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重新审视准稳态近似:酶动力学中的时间尺度、小参数、奇点和规范形式。

The quasi-steady-state approximations revisited: Timescales, small parameters, singularities, and normal forms in enzyme kinetics.

机构信息

Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.

Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.

出版信息

Math Biosci. 2020 Jul;325:108339. doi: 10.1016/j.mbs.2020.108339. Epub 2020 Mar 14.

Abstract

In this work, we revisit the scaling analysis and commonly accepted conditions for the validity of the standard, reverse and total quasi-steady-state approximations through the lens of dimensional Tikhonov-Fenichel parameters and their respective critical manifolds. By combining Tikhonov-Fenichel parameters with scaling analysis and energy methods, we derive improved upper bounds on the approximation error for the standard, reverse and total quasi-steady-state approximations. Furthermore, previous analyses suggest that the reverse quasi-steady-state approximation is only valid when initial enzyme concentrations greatly exceed initial substrate concentrations. However, our results indicate that this approximation can be valid when initial enzyme and substrate concentrations are of equal magnitude. Using energy methods, we find that the condition for the validity of the reverse quasi-steady-state approximation is far less restrictive than was previously assumed, and we derive a new "small" parameter that determines the validity of this approximation. In doing so, we extend the established domain of validity for the reverse quasi-steady-state approximation. Consequently, this opens up the possibility of utilizing the reverse quasi-steady-state approximation to model enzyme catalyzed reactions and estimate kinetic parameters in enzymatic assays at much lower enzyme to substrate ratios than was previously thought. Moreover, we show for the first time that the critical manifold of the reverse quasi-steady-state approximation contains a singular point where normal hyperbolicity is lost. Associated with this singularity is a transcritical bifurcation, and the corresponding normal form of this bifurcation is recovered through scaling analysis.

摘要

在这项工作中,我们通过维度的 Tikhonov-Fenichel 参数及其各自的临界流形,重新审视了标准、反向和总准稳态近似的标度分析和普遍接受的有效性条件。通过将 Tikhonov-Fenichel 参数与标度分析和能量方法相结合,我们为标准、反向和总准稳态近似的逼近误差导出了改进的上界。此外,先前的分析表明,只有当初始酶浓度远远超过初始底物浓度时,反向准稳态近似才有效。然而,我们的结果表明,当初始酶和底物浓度相同时,该近似也可以有效。通过能量方法,我们发现反向准稳态近似的有效性条件比之前假设的要宽松得多,并且我们推导出了一个新的“小”参数,该参数决定了该近似的有效性。这样做,我们扩展了反向准稳态近似的有效范围。因此,这为利用反向准稳态近似来模拟酶催化反应并在比以前认为更低的酶与底物比的酶促测定中估计动力学参数提供了可能性。此外,我们首次表明,反向准稳态近似的临界流形包含一个奇异点,在该点处失去了正常双曲性。与这个奇点相关的是一个超越临界分岔,通过标度分析恢复了这个分岔的相应正规形式。

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