Operating regimes of signaling cycles: statics, dynamics, and noise filtering

• Published in: PLoS computational biology Vol. 3; no. 12; p. e246
• Main Authors: Gomez-Uribe, Carlos, Verghese, George C, Mirny, Leonid A
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01-12-2007; Public Library of Science (PLoS)
• Subjects: Adaptation, Physiological - physiology; Algorithms; Amino Acid Sequence; Animals; Biochemistry; Biological Clocks - physiology; Biophysics; Computational Biology; Computer Simulation; Eukaryotes; Experiments; Feedback - physiology; Humans; Kinases; Kinetics; Models, Biological; Models, Statistical; Molecular Sequence Data; Phosphorylation; Proteins; Proteome - chemistry; Proteome - metabolism; Random variables; Signal Processing, Computer-Assisted; Signal Transduction - physiology; Studies; Adaptation, Physiological; Amino Acid Sequence; Signal Transduction; Humans; Molecular Sequence Data; Proteome; Models, Statistical; Algorithms; Animals; Feedback; Models, Biological; Computer Simulation; Signal Processing, Computer-Assisted; Biological Clocks; Kinetics
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.0030246

A ubiquitous building block of signaling pathways is a cycle of covalent modification (e.g., phosphorylation and dephosphorylation in MAPK cascades). Our paper explores the kind of information processing and filtering that can be accomplished by this simple biochemical circuit. Signaling cycles are particularly known for exhibiting a highly sigmoidal (ultrasensitive) input-output characteristic in a certain steady-state regime. Here, we systematically study the cycle's steady-state behavior and its response to time-varying stimuli. We demonstrate that the cycle can actually operate in four different regimes, each with its specific input-output characteristics. These results are obtained using the total quasi-steady-state approximation, which is more generally valid than the typically used Michaelis-Menten approximation for enzymatic reactions. We invoke experimental data that suggest the possibility of signaling cycles operating in one of the new regimes. We then consider the cycle's dynamic behavior, which has so far been relatively neglected. We demonstrate that the intrinsic architecture of the cycles makes them act--in all four regimes--as tunable low-pass filters, filtering out high-frequency fluctuations or noise in signals and environmental cues. Moreover, the cutoff frequency can be adjusted by the cell. Numerical simulations show that our analytical results hold well even for noise of large amplitude. We suggest that noise filtering and tunability make signaling cycles versatile components of more elaborate cell-signaling pathways.