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Method for constructing dynamic metabolic network based on topological structure of elementary reactions

A technology of elementary reaction and metabolic network, applied in special data processing applications, electrical digital data processing, instruments, etc., can solve the problem that the rate constant of elementary reaction cannot be completely experimentally determined.

Active Publication Date: 2018-05-11
EAST CHINA UNIV OF SCI & TECH
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Problems solved by technology

[0004] The purpose of the present invention is to propose a new method for constructing a metabolic network according to the topological structure of the elementary reaction, which can determine the elementary reaction rate constants involved in all enzyme reactions in the metabolic network through a single in vitro reaction (i.e. isolated reaction) rate experiment, In order to overcome the problem that there are too many elementary reaction rate constants and cannot be completely experimentally determined

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  • Method for constructing dynamic metabolic network based on topological structure of elementary reactions
  • Method for constructing dynamic metabolic network based on topological structure of elementary reactions
  • Method for constructing dynamic metabolic network based on topological structure of elementary reactions

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Embodiment 1

[0112]Enzyme reaction: glucose 6 phosphate → fructose 6 phosphate, the enzyme is phosphoglucose isomerase, molecular weight M=12000Da.

[0113] This reaction is an irreversible reaction with a single substrate and a single product, and the elementary reaction formula is as follows,

[0114]

[0115] Where S represents glucose 6 phosphate, E represents glucose phosphate isomerase, P represents fructose 6 phosphate, EP represents enzyme complex, k 1 、k 2 and k 3 is the elementary reaction rate constant.

[0116] Under the pseudo-steady state assumption, the elementary reaction kinetic equation is:

[0117] The classic Michaelis-Menten equation for a substrate single-product reaction is:

[0118] Among them, the Michaelis Kinetic parameters include the Michaelis constant K m and catalytic constant k cat .

[0119] k 1 、k 2 、k 3 and K m 、k cat There are the following correlations,

[0120]

[0121] And the Michaelis constant K can be obtained by experiment ...

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Abstract

The invention discloses a constructing method for a dynamic metabolic network. The method comprises the steps that (a), for the dynamic metabolic network to be constructed, all isolated reactions andregulation reactions are found out, the number of redundant elementary reaction rate constants in each isolated reaction is determined; (b), Michaelis Menten kinetic parameters of all the isolated reactions and the regulation reactions are obtained from in vitro experiments or from existing enzymology databases; (c / d), for each isolated reaction and regulation reaction, absolute values and / or relative values of all the other basic reaction rate constants are calculated; (e) by steps (c) and (d), the rate constants of the elementary reactions are obtained, by computers, a dynamic metabolic network of an elementary reaction topological structure is constructed. The method does not need to deduce the analytical formulas of the Michaelis Menten kinetic rate equations one by one, under the premise of the thermodynamic equilibrium constants, the method is easy to obtain the elementary reaction rate constants involved in the regulation reactions, and suitable for constructing a large-scalemetabolic network by computers.

Description

technical field [0001] The invention belongs to the field of enzyme reaction kinetics, and in particular relates to a method for constructing a dynamic metabolic network according to the topological structure of elementary reactions. Background technique [0002] Existing models describing metabolic networks are mainly divided into two types: 1) Chemometric models based on network topology (O'Brien, E.J. et al., Cell, 2015:161, 971-987; Schuster et al., Nature Biotechnology , 2000:18,326-332); 2) Introduce the dynamic metabolic network model of metabolite concentration, enzyme amount and metabolic regulation (Khodayari, A.et al., Metabolic Engineering.2014,25:50-62). The former only involves metabolic flow (that is, the reaction rate), and the method is simple, but the information is limited; the latter is more comprehensive, but obtaining model parameters is a huge challenge. [0003] Regarding the dynamic metabolic network model, compared with the empirical or semi-empiri...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/12
CPCG16B5/00
Inventor 赵阔潘天宇魏冰洁陈楚赟仇隽张丽梅关岳
Owner EAST CHINA UNIV OF SCI & TECH
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