128 research outputs found
Statistics of reversible bond dynamics observed in force-clamp spectroscopy
We present a detailed analysis of two-state trajectories obtained from
force-clamp spectroscopy (FCS) of reversibly bonded systems. FCS offers the
unique possibility to vary the equilibrium constant in two-state kinetics, for
instance the unfolding and refolding of biomolecules, over many orders of
magnitude due to the force dependency of the respective rates. We discuss two
different kinds of counting statistics, the event-counting usually employed in
the statistical analysis of two-state kinetics and additionally the so-called
cycle-counting. While in the former case all transitions are counted,
cycle-counting means that we focus on one type of transitions. This might be
advantageous in particular if the equilibrium constant is much larger or much
smaller than unity because in these situations the temporal resolution of the
experimental setup might not allow to capture all transitions of an
event-counting analysis. We discuss how an analysis of FCS data for complex
systems exhibiting dynamic disorder might be performed yielding information
about the detailed force-dependence of the transition rates and about the time
scale of the dynamic disorder. In addition, the question as to which extent the
kinetic scheme can be viewed as a Markovian two-state model is discussed.Comment: 25 pages, 10 figures, Phys. Rev. E, in pres
Force-clamp spectroscopy of reversible bond breakage
We consider reversible breaking of adhesion bonds or folding of proteins
under the influence of a constant external force. We discuss the stochastic
properties of the unbinding/rebinding events and analyze their mean number and
their variance in the framework of simple two-state models. In the
calculations, we exploit the analogy to single molecule fluorescence and
particularly between unbinding/rebinding and photon emission events.
Environmental fluctuation models are used to describe deviations from Markovian
behavior. The second moment of the event-number distribution is found to be
very sensitive to possible exchange processes and can thus be used to identify
temporal fluctuations of the transition rates.Comment: 8 pages, 4 figure
Dynamic force spectroscopy: analysis of reversible bond-breaking dynamics
The problem of diffusive bond-dissociation in a double well potential under
application of an external force is scrutinized. We compute the probability
distribution of rupture forces and present a detailed discussion of the
influence of finite rebinding probabilities on the dynamic force spectrum. In
particular, we focus on barrier crossing upon extension, i.e. under linearly
increased load, and upon relaxation starting from completely separated bonds.
For large loading rates the rupture force and the rejoining force depend on the
loading rate in the expected manner determined by the shape of the potential.
For small loading rates the mean forces obtained from pull and relax modes
approach each other as the system reaches equilibrium. We investigate the
dependence of the rupture force distributions and mean rupture forces on
external parameters like cantilever stiffness and influence of a soft linker.
We find that depending on the implementation of a soft linker the equilibrium
rupture force is either unaffected by the presence of the linker or changes in
a predictable way with the linker-compliance. Additionally, we show that it is
possible to extract the equilibrium constant of the on- and off-rates from the
determination of the equilibrium rupture forces.Comment: 32 pages, 14 figure
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Hydrophobic mismatch sorts SNARE proteins into distinct membrane domains
The clustering of proteins and lipids in distinct microdomains is emerging as an important principle for the spatial patterning of biological membranes. Such domain formation can be the result of hydrophobic and ionic interactions with membrane lipids as well as of specific proteinâprotein interactions. Here using plasma membrane-resident SNARE proteins as model, we show that hydrophobic mismatch between the length of transmembrane domains (TMDs) and the thickness of the lipid membrane suffices to induce clustering of proteins. Even when the TMDs differ in length by only a single residue, hydrophobic mismatch can segregate structurally closely homologous membrane proteins in distinct membrane domains. Domain formation is further fine-tuned by interactions with polyanionic phosphoinositides and homo and heterotypic protein interactions. Our findings demonstrate that hydrophobic mismatch contributes to the structural organization of membranes
Size Matters: Problems and Advantages Associated with Highly Miniaturized Sensors
There is no doubt that the recent advances in nanotechnology have made it possible to realize a great variety of new sensors with signal transduction mechanisms utilizing physical phenomena at the nanoscale. Some examples are conductivity measurements in nanowires, deflection of cantilevers and spectroscopy of plasmonic nanoparticles. The fact that these techniques are based on the special properties of nanostructural entities provides for extreme sensor miniaturization since a single structural unit often can be used as transducer. This review discusses the advantages and problems with such small sensors, with focus on biosensing applications and label-free real-time analysis of liquid samples. Many aspects of sensor design are considered, such as thermodynamic and diffusion aspects on binding kinetics as well as multiplexing and noise issues. Still, all issues discussed are generic in the sense that the conclusions apply to practically all types of surface sensitive techniques. As a counterweight to the current research trend, it is argued that in many real world applications, better performance is achieved if the active sensor is larger than that in typical nanosensors. Although there are certain specific sensing applications where nanoscale transducers are necessary, it is argued herein that this represents a relatively rare situation. Instead, it is suggested that sensing on the microscale often offers a good compromise between utilizing some possible advantages of miniaturization while avoiding the complications. This means that ensemble measurements on multiple nanoscale sensors are preferable instead of utilizing a single transducer entity
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