Biomedical Engineering Reference
In-Depth Information
Fig. 6.1 (a) Schematic diagram of protein nanopore translocation experiment. (b) Illustration the
shapes of proteins and an unfolded protein translocation in a nanopore. (c) Several recorded
Laminin (L6274, Sigma-Aldrich) current blockage events in partially denatured condition (in
3 M Guanidine HCl at pH 7 and 1 M KCl). The insert is an illustrated structure of Laminin at its
native state (taken from
http://www.sigmaaldrich.com
). (d) The Ipoint histogram or the instanta-
neous time distribution of blockade current
DI
b
over all events
ionic current caused by the translocating protein is a time dependent quantity,
DI
b
(
t
). Separating the translocation-relative variability in
DI
b
(
t
) from the noise-
related variability in
DI
b
(
t
) is an ongoing challenge. In this chapter, we consider the
mean current blockage amplitude
DI
b
and the dwell time
t
d
while a protein molecule
stays in a nanopore.
6.1.4 Event Classification
Analysis of protein translocation current blockage events has been a challenging
task due to their complexity. For initial analysis of a data set, we usually first
generate the instantaneous time distribution of blockade current
DI
b
over all events
(Fig.
6.1d
), called
I
point
histogram [
16
]. The
I
point
histogram can help us to identify
possible peak values of
DI
b
that can be used to set a trigger line to classify events.
To classify events, a MATLAB based program has been developed. Using a trigger
line at approximately half the value of an interested peak, the MATLAB program
can select a group of events, calculate the mean blockage current
DI
b
and the time
duration
t
d
of each event. When the current,
I
(
t
), crosses the trigger line the event
is considered to start, and the event stops when the current crosses the trigger line
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