569 research outputs found
Jamming proteins with slipknots and their free energy landscape
Theoretical studies of stretching proteins with slipknots reveal a surprising
growth of their unfolding times when the stretching force crosses an
intermediate threshold. This behavior arises as a consequence of the existence
of alternative unfolding routes that are dominant at different force ranges.
Responsible for longer unfolding times at higher forces is the existence of an
intermediate, metastable configuration where the slipknot is jammed.
Simulations are performed with a coarsed grained model with further
quantification using a refined description of the geometry of the slipknots.
The simulation data is used to determine the free energy landscape (FEL) of the
protein, which supports recent analytical predictions.Comment: 5 page
Mean first passage time analysis reveals rate-limiting steps, parallel pathways and dead ends in a simple model of protein folding
We have analyzed dynamics on the complex free energy landscape of protein
folding in the FOLD-X model, by calculating for each state of the system the
mean first passage time to the folded state. The resulting kinetic map of the
folding process shows that it proceeds in jumps between well-defined, local
free energy minima. Closer analysis of the different local minima allows us to
reveal secondary, parallel pathways as well as dead ends.Comment: 7 page
Refolding dynamics of stretched biopolymers upon force quench
Single molecule force spectroscopy methods can be used to generate folding
trajectories of biopolymers from arbitrary regions of the folding landscape. We
illustrate the complexity of the folding kinetics and generic aspects of the
collapse of RNA and proteins upon force quench, using simulations of an RNA
hairpin and theory based on the de Gennes model for homopolymer collapse. The
folding time, , depends asymmetrically on and
where () is the stretch (quench) force, and
is the transition mid-force of the RNA hairpin. In accord with
experiments, the relaxation kinetics of the molecular extension, , occurs
in three stages: a rapid initial decrease in the extension is followed by a
plateau, and finally an abrupt reduction in that occurs as the native
state is approached.
The duration of the plateau increases as decreases
(where is the time in which the force is reduced from to ).
Variations in the mechanisms of force quench relaxation as is altered
are reflected in the experimentally measurable time-dependent entropy, which is
computed directly from the folding trajectories. An analytical solution of the
de Gennes model under tension reproduces the multistage stage kinetics in
. The prediction that the initial stages of collapse should also be a
generic feature of polymers is validated by simulation of the kinetics of
toroid (globule) formation in semiflexible (flexible) homopolymers in poor
solvents upon quenching the force from a fully stretched state. Our findings
give a unified explanation for multiple disparate experimental observations of
protein folding.Comment: 31 pages 11 figure
Single-molecule fluorescence studies of intrinsically disordered proteins and liquid phase separation
Intrinsically disordered proteins (IDPs) are ubiquitous in proteomes and serve in a range of cellular functions including signaling, regulation, transport and enzyme function. IDP misfunction and aggregation are also associated with several diseases including neurodegenerative diseases and cancer. During the past decade, single-molecule methods have become popular for detailed biophysical and structural studies of these complex proteins. This work has included recent applications to cellular liquid-liquid phase separation (LLPS), relevant for functional dynamics of membraneless organelles such as the nucleolus and stress granules. In this concise review, we cover the conceptual motivations for development and application of single-molecule fluorescence methods for such IDP studies. We follow with a few key examples of systems and biophysical problems that have been addressed, and conclude with thoughts for emerging and future directions
Picosecond fluctuating protein energy landscape mapped by pressure–temperature molecular dynamics simulation
