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Register a new userEquilibrium properties and force-driven unfolding pathways of RNA molecules
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The mechanical unfolding of a simple RNA hairpin and of a 236--bases portion of the Tetrahymena thermophila ribozyme is studied by means of an Ising--like model. Phase diagrams and free energy landscapes are computed exactly and suggest a simple two--state behaviour for the hairpin and the presence of intermediate states for the ribozyme. Nonequilibrium simulations give the possible unfolding pathways for the ribozyme, and the dominant pathway corresponds to the experimentally observed one.
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We study the mechanical unfolding pathways of the $FnIII_{10}$ domain of fibronectin by means of an Ising--like model, using both constant force and constant velocity protocols. At high forces and high velocities our results are consistent with experiments and previous computational studies. Moreover, the simplicity of the model allows us to probe the biologically relevant low force regime, where we predict the existence of two intermediates with very close elongations. The unfolding pathway is characterized by stochastic transitions between these two intermediates.
Deviations from linearity in the dependence of the logarithm of protein unfolding rates, $log k_u(f)$, as a function of mechanical force, $f$, measurable in single molecule experiments, can arise for many reasons. In particular, upward curvature in $log k_u(f)$ as a function of $f$ implies that the underlying energy landscape must be multidimensional with the possibility that unfolding ensues by parallel pathways. Here, simulations using the SOP-SC model of a wild type $beta$-sandwich protein and several mutants, with immunoglobulin folds, show upward curvature in the unfolding kinetics. There are substantial changes in the structures of the transition state ensembles as force is increased, signaling a switch in the unfolding pathways. Our results, when combined with previous theoretical and experimental studies, show that parallel unfolding of structurally unrelated single domain proteins can be determined from the dependence of $log k_u(f)$ as a function of force (or $log k_u[C]$ where $[C]$ is the denaturant concentration).
We propose a lattice model for RNA based on a self-interacting two-tolerant trail. Self-avoidance and elements of tertiary structure are taken into account. We investigate a simple version of the model in which the native state of RNA consists of just one hairpin. Using exact arguments and Monte Carlo simulations we determine the phase diagram for this case. We show that the denaturation transition is first order and can either occur directly or through an intermediate molten phase.
Using analytical techniques and Langevin dynamics simulations, we investigate the dynamics of polymer translocation through a nanochannel embedded in two dimensions under an applied external field. We examine the translocation time for various ratio of the channel length $L$ to the polymer length $N$. For short channels $Lll N$, the translocation time $tau sim N^{1+ u}$ under weak driving force $F$, while $tausim F^{-1}L$ for long channels $Lgg N$, independent of the chain length $N$. Moreover, we observe a minimum of translocation time as a function of $L/N$ for different driving forces and channel widths. These results are interpreted by the waiting time of a single segment.
Using analytical techniques and Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a narrow channel of width $R$ embedded in two dimensions, driven by a force proportional to the number of monomers in the channel. Such a setup mimics typical experimental situations in nano/micro-fluidics. During the the translocation process if the monomers in the channel can sufficiently quickly assume steady state motion, we observe the scaling $tausim N/F$ of the translocation time $tau$ with the driving force $F$ per bead and the number $N$ of monomers per chain. With smaller channel width $R$, steady state motion cannot be achieved, effecting a non-universal dependence of $tau$ on $N$ and $F$. From the simulations we also deduce the waiting time distributions under various conditions for the single segment passage through the channel entrance. For different chain lengths but the same driving force, the curves of the waiting time as a function of the translocation coordinate $s$ feature a maximum located at identical $s_{mathrm{max}}$, while with increasing the driving force or the channel width the value of $s_{mathrm{max}}$ decreases.
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