An Elementary Metabolite Unit (EMU) based method of isotopically nonstationary flux analysis
An Elementary Metabolite Unit (EMU) based method of isotopically nonstationary flux analysis
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DOI：
10.1002/bit.21632
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发表时间：
2008-02-15
影响因子：
3.8
通讯作者：
Stephanopoulos, Gregory
中科院分区：
文献类型：
--
作者：
Young, Jarney D.;Walther, Jason L.;Stephanopoulos, Gregory
非平稳代谢通量分析（NMFA）目前是一项计算量非常大的工作，特别是对于大型反应网络。我们将基本代谢物单位（EMU）理论应用于NMFA，大大降低了计算难度。我们还引入了分块解耦，这是一种新的方法，它系统地、全面地将动车组方程组分解成更小的子问题，以进一步降低计算难度。这些改进使模拟时间减少了5000倍，从而可以使用NMFA分析全新且更复杂的问题集。我们模拟了一个大型大肠杆菌网络的一系列非平稳和平稳GC/MS测量，然后用于估计参数及其相关的置信区间。我们发现仅使用非平稳标记数据和外部通量测量就可以成功地估计通量。近平稳和平稳时间点的加入提高了大多数参数的精度。与以前的报告相反，非平稳估计的精度证明与完全基于平稳数据的估计精度相当。最后，我们将基于emu的NMFA应用于棕色脂肪细胞的实验非平稳测量，并成功地估计了通量和一些代谢物浓度。通过使用NFMA代替传统的MFA，实验只需要6小时，而不是50小时（大多数代谢物标记达到同位素稳态99%所需的时间）。
Nonstationary metabolic flux analysis (NMFA) is at present a very computationally intensive exercise, especially for large reaction networks. We applied elementary metabolite unit (EMU) theory to NMFA, dramatically reducing computational difficulty. We also introduced block decoupling, a new method that systematically and comprehensively divides EMU systems of equations into smaller subproblems to further reduce computational difficulty. These improvements led to a 5000-fold reduction in simulation times, enabling an entirely new and more complicated set of problems to be analyzed with NMFA. We simulated a series of nonstationary and stationary GC/MS measurements for a large E. coli network that was then used to estimate parameters and their associated confidence intervals. We found that fluxes could be successfully estimated using only nonstationary labeling data and external flux measurements. Addition of near-stationary and stationary time points increased the precision of most parameters. Contrary to prior reports, the precision of nonstationary estimates proved to be comparable to the precision of estimates based solely on stationary data. Finally, we applied EMU-based NMFA to experimental nonstationary measurements taken from brown adipocytes and successfully estimated fluxes and some metabolite concentrations. By using NFMA instead of traditional MFA, the experiment required only 6 h instead of 50 (the time necessary for most metabolite labeling to reach 99% of isotopic steady state).