Biomedical Engineering Reference
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Fig. 6.8 (a) Structure of wild type SNase with basic (positive at pH 7.8) residues labeled
dark
and
acidic (negative at pH 7.8) residues labeled
light grey
.(b) Electrostatic contribution to transloca-
tion potential for several mutants of SNase at pH 7.8 illustrating how sequence can change the
location, number, and depth of electrostatic barriers. (c) Future nanopore measurement with
improved signal to noise ratio would allow of distinguishing single site mutant proteins
the barriers present during translocation. The linear translocation of seven selected
SNase mutants in a nanopore at pH. 7.8 (Fig.
6.8b
) shows their electrical potential
profiles vary significantly. The potential well depth or barrier height could vary by a
factor of 5 between the SNase mutants.
Varying the electrostatic potential allows changing the electrical potential barrier
height
DU
{
values systematically. Systematically changing the electrical potential
barrier height
DU
{
values will change the protein dwell time t
d
in a pore as described
in Eq. (6.5). Our data analysis tools have enabled us to predict a 2Dmap of stall point
volumes (
L
AA
) vs. time durations (
t
d
) shown in Fig.
6.8c
from a future nanopore
measurement of these SNase mutant proteins.
A 2D map illustrated in Fig.
6.8c
, in principle, would be able to detect single
site or multi-site mutants. Furthermore, a 2D map of excluded volume (
DI
b
)
and time duration (
t
d
) measured under different pH and voltage could allow
identification and resolution of proteins.
L
or
6.8.2 Open Challenges
Several challenges must be overcome to make the 2D map in Fig.
6.8c
become a
reality. One of such challenges is to find the correlation between protein primary
charge sequence and the dwell time or the theoretical connection between the
measured distributions of translocation times with the sequence and structural
properties of the proteins.
At the present time, a quantitative theory for phenomenon of protein dwell
time in a nanopore is not available and systematic studies of the sequence and
condition effects on protein translocation are almost non-existent. As a result, a full
explanation of the dwell time distribution remains an unsolved problem.
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