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Biophys J. 2015 Feb 17;108(4):986-996. doi: 10.1016/j.bpj.2014.12.011.

Phosphatase specificity and pathway insulation in signaling networks.

Author information

1
Center for Computational Biology, University of Kansas, Lawrence, Kansas.
2
Center for Computational Biology, University of Kansas, Lawrence, Kansas; Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas; Santa Fe Institute, Santa Fe, New Mexico. Electronic address: deeds@ku.edu.

Abstract

Phosphatases play an important role in cellular signaling networks by regulating the phosphorylation state of proteins. Phosphatases are classically considered to be promiscuous, acting on tens to hundreds of different substrates. We recently demonstrated that a shared phosphatase can couple the responses of two proteins to incoming signals, even if those two substrates are from otherwise isolated areas of the network. This finding raises a potential paradox: if phosphatases are indeed highly promiscuous, how do cells insulate themselves against unwanted crosstalk? Here, we use mathematical models to explore three possible insulation mechanisms. One approach involves evolving phosphatase KM values that are large enough to prevent saturation by the phosphatase's substrates. Although this is an effective method for generating isolation, the phosphatase becomes a highly inefficient enzyme, which prevents the system from achieving switch-like responses and can result in slow response kinetics. We also explore the idea that substrate degradation can serve as an effective phosphatase. Assuming that degradation is unsaturatable, this mechanism could insulate substrates from crosstalk, but it would also preclude ultrasensitive responses and would require very high substrate turnover to achieve rapid dephosphorylation kinetics. Finally, we show that adaptor subunits, such as those found on phosphatases like PP2A, can provide effective insulation against phosphatase crosstalk, but only if their binding to substrates is uncoupled from their binding to the catalytic core. Analysis of the interaction network of PP2A's adaptor domains reveals that although its adaptors may isolate subsets of targets from one another, there is still a strong potential for phosphatase crosstalk within those subsets. Understanding how phosphatase crosstalk and the insulation mechanisms described here impact the function and evolution of signaling networks represents a major challenge for experimental and computational systems biology.

PMID:
25692603
PMCID:
PMC4336360
DOI:
10.1016/j.bpj.2014.12.011
[Indexed for MEDLINE]
Free PMC Article

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