Biomedical Engineering Reference
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quantitatively with the volume calculated at the stall points for the
b
GLa and HPr
in Fig.
6.5d
(right axis). The broader distribution of
LGa is likely caused
by contributions from the translocation of looped configurations due to the
presence of disulfide bonds in
DI
b
for
b
b
LGa [
35
].
6.5.3 Parameters Affecting the Linear Translocation Potential
The net charge profile
Q
AA
is not only a function of protein primary charge
sequence, it also depends on the nanopore effective length
H
eff
and solution pH
as illustrated in Fig.
6.6
. Changing the thickness of the pore changes the length of
the segment of the unfolded protein that is exposed to the nanopore environment.
The translocation potential changes significantly with pore thickness because of the
changes in coarse grain sampling of the local structure. In this case, changing the
pore thickness will change the presence or absence of stall points. In the limit of
thick pores,
l
m
< H
eff
, there will be no stall points.
Varying solution pH systematically changes the charge sequence of the same
protein to vary the electrostatic translocation potential. Changing the pH alters the
number, depth, and location of stall points along the polypeptide chain as shown in
Fig.
6.6b
for bacterial
L
-lactate dehydrogenase.
In addition, the depth of the potential well
DU
{
is deeper or the barrier height is
larger at a higher voltage. This analysis implies the linear translocation potential
profile depends on the protein charge sequence, nanopore thickness, solution pH,
and applied voltage.
Fig. 6.6 Nanopore length
H
eff
and solution pH effects on translocation potential profile:
(a) translocation potential profile at four different pore thicknesses (
H
eff
5, 10, 20, 30 nm) for
ferritin heavy chain (PDB file:
2Z6M, 176 aa
). (b) The predicted potentials for linear translocation
of bacterial
L
-lactate dehydrogenase (PDB file:
1LLD, 319 aa
) through a 10 nm pore at pH
¼
¼
5.0,
6.0, 7.0, and 10.5 as labeled in the figure
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