Signal transducing protein networks are topologically tightly organized macromolecular protein complexes that act like specialized molecular machines. These machines are composed of constitutive building blocks including specific nodes in combination with multifunctional scaffolds and highly dynamic interactions, moving in and out of a complex. Specificity within these complexes is conferred using combinatory principles combined with specific signaling in- and outputs. The main aim of the DYNAMO consortium is a systems biology approach to analyze dynamics of membrane associated protein complexes. For this purpose the consortium develops novel measurement techniques to determine the state of protein complexes in vivo and novel mathematical modeling techniques to describe these networks in silico.
Two different model systems covering different dynamic aspects are studied: (1) the light signalling by rhodopsin and (2) protein translocation through the mitochondrial protein import.
The task of the ISYS within the DYNAMO consortium is to develop novel, application-oriented methods for the mathematical modeling of protein complexes, since the conventional modeling methods run into severe problems due to the combinatorial explosion of the number of different protein complexes. We aim for unifying several approaches for modeling and model reduction and integrating them into a method tailored for the description of the dynamics of protein complexes.