Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification

Kadir, Tuty Asmawaty Abdul; Mannan, Ahmad A; Kierzek, Andrzej M; McFadden, Johnjoe; Shimizu, Kazuyuki

doi:10.1186/1475-2859-9-88

Table 2 Model parameters

From: Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification

Enzyme	Kinetic parameter values	Original source
Cell growth	μ_m = 0.6, K_s= 0.1, μ_mA= 0.9, K_sA = 0.01, X_m = 2.3	estimated
Glk	$v_{G l k}^{\max} = 4.503 m m o l / g D C W . h, K_{m}^{G L C} = 0.12 m M, K_{m}^{A A T P} = 0.5 m M$	[49]
PTS	$v_{P T S}^{\max} = 25.739 m m o l / g D C W . h, K_{a 1} = 1.0 m M, K_{a 2} = 0.01 m M, K_{a 3} = 1.0, n_{G 6 P} = 4$ , K_{G 6p}= 0.5mM	[8, 33]
Pgi	$v_{P G I}^{max} = 26.3711 m m o l / g D C W . h, K_{G 6 P} = 2.46 m M, K_{F 6 P} = 0.2 m M, K_{e q} = 0.43 m M$ , $K_{6 p g i n h}^{^{G 6 P}} = 0.2 m M, K_{6 p g i n h}^{^{F 6 P}} = 0.2 m M$	[8]
Pfk	$v_{P f k}^{\max} = 24.613 m m o l / g D C W . h, K_{(A T P)} = 4.27 m M, K_{(A T P, A D P)} = 4.6944 m M$ , $K_{a (A D P, A M P)} = 1.1118 m M, K_{b (A D P, A M P)} = 98.88 m M, n_{P f k} = 4, L_{P f k} = 1000, K_{s}^{F 6 P} = 0.14 m M$ , K_PEP= 3.26mM	[8]
Aldo	$v_{A l d o}^{max} = 2.8337 m m o l / g D C W . h, K_{F D P} = 0.133 m M, K_{G A P} = 0.088 m M, K_{D H A P} = 0.088 m M$ , $K_{i n h}^{G A P} = 0.6 m M, K_{e q} = 0.14 m M, V_{b l f} = 2$	[8]
GAPDH	$v_{G A P D H}^{max} = 121.29 m m o l / g D C W . h, K_{G A P} = 0.15 m M, K_{P G P} = 0.1 m M, K_{N A D} = 0.45 m M$ , K_NADH= 0.02mM, K_eq= 0.63	[8]
Pyk	$v_{P y k}^{max} = 1.0849 m m o l / g D C W . h, K_{P E P} = 0.31 m M, K_{F D P} = 0.19 m M, K_{A M P} = 0.2 m M, n_{P y k} = 4$ K_ATP= 22.5mM, K_ADP= 0.26mM, L_Pyk= 1000,	[8]
PDH	$v_{P D H}^{\max} = 27171 m m o l / g D C W . h, K_{m}^{P Y R} = 1 m M, K_{m}^{N A D} = 0.4 m M, K_{m}^{A c C o A} = 0.008 m M$ , $K_{m}^{N A D H} = 0.1 m M, K_{m}^{C O A} = 0.014 m M, K_{i}^{P D H} = 46.4 m M$	[40]
CS	$v_{C S}^{\max} = 17.36 m m o l / g D C W . h, K_{d 1}^{H} = 0.00001 m M, K_{d 2}^{H} = 0.0002 m M, K_{m}^{A c C o A} = 0.18 m M$ , $K_{m}^{O A A} = 0.04 m M, K_{d}^{A c C o A} = 0.1 m M, K_{i}^{A T P} = 0.58 m M, K_{ι 1}^{2 K G} = 0.015 m M, K_{i 2}^{2 K G} = 0.256 m M$ , $K_{i 1}^{N A D H} = 0.00033 m M, K_{i 2}^{N A D H} = 0.0084 m M, K_{c a t 0} = 1$	[43]
ICDH	$v_{I C D H}^{\max} = 24.42 m m o l / g D C W . h, K_{e q} = 1000 m M, k_{f} = 4830 - 1 / min, K_{m}^{2 k G} = 0.038 m M$ , $K_{m}^{i C i T} = 0.0059 m M, K_{d}^{N A D P} = 0.0013 m M, K_{m}^{N A D P} = 0.0227 m M, K_{d}^{N A D H} = 0.12 m M$ , $K_{d}^{i C i T} = 0.03 m M, K_{e i n h}^{N A D P H} = 0.007 m M, K_{e k n h}^{2K G} = 5.5 m M, K_{d}^{c o_{2}} = 1.6 m M, K_{e k e}^{c o_{2}} = 1.6 m M$ , $K_{e k n}^{N A D P} = 0.00016 m M, K_{m}^{N A D P H} = 0.0036 m M, K_{e n h e}^{N A D P H} = 0.028 m M$	[44]
Icl	$V_{I c l_{-} f}^{max} = 3.8315 m m o l / g D C W . h, v_{I c l_r}^{\max} = 2.585 / 100 m m o l / g D C W . h, K_{m}^{i C i T} = 0.604 m M$ , $K_{m}^{S U C} = 0.59 m M, K_{m}^{G O X} = 0.13 m M, K_{I}^{^{I C L}} = 0.003 m M$	[46]
