SSB toolkit: from molecular structure to subcellular signaling pathways

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

We present, here, an open-source systems biology toolkit to simulate mathematical models of the signal-transduction pathways of G-protein coupled receptors (GPCRs). By merging structural macromolecular data with systems biology simulations, we developed a framework to simulate the signal-transduction kinetics induced by ligand-GPCR interactions, as well as the consequent change of concentration of signaling molecular species, as a function of time and ligand concentration. Therefore, this tool brings to the light the possibility to investigate the subcellular effects of ligand binding upon receptor activation, deepening the understanding of the relationship between the molecular level of ligand-target interactions and higher-level cellular and physiologic or pathological response mechanisms.

Authors 4

1. Rui Pedro Ribeiro

   Forschungszentrum Jülich

   Affiliation as printed

   IAS-5 / INM-9, Forschungszentrum Jülich, Germany

2. Jonas Goßen Aachen Faculty of Mathematics, Computer Science and Natural Sciences

   Forschungszentrum Jülich · RWTH Aachen University

   Affiliation as printed

   Faculty of Mathematics, Computer Science and Natural Sciences RWTH Aachen University

   IAS-5 / INM-9, Forschungszentrum Jülich, Germany

3. Giulia Rossetti Aachen Department of Neurology

   Forschungszentrum Jülich · Universitätsklinikum Aachen · Jülich Supercomputing Centre · RWTH Aachen University

   Affiliation as printed

   Department of Neurology, University Hospital Aachen, RWTH Aachen, Germany

   IAS-5 / INM-9, Forschungszentrum Jülich, Germany

   Jülich Supercomputing Center, Forschungszentrum Jülich, Germany

4. Alejandro Giorgetti corresponding

   University of Verona · Forschungszentrum Jülich

   Affiliation as printed

   Department of Biotechnology, University of Verona, Italy

   IAS-5 / INM-9, Forschungszentrum Jülich, Germany