Yokota 1985 photorespiration model
The Yokota 1985 model is a kinetic description of the photorespiratory C2 cycle in plant chloroplasts and peroxisomes. Glycolate generated by Rubisco oxygenase flows through glyoxylate, glycine, serine and hydroxypyruvate, while the hydrogen peroxide produced by glycolate oxidase is scavenged by catalase.
Every enzymatic step follows Michaelis–Menten kinetics, so the model traces how carbon and reducing equivalents move through the photorespiratory pathway under varying conditions.
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\begin{align*}
\frac{d glycolate}{dt} &= kf\_phosphoglycolate\_phosphatase \\
& - \frac{glycolate \cdot vmax\_glycolate\_oxidase}{glycolate + km\_glycolate\_oxidase\_s} \\
\frac{d glyoxylate}{dt} &= \frac{glycolate \cdot vmax\_glycolate\_oxidase}{glycolate + km\_glycolate\_oxidase\_s} \\
& - \frac{glyoxylate \cdot vmax\_glycine\_transaminase}{glyoxylate + km\_glycine\_transaminase\_s} \\
& - \frac{glyoxylate \cdot serine \cdot vmax\_serine\_glyoxylate\_transaminase}{glyoxylate \cdot serine + \frac{glyoxylate}{km\_serine\_glyoxylate\_transaminase\_glyoxylate} + \frac{serine}{km\_serine\_glyoxylate\_transaminase\_serine} + \frac{1}{km\_serine\_glyoxylate\_transaminase\_glyoxylate \cdot km\_serine\_glyoxylate\_transaminase\_serine}} \\
\frac{d glycine}{dt} &= \frac{glyoxylate \cdot vmax\_glycine\_transaminase}{glyoxylate + km\_glycine\_transaminase\_s} \\
& - 2 \cdot \frac{glycine \cdot vmax\_glycine\_decarboxylase}{glycine + km\_glycine\_decarboxylase\_s} \\
& + \frac{glyoxylate \cdot serine \cdot vmax\_serine\_glyoxylate\_transaminase}{glyoxylate \cdot serine + \frac{glyoxylate}{km\_serine\_glyoxylate\_transaminase\_glyoxylate} + \frac{serine}{km\_serine\_glyoxylate\_transaminase\_serine} + \frac{1}{km\_serine\_glyoxylate\_transaminase\_glyoxylate \cdot km\_serine\_glyoxylate\_transaminase\_serine}} \\
\frac{d serine}{dt} &= \frac{glycine \cdot vmax\_glycine\_decarboxylase}{glycine + km\_glycine\_decarboxylase\_s} \\
& - \frac{glyoxylate \cdot serine \cdot vmax\_serine\_glyoxylate\_transaminase}{glyoxylate \cdot serine + \frac{glyoxylate}{km\_serine\_glyoxylate\_transaminase\_glyoxylate} + \frac{serine}{km\_serine\_glyoxylate\_transaminase\_serine} + \frac{1}{km\_serine\_glyoxylate\_transaminase\_glyoxylate \cdot km\_serine\_glyoxylate\_transaminase\_serine}} \\
\frac{d hydroxypyruvate}{dt} &= \frac{glyoxylate \cdot serine \cdot vmax\_serine\_glyoxylate\_transaminase}{glyoxylate \cdot serine + \frac{glyoxylate}{km\_serine\_glyoxylate\_transaminase\_glyoxylate} + \frac{serine}{km\_serine\_glyoxylate\_transaminase\_serine} + \frac{1}{km\_serine\_glyoxylate\_transaminase\_glyoxylate \cdot km\_serine\_glyoxylate\_transaminase\_serine}} \\
& - \frac{hydroxypyruvate \cdot vmax\_glycerate\_dehydrogenase}{hydroxypyruvate + km\_glycerate\_dehydrogenase\_s} \\
\frac{d H2O2}{dt} &= \frac{glycolate \cdot vmax\_glycolate\_oxidase}{glycolate + km\_glycolate\_oxidase\_s} \\
& - \frac{H2O2 \cdot vmax\_catalase}{H2O2 + km\_catalase\_s}
\end{align*}Edit analysis
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