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.
Ferrell JE Jr, Ha SH. Ultrasensitivity part iii: cascades, bistable switches, and oscillators. Trends in Biochemical Sciences. 2014;39(12):612–8.
Article CAS PubMed PubMed Central 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.
Article PubMed PubMed Central 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.
Article CAS PubMed PubMed Central 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.
Article CAS PubMed Google Scholar
Walsh CT, Wencewicz TA. Prospects for new antibiotics: a molecule-centered perspective. The Journal of Antibiotics. 2014;67(1):7–22.
Article CAS PubMed 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.
Article PubMed PubMed Central 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.
Article PubMed PubMed Central 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.
Fell DA. Metabolic control analysis: a survey of its theoretical and experimental development. Biochemical Journal. 1992;286(2):313–30.
Article CAS PubMed PubMed Central 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.
Article CAS PubMed Google Scholar
Sauro HM, Kholodenko BN. Quantitative analysis of signaling networks. Progress in Biophysics and Molecular Biology. 2004;86(1):5–43.
Article CAS PubMed 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.
Article CAS PubMed 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.
Huang CY, Ferrell JE. Ultrasensitivity in the mitogen-activated protein kinase cascade. Proceedings of the National Academy of Sciences. 1996;93(19):10078–83.
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.
Article CAS PubMed 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.
• 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.
Article CAS PubMed 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.
Article CAS PubMed PubMed Central 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.
Article CAS PubMed Google Scholar
Miyazono K. Positive and negative regulation of tgf-beta signaling. Journal of Cell Science. 2000;113(7):1101–9.
Article CAS PubMed 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.
Article CAS PubMed 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.
Article CAS PubMed 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.
Article PubMed PubMed Central Google Scholar
Bechhoefer J. Feedback for physicists: A tutorial essay on control. Reviews of Modern Physics. 2005;77(3):783.
Rao CV, Wolf DM, Arkin AP. Control, exploitation and tolerance of intracellular noise. Nature. 2002;420(6912):231–7.
Article CAS PubMed Google Scholar
Sauro HM. Control and regulation of pathways via negative feedback. Journal of The Royal Society Interface. 2017;14(127):20160848.
Article PubMed PubMed Central 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.
Article CAS PubMed PubMed Central Google Scholar
Black HS. Stabilized feedback amplifiers. Bell System Technical Journal. 1934;13(1):1–18.
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.
Article CAS PubMed PubMed Central 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.
Comments (0)