. 2015 Oct 7;7:17. doi: 10.3389/fnsyn.2015.00017

Table 1.

Chemical kinetic rates and diffusion constants of molecules in model.

Parameter	Value	Temperature (°C)	Source
Calcium
Diffusion constant	2.2 × 10⁻⁶ cm²s⁻¹	34	Allbritton et al., 1992
Glutamate
Diffusion constant	2.2 × 10⁻⁶ cm²s⁻¹	34	Bartol, 1992; Elowitz et al., 1999; Ellis, 2001
AMPAR		34	Jonas et al., 1993
k_C0C1	9.18 × 10⁶ M⁻¹s⁻¹	34
k_C1C0	8520 s⁻¹	34
k_C1C2	5.68 × 10⁷ M⁻¹s⁻¹	34
k_C2C1	6520 s⁻¹	34
k_C2O	8480 s⁻¹	34
k_OC2	1800 s⁻¹	34
k_C3C4	2.54 × 10⁶ M⁻¹s⁻¹	34
k_C4C3	91.4 s⁻¹	34
k_C1C3	5780 s⁻¹	34
k_C3C1	78.4 s⁻¹	34
k_C2C4	344 s⁻¹	34
k_C4C2	1.45 s⁻¹	34
k_OC5	35.4 s⁻¹	34
k_C5O	8.0 s⁻¹	34
k_C4C5	33.6 s⁻¹	34
k_C5C4	380.8 s⁻¹	34
NMDAR: GluN2A/2B		34	Vargas-Caballero and Robinson, 2004
k_C0C1	2 × 10⁷ M⁻¹s⁻¹	34
k_C1C0	11.0 s⁻¹	34
k_C1C2	1.0 × 10⁷ M⁻¹s⁻¹	34
k_C2C1	22.0 s⁻¹	34
k_C2O	93.0 s⁻¹	34
k_OC2	183.2 s⁻¹	34
k_C2Ob	97.0 s⁻¹	34
k_OC2b	574 s⁻¹	34
k_C2D	16.8 s⁻¹	34
k_DC2	3.6 s⁻¹	34
k_B(V_m)	$1200 e^{(\frac{- V_{m}}{17})}$ s⁻¹	34	Rate at 1 mM Mg²⁺
k_U(V_m)	$10800 e^{(\frac{V_{m}}{47})}$ s⁻¹	34
L-type and R-type VDCCs		34	Bischofberger et al., 2002
γ	3.72 pS	34	Church and Stanley, 1996 and Q₁₀ 1.55
α_i(V_m)	$α_{i o} e^{(\frac{V_{m}}{V_{i}})}$
β_i(V_m)	$β_{i o} e^{(\frac{V_{m}}{V_{i}})}$
α_1o	8.08 ms⁻¹	34
α_2o	13.4 ms⁻¹	34
α_3o	8.78 ms⁻¹	34
α_4o	34.7 ms⁻¹	34
β_1o	5.76 ms⁻¹	34
β_2o	12.6 ms⁻¹	34
β_3o	16.3 ms⁻¹	34
β_4o	3.68 ms⁻¹	34
V₁	49.14 mV
V₂	42.08 mV
V₃	55.31 mV
V₄	26.55 mV
k_Ca(V_m)	$\frac{γ V_{m} N_{A} (0.393 - e^{\frac{- V_{m}}{80.36}})}{2 F (1 - e^{\frac{V_{m}}{80.36}})}$
GluT: GLT1/GLAST		34	Otis and Jahr, 1998; Geiger et al., 1999
kT0T1	3.6 × 10⁷ M⁻¹s⁻¹	34
kT1T0	360 s⁻¹	34
kT1T2	360 s⁻¹	34
kT2T0	51.4 s⁻¹	34
Immobile Calcium-Binding Protein (CBP)			Calibrated (see text)
Association rate	2.47 × 10⁸ M⁻¹s⁻¹	34	Calibrated (see text)
Dissociation rate	524 s⁻¹	34	Calibrated (see text)
Diffusion constant	0 μm²s⁻¹
Calbindin		34	Nagerl et al., 2000
kM0M1	17.4 × 10⁷ M⁻¹s⁻¹	34
kM1M2	8.7 × 10⁷ M⁻¹s⁻¹	34
kM1M0	35.8 s⁻¹	34
kM2M1	71.6 s⁻¹	34
kH0H1	2.2 × 10⁷ M⁻¹s⁻¹	34
kH1H2	1.1 × 10⁷ M⁻¹ s⁻¹	34
kH1H0	2.6 s⁻¹	34
kH2H1	5.2 s⁻¹	34
Diffusion constant	0.28 × 10⁻⁶ cm²s⁻¹	34
PMCA		37	Penheiter et al., 2003; Brini and Carafoli, 2009
k₁	1.5 × 10⁸ M⁻¹s⁻¹	37
k₂	15 s⁻¹	37
k₃	12 s⁻¹	37
k_LEAK	4.3 s⁻¹		Gives 100 nM resting Calcium
NCX		34	Hilgemann et al., 1991
k₁	3 × 10⁸ M⁻¹s⁻¹	34
k₂	300 s⁻¹	34
k₃	600 s⁻¹	34
k_LEAK	19.4 s⁻¹		Gives 100 nM resting Calcium
SERCA2b		37	Higgins et al., 2006
k_X0X1	2 × 10⁸ M⁻¹s⁻¹	37
k_X1X0	83.7 s⁻¹	37
k_X1X2	1 × 10⁸ M⁻¹s⁻¹	37
k_X2X1	167.4 s⁻¹	37
k_X2Y2	0.6 s⁻¹	37
k_Y2X2	0.097 s⁻¹	37
k_X0Y0	1.2 × 10⁻³	37
k_Y0X0	0.4 s⁻¹	37
k_Y0Y1	60 × 10⁻⁶ M	37	Assume 60 μM [Ca²⁺] in ER
	×2 × 10⁵ M⁻¹s⁻¹
k_Y1Y0	30.02 s⁻¹	37
k_Y1Y2	60 × 10⁻⁶ M	37	Assume 60 μM [Ca²⁺] in ER
	×1 × 10⁵ M⁻¹s⁻¹
k_Y2Y1	60.04 s⁻¹	37
Fluo4
Association-rate	8.0 × 10⁸ M⁻¹s⁻¹	35	Naraghi, 1997
Dissociation-rate	240 s⁻¹	35	Kd = 300 nM, Maravall et al., 2000
Diffusion constant	0.84 × 10⁻⁶ cm²s⁻¹	34	Calculated (see text)
OGB1
Association-rate	8.0 × 10⁸ M⁻¹s⁻¹	35	Naraghi, 1997
Dissociation-rate	160 s⁻¹	35	Kd = 200 nM, Maravall et al., 2000
Diffusion constant	0.84 × 10⁻⁶ cm²s⁻¹		Calculated (see text)

The parameters used in the model of spine Ca²⁺ transients are listed, along with literature sources. Parameters were adjusted to reflect a range of 34–37°C, as described in the Methods and Results Sections. The usage of the parameters in kinetic models of each protein are shown in Figures 2, 3.