Page 34 - YORAM RUDY BOOK FINAL

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When paced at slow rate (CL=4000ms) with I block, Pcell develops EADs. Interestingly, the
Kr
simulations (see reference ) show that the ionic mechanism of EAD formation is different in Pcell
93
from that in Vcell. As shown earlier, recovery and reactivation of I CaL underlies EAD formation in
Vcell. In Pcell EAD generation is mostly attributable to reactivation of I NaL2 (type 2 component
of I NaL ).

2.8. Structure – Function Relationship of an Ion Channel During Gating

Reductionist Approach at the Molecular Scale

Markov models of ion channels represent kinetic states of the channel and reproduce
the kinetics of channel opening and closing. However, the structural molecular conformations
represented by the Markov model states are not identified. A Markov scheme is not a unique
model of the channel function and different schemes that fit the same experimental data can

be interpreted differently in terms of underlying gating mechanisms. To overcome this
limitation, and relate explicitly molecular structure and channel function, a multiscale
computational approach that combines molecular dynamics and continuum electrostatics was

introduced and applied to link KCNQ1 and I movement during gating to the ionic current they
Ks
generate and to the cardiac action potential. A molecular model of KCNQ1 is constructed by
101
aligning the KCNQ1 sequence with K 1.2 and using the known crystal structure of K 1.2 (in the open
v v
state) as a template (Figure 2.20A). This homology-based model is then refined by minimizing
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an objective function that accounts for this alignment, as well as van der Waals forces, dihedral

angles, bond lengths and torsions, and Coulombic interactions, using the computer software
Modeller . As shown in Figure 2.20A, there is good agreement between KCNQ1 and K 1.2 with
103
v
respect to position of charged residues. Further refinement of the model is done with molecular
dynamics simulations (using the NAMD simulation package) to include lipid and water mole-
104
cules surrounding the channel protein (Figure 2.20B, C).

The voltage-sensing region of each of the four KCNQ1 channel subunits includes the
transmembrane segments S1-S4 (Figure 2.20B-D). S4 contains a series of positively charged

residues (R1-R6) that interact with negatively charged residues on S2 and S3 (see Figure 2.20F,
top). During channel gating, S4 moves up and down through the membrane approximately 12
Angstrom 105,106 (up towards the extracellular space during activation and down toward the

intracellular space during channel closing) and rotates about its axis (a simplifying assumption
is made that S4 remains rigid and that other helices do not move). The simulated movement
(translation and rotation) of S4 is shown in Figure 2.20D. During this movement, positive charges
on S4 interact with different negative charges on S2 and S3, generating an electrostatic energy at
each protein conformation that can be computed using the Poisson-Boltzmann equation. 107,108,109

As an approximation, other forces (van der Waals force, bending and twisting of residues into
favorable and unfavorable conformations) are not considered.