Mark I Borkum1, Patrick N Reardon1, Ronald C Taylor2, Nancy G Isern1. 1. Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, WA 99354 USA. 2. Biological Sciences Division, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, WA 99354 USA.
Abstract
BACKGROUND: Isotopic labeling is an analytic technique that is used to track the movement of isotopes through reaction networks. In general, the applicability of isotopic labeling techniques is limited to the investigation of reaction networks that consider homonuclear moieties, whose atoms are of one tracer element with two isotopes, distinguished by the presence of one additional neutron. RESULTS: This article presents a reformulation of the modeling framework for isotopic labeling, generalized to arbitrarily large, heteronuclear moieties, arbitrary numbers of isotopic tracer elements, and arbitrary numbers of isotopes per element, distinguished by arbitrary numbers of additional neutrons. CONCLUSIONS: With this work, it is now possible to simulate the isotopic labeling states of metabolites in completely arbitrary biochemical reaction networks.
BACKGROUND: Isotopic labeling is an analytic technique that is used to track the movement of isotopes through reaction networks. In general, the applicability of isotopic labeling techniques is limited to the investigation of reaction networks that consider homonuclear moieties, whose atoms are of one tracer element with two isotopes, distinguished by the presence of one additional neutron. RESULTS: This article presents a reformulation of the modeling framework for isotopic labeling, generalized to arbitrarily large, heteronuclear moieties, arbitrary numbers of isotopic tracer elements, and arbitrary numbers of isotopes per element, distinguished by arbitrary numbers of additional neutrons. CONCLUSIONS: With this work, it is now possible to simulate the isotopic labeling states of metabolites in completely arbitrary biochemical reaction networks.
Authors: Héctor García Martín; Vinay Satish Kumar; Daniel Weaver; Amit Ghosh; Victor Chubukov; Aindrila Mukhopadhyay; Adam Arkin; Jay D Keasling Journal: PLoS Comput Biol Date: 2015-09-17 Impact factor: 4.475