195,465 research outputs found
On the form of growing strings
Patterns and forms adopted by Nature, such as the shape of living cells, the
geometry of shells and the branched structure of plants, are often the result
of simple dynamical paradigms. Here we show that a growing self-interacting
string attached to a tracking origin, modeled to resemble nascent polypeptides
in vivo, develops helical structures which are more pronounced at the growing
end. We also show that the dynamic growth ensemble shares several features of
an equilibrium ensemble in which the growing end of the polymer is under an
effective stretching force. A statistical analysis of native states of proteins
shows that the signature of this non-equilibrium phenomenon has been fixed by
evolution at the C-terminus, the growing end of a nascent protein. These
findings suggest that a generic non-equilibrium growth process might have
provided an additional evolutionary advantage for nascent proteins by favoring
the preferential selection of helical structures.Comment: 4 pages, 3 figures. Accepted for publication in Phys. Rev. Let
Determination of protein binding affinities within hydrogel-based molecularly imprinted polymers (HydroMIPs)
Hydrogel-based molecularly imprinted polymers (HydroMIPs) were prepared for several proteins (haemoglobin, myoglobin and catalase) using a family of acrylamide-based monomers. Protein affinity towards the HydroMIPs was investigated under equilibrium conditions and over a range of concentrations using specific binding with Hill slope saturation profiles. We report HydroMIP binding affinities, in terms of equilibrium dissociation constants (Kd) within the micro-molar range (25 ± 4 mM, 44 ± 3 mM, 17 ± 2 mM for haemoglobin, myoglobin and catalase respectively within a polyacrylamide-based MIP). The extent of non-specific binding or cross-selectivity for non-target proteins has also been assessed. It is concluded that both selectivity and affinity for both cognate and non-cognate proteins towards the MIPs were dependent on the concentration and the complementarity of their structures and size. This is tentatively attributed to the formation of protein complexes during both the polymerisation and rebinding stages at high protein concentrations. We have used atomic force spectroscopy to characterize molecular interactions in the MIP cavities using protein-modified AFM tips. Attractive and repulsive force curves were obtained for the MIP and NIP (non-imprinted polymer) surfaces (under protein loaded or unloaded states). Our force data suggest that we have produced selective cavities for the template protein in the MIPs and we have been able to quantify the extent of non-specific protein binding on, for example, a non-imprinted polymer (NIP) control surface
Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation
Gene expression is controlled primarily by interactions between transcription
factor proteins (TFs) and the regulatory DNA sequence, a process that can be
captured well by thermodynamic models of regulation. These models, however,
neglect regulatory crosstalk: the possibility that non-cognate TFs could
initiate transcription, with potentially disastrous effects for the cell. Here
we estimate the importance of crosstalk, suggest that its avoidance strongly
constrains equilibrium models of TF binding, and propose an alternative
non-equilibrium scheme that implements kinetic proofreading to suppress
erroneous initiation. This proposal is consistent with the observed covalent
modifications of the transcriptional apparatus and would predict increased
noise in gene expression as a tradeoff for improved specificity. Using
information theory, we quantify this tradeoff to find when optimal proofreading
architectures are favored over their equilibrium counterparts.Comment: 5 pages, 3 figure
Reliable protein folding on non-funneled energy landscapes: the free energy reaction path
A theoretical framework is developed to study the dynamics of protein
folding. The key insight is that the search for the native protein conformation
is influenced by the rate r at which external parameters, such as temperature,
chemical denaturant or pH, are adjusted to induce folding. A theory based on
this insight predicts that (1) proteins with non-funneled energy landscapes can
fold reliably to their native state, (2) reliable folding can occur as an
equilibrium or out-of-equilibrium process, and (3) reliable folding only occurs
when the rate r is below a limiting value, which can be calculated from
measurements of the free energy. We test these predictions against numerical
simulations of model proteins with a single energy scale.Comment: 13 pages, 9 figure
Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise
The Jarzynski equality and the fluctuation theorem relate equilibrium free
energy differences to non-equilibrium measurements of the work. These relations
extend to single-molecule experiments that have probed the finite-time
thermodynamics of proteins and nucleic acids. The effects of experimental error
and instrument noise have not previously been considered. Here, we present a
Bayesian formalism for estimating free-energy changes from non-equilibrium work
measurements that compensates for instrument noise and combines data from
multiple driving protocols. We reanalyze a recent set of experiments in which a
single RNA hairpin is unfolded and refolded using optical tweezers at three
different rates. Interestingly, the fastest and farthest-from-equilibrium
measurements contain the least instrumental noise, and therefore provide a more
accurate estimate of the free energies than a few slow, more noisy,
near-equilibrium measurements. The methods we propose here will extend the
scope of single-molecule experiments; they can be used in the analysis of data
from measurements with AFM, optical, and magnetic tweezers.Comment: 8 page
Thermodynamic bounds on the ultra- and infra-affinity of Hsp70 for its substrates
The 70 kDa Heat Shock Proteins Hsp70 have several essential functions in
living systems, such as protecting cells against protein aggregation, assisting
protein folding, remodeling protein complexes and driving the translocation
into organelles. These functions require high affinity for non-specific
amino-acid sequences that are ubiquitous in proteins. It has been recently
shown that this high affinity, called ultra-affinity, depends on a process
driven out of equilibrium by ATP hydrolysis. Here we establish the
thermodynamic bounds for ultra-affinity, and further show that the same
reaction scheme can in principle be used both to strengthen and to weaken
affinities (leading in this case to infra-affinity). We show that cofactors are
essential to achieve affinity beyond the equilibrium range. Finally, biological
implications are discussed.Comment: 14 pages, 5 figure
Dynamical phase transition of a periodically driven DNA
Replication and transcription are two important processes in living systems.
To execute such processes, various proteins work far away from equilibrium in a
staggered way. Motivated by this, aspects of hysteresis during unzipping of DNA
under a periodic drive in non-equilibrium conditions are studied. A steady
state phase diagram of a driven DNA is proposed which is experimentally
verifiable. As a two state system, we also compare the results of DNA with that
of an Ising magnet under an asymmetrical variation of magnetic field.Comment: 8 pages, 6 figures, Accepted version in PR
Characterization of the low temperature properties of a simplified protein model
Prompted by results that showed that a simple protein model, the frustrated
G\=o model, appears to exhibit a transition reminiscent of the protein
dynamical transition, we examine the validity of this model to describe the
low-temperature properties of proteins. First, we examine equilibrium
fluctuations. We calculate its incoherent neutron-scattering structure factor
and show that it can be well described by a theory using the one-phonon
approximation. By performing an inherent structure analysis, we assess the
transitions among energy states at low temperatures. Then, we examine
non-equilibrium fluctuations after a sudden cooling of the protein. We
investigate the violation of the fluctuation--dissipation theorem in order to
analyze the protein glass transition. We find that the effective temperature of
the quenched protein deviates from the temperature of the thermostat, however
it relaxes towards the actual temperature with an Arrhenius behavior as the
waiting time increases. These results of the equilibrium and non-equilibrium
studies converge to the conclusion that the apparent dynamical transition of
this coarse-grained model cannot be attributed to a glassy behavior
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