Multiple barriers in forced rupture of protein complexes

Curvatures in the most probable rupture force ($f^*$) versus log-loading rate ($\log{r_f}$) observed in dynamic force spectroscopy (DFS) on biomolecular complexes are interpreted using a one-dimensional free energy profile with multiple barriers or a single barrier with force-dependent transition state. Here, we provide a criterion to select one scenario over another. If the rupture dynamics occurs by crossing a single barrier in a physical free energy profile describing unbinding, the exponent $\nu$, from $(1- f^*/f_c)^{1/\nu}\sim(\log r_f)$ with $f_c$ being a critical force in the absence of force, is restricted to $0.5 \leq \nu \leq 1$. For biotin-ligand complexes and leukocyte-associated antigen-1 bound to intercellular adhesion molecules, which display large curvature in the DFS data, fits to experimental data yield $\nu<0.5$, suggesting that ligand unbinding is associated with multiple-barrier crossing.Comment: 8 pages, 5 figure

Force-induced Unbinding Dynamics in a Multidimensional Free Energy Landscape

We examined theory for force-induced unbinding on a two-dimensional free energy surface where the internal dynamics of biomolecules is coupled with the rupture process under constant tension f. We show that only if the transition state ensemble is narrow and activation barrier is high, the f-dependent rupture rate in the 2D potential surface can faithfully be described using an effective 1D energy profile.Comment: 11 pages, 3 figure

Urea-induced denaturation of PreQ1-riboswitch

Urea, a polar molecule with a large dipole moment, not only destabilizes the folded RNA structures, but can also enhance the folding rates of large ribozymes. Unlike the mechanism of urea-induced unfolding of proteins, which is well understood, the action of urea on RNA has barely been explored. We performed extensive all atom molecular dynamics (MD) simulations to determine the molecular underpinnings of urea-induced RNA denaturation. Urea displays its denaturing power in both secondary and tertiary motifs of the riboswitch (RS) structure. Our simulations reveal that the denaturation of RNA structures is mainly driven by the hydrogen bonds and stacking interactions of urea with the bases. Through detailed studies of the simulation trajectories, we found that geminate pairs between urea and bases due to hydrogen bonds and stacks persist only ~ (0.1-1) ns, which suggests that urea-base interaction is highly dynamic. Most importantly, the early stage of base pair disruption is triggered by penetration of water molecules into the hydrophobic domain between the RNA bases. The infiltration of water into the narrow space between base pairs is critical in increasing the accessibility of urea to transiently disrupted bases, thus allowing urea to displace inter base hydrogen bonds. This mechanism, water-induced disruption of base-pairs resulting in the formation of a "wet" destabilized RNA followed by solvation by urea, is the exact opposite of the two-stage denaturation of proteins by urea. In the latter case, initial urea penetration creates a dry-globule, which is subsequently solvated by water penetration leading to global protein unfolding. Our work shows that the ability to interact with both water and polar, non-polar components of nucleotides makes urea a powerful chemical denaturant for nucleic acids.Comment: 41 pages, 18 figure