tailieunhanh - Báo cáo khoa học: What makes biochemical networks tick? A graphical tool for the identification of oscillophores

In view of the increasing number of reported concentration oscillations in living cells, methods are needed that can identify the causes of these oscillations. These causes always derive from the influences that concentrations have on reaction rates. The influences reach over many molecular reaction steps and are defined by the detailed molecular topology of the network. So-called autoinfluence paths , which quantify the influence of one molecular species upon itself through a particular path through the network, can have positive or negative values | Eur. J. Biochem. 271 3877-3887 2004 FEBS 2004 doi What makes biochemical networks tick A graphical tool for the identification of oscillophores Boris N. Goldstein1 Gennady Ermakov1 Josep J. Centelles3 Hans V. Westerhoff2 and Marta Cascante3 1 Institute of Theoretical and Experimental Biophysics Russian Academy of Sciences Pushchino Moscow Region Russia BioCentrum Amsterdam Departments of Molecular Cell Physiology IMC VUA and Mathematical Biochemistry SILS UvA Amsterdam the Netherlands 3Department of Biochemistry and Molecular Biology Faculty of Chemistry and CeRQT at Barcelona Scientific Parc University of Barcelona Spain In view of the increasing number of reported concentration oscillations in living cells methods are needed that can identify the causes of these oscillations. These causes always derive from the influences that concentrations have on reaction rates. The influences reach over many molecular reaction steps and are defined by the detailed molecular topology of the network. So-called autoinfluence paths which quantify the influence of one molecular species upon itself through a particular path through the network can have positive or negative values. The former bring a tendency towards instability. In this molecular context a new graphical approach is presented that enables the classification of network topologies into oscillophoretic and non-oscillophoretic . into ones that can and ones that cannot induce concentration oscillations. The network topologies are formulated in terms of a set of uni-molecular and bi-molecular reactions organized into branched cycles of directed reactions and presented as graphs. Subgraphs of the network topologies are then classified as negative ones which can and positive ones which cannot give rise to oscillations. A subgraph is oscillophoretic negative when it contains more positive than negative autoinfluence paths. Whether the former generates oscillations depends on the values of