Only a Topological Method Can Identify All Possible Network Structures Capable of Robust Perfect Adaptation

Overview

Journal PLoS Comput Biol

Specialty Biology

Date 2023 Nov 22

PMID 37992051

Authors

Robyn P Araujo

Lance A Liotta

Affiliations

Soon will be listed here.

Citing Articles

A distributed integral control mechanism for regulation of cholesterol concentration in the human retina.

Scheepers R, Levi N, Araujo R R Soc Open Sci. 2024; 11(10):240432.

PMID: 39479233 PMC: 11521609. DOI: 10.1098/rsos.240432.

References

Briat C, Gupta A, Khammash M . Antithetic Integral Feedback Ensures Robust Perfect Adaptation in Noisy Biomolecular Networks. Cell Syst. 2016; 2(1):15-26. DOI: 10.1016/j.cels.2016.01.004. View

Barkai N, Leibler S . Robustness in simple biochemical networks. Nature. 1997; 387(6636):913-7. DOI: 10.1038/43199. View

Araujo R, Liotta L . Design Principles Underlying Robust Adaptation of Complex Biochemical Networks. Methods Mol Biol. 2023; 2634:3-32. PMC: 10720973. DOI: 10.1007/978-1-0716-3008-2_1. View

Khammash M . Perfect adaptation in biology. Cell Syst. 2021; 12(6):509-521. DOI: 10.1016/j.cels.2021.05.020. View

Filo M, Kumar S, Khammash M . A hierarchy of biomolecular proportional-integral-derivative feedback controllers for robust perfect adaptation and dynamic performance. Nat Commun. 2022; 13(1):2119. PMC: 9018779. DOI: 10.1038/s41467-022-29640-7. View

Bhattacharya P, Raman K, Tangirala A . Discovering adaptation-capable biological network structures using control-theoretic approaches. PLoS Comput Biol. 2022; 18(1):e1009769. PMC: 8809615. DOI: 10.1371/journal.pcbi.1009769. View

Anastassov S, Filo M, Chang C, Khammash M . A cybergenetic framework for engineering intein-mediated integral feedback control systems. Nat Commun. 2023; 14(1):1337. PMC: 10008564. DOI: 10.1038/s41467-023-36863-9. View

Araujo R, Liotta L . Universal structures for adaptation in biochemical reaction networks. Nat Commun. 2023; 14(1):2251. PMC: 10119132. DOI: 10.1038/s41467-023-38011-9. View

Gupta A, Khammash M . Universal structural requirements for maximal robust perfect adaptation in biomolecular networks. Proc Natl Acad Sci U S A. 2022; 119(43):e2207802119. PMC: 9618122. DOI: 10.1073/pnas.2207802119. View

10.

Frei T, Chang C, Filo M, Arampatzis A, Khammash M . A genetic mammalian proportional-integral feedback control circuit for robust and precise gene regulation. Proc Natl Acad Sci U S A. 2022; 119(24):e2122132119. PMC: 9214505. DOI: 10.1073/pnas.2122132119. View

11.

Filo M, Chang C, Khammash M . Biomolecular feedback controllers: from theory to applications. Curr Opin Biotechnol. 2023; 79:102882. DOI: 10.1016/j.copbio.2022.102882. View

12.

Jeynes-Smith C, Araujo R . Protein-protein complexes can undermine ultrasensitivity-dependent biological adaptation. J R Soc Interface. 2023; 20(198):20220553. PMC: 9810431. DOI: 10.1098/rsif.2022.0553. View

13.

Aoki S, Lillacci G, Gupta A, Baumschlager A, Schweingruber D, Khammash M . A universal biomolecular integral feedback controller for robust perfect adaptation. Nature. 2019; 570(7762):533-537. DOI: 10.1038/s41586-019-1321-1. View

14.

Gutierrez Mena J, Kumar S, Khammash M . Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback. Nat Commun. 2022; 13(1):4808. PMC: 9381578. DOI: 10.1038/s41467-022-32392-z. View

15.

Jeynes-Smith C, Araujo R . Ultrasensitivity and bistability in covalent-modification cycles with positive autoregulation. Proc Math Phys Eng Sci. 2022; 477(2252):20210069. PMC: 8331239. DOI: 10.1098/rspa.2021.0069. View

16.

Araujo R, Liotta L . The topological requirements for robust perfect adaptation in networks of any size. Nat Commun. 2018; 9(1):1757. PMC: 5931626. DOI: 10.1038/s41467-018-04151-6. View

17.

Tyson J, Chen K, Novak B . Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol. 2003; 15(2):221-31. DOI: 10.1016/s0955-0674(03)00017-6. View

18.

Shinar G, Feinberg M . Structural sources of robustness in biochemical reaction networks. Science. 2010; 327(5971):1389-91. DOI: 10.1126/science.1183372. View

19.

Doyle J . Even Noisy Responses Can Be Perfect If Integrated Properly. Cell Syst. 2016; 2(2):73-5. DOI: 10.1016/j.cels.2016.02.012. View

20.

Ma W, Trusina A, El-Samad H, Lim W, Tang C . Defining network topologies that can achieve biochemical adaptation. Cell. 2009; 138(4):760-73. PMC: 3068210. DOI: 10.1016/j.cell.2009.06.013. View