Abstract
Background: Many computer studies have employed either dynamic simulation or metabolic flux analysis (MFA) to predict the behaviour of biochemical pathways. Dynamic simulation determines the time evolution of pathway properties in response to environmental changes, whereas MFA provides only a snapshot of pathway properties within a particular set of environmental conditions. However, owing to the large amount of kinetic data required for dynamic simulation, MFA, which requires less information, has been used to manipulate large-scale pathways to determine metabolic outcomes. Results: Here we describe a simulation method based on cooperation between kinetics-based dynamic models and MFA-based static models. This hybrid method enables quasi-dynamic simulations of large-scale metabolic pathways, while drastically reducing the number of kinetics assays needed for dynamic simulations. The dynamic behaviour of metabolic pathways predicted by our method is almost identical to that determined by dynamic kinetic simulation. Conclusion: The discrepancies between the dynamic and the hybrid models were sufficiently small to prove that an MFA-based static module is capable of performing dynamic simulations as accurately as kinetic models. Our hybrid method reduces the number of biochemical experiments required for dynamic models of large-scale metabolic pathways by replacing suitable enzyme reactions with a static module.
| Original language | English |
|---|---|
| Article number | 42 |
| Journal | Theoretical Biology and Medical Modelling |
| Volume | 2 |
| DOIs | |
| Publication status | Published - 2005 Oct 4 |
Fingerprint
ASJC Scopus subject areas
- Health Informatics
- Medicine(all)
Cite this
Hybrid dynamic/static method for large-scale simulation of metabolism. / Yugi, Katsuyuki; Nakayama, Yoichi; Kinoshita, Ayako; Tomita, Masaru.
In: Theoretical Biology and Medical Modelling, Vol. 2, 42, 04.10.2005.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Hybrid dynamic/static method for large-scale simulation of metabolism
AU - Yugi, Katsuyuki
AU - Nakayama, Yoichi
AU - Kinoshita, Ayako
AU - Tomita, Masaru
PY - 2005/10/4
Y1 - 2005/10/4
N2 - Background: Many computer studies have employed either dynamic simulation or metabolic flux analysis (MFA) to predict the behaviour of biochemical pathways. Dynamic simulation determines the time evolution of pathway properties in response to environmental changes, whereas MFA provides only a snapshot of pathway properties within a particular set of environmental conditions. However, owing to the large amount of kinetic data required for dynamic simulation, MFA, which requires less information, has been used to manipulate large-scale pathways to determine metabolic outcomes. Results: Here we describe a simulation method based on cooperation between kinetics-based dynamic models and MFA-based static models. This hybrid method enables quasi-dynamic simulations of large-scale metabolic pathways, while drastically reducing the number of kinetics assays needed for dynamic simulations. The dynamic behaviour of metabolic pathways predicted by our method is almost identical to that determined by dynamic kinetic simulation. Conclusion: The discrepancies between the dynamic and the hybrid models were sufficiently small to prove that an MFA-based static module is capable of performing dynamic simulations as accurately as kinetic models. Our hybrid method reduces the number of biochemical experiments required for dynamic models of large-scale metabolic pathways by replacing suitable enzyme reactions with a static module.
AB - Background: Many computer studies have employed either dynamic simulation or metabolic flux analysis (MFA) to predict the behaviour of biochemical pathways. Dynamic simulation determines the time evolution of pathway properties in response to environmental changes, whereas MFA provides only a snapshot of pathway properties within a particular set of environmental conditions. However, owing to the large amount of kinetic data required for dynamic simulation, MFA, which requires less information, has been used to manipulate large-scale pathways to determine metabolic outcomes. Results: Here we describe a simulation method based on cooperation between kinetics-based dynamic models and MFA-based static models. This hybrid method enables quasi-dynamic simulations of large-scale metabolic pathways, while drastically reducing the number of kinetics assays needed for dynamic simulations. The dynamic behaviour of metabolic pathways predicted by our method is almost identical to that determined by dynamic kinetic simulation. Conclusion: The discrepancies between the dynamic and the hybrid models were sufficiently small to prove that an MFA-based static module is capable of performing dynamic simulations as accurately as kinetic models. Our hybrid method reduces the number of biochemical experiments required for dynamic models of large-scale metabolic pathways by replacing suitable enzyme reactions with a static module.
UR - http://www.scopus.com/inward/record.url?scp=26844531259&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=26844531259&partnerID=8YFLogxK
U2 - 10.1186/1742-4682-2-42
DO - 10.1186/1742-4682-2-42
M3 - Article
C2 - 16202166
AN - SCOPUS:26844531259
VL - 2
JO - Theoretical Biology and Medical Modelling
JF - Theoretical Biology and Medical Modelling
SN - 1742-4682
M1 - 42
ER -