Mechanical Unfolding of Proteins-A Comparative Nonequilibrium Molecular Dynamics Study.

Mechanical signals regulate functions of mechanosensitive proteins by inducing structural changes that are determinant for force-dependent interactions. Talin is a focal adhesion protein that is known to extend under mechanical load, and it has been shown to unfold via intermediate states. Here, we compared different nonequilibrium molecular dynamics (MD) simulations to study unfolding of the talin rod. We combined boxed MD (BXD), steered MD, and umbrella sampling (US) techniques and provide free energy profiles for unfolding of talin rod subdomains. We conducted BXD, steered MD, and US simulations at different detail levels and demonstrate how these different techniques can be used to study protein unfolding under tension. Unfolding free energy profiles determined by BXD suggest that the intermediate states in talin rod subdomains are stabilized by force during unfolding, and US confirmed these results.

Fully Atomistic Simulations of Protein Unfolding in Low Speed Atomic Force Microscope and Force Clamp Experiments with the Help of Boxed Molecular Dynamics.

The results of boxed dynamics (BXD) fully atomistic simulations of protein unfolding by atomic force microscopy (AFM) in both force clamp (FC) and velocity clamp (VC) modes are reported. In AFM experiments the unfolding occurs on a time scale which is too long for standard atomistic molecular dynamics (MD) simulations, which are usually performed with the addition of forces which exceed those of experiment by many orders of magnitude. BXD can reach the time scale of slow unfolding and sample the very high free energy unfolding pathway, reproducing the experimental dependence of pulling force against extension and extension against time. Calculations show the presence of the pulling force "humps" previously observed in the VC AFM experiments and allow the identification of intermediate protein conformations responsible for them. Fully atomistic BXD simulations can estimate the rate of unfolding in the FC experiments up to the time scale of seconds.

Hydrotrope accumulation around the drug: the driving force for solubilization and minimum hydrotrope concentration for nicotinamide and urea.

Nicotinamide is an effective non-micellar hydrotrope (solubilizer) for drugs with low aqueous solubility. To clarify the molecular basis of nicotinamide's hydrotropic effectiveness, we present here a rigorous statistical thermodynamic theory, based on the Kirkwood-Buff theory of solutions, and our recent application of it to hydrotropy. We have shown that (i) nicotinamide self-association reduces solubilization efficiency, contrary to the previous hypothesis which claimed that self-association drives solubilization and (ii) the minimum hydrotrope concentration (MHC), namely, the threshold concentration above which solubility suddenly increases, is caused not by the bulk-phase self-association of nicotinamides as has been postulated previously, but by the enhancement of nicotinamide-nicotinamide interaction around the drug molecules. We have thus established a new view of hydrotropy - it is nicotinamide's non-stoichiometric accumulation around the drug that is the basis of solubility increase above MHC.

Hydrotropy: binding models vs. statistical thermodynamics.

Hydrophobic drugs can often be solubilized by the addition of hydrotropes. We have previously shown that preferential drug-hydrotrope association is one of the major factors of increased solubility (but not "hydrotrope clustering" or changes in "water structure"). How, then, can we understand this drug-hydrotrope interaction at a molecular level? Thermodynamic models based upon stoichiometric solute-water and solute-hydrotrope binding have long been used to understand solubilization microscopically. Such binding models have shown that the solvation numbers or coordination numbers of the water and hydrotrope molecules around the drug solute is the key quantity for solute-water and solute-hydrotrope interaction. However, we show that a rigorous statistical thermodynamic theory (the fluctuation solution theory originated by Kirkwood and Buff) requires the total reconsideration of such a paradigm. Here we show that (i) the excess solvation number (the net increase or decrease, relative to the bulk, of the solvent molecules around the solute), not the coordination number, is the key quantity for describing the solute-hydrotrope interaction; (ii) solute-hydrotrope binding is beyond the reach of the stoichiometric models because long-range solvation structure plays an important role.

Mechanism of hydrophobic drug solubilization by small molecule hydrotropes.

Drugs that are poorly soluble in water can be solubilized by the addition of hydrotropes. Albeit known for almost a century, how they work at a molecular basis is still controversial due to the lack of a rigorous theoretical basis. To clear up this situation, a combination of experimental data and Fluctuation Theory of Solutions (FTS) has been employed; information on the interactions between all the molecular species present in the solution has been evaluated directly. FTS has identified two major factors of hydrotrope-induced solubilization: preferential hydrotrope-solute interaction and water activity depression. The former is dominated by hydrotrope-solute association, and the latter is enhanced by ionic dissociation and hindered by the self-aggregation of the hydrotropes. Moreover, in stark contrast to previous hypotheses, neither the change of solute hydration nor the water structure accounts for hydrotropy. Indeed, the rigorous FTS poses serious doubts over the other common hypothesis: self-aggregation of the hydrotrope hinders, rather than promotes, solubilization.