Microscopic statistical pressure fluctuations can, in principle, lead to corresponding fluctuations in the shape of a protein energy landscape. To examine this, nanosecond molecular dynamics simulations of lysozyme are performed covering a range of temperatures and pressures. The well known dynamical transition with temperature is found to be pressure-independent, indicating that the effective energy barriers separating conformational substates are not significantly influenced by pressure. In contrast, vibrations within substates stiffen with pressure, due to increased curvature of the local harmonic potential in which the atoms vibrate. The application of pressure is also shown to selectively increase the damping of the anharmonic, low-frequency collective modes in the protein, leaving the more local modes relatively unaffected. The critical damping frequency, i.e., the frequency at which energy is most efficiently dissipated, increases linearly with pressure. The results suggest that an invariant description of protein energy landscapes should be subsumed by a fluctuating picture and that this may have repercussions in, for example, mechanisms of energy dissipation accompanying functional, structural, and chemical relaxation
Large phenotype jumps in biomolecular evolution
By defining the phenotype of a biopolymer by its active three-dimensional
shape, and its genotype by its primary sequence, we propose a model that
predicts and characterizes the statistical distribution of a population of
biopolymers with a specific phenotype, that originated from a given genotypic
sequence by a single mutational event. Depending on the ratio g0 that
characterizes the spread of potential energies of the mutated population with
respect to temperature, three different statistical regimes have been
identified. We suggest that biopolymers found in nature are in a critical
regime with g0 in the range 1-6, corresponding to a broad, but not too broad,
phenotypic distribution resembling a truncated Levy flight. Thus the biopolymer
phenotype can be considerably modified in just a few mutations. The proposed
model is in good agreement with the experimental distribution of activities
determined for a population of single mutants of a group I ribozyme.Comment: to appear in Phys. Rev. E; 7 pages, 6 figures; longer discussion in
VII, new fig.
Origins of Chevron Rollovers in Non-Two-State Protein Folding Kinetics
Chevron rollovers of some proteins imply that their logarithmic folding rates
are nonlinear in native stability. This is predicted by lattice and continuum
G\=o models to arise from diminished accessibilities of the ground state from
transiently populated compact conformations under strongly native conditions.
Despite these models' native-centric interactions, the slowdown is due partly
to kinetic trapping caused by some of the folding intermediates' nonnative
topologies. Notably, simple two-state folding kinetics of small single-domain
proteins are not reproduced by common G\=o-like schemes.Comment: 10 pages, 4 Postscript figures (will appear on PRL
Expression of PAFR as Part of a Prosurvival Response to Chemotherapy: A Novel Target for Combination Therapy in Melanoma
Melanoma cells express the platelet-activating factor receptor (PAFR) and, thus, respond to PAF, a bioactive lipid produced by both tumour cells and those in the tumour microenvironment such as macrophages. Here, we show that treatment of a human melanoma SKmel37 cell line with cisplatin led to increased expression of PAFR and its accumulation. In the presence of exogenous PAF, melanoma cells were significantly more resistant to cisplatin-induced cell death. Inhibition of PAFR-dependent signalling pathways by a PAFR antagonist (WEB2086) showed chemosensitisation of melanoma cells in vitro. Nude mice were inoculated with SKmel37 cells and treated with cisplatin and WEB2086. Animals treated with both agents showed significantly decreased tumour growth compared to the control group and groups treated with only one agent. PAFR accumulation and signalling are part of a prosurvival program of melanoma cells, therefore constituting a promising target for combination therapy for melanomas
Expression of PAFR as Part of a Prosurvival Response to Chemotherapy: A Novel Target for Combination Therapy in Melanoma
Melanoma cells express the platelet-activating factor receptor (PAFR) and, thus, respond to PAF, a bioactive lipid produced by both tumour cells and those in the tumour microenvironment such as macrophages. Here, we show that treatment of a human melanoma SKmel37 cell line with cisplatin led to increased expression of PAFR and its accumulation. In the presence of exogenous PAF, melanoma cells were significantly more resistant to cisplatin-induced cell death. Inhibition of PAFR-dependent signalling pathways by a PAFR antagonist (WEB2086) showed chemosensitisation of melanoma cells in vitro. Nude mice were inoculated with SKmel37 cells and treated with cisplatin and WEB2086. Animals treated with both agents showed significantly decreased tumour growth compared to the control group and groups treated with only one agent. PAFR accumulation and signalling are part of a prosurvival program of melanoma cells, therefore constituting a promising target for combination therapy for melanomas
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