Structural and dynamical analyses of the kinase network derived from the transpath database.
We analyze the structural design and the dynamical properties of a protein kinase network derived from the Transpath database. We consider structural properties, such as feedback cycles, pathway lengths, fraction of shortest pathways and crosstalk. Dynamic characteristics of the network are analyzed by using nonlinear differential equations with a special focus on kinase amplitudes and signal propagation times. Comparison with random networks shows that the cellular kinase network exhibits special features which might be a result of natural selection. In particular, the Transpath network contains no cycles, and input kinases and output kinases are generally connected by shortest signalling routes. Moreover, it displays a characteristic spectrum of cross-talk between different pathways.
Binder
Bernd
B
Theoretical Biophysics, Institute of Biology, Humboldt University Berlin, Berlin, Germany. bernd.binder@rz.hu-berlin.de
Heinrich
Reinhart
R
D000465:Algorithms; D016208:Databases, Factual; D004789:Enzyme Activation; D007700:Kinetics; D020930:MAP Kinase Kinase Kinases / Q000378:metabolism; D020929:Mitogen-Activated Protein Kinase Kinases / Q000378:metabolism; D020928:Mitogen-Activated Protein Kinases / Q000378:metabolism; D008954:Models, Biological; D008962:Models, Theoretical; D016571:Neural Networks, Computer; D010766:Phosphorylation; D010770:Phosphotransferases / Q000378:metabolism*; D011494:Protein Kinases / Q000378:metabolism; D012641:Selection, Genetic; D015398:Signal Transduction; D012984:Software
D010770:Phosphotransferases; D011494:Protein Kinases; D020928:Mitogen-Activated Protein Kinases; D020930:MAP Kinase Kinase Kinases; D020929:Mitogen-Activated Protein Kinase Kinases