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Funneled Landscape Leads to Robustness of Cell Networks: Yeast Cell Cycle

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  • Jin Wang
  • Bo Huang
  • Xuefeng Xia
  • Zhirong Sun

Abstract

We uncovered the underlying energy landscape for a cellular network. We discovered that the energy landscape of the yeast cell-cycle network is funneled towards the global minimum (G0/G1 phase) from the experimentally measured or inferred inherent chemical reaction rates. The funneled landscape is quite robust against random perturbations. This naturally explains robustness from a physical point of view. The ratio of slope versus roughness of the landscape becomes a quantitative measure of robustness of the network. The funneled landscape can be seen as a possible realization of the Darwinian principle of natural selection at the cellular network level. It provides an optimal criterion for network connections and design. Our approach is general and can be applied to other cellular networks.Synopsis: Cellular networks are in general quite robust and perform their biological functions against environmental perturbations. There are so far very few studies of why networks should be robust and perform biological functions from the physical point of view. In this work, Wang, Huang, Xia, and Sun studied the global properties of the network from physical perspectives. The aim of this paper is to provide a conceptual framework and a tool to study the global nature of the cellular network. The main conclusion is that by uncovering the underlying potential landscape of the budding yeast cell cycle the authors show that it is funneled and robust against the perturbation from kinetic rates and environmental disturbances through noise. This provides the physical explanation of the robustness and stability of the network for performing biological functions. They believe the energy landscape is useful in exploring global properties of protein–protein interaction networks. They also believe the funneled landscape may provide a possible quantitative realization of the Darwinian principle of natural selection at the cellular network level. Finally, Wang et al. derived a quantitative criterion for robustness of the network function. This criterion may provide a novel algorithm for optimizing the network connections to improve the design of synthetic networks.

Suggested Citation

  • Jin Wang & Bo Huang & Xuefeng Xia & Zhirong Sun, 2006. "Funneled Landscape Leads to Robustness of Cell Networks: Yeast Cell Cycle," PLOS Computational Biology, Public Library of Science, vol. 2(11), pages 1-10, November.
    • Handle: RePEc:plo:pcbi00:0020147
    DOI: 10.1371/journal.pcbi.0020147
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    Cited by:

    1. Keun-Young Kim & Jin Wang, 2007. "Potential Energy Landscape and Robustness of a Gene Regulatory Network: Toggle Switch," PLOS Computational Biology, Public Library of Science, vol. 3(3), pages 1-13, March.
    2. Wio, H.S. & Deza, J.I. & Sánchez, A.D. & García-García, R. & Gallego, R. & Revelli, J.A. & Deza, R.R., 2022. "The nonequilibrium potential today: A short review," Chaos, Solitons & Fractals, Elsevier, vol. 165(P1).
    3. Li Xu & Jin Wang, 2018. "Landscape and flux for quantifying global stability and dynamics of game theory," PLOS ONE, Public Library of Science, vol. 13(8), pages 1-27, August.

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