POTASSIUM-DEPENDENT MOLECULES 227
should be accessible from the membrane ’ s exterior, while glu28, asp72 and
glu93 should be accessible from inside the membrane for all conformations
(see Figure 5.4 ). In these models, KvAP arginine residues that will interact
with the acidic residues are numberedR1 (arg117), R2 (arg 120), R3 (arg123),
R4 (arg126), R6 (arg133), and R7 (lys136). R5 is not included because KvAP
has no charged residue at this position. The comparable positions in the Shaker
protein would beR1 (arg362), R2 (arg365), R3 (arg368), R4 (arg371), R5
(lys374), R6 (arg377), and R7 (lys380). In the fi rst model — pore open — R1 and
R2 reside in the external aqueous phase, R3 is exposed but near E3b, R4 is
nearE1b, R6 salt bridges to D2a , and K7 is near D2b. Now the helical screw
model comes into play as one inward helical screw step translates the S4 helix
by∼ 4.5 Å further into the membrane and rotates it ∼ 60 ° about its axis. (See
the movie and Figure 4 of reference 36.) After two helical screw steps the
following interactions occur: R1 - E3b, R2 - E1b, R3 - D2a, R4 - E3a, R6 - D2b , and
K7 - E1a. The pattern results in the positively charged S4 residues remaining in
the core of the voltage sensor domain where continued interaction with the
electronegative core residues lowers the electrostatic barrier to the movement
and allows the arginine residues to remain protonated and to carry the positive
gating charge through the membrane. Two more helical screw steps move S4
toward the intracellular side of the membrane as the resting state (pore closed)
confi guration is achieved. The transition states are not meant to be energy -
minimized conformations but rather possible steps along a continuum.
To carry their model further, Guy and co - workers now docked the voltage
sensor domain with the ion conduction pore domain forming a covalent linkage
between S4 and S5 through the S4 – S5 linker (Loop 4 – 5). The pore forming
domain from the X - ray crystallographic structure of the full - length KvAP
channel (PDB: 1ORQ) was used for the open conformation. Modeling for the
closed conformations of KvAP were taken from the KcsA structure (PDB:
1BL8). It was assumed that interactions between S4 and the pore - forming
domain for KvAP would be similar to those for the Shaker protein, as experi-
mental results exist for Shaker. The experimental results indicate that interact-
ing residues between domains are more likely to be conserved among different
proteins than those exposed to lipid. These are the same concepts discussed
in determining tolerant versus nontolerant residues in the reference 28 model
discussed above. Experiments indicate that the voltage sensor domain docks
on the pore - forming domain so that water - fi lled crevasses or clefts around the
central barrier (crossing point of S4 and S2 helices in the sensor domain) form
between the two domains. The conclusion from many such experiments pre-
dicts that the voltage sensor domain X - ray structure (PDB: 1ORS) shows this
domain in a native conformation. The open conformation PDB: 1ORS domain
was docked with the open conformation pore - forming domain so that con-
served residues interacted to the maximum amount and in a manner consistent
with the experimental studies on Shaker channels. The docking arrangement
caused residues near the S4 helix ’ N - terminal end to interact with residues in
the C - terminal end of the S5 helix of an adjacent tetramer subunit. The authors