google Scholar 

Stroschein SL, Wang W, Zhou S, Zhou Q, Luo K. Negative feedback regulation of tgf-β signaling by the snon oncoprotein. Science. 1999;286(5440):771–4.

CAS  PubMed  Article  Google Scholar 

Cornish-Bowden A, Cárdenas ML. Information transfer in metabolic pathways: effects of irreversible steps in computer models. European Journal of Biochemistry. 2001;268(24):6616–24.

CAS  PubMed  Article  Google Scholar 

• Del Vecchio, D., Ninfa, A.J., Sontag, E.D.: Modular cell biology: retroactivity and insulation. Molecular Systems Biology 4(1), 161 (2008). This paper demonstrated the effects of retroactivity on upstream components and introduced an amplifier based compensatory mechanism.

Ventura AC, Sepulchre JA, Merajver SD. A hidden feedback in signaling cascades is revealed. PLoS Comput Biol. 2008;4(3):e1000041.

PubMed  PubMed Central  Article  CAS  Google Scholar 

Bechhoefer J. Feedback for physicists: A tutorial essay on control. Reviews of Modern Physics. 2005;77(3):783.

Article  Google Scholar 

Rao CV, Wolf DM, Arkin AP. Control, exploitation and tolerance of intracellular noise. Nature. 2002;420(6912):231–7.

CAS  PubMed  Article  Google Scholar 

Sauro HM. Control and regulation of pathways via negative feedback. Journal of The Royal Society Interface. 2017;14(127):20160848.

PubMed  PubMed Central  Article  Google Scholar 

Muzzey D, Gómez-Uribe CA, Mettetal JT, van Oudenaarden A. A systems-level analysis of perfect adaptation in yeast osmoregulation. Cell. 2009;138(1):160–71.

CAS  PubMed  PubMed Central  Article  Google Scholar 

Black HS. Stabilized feedback amplifiers. Bell System Technical Journal. 1934;13(1):1–18.

Article  Google Scholar 

Andrews SS, Peria WJ, Richard CY, Colman-Lerner A, Brent R. Push-pull and feedback mechanisms can align signaling system outputs with inputs. Cell Systems. 2016;3(5):444–55.

CAS  PubMed  PubMed Central  Article  Google Scholar 

Nevozhay D, Adams RM, Murphy KF, Josić K, Balázsi G. Negative autoregulation linearizes the dose-response and suppresses the heterogeneity of gene expression. Proceedings of the National Academy of Sciences. 2009;106(13):5123–8.

CAS  Article  Google Scholar 

• Nunns, H., Goentoro, L.: Signaling pathways as linear transmitters. Elife. 2018; 7, e33617. The authors investigated the mechanisms that three different biological pathways use to produce linear signaling

Sauro, H.M., Ingalls, B.: Mapk cascades as feedback amplifiers. arXiv (2007)

Andrews SS, Brent R, Balázsi G. Signaling systems: Transferring information without distortion. Elife. 2018;7:e41894.

PubMed  PubMed Central  Article  Google Scholar 

Cao Y, Wang H, Ouyang Q, Tu Y. The free-energy cost of accurate biochemical oscillations. Nature Physics. 2015;11(9):772–8.

CAS  PubMed  PubMed Central  Article  Google Scholar 

Hoffmann A, Levchenko A, Scott ML, Baltimore D. The iĸb-nf-ĸb signaling module: temporal control and selective gene activation. Science. 2002;298(5596):1241–5.

CAS  PubMed  Article  Google Scholar 

Boiteux A, Goldbeter A, Hess B. Control of oscillating glycolysis of yeast by stochastic, periodic, and steady source of substrate: A model and experimental study. Proc Nat Acad Sci USA. 1975;72(10):3829–33.

CAS  PubMed  PubMed Central  Article  Google Scholar 

Shankaran H, Ippolito DL, Chrisler WB, Resat H, Bollinger N, Opresko LK, Wiley HS. Rapid and sustained nuclear-cytoplasmic erk oscillations induced by epidermal growth factor. Molecular Systems Biology. 2009;5(1):332.

PubMed  PubMed Central  Article  CAS  Google Scholar 

Shankaran H, Wiley HS. Oscillatory dynamics of the extracellular signal-regulated kinase pathway. Current Opinion in Genetics & Development. 2010;20(6):650–5.

CAS  Article  Google Scholar 

Ferrell JE, Machleder EM. The biochemical basis of an all-or-none cell fate switch in xenopus oocytes. Science. 1998;280(5365):895–8.

留言 (0)

沒有登入
gif