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Computational modeling of cellular signaling processes embedded into dynamic spatial contexts.

ABSTRACT: Cellular signaling processes depend on spatiotemporal distributions of molecular components. Multicolor, high-resolution microscopy permits detailed assessment of such distributions, providing input for fine-grained computational models that explore mechanisms governing dynamic assembly of multimolecular complexes and their role in shaping cellular behavior. However, it is challenging to incorporate into such models both complex molecular reaction cascades and the spatial localization of signaling components in dynamic cellular morphologies. Here we introduce an approach to address these challenges by automatically generating computational representations of complex reaction networks based on simple bimolecular interaction rules embedded into detailed, adaptive models of cellular morphology. Using examples of receptor-mediated cellular adhesion and signal-induced localized mitogen-activated protein kinase (MAPK) activation in yeast, we illustrate the capacity of this simulation technique to provide insights into cell biological processes. The modeling algorithms, implemented in a new version of the Simmune toolset, are accessible through intuitive graphical interfaces and programming libraries.

SUBMITTER: Angermann BR

PROVIDER: S-EPMC3448286 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature

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Computational modeling of cellular signaling processes embedded into dynamic spatial contexts.

Angermann Bastian R BR Klauschen Frederick F Garcia Alex D AD Prustel Thorsten T Zhang Fengkai F Germain Ronald N RN Meier-Schellersheim Martin M

Nature methods 20120129 3

Cellular signaling processes depend on spatiotemporal distributions of molecular components. Multicolor, high-resolution microscopy permits detailed assessment of such distributions, providing input for fine-grained computational models that explore mechanisms governing dynamic assembly of multimolecular complexes and their role in shaping cellular behavior. However, it is challenging to incorporate into such models both complex molecular reaction cascades and the spatial localization of signali ...[more]

PMID: 22286385

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Dataset Information

Computational modeling of cellular signaling processes embedded into dynamic spatial contexts.

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Computational modeling of cellular signaling processes embedded into dynamic spatial contexts.

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