Biomedical Engineering Reference
In-Depth Information
development in the pharmaceutical industry to the fundamental sciences for
providing an understanding of protein structure-function relationships.
The field of nanopore science is relatively new, especially in regard to the
detection of single proteins. As the field progresses, we envision a shift from simply
detecting single proteins to the development of functional protein assays. Further-
more, as many researchers pursue the use of nanopores for sequencing DNA and
RNA, it is possible that nanopores will be used in a similar manner to probe the
amino acid sequence of proteins. It is in this context, that we review progress in
characterizing the function of proteins with nanopores.
9.2 Characterizing the Size, Charge, and Conformation
of Proteins from Nanopore Recordings
A series of recent reports have demonstrated the use of nanopores for determining
basic characteristics of proteins such as size, charge, and conformation. Here we
describe the details of sensing proteins in nanopores and of these reports.
9.2.1 Determining the Size of Proteins with Nanopores
The amplitude of the current fluctuations due to protein translocation through
a nanopore is directly proportional to the volume of the protein given that the
protein has roughly a spherical shape [
11
,
13
,
16
,
40
]. The underlying physical
model that relates protein size to the amplitude of these current fluctuations was
derived by Maxwell [
31
] and later improved by DeBlois and Bean in 1970 [
11
].
Based on their findings, the passage of a spherical particle through a
cylindrical
nanopore reduces the current through the pore in a time dependent fasion,
DI
(
t
), that
is directly proportional to the conducting volume excluded by the protein,
LðtÞ
:
DIðtÞ¼
s
E
l
p
d
m
d
p
;
l
m
l
p
LðtÞ
1
þ f
;
(9.1)
m
1
)isthe
conductivity of the solution,
E
(V) is the voltage drop across the nanopore, and
l
p
(m) is
the length of the nanopore. A dimensionless correction factor,
f
, can account for
deviations when the diameter of the molecule,
d
m
, is similar to the diameter of the
pore,
d
p
, or the length of the molecule,
l
m
, is similar to length of the pore,
l
p
. This
f
factor is described in greater detail in DeBlois and Bean; under most experimental
conditions it can be neglected [
11
]. In addition, when
l
p
is comparable to
d
p
,theterm
l
p
should be substituted for (
l
p
+0.8
(m
3
) is approximately equal to the volume of the protein,
O
1
where
L
s
(
d
p
) to account for the access resistance of the pore
(access resistance results from electric field lines converging from the bulk solution to
the opening of nanopores) [
17
]. Finally, it should be noted that machined nanopores
are not perfectly cylindrical. Equation (
9.1
) is, however, suitable for estimating
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