In silico labeling reveals the time-dependent label half-life and transit-time in dynamical systems

• Verfasst von: Maiwald, Thomas [VerfasserIn]
• Verfasst von: Schilling, Marcel [VerfasserIn]
• Verfasst von: Becker, Verena [VerfasserIn]
• Verfasst von: Klingmüller, Ursula [VerfasserIn]
• Titel: In silico labeling reveals the time-dependent label half-life and transit-time in dynamical systems
• Verf.angabe: Thomas Maiwald, Julie Blumberg, Andreas Raue, Stefan Hengl, Marcel Schilling, Sherwin KB Sy, Verena Becker, Ursula Klingmüller and Jens Timmer
• E-Jahr: 2012
• Jahr: 27 February 2012
• Umfang: 11 S.
• Fussnoten: Gesehen am 31.08.2018
• Titel Quelle: Enthalten in: BMC systems biology
• Ort Quelle: London : BioMed Central, 2007
• Jahr Quelle: 2012
• Band/Heft Quelle: 6(2012) Artikel-Nummer 13, 11 Seiten
• ISSN Quelle: 1752-0509
• DOI: doi:10.1186/1752-0509-6-13
• Datenträger: Online-Ressource
• Sprache: eng
• K10plus-PPN: 1580585515

Abstract

Mathematical models of dynamical systems facilitate the computation of characteristic properties that are not accessible experimentally. In cell biology, two main properties of interest are (1) the time-period a protein is accessible to other molecules in a certain state - its half-life - and (2) the time it spends when passing through a subsystem - its transit-time. We discuss two approaches to quantify the half-life, present the novel method of in silico labeling, and introduce the label half-life and label transit-time. The developed method has been motivated by laboratory tracer experiments. To investigate the kinetic properties and behavior of a substance of interest, we computationally label this species in order to track it throughout its life cycle. The corresponding mathematical model is extended by an additional set of reactions for the labeled species, avoiding any double-counting within closed circuits, correcting for the influences of upstream fluxes, and taking into account combinatorial multiplicity for complexes or reactions with several reactants or products. A profile likelihood approach is used to estimate confidence intervals on the label half-life and transit-time.