Biomedical Engineering Reference
In-Depth Information
silico mutagenesis of the influential residue (Leu118) to a negative charge residue
(glutamate or aspartate) and positive charge residue (lysine or arginine) was
undertaken, with production MD simulations performed for 10 ns. The conforma-
tional changes in the binding pocket we investigated by taking a set of snapshots
from each trajectory, with the re-docking of the agonist. The wild-type, L118E and
L118D bound acetylcholine, however L118K and L118R did not.
The blocking process leads the ion channel to undergo a large conformational
change. MD simulations have been used to assess the transition path between open
and resting (close) state. The mammalian voltage-gated potassium channel Kv1.5
has a specific region that controls the open and close states, that is the ProValPro-
type and Gly-type of bending hinge. A combination of homology, docking and
MD simulations revealed that the blocker, R(+)-bupivacaine, selectively binds to
the open-state of Kv1.5, for the K
+
ion occupancy state 0101, inside the pore at
the ProValPro-type of bending hinge [
42
]. MD simulations also suggested that the
ProValPro-bend appeared much more flexible than the Gly-bend, however, the
open-state channel cannot turn to the close-state with bupivacaine bound. Important
residues in the Kv1.5 for ligand recognition are hydrophobic amino residues;
Val505, Ile508, Val512, and Val516 [
45
].
Almost blockers bind at the C-loop region of nicotinic acetylcholine receptor
(nAChR) where the C-loop plays as the flexible gate outside the pore. The C-loop is
known to have high flexibility and distinguished from other. The dynamics of
C-loop region were captured within 5 ns of MD simulations in acetylcholine
binding protein (AChBP) representing the nAChR. The C-loop has less movement
when blockers bind inside the pocket, especially blockers contained aromatic sub-
stituents, which can form the cage stabilized in the C-loop region [
49
]. MD simu-
lations also demonstrated that transition motion in gating of nAChR depend on the
tilting of the M2 helices [
77
]. Selective binding of the blockers is supported by
kinetics experiment when imipramine binds to the desensitized state of Torpedo
AChR about fivefold higher affinity than the resting state [
40
]. Although some part
of the channel shows high flexibility, there needs to be a very stable part also.
Comparison of the stable and deformation of ligand binding domain (LBD) in
Glycine receptor (GlyR), which is similar to the nAChR, from 500 ps MD
simulations indicated fairly similar structure. This suggested that the
b
-sandwich
core is relatively inflexible [
78
].
3.3 MD Simulation Protocols
Simulation results that provided an insight into the dynamics and other properties of
the system depend on how well the initial models were generated and the choice of
simulation protocol, which can be varied from each specific system. In this section,
we review recent MD methodology applied on ion channel and blockers.
Partial atomic charge and force field parameters must first be assigned to a ligand
[
45
]. Prior to the initial model, specific known state maybe loaded by carefully
