61 research outputs found
A Theoretical Model for the Mechanical Unfolding of Repeat Proteins
AbstractWe consider the mechanical stretching of a polypeptide chain formed by multiple interacting repeats. The folding thermodynamics and the interactions among the repeats are described by the Ising model. Unfolded repeats act as soft entropic springs, whereas folded repeats respond to a force as stiffer springs. We show that the resulting force-extension curve may exhibit a pronounced force maximum corresponding to the unfolding of the first repeat. This event is followed by the unfolding of the remaining repeats, which takes place at a lower force. As the protein extension is increased, the force-extension curve of a sufficiently long repeat protein displays a plateau, where the force remains nearly constant and the protein unfolds sequentially so that the number of unfolded repeats is proportional to the extension. Such a sequential mechanical unfolding mechanism is displayed even by the repeat proteins whose thermal denaturation is highly cooperative, provided that they are long enough. By contrast, the unfolding of short repeat progressions can be cooperative
A Kinetic Model for the Enzymatic Action of Cellulase
We develop a mechanochemical model for the dynamics of cellulase, a two-domain enzyme connected by a peptide linker, as it extracts and hydrolyzes a cellulose polymer from a crystalline substrate. We consider two random walkers, representing the catalytic domain (CD) and the carbohydrate binding module (CBM), whose rates for stepping are biased by the coupling through the linker and the energy required to lift the cellulose polymer from the crystalline surface. Our results show that the linker length and stiffness play a critical role in the cooperative action of the CD and CBM domains and that, for a given linker length, the steady-state hydrolysis shows a maximum at some intermediate linker stiffness. The maximum hydrolysis rate corresponds to a transition of the linker from a compressed to an extended conformation, where the system exhibits maximum fluctuation, as measured by the variance of the separation distance between the two domains and the dispersion around the mean hydrolysis speed. In the range of experimentally known values of the parameters of our model, improving the intrinsic hydrolytic activity of the CD leads to a proportional increase in the overall hydrolysis rate
Nonequilibrium statistical mechanics of money/energy exchange models
Many-body dynamical models in which Boltzmann statistics can be derived
directly from the underlying dynamical laws without invoking the fundamental
postulates of statistical mechanics are scarce. Interestingly, one such model
is found in econophysics and in chemistry classrooms: the money game, in which
players exchange money randomly in a process that resembles elastic
intermolecular collisions in a gas, giving rise to the Boltzmann distribution
of money owned by each player. Although this model offers a pedagogical example
that demonstrates the origins of Boltzmann statistics, such demonstrations
usually rely on computer simulations - a proof of the exponential steady-state
distribution in this model has only become available in recent years. Here, we
study this random money/energy exchange model, and its extensions, using a
simple mean-field-type approach that examines the properties of the
one-dimensional random walk performed by one of its participants. We give a
simple derivation of the Boltzmann steady-state distribution in this model.
Breaking the time-reversal symmetry of the game by modifying its rules results
in non-Boltzmann steady-state statistics. In particular, introducing "unfair"
exchange rules in which a poorer player is more likely to give money to a
richer player than to receive money from that richer player, results in an
analytically provable Pareto-type power-law distribution of the money in the
limit where the number of players is infinite, with a finite fraction of
players in the "ground state" (i.e., with zero money). For a finite number of
players, however, the game may give rise to a bimodal distribution of money and
to bistable dynamics, in which a participant's wealth jumps between poor and
rich states. The latter corresponds to a scenario where the player accumulates
nearly all the available money in the game
Theoretical studies of the kinetics of mechanical unfolding of cross-linked polymer chains and their implications for single molecule pulling experiments
We have used kinetic Monte Carlo simulations to study the kinetics of
unfolding of cross-linked polymer chains under mechanical loading. As the ends
of a chain are pulled apart, the force transmitted by each crosslink increases
until it ruptures. The stochastic crosslink rupture process is assumed to be
governed by first order kinetics with a rate that depends exponentially on the
transmitted force. We have performed random searches to identify optimal
crosslink configurations whose unfolding requires a large applied force
(measure of strength) and/or large dissipated energy (measure of toughness). We
found that such optimal chains always involve cross-links arranged to form
parallel strands. The location of those optimal strands generally depends on
the loading rate. Optimal chains with a small number of cross-links were found
to be almost as strong and tough as optimal chains with a large number of
cross-links. Furthermore, optimality of chains with a small number of
cross-links can be easily destroyed by adding cross-links at random. The
present findings are relevant for the interpretation of single molecule force
probe spectroscopy studies of the mechanical unfolding of load-bearing
proteins, whose native topology often involves parallel strand arrangements
similar to the optimal configurations identified in the study
Preface: Special Topic on Single-Molecule Biophysics
Single-molecule measurements are now almost routinely used to study biological systems and processes. The scope of this special topic emphasizes the physics side of single-molecule observations, with the goal of highlighting new developments in physical techniques as well as conceptual insights that single-molecule measurements bring to biophysics. This issue also comprises recent advances in theoretical physical models of single-molecule phenomena, interpretation of single-molecule signals, and fundamental areas of statistical mechanics that are related to single-molecule observations. A particular goal is to illustrate the increasing synergy between theory, simulation, and experiment in single-molecule biophysics
Two-dimensional fluorescence resonance energy transfer as a probe for protein folding: A theoretical study
We describe a two-dimensional (2D), four-color fluorescence resonance energy transfer (FRET) scheme, in which the conformational dynamics of a protein is followed by simultaneously observing the FRET signal from two different donor-acceptor pairs. For a general class of models that assume Markovian conformational dynamics, we relate the properties of the emission correlation functions to the rates of elementary kinetic steps in the model. We further use a toy folding model that treats proteins as chains with breakable cross-links to examine the relationship between the cooperativity of folding and FRET data and to establish what additional information about the folding dynamics can be gleaned from 2D, as opposed to one-dimensional FRET experiments. We finally discuss the potential advantages of the four-color FRET over the three-color FRET technique
Transition path dynamics of a nanoparticle in a bistable optical trap
Many processes in chemistry, physics, and biology involve rare events in
which the system escapes from a metastable state by surmounting an activation
barrier. Examples range from chemical reactions, protein folding, and
nucleation events to the catastrophic failure of bridges. A challenge in
understanding the underlying mechanisms is that the most interesting
information is contained within the rare transition paths, the exceedingly
short periods when the barrier is crossed. To establish a model process that
enables access to all relevant timescales, although highly disparate, we probe
the dynamics of single dielectric particles in a bistable optical trap in
solution. Precise localization by high-speed tracking enables us to resolve the
transition paths and relate them to the detailed properties of the 3D potential
within which the particle diffuses. By varying the barrier height and shape,
the experiments provide a stringent benchmark of current theories of transition
path dynamics
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