Calcium is a vital second

messenger

• Ca2+ plays an equally important role in practically every

cell type.

• Ca2+ controls secretion, cell movement, muscular

contraction, cell differentiation, ciliary beating, and so on.

• Important in both excitable and non-excitable cells.

•Well regulated in cells

Typical Calcium
Oscillations

A: Hepatocytes
B: Rat parotid gland
C: Gonadotropes
D: Hamster eggs (post-
fertilization)
E, F: Insulinoma cells
Summary of calcium
homeostasis Ca2+
PM pumps

ICa
RyR
Ca2+ leak

ER IPR

Ca2+-B
serca
(buffering)

Mitochondria
Calcium metabolism in neurons
Calcium excitability
• Both IPR and RyR release calcium in an excitable manner. They
both respond to a calcium challenge by the release of even more
calcium.

• The precise mechanisms are not known for sure (although

detailed models can be constructed).

• An IPR behaves like a Na+ channel (in some ways). In response

to an increase in [Ca2+] it first activates quickly, and then inactivates
slowly, resulting in the short-term release of a large amount of
calcium.

• A lot of attention has been focused on IPR and RyR. Less on

pumping. But the dynamics of pumping is equally important.
IP3 Receptor pathway
Ryanodine Receptor pathway
 Generic modeling
Total buffer
Set up a typical reaction diffusion equation for calcium:
∂c
= D∇ 2c + (J IPR + J RyR − J serca ) + (J leak − J PM + J I ) + (J m, out − J m,in ) − k1c(bt − b) + k2 b
∂t

mitochondrial buffering
ER fluxes PM fluxes
fluxes

• This reaction-diffusion equation is coupled to a system of o.d.e.s (or p.d.e.s),

describing the various receptor states, IP3, the reaction and diffusion of the buffers,
calcium inside the ER or mitochondria, or any other important species.

• The specifics of the coupled o.d.e.s depend on which particular model is being used.

• Sometimes the PM fluxes appear only as boundary conditions, sometimes not,

depending on the exact assumptions made about the spatial properties of the cell.

• In general the buffering flux is a sum of terms, describing buffering by multiple

diffusing buffers.
 Calcium diffusion
• Assume uniform calcium flux across compartment membrane →
only need to consider radial (1D) diffusion.
• Fick´s first law: flux JCa (in mol/s) through area a is proportional to
negative concentration gradient:

∂ [Ca 2+ ]
JCa = −a DCa
∂x
• Discretised concentration change in volume vi:

[Ca ]
2+
i, t +1 [
− Ca 2 + ]
i, t
=DCa
[
ai ,i +1 Ca 2 + ]
i +1,t [
− Ca 2 + ]
i ,t

∆t vi ∆x
• Only parameter: diffusion constant DCa. Depends on ion size and
medium, e.g. DCa (water) ~ 600 µm2/s, DCa (cytoplasm) ~ 200 µm2/s.
 Calcium diffusion: spatial discretization

• Spatial discretisation depending on structure of compartment and

location of calcium influx. Divide cylindrical compartments into shells,
spines into stacked cylinders.

Limitations:
• Localised calcium fluxes → local calcium domains.
• Calcium induced calcium release → calcium waves, calcium sparks.
→ Model 3D diffusion (computationally expensive).
 Calcium dynamics: exponentially decaying pool

[
d Ca 2 +]=
I Ca
([ ] [
− β Ca 2+ − Ca 2 + ] )
min
dt 2 Fv
Advantage: only three parameters
• [Ca2+]min baseline calcium concentration ~50nM.
•β decay rate constant, summarises diffusion, buffering,
pumps and exchangers.
•v volume of calcium pool, usually submembrane shell
(relevant for activation of KCa channels).

Limitations:
• Not possible to study calcium dependent processes in the cytoplasm
(e.g. calcium induced calcium release CICR).
• Different KCa channels sense different [Ca2+]?

Possible extension:
• Use several calcium pools with different βi.
 Calcium buffers
k1
For each diffusion shell →

→
J
Ca 2+ + B CaB
and each buffer: ←
k2

d [Ca 2+ ]
= −k1[Ca 2+ ][ B] + k2 [CaB ] + J
dt
Four parameters for each buffer:
• Forward and backward rate constants k1 and k2.
• Total concentration [B]T = [B] + [CaB].
• Diffusion constant DB.

Derived parameters (assume rapid [Ca 2 + ] [ B] k2

buffer approximation, i.e. steady-state): KD = =
[CaB ] k1
• Dissociation constant
• Buffer capacity d [CaB ] K D [B ]T [B]T
κ= = ≈
(between 50 and 4000 in neurons) [ ] (K + [Ca ] )
d Ca 2+ D
2+ 2
KD
d [Ca ]
• Buffering factor 2+
1
β = =
d [Ca ] 1 + κ
2+
T
 Calcium buffers: Rapid Buffer Approximation (RBA)

Rapid buffer assumption (calcium and buffer are in equilibrium):

d[Ca 2+ ] d[Ca 2+ ] d [Ca 2+ ]T

= 2+
=βJ
dt d[Ca ]T dt

Apparent diffusion constant:

DCa , app = β ( DCa + DBκ )

Fixed buffers → slower calcium diffusion (0 < β < 1).

