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Deviant effects in molecular reaction pathways

Nature Biotechnology volume 24, pages 1235–1240 (2006)Cite this article

Abstract

In biological networks, any manifestations of behaviors substantially 'deviant' from the predictions of continuous-deterministic classical chemical kinetics (CCK) are typically ascribed to systems with complex dynamics and/or a small number of molecules. Here we show that in certain cases such restrictions are not obligatory for CCK to be largely incorrect. By systematically identifying properties that may cause significant divergences between CCK and the more accurate discrete-stochastic chemical master equation (CME) system descriptions, we comprehensively characterize potential CCK failure patterns in biological settings, including consequences of the assertion that CCK is closer to the 'mode' rather than the 'average' of stochastic reaction dynamics, as generally perceived. We demonstrate that mechanisms underlying such nonclassical effects can be very simple, are common in cellular networks and result in often unintuitive system behaviors. This highlights the importance of deviant effects in biotechnologically or biomedically relevant applications, and suggests some approaches to diagnosing them in situ.

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Figure 1: Characteristic CME distribution examples.
Figure 2: A signaling pathway motif.
Figure 3: Type I system evolution.
Figure 4: Type II system evolution.
Figure 5: Type III deviant behavior.

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Authors and Affiliations

  1. Department of Bioengineering, Physical Biosciences Division, Howard Hughes Medical Institute, University of California at Berkeley, Center for Synthetic Biology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS 977-257, Berkeley, 94720, California, USA

    Michael S Samoilov & Adam P Arkin

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  1. Michael S Samoilov
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  2. Adam P Arkin
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Correspondence to Michael S Samoilov or Adam P Arkin.

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Samoilov, M., Arkin, A. Deviant effects in molecular reaction pathways. Nat Biotechnol 24, 1235–1240 (2006). https://doi.org/10.1038/nbt1253

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