Glyceraldehyde-3-phosphate dehydrogenase

The Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) enzyme serves two functions in glycolytic pathway. First the enzyme transfers a hydrogen (H-) from glyceraldehyde phosphate (Gly3P) to the oxidizing agent Nicotinamide Adenine Dinucleotide (NAD+) to form NADH. Next it adds a phosphate (P) from the cytosol to the oxidized Gly3P to form 1, 3-bisphosphoglycerate.

Chemical equation

$NAD + Gly3P + Pi \rightleftharpoons 1,3BPG + NADH$

Rate equation

Ordererd Ter-Bi reversible Michaelis-Menten equation for non-interacting substrates.

$v = \frac{ V_{mf}\frac{[NAD][Gly3P][Pi]}{K_{NAD}K_{Gly3P}K_{Pi}} - V_{mr} \frac{[1,3BPG][NADH]}{K_{1,3BPG}K_{NADH}} }{1 + \frac{[NAD]}{K_{NAD}} + \frac{[NAD][Gly3P]}{K_{NAD}K_{Gly3P}} + \frac{[NAD][Gly3P][Pi]}{K_{NAD}K_{Gly3P}K_{Pi}} + \frac{[1,3BPG][NADH]}{K_{1,3BPG}K_{NADH}} +\frac{[NADH]}{K_{NADH}} }$

Modified rate law for taking Thermodynamic constant into consideration

$v = \frac{ V_{mf}\frac{[NAD][Gly3P][Pi]}{K_{NAD}K_{Gly3P}K_{Pi}} \left( 1 - \frac{[1,3BPG][NADH]}{K_{eq}[NAD][Gly3P][Pi]} \right)}{1 + \frac{[NAD]}{K_{NAD}} + \frac{[NAD][Gly3P]}{K_{NAD}K_{Gly3P}} + \frac{[NAD][Gly3P][Pi]}{K_{NAD}K_{Gly3P}K_{Pi}} + \frac{[1,3BPG][NADH]}{K_{1,3BPG}K_{NADH}} +\frac{[NADH]}{K_{NADH}} }$

Parameters

Parameter	Value	Units	Organism	Remarks
$V_{mf}$	0.58	$mM \times min^{-1}$	HeLa cell line
$V_{mr}$	0.72	$mM \times min^{-1}$
$Km_{Gly3P}$	0.19	mM
$Km_{1,3BPG}$	0.022	mM
$Km_{NAD+}$	0.09	mM
$Km_{NADH}$	0.01	mM
$Km_{Pi}$	29	mM

Parameters with uncertainty

• Four values of $Km_{NADH}$ have been collected from Lambeir et. al. (1991) for different organisms. $Km_{NADH} = 0.007$ for Trypanosoma brucei, $Km_{NADH} = 0.01$ for Homo sapiens, $Km_{NADH} = 0.012$ for Geobacillus stearothermophilus and $Km_{NADH} = 0.012$ for Oryctolagus cuniculus. Calculating mean and std. dev. from these 4 values gives $Km_{NADH} = 0.01025 \pm 0.002046$

• Three values collected under different conditions from human cell is reported for $Km_{NAD+}$ in Ryzlak (1998) et. al. . Those values are 0.01, 0.02, 0.027. The mean and Std. Dev. from these three values are $Km_{NAD+} = 0.019 \pm 0.007$

• Three values for $Km_{1,3BPG}$ have also been reported under different conditions from human cell in Ryzlak (1998) et. al. . Those values are 0.01, 0.012, 0.018. The mean and Std. Dev. from these three values are $Km_{1,3BPG} = 0.013 \pm 0.0035$

• Three values for $Km_{Gly3P}$ have also been reported under different conditions from human cell in Ryzlak (1998) et. al. . Those values are 0.032, 0.035, 0.042. The mean and Std. Dev. from these three values are $Km_{Gly3P} = 0.036 \pm 0.0042$

Parameter	Value	Units	Organism	Remarks
$V_{mf}$	$2 \pm 0.74 (5)$	$mM \times min^{-1}$	HeLa cell line
$V_{mr}$	$2.5 \pm 0.8$ (5)	$mM \times min^{-1}$
$Km_{Gly3P}$	$0.036 \pm 0.0042$	mM	Human brain
$Km_{1,3BPG}$	$0.013 \pm 0.0035$	mM	Human brain
$Km_{NAD+}$	$0.019 \pm 0.007$	mM	Human brain
$Km_{NADH}$	$0.01025 \pm 0.002046$	mM	Multiple organism
$Km_{Pi}$	$4 \pm 0.2$	mM	Normal tissue in human

Equilibrium constant

Equilibrium constant	Conditions	Source
0.078	pH=7, T=25°C	Lehninger, (2008) p 553: $\Delta G' = 6.3\ kJ.mol^{-1}$, $Keq = exp(-\frac{\Delta G'}{RT}) = exp(\frac{-6300}{8.31*298.15}) \approx 0.078$
0.067	pH=7, T=25°C	Voet et al. from Newshole et al. (1973) p 97: $\Delta G' = 6.7\ kJ.mol^{-1}$, $Keq = exp(-\frac{\Delta G'}{RT}) = exp(\frac{-6300}{8.31*298.15}) \approx 0.067$
0.08	pH=7, T=298.15 Kelvin	Corrected for pH from Cori et al. 1950 (NIST database [50COR/VEL_252]) pH=7.09

• The mean and Std. Dev. for Keq would be $0.075 \pm 0.007$