dorsal/arxiv
View SchemaThresholds, long delays and stability from generalized allosteric effect in protein networks
| Authors | Roberto Chignola, Chiara Dalla Pellegrina, Alessio Del Fabbro, Edoardo Milotti |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0601045 |
| URL | https://arxiv.org/abs/q-bio/0601045 |
| DOI | 10.1016/j.physa.2006.03.044 |
Abstract
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation are well-known to play a pivotal role in the intracellular transduction of activation and death signals. A protein can have multiple sites where chemical groups can reversibly attach in processes such as phosphorylation or nitrosylation. A microscopic description of these processes must take into account the intrinsic probabilistic nature of the underlying reactions. We apply combinatorial considerations to standard enzyme kinetics and in this way we extend to the dynamic regime a simplified version of the traditional models on the allosteric regulation of protein functions. We link a generic modification chain to a downstream Michaelis-Menten enzymatic reaction and we demonstrate numerically that this accounts both for thresholds and long time delays in the conversion of the substrate by the enzyme. The proposed mechanism is stable and robust and the higher the number of modification sites, the greater the stability. We show that a high number of modification sites converts a fast reaction into a slow process, and the slowing down depends on the number of sites and may span many orders of magnitude; in this way multisite modification of proteins stands out as a general mechanism that allows the transfer of information from the very short time scales of enzyme reactions (milliseconds) to the long time scale of cell response (hours).
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"abstract": "Post-transductional modifications tune the functions of proteins and regulate\nthe collective dynamics of biochemical networks that determine how cells\nrespond to environmental signals. For example, protein phosphorylation and\nnitrosylation are well-known to play a pivotal role in the intracellular\ntransduction of activation and death signals. A protein can have multiple sites\nwhere chemical groups can reversibly attach in processes such as\nphosphorylation or nitrosylation. A microscopic description of these processes\nmust take into account the intrinsic probabilistic nature of the underlying\nreactions. We apply combinatorial considerations to standard enzyme kinetics\nand in this way we extend to the dynamic regime a simplified version of the\ntraditional models on the allosteric regulation of protein functions. We link a\ngeneric modification chain to a downstream Michaelis-Menten enzymatic reaction\nand we demonstrate numerically that this accounts both for thresholds and long\ntime delays in the conversion of the substrate by the enzyme. The proposed\nmechanism is stable and robust and the higher the number of modification sites,\nthe greater the stability. We show that a high number of modification sites\nconverts a fast reaction into a slow process, and the slowing down depends on\nthe number of sites and may span many orders of magnitude; in this way\nmultisite modification of proteins stands out as a general mechanism that\nallows the transfer of information from the very short time scales of enzyme\nreactions (milliseconds) to the long time scale of cell response (hours).",
"arxiv_id": "q-bio/0601045",
"authors": [
"Roberto Chignola",
"Chiara Dalla Pellegrina",
"Alessio Del Fabbro",
"Edoardo Milotti"
],
"categories": [
"q-bio.CB",
"q-bio.SC"
],
"doi": "10.1016/j.physa.2006.03.044",
"title": "Thresholds, long delays and stability from generalized allosteric effect in protein networks",
"url": "https://arxiv.org/abs/q-bio/0601045"
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