6 research outputs found
Visualization 1.mp4
Manipulation of a microbubble between two horizontally opposed optical fibers due to the switching of the temperature gradient
Carbohydrate Affinity for the Glucose–Galactose Binding Protein Is Regulated by Allosteric Domain Motions
Protein function, structure, and dynamics are intricately
correlated,
but studies on structure–activity relationships are still only
rarely complemented by a detailed analysis of dynamics related to
function (functional dynamics). Here, we have applied NMR to investigate
the functional dynamics in two homologous periplasmic sugar binding
proteins with bidomain composition: <i>Escherichia coli</i> glucose/galactose (GGBP) and ribose (RBP) binding proteins. In contrast
to their structural and functional similarity, we observe a remarkable
difference in functional dynamics: For RBP, the absence of segmental
motions allows only for isolated structural adaptations upon carbohydrate
binding in line with an <i>induced fit</i> mechanism; on
the other hand, GGBP shows extensive segmental mobility in both <i>apo</i> and <i>holo</i> states, enabling selection
of the most favorable conformation upon carbohydrate binding in line
with a <i>population shift</i> mechanism. Collective segmental
motions are controlled by the hinge composition: by swapping two identified
key residues between RBP and GGBP we also interchange their segmental
hinge mobility, and the doubly mutated GGBP* no longer experiences
changes in conformational entropy upon ligand binding while the complementary
RBP* shows the segmental dynamics observed in wild-type GGBP. Most
importantly, the segmental interdomain dynamics always increase the
apparent substrate affinity and thus, are functional, underscoring
the allosteric control that the hinge region exerts on ligand binding
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Calibration-Free Electrochemical Biosensors Supporting Accurate Molecular Measurements Directly in Undiluted Whole Blood
The
need to calibrate to correct for sensor-to-sensor fabrication
variation and sensor drift has proven a significant hurdle in the
widespread use of biosensors. To maintain clinically relevant (±20%
for this application) accuracy, for example, commercial continuous
glucose monitors require recalibration several times a day, decreasing
convenience and increasing the chance of user errors. Here, however,
we demonstrate a “dual-frequency” approach for achieving
the calibration-free operation of electrochemical biosensors that
generate an output by using square-wave voltammetry to monitor binding-induced
changes in electron transfer kinetics. Specifically, we use the square-wave
frequency dependence of their response to produce a ratiometric signal,
the ratio of peak currents collected at responsive and non- (or low)
responsive square-wave frequencies, which is largely insensitive to
drift and sensor-to-sensor fabrication variations. Using electrochemical
aptamer-based (E-AB) biosensors as our test bed, we demonstrate the
accurate and precise operation of sensors against multiple drugs,
achieving accuracy in the measurement of their targets of within better
than 20% across dynamic ranges of up to 2 orders of magnitude without
the need to calibrate each individual sensor
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Simulation-Based Approach to Determining Electron Transfer Rates Using Square-Wave Voltammetry
The
efficiency with which square-wave voltammetry differentiates
faradic and charging currents makes it a particularly sensitive electroanalytical
approach, as evidenced by its ability to measure nanomolar or even
picomolar concentrations of electroactive analytes. Because of the
relative complexity of the potential sweep it uses, however, the extraction
of detailed kinetic and mechanistic information from square-wave data
remains challenging. In response, we demonstrate here a numerical
approach by which square-wave data can be used to determine electron
transfer rates. Specifically, we have developed a numerical approach
in which we model the height and the shape of voltammograms collected
over a range of square-wave frequencies and amplitudes to simulated
voltammograms as functions of the heterogeneous rate constant and
the electron transfer coefficient. As validation of the approach,
we have used it to determine electron transfer kinetics in both freely
diffusing and diffusionless surface-tethered species, obtaining electron
transfer kinetics in all cases in good agreement with values derived
using non-square-wave methods
Subsecond-Resolved Molecular Measurements in the Living Body Using Chronoamperometrically Interrogated Aptamer-Based Sensors
Electrochemical,
aptamer-based (E-AB) sensors support the continuous,
real-time measurement of specific small molecules directly in situ
in the living body over the course of many hours. They achieve this
by employing binding-induced conformational changes to alter electron
transfer from a redox-reporter-modified, electrode-attached aptamer.
Previously we have used voltammetry (cyclic, alternating current,
and square wave) to monitor this binding-induced change in transfer
kinetics indirectly. Here, however, we demonstrate the potential advantages
of employing chronoamperometry to measure the change in kinetics directly.
In this approach target concentration is reported via changes in the
lifetime of the exponential current decay seen when the sensor is
subjected to a potential step. Because the lifetime of this decay
is independent of its amplitude (e.g., insensitive to variations in
the number of aptamer probes on the electrode), chronoamperometrically
interrogated E-AB sensors are calibration-free and resistant to drift.
Chronoamperometric measurements can also be performed in a few hundred
milliseconds, improving the previous few-second time resolution of
E-AB sensing by an order of magnitude. To illustrate the potential
value of the approach we demonstrate here the calibration-free measurement
of the drug tobramycin in situ in the living body with 300 ms time
resolution and unprecedented, few-percent precision in the determination
of its pharmacokinetic phases
Unraveling the Conformational Landscape of Ligand Binding to Glucose/Galactose-Binding Protein by Paramagnetic NMR and MD Simulations
Protein dynamics
related to function can nowadays be structurally
well characterized (i.e., instances obtained by high resolution structures),
but they are still ill-defined energetically, and the energy landscapes
are only accessible computationally. This is the case for glucose–galactose
binding protein (GGBP), where the crystal structures of the apo and
holo states provide structural information for the domain rearrangement
upon ligand binding, while the time scale and the energetic determinants
for such concerted dynamics have been so far elusive. Here, we use
GGBP as a paradigm to define a functional conformational landscape,
both structurally and energetically, by using an innovative combination
of paramagnetic NMR experiments and MD simulations. Anisotropic NMR
parameters induced by self-alignment of paramagnetic metal ions was
used to characterize the ensemble of conformations adopted by the
protein in solution while the rate of interconversion between conformations
was elucidated by long molecular dynamics simulation on two states
of GGBP, the closed-liganded (<i>holo_cl</i>) and open-unloaded
(<i>apo_op</i>) states. Our results demonstrate that, in
its apo state, the protein coexists between open-like (68%) and closed-like
(32%) conformations, with an exchange rate around 25 ns. Despite such
conformational heterogeneity, the presence of the ligand is the ultimate
driving force to unbalance the equilibrium toward the <i>holo_cl</i> form, in a mechanism largely governed by a conformational selection
mechanism