Mobile buffers → faster calcium diffusion.
Calcium buffers: Excess Buffer Approximation (EBA)

Besides RBA another simplification, excess buffer approximation,

can be used to reduce the Ca and buffer system.

Excess buffer approximation (Neher, 1986; Smith, 1996)

assumes that mobile buffer is present in excess and cannot
be saturated; B (and BTot) does not change due to Ca changes.

∂ Ca
= Dc ∇2Ca − k + Btot (Ca − Cabk ) + σδ (r )
∂t

where Cabk is the “bulk calcium” concentration, far from the

channel.
 Steady-state EBA
Steady State EBA

σ
Ca = e −r / λ + Cabk
4πDc r

Where λ is the characteristic length, which depends on the

calcium diffusion coefficient, the buffer binding rate, and
the free buffer far from the channel,

Dc
λ=
k + Bbk
 EBA vs. RBA
• EBA appropriate when the saturability of mobile buffer is
negligible. For example, this is the case for millimolar
concentrations of Calbindin-D28K in the saccular hair cell.
• RBA appropriate when there is significant saturability of mobile
buffer and when buffer kinetics are fast relative to Ca2+ diffusion.
This is often the case near Ca2+ channels in synapses, and near
IP3 or ryanodine receptors in the ER/SR.
• Smith et al. (2001) did an asymptotic analysis of buffered Ca2+
diffusion near a point source, and determined mathematical
conditions for when RBA or EBA are appropriate.

lim B ≈ Bbk (EBA) lim B ≈ 0 (RBA)

r→ 0 r →0
buffer unperturbed buffer saturates
 Calcium buffers: examples

k1 (µM-1s-1) k2 (s-1) KD (µM) D (µm2s-1)

Endogenous
Troponin-C 90-100 7-300 0.05-3 0
Calmodulin 100-500 37-470 0.2-2.0 32
Calbindin-D28k 20 8.6 0.4-1.0 27
Parvalbumin 6 1 0.00037 36

Exogenous
EGTA 1.5 0.3 0.2 113
BAPTA 600 100 0.1-0.7 95
Fura-2 600 80-100 0.13-0.6 30-95
Ca Green-1 700 170 0.19-0.25 84

Smith (2001)

Calcium indicator dyes distort the spatio-temporal profile of calcium

and should be included in the model.
 IP 3 induced calcium release
• Can be modelled using Hodgkin-Huxley like formalism (Li & Rinzel 1994).
J = Vmax m3 h3 ([Ca 2 + ]store − [Ca 2+ ])
dm m∞ − m dh h∞ − h
= =
dt τm dt τh
• mss , hss , τm and τh are functions of [Ca2+ ] and [IP3], e.g.

[ IP3 ] [Ca 2 + ]
m∞ =
[ IP3 ] + K IP3 [Ca 2+ ] + K Ca 2+
• IP3 production in response to metabotropic glutamate receptor activation
can be modelled with an alpha function (analogous to gAMPA):
d [ IP3 ] −t / t
= γ t e peak − β ([ IP3 ] − [ IP3 ]min )
dt

• Positive feedback of Ca2+ on IP3 production → model production of IP3

by PLC, G protein activation of PLC etc. explicitly…
 Calcium influx and efflux
Plasma membrane
• Ca2+ ATPase
• 3 Na+ / Ca2+ exchanger
• Electrogenic → affect resting membrane potential and excitability.

Intracellular calcium stores

• Ca2+ ATPase
• Calcium induced calcium release CICR
• IP3 induced calcium release IICR
• Calcium dependent → waves, sparks, coincidence detection…

Ca2+ ATPase model

• Time dependent or steady state
Vmax [Ca 2+ ]n
J∞ = n
K + [Ca 2+ ]n
dJ J ∞ − J
=
dt τJ
 Stochasticity in intracellular Ca dynamics
• Intracellular pathways can involve very small numbers of ions
or molecules.
• 100 nM [Ca2+] = 5 calcium ions in a spine head with 0.5 µm diameter.
• Use stochastic simulation methods instead of mass action kinetics.
k1
→
A + B AB
• Probability that one molecule of A ←
k2
changes to AB during the time ∆t:
p ( A → AB) = 1 − e − k1 ∆t

• Stochastic methods are computationally expensive

→ Use adaptive stochastic methods that switch to deterministic
calculations for large numbers of molecules (Vasudeva & Bhalla, 2003).

• Representation of spatial microstructure: use Monte-Carlo simulation

where all molecules are represented individually and perform random
walks. Simulation software: MCell