TY - JOUR

T1 - A Promising Method for Calculating True Steady-State Metabolite Concentrations in Large-Scale Metabolic Reaction Network Models

AU - Miyawaki-Kuwakado, Atsuko

AU - Komori, Soichiro

AU - Shiraishi, Fumihide

N1 - Funding Information:
This work was supported by JSPS Science Grant-in-Aid for JSPS Research Fellow Grant Number 17J04007.

PY - 2020/1/1

Y1 - 2020/1/1

N2 - The calculation of steady-state metabolite concentrations in metabolic reaction network models is the first step in the sensitivity analysis of a metabolic reaction system described by differential equations. However, this calculation becomes very difficult when the number of differential equations is more than 100. In the present study, therefore, we investigated a calculation procedure for obtaining true steady-state metabolite concentrations both efficiently and accurately even in large-scale network models. For convenience, a linear pathway model composed of a simple Michaelis-Menten rate law and two TCA cycle models were used as case studies. The calculation procedure is as follows: first solve the differential equations by a numerical method for solving initial-value problems until the upper several digits of the calculated values stabilize, and then use these values as initial guesses for a root-finding technique. An intensive investigation indicates that the S-system technique, finding roots in logarithmic space and providing a broader convergence region, is superior to the Newton-Raphson technique, and the algorithm using the S-system technique successfully provides true steady-state values with machine accuracy even with 1,500 differential equations. The complex-step method is also shown to contribute to shortening the calculation time and enhancing the accuracy. The program code has been deposited to https://github.com/BioprocessdesignLab/Steadystateconc.

AB - The calculation of steady-state metabolite concentrations in metabolic reaction network models is the first step in the sensitivity analysis of a metabolic reaction system described by differential equations. However, this calculation becomes very difficult when the number of differential equations is more than 100. In the present study, therefore, we investigated a calculation procedure for obtaining true steady-state metabolite concentrations both efficiently and accurately even in large-scale network models. For convenience, a linear pathway model composed of a simple Michaelis-Menten rate law and two TCA cycle models were used as case studies. The calculation procedure is as follows: first solve the differential equations by a numerical method for solving initial-value problems until the upper several digits of the calculated values stabilize, and then use these values as initial guesses for a root-finding technique. An intensive investigation indicates that the S-system technique, finding roots in logarithmic space and providing a broader convergence region, is superior to the Newton-Raphson technique, and the algorithm using the S-system technique successfully provides true steady-state values with machine accuracy even with 1,500 differential equations. The complex-step method is also shown to contribute to shortening the calculation time and enhancing the accuracy. The program code has been deposited to https://github.com/BioprocessdesignLab/Steadystateconc.

UR - http://www.scopus.com/inward/record.url?scp=85049850426&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85049850426&partnerID=8YFLogxK

U2 - 10.1109/TCBB.2018.2853724

DO - 10.1109/TCBB.2018.2853724

M3 - Article

C2 - 30004883

AN - SCOPUS:85049850426

VL - 17

SP - 27

EP - 36

JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics

JF - IEEE/ACM Transactions on Computational Biology and Bioinformatics

SN - 1545-5963

IS - 1

M1 - 8410022

ER -