MS	$K_{M S_f}^{\max} = 3.6968 m m o l / g D C W . h, K_{M S_r}^{max} = 13.742 / 100 m m o l / g D C W . h, K_{m}^{G O X} = 2 m M$ , $K_{m}^{A c C o A} = 0.01 m M, K_{m}^{M A L} = 1 m M, K_{m}^{C o A} = 0.1 m M$	[46]
2KGDH	$v_{2 K G D H}^{\max} = 137.435 m m o l / g D C W . h, K_{m}^{2 K G} = 1.0 m M, K_{I}^{2 K G} = 0.75 m M, K_{m}^{C o A} = 0.002 m M$ , $K_{m}^{N A D} = 0.07 m M, K_{m}^{S U C} = 1.0 m M, K_{m}^{N A D H} = 0.018 m M, K_{Z} = 1.5$	[45]
SDH	$K_{m}^{S U C} = 0.1, v_{S D H 1} = 1.1334 m m o l / g D C W . h, v_{S D H 2} = 1.1334 m m o l / g D C W . h, K_{e q} = 10$	[45]
MDH	$v_{M D H 1} = 25.874 m m o l / g D C W . h, v_{M D H 2} = 25.874 m m o l / g D C W . h, K_{e q} = 1.0, K_{I}^{N A D} = 0.31 m M$ , $K_{I}^{N A D H} = 0.04 m M, K_{I}^{M A L} = 3.30 m M, K_{I}^{O A A} = 0.27 m M, K_{m}^{N A D} = 0.1 m M, K_{m}^{N A D H} = 0.04 m M$ , $K_{m}^{M A L} = 1.33 m M, K_{m}^{O A A} = 0.27 m M, K_{I I}^{N A D} = 0.31 m M, K_{I I}^{O A A} = 0.17 m M$	[45]
FUM	$v_{F U M 1} = 1.1334 m m o l / g D C W . h, V_{F U M 2} = 1.1334 m m o l / g D C W . h, K_{e q} = 10, K_{m}^{F U M} = 0.1 m M$	[45]
Ppc	$v_{P p c}^{\max} = 0.1885 m m o l / g D C W . h, K_{m}^{P E P} = 0.323 l m M, k_{1} = 0.03176, k_{2} = 1.2878 m M$ , k₃ = 0.0542mM, k₄ = 0.8139mM, k₅ = 0.0939mM, k₆ = 0.2693mM	[38]
Pck	$v_{P c k}^{\max} = 4.5116 m m o l / g D C W . h, K_{m}^{A T P} = 0.06 m M, K_{I}^{A T P} = 0.04 m M, K_{i}^{A T P} = 0.04 m M$ , $K_{m}^{O A A} = 0.67 m M, K_{i}^{P E P} = 0.06 m M, K_{I}^{O A A} = 0.67 m M, K_{m}^{P E P} = 0.07 m M, K_{i}^{A D P} = 0.04 m M$	[15]
Mez	$v_{M e z}^{\max} = 0.069945 m m o l / g D C W . h, K_{m}^{M A L} = 0.37 m M, K_{e q} = 0.10$	[45]
Pta	$v_{P t a}^{max} = 12.585 m m o l / g D C W . h, K_{i}^{A c C o A} = 0.2 m M, K_{m}^{P} = 2.6 m M, K_{i}^{P} = 2.6 m M$ , $K_{m}^{A C P} = 0.7 m M, K_{i}^{A C P} = 0.2 m M, K_{i}^{c o A} = 0.029 m M, K_{e q} = 0.0281 m M$	[40]
Ack	$v_{A c k}^{\max} = 2865.3 m m o l / g D C W . h, K_{m}^{A C P} = 0.16 m M, K_{m}^{A D P} = 0.5 m M, K_{m}^{A C E} = 7 m M$ , $K_{m}^{A T P} = 0.07 m M, K_{e q} = 174.217 m M$	[40]
Acs	$v_{A c s}^{max} = 17.9068 m m o l / g D C W . h K = 0.089971 m m o l / g D C W . h, K_{m} = 0.07 m M$	[42]
G6PDH	$v_{G 6 P D H}^{max} = 0.97922 m m o l / g D C W . h, K_{G 6 P} = 14.4 m M, K_{N A D P} = 0.015 m M, K_{N A D P H}^{N A D P} = 0.01 m M,$ $K_{N A D P H}^{G 6 P} = 0.18 m M$	[8]
6PGDH	$v_{6 G P D H}^{max} = 1.81 m m o l / g D C W . h, K_{G 6 P} = 0.1 m M, K_{N A D P} = 0.028 m M, K_{N A D}_{P i n h} = 0.01 m M$ , K_ATPinh= 3.0mM	[8]
Rpe	$v_{R p e}^{\max} = 18.485 m m o l / g D C W . h, K_{e q}^{R p e} = 1.4 m M$	[8]
Rpi	$v_{R p i}^{\max} = 13.318 m m o l / g D C W . h K_{e q}^{R p i} = 4.0 m M$	[8]
TktA	$v_{T k t A}^{\max} = 29.348 m m o l / g D C W . h, K_{e q}^{T k t A} = 1.2 m M$	[8]
TktB	$v_{T K t B}^{\max} = 316.22 m m o l / g D C W . h, K_{e q}^{T k t B} = 10.0 m M$	[8]
Tal	$v_{T a l}^{\max} = 24.499 m m o l / g D C W . h, K_{e q}^{T a l} = 1.05 m M$	[8]

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