Week 4 MD simulations of ion channels and transporters •Lecture 7: Biophysics of a single neuron; propagation of action potential and ion channels; neurotransmission at synapses and transporters; MD simulations of gramicidin and potassium channels. •Lecture 8: Primary and secondary active transporters; Na-K pump and ABC transporters use energy from ATP; secondary active transporters use the membrane potential; MD simulations of glutamate transporters.
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Week 4 MD simulations of ion channels and transporters Lecture 7: Biophysics of a single neuron; propagation of action potential and ion channels; neurotransmission.
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Week 4
MD simulations of ion channels and transporters
•Lecture 7: Biophysics of a single neuron; propagation of action
potential and ion channels; neurotransmission at synapses and
transporters; MD simulations of gramicidin and potassium channels.
•Lecture 8: Primary and secondary active transporters; Na-K pump and
ABC transporters use energy from ATP; secondary active transporters
use the membrane potential; MD simulations of glutamate transporters.
Structure of a neuron
Signal transmission in salt water
Problem of signal transmission in salt water
Diffusion wouldn’t work: <x2>=2Dt, L=1 m, D~10-9 m2/s, t~16 years!
year 1 s105.2
kT 40 eV 1for m/s1040
7
9
d
d
vL
t
LD
kTeV
kTD
LeVF
vIf we apply
a potential difference V
Propagation of the action potential
1. Change of membrane voltage opens the sodium channels.
2. Na+ ions flow into the cell, which collapses the membrane potential from
−60 mV to 0.
3. This triggers the opening of the potassium channels, while the sodium
channels shut down stochastically.
4. K+ ions flow outside the cell, restoring the membrane potential. The
potassium channels shut down, returning the system to (1).
5. This process is repeated along the axon, which propagates the action
Crystal structure of potassium channel (MacKinnon, 1998; Nobel 2003).
Reveals the mechanisms of selectivity and voltage gating
The selectivity filter has the
right size to bind the
dehydrated K+ ions (r=1.3 Å)
but it is too large for the
smaller Na+ ions (r=0.9 Å).
Voltage-gated
ion channels are
life’s transistors.
Selectivity filter
Crystal structure of a sodium channel (Caterall, 2011)
Selectivity filter in Nav (yellow)
is wider than in Kv (blue), and
can accommodate a hydrated
Na+ ion.
Neurons communicate via neurotransmitters at synapses
Vesicles contain hundreds of neurotransmitters. They travel about 10 nm across the cleft and bind to receptors, which starts another action potential.
Synaptic transmission
1. When the action potential reaches an axon bulb, it triggers opening of the calcium channels and calcium ions move in.
2. The rise in calcium concentration causes synaptic vesicles containing neurotransmitters to move towards the membrane.
3. Synaptic vesicles merge with the membrane and release neurotransmitters into the synaptic cleft.
4. Neurotransmitters diffuse across the synaptic cleft (~ nm) and bind to receptor proteins on the postsynaptic membrane. Excitatory neurotransmitters open sodium channels, and sodium ions move in.
5. If sufficient excitatory neurotransmitter binds to receptors, an action potential is produced in the postsynaptic membrane and travels along the axon of the second neuron.
6. To prevent continuous stimulation or inhibition of the postsynaptic membrane, neurotransmitters are broken down by enzymes or are reabsorbed through the presynaptic membrane by transporters.
Ion channels in the central nervous system
Voltage-gated ion channels in CNS
sodium and potassium channels are involved in the propagation
of action potential
calcium channels facilitate release of nerotransmitters at the
axon terminal.
Ligand-gated channels in synapses:
glutamate receptor channels: glutamate is the major excitatory
neurotransmitter in CNS – its binding opens a sodium channel
GABA (g aminobutyric acid) and glycine receptor channels:
inhibitory neurotransmitters
NACh (nicotinic acetylcholine) receptor channels: neuromuscular
junctions
What did we know about ion channels a decade ago?
A lot about their function:
• I-V curves, conductance-concentration curves
• Selectivity sequences for ions
• Gating properties
But not much about structure:
Water filled holes in the membrane
that open and close in response
to voltage change, chemicals, etc.
Without structure, we cannot answer even the most basic questions
about how channels select ions and how the gates open and close.
Thus most work on ion channels before 1998 were done on gramicidin,
which is an antibacterial drug (NMR structure, 1971). After 1998, all the
work focused on potassium channels (and now on sodium channels!).
MD simulations of ion channels
What we can do with MD simulations at present:
• Conductance calculations require more than microsecond MD
simulations, so we cannot determine it directly from MD by counting
ions crossing the channel.
Compromise solution: determine the free energy profiles from MD or
continuum electrostatics and use them in BD simulations.
• Ion selectivity ratios can be determined from MD-free energy
perturbation calculations.
• Gating happens in ms time domain so cannot be accessed directly
with brute-force MD. However targeted MD simulations and coarse-
grained models have been used to study gating.
• The recent entrance of ANTON – the special purpose MD machine –
to the field has allowed extension of these limits.
A prerequisite for MD simulation of an ion channel is the availability of the
crystal structure or a good homology model. Because MD is an atomistic
model, it does not forgive any errors in the molecular structure of a
channel model.
What is available:
• Gramicidin: Antibacterial peptide, structure known since the 70’ties.
• Potassium channels: KcsA (1998), followed by many others, including
voltage-gated potassium channels.
• Sodium channels: The latest entry. However the initial rush has been
moderated by the difficulty of constructing homology models from
bacterial crystal structure.
• Calcium channels: The hardest one to crack due to lack of symmetry.
But BD simulations has given a good account of the conductance data.