Memory effects in biochemical networks as the natural counterpart of extrinsic noise

JOURNAL OF THEORETICAL BIOLOGY

卷:357

Article

Rubin, Katy J.¹  Lawler, Katherine²  Sollich, Peter¹  Ng, Tony^3,4 

[1] Kings Coll London, Dept Math, London WC2R 2LS, England

[2] Kings Coll London, Inst Math & Mol Biomed, London SE1 1UL, England

[3] Kings Coll London, Div Canc Studies, Richard Dimbleby Dept Canc Res, London SE1 1UL, England

[4] UCL, UCL Canc Inst, London WC1E 6DD, England

关键词: Subnetworks;    Model reduction;    Memory function;    Protein interaction networks;   

DOI  :  10.1016/j.jtbi.2014.06.002

来源: Elsevier

【 摘 要 】

We show that in the generic situation where a biological network, e.g. a protein interaction network, is in fact a subnetwork embedded in a larger bulk network, the presence of the bulk causes not just extrinsic noise but also memory effects. This means that the dynamics of the subnetwork will depend not only on its present state, but also its past. We use projection techniques to get explicit expressions for the memory functions that encode such memory effects, for generic protein interaction networks involving binary and unary reactions such as complex formation and phosphorylation. Remarkably, in the limit of low intrinsic copy-number noise such expressions can be obtained even for nonlinear dependences on the past. We illustrate the method with examples from a protein interaction network around epidermal growth factor receptor (EGFR), which is relevant to cancer signalling. These examples demonstrate that inclusion of memory terms is not only important conceptually but also leads to substantially higher quantitative accuracy in the predicted subnetwork dynamics. (C) 2014 Elsevier Ltd. All rights reserved.

【 授权许可】

Free