Navigating in foldonia: Using accelerated molecular dynamics to explore stability, unfolding and self-healing of the β-solenoid structure formed by a silk-like polypeptide

<div><p>The β roll molecules with sequence (GAGAGAGQ)₁₀ stack via hydrogen bonding to form fibrils which have been themselves been used to make viral capsids of DNA strands, supramolecular nanotapes and pH-responsive gels. Accelerated molecular dynamics (aMD) simulations are used to investigate the unfolding of a stack of two β roll molecules, (GAGAGAGQ)₁₀, to shed light on the folding mechanism by which silk-inspired polypeptides form fibrils and to identify the dominant forces that keep the silk-inspired polypeptide in a β roll configuration. Our study shows that a molecule in a stack of two β roll molecules unfolds in a step-wise fashion mainly from the C terminal. The bottom template is found to play an important role in stabilizing the β roll structure of the molecule on top by strengthening the hydrogen bonds in the layer that it contacts. Vertical hydrogen bonds within the β roll structure are considerably weaker than lateral hydrogen bonds, signifying the importance of lateral hydrogen bonds in stabilizing the β roll structure. Finally, an intermediate structure was found containing a β hairpin and an anti-parallel β sheet consisting of strands from the top and bottom molecules, revealing the self-healing ability of the β roll stack.</p></div

Simulation lengths and threshold energies for the three different types of accelerated MD simulations (aMD).

<p>Simulation lengths and threshold energies for the three different types of accelerated MD simulations (aMD).</p

Linear Viscoelasticity of Polyelectrolyte Complex Coacervates

Two flexible, oppositely charged polymers can form liquid-like complex coacervate phases with rich but poorly understood viscoelastic properties. They serve as an experimental model system for many biological and man-made materials made from oppositely charged macromolecules. We use rheology to systematically study the viscoelastic properties as a function of salt concentration, chain length, chain length matching, and mixing stoichiometry of model complex coacervates of poly­(<i>N</i>,<i>N</i>-dimethylaminoethyl methacrylate), PDMAEMA, and poly­(acrylic acid), PAA. The dynamics of making and breaking ionic bonds between the oppositely charged chains underlie all linear viscoelastic properties of the complex coacervates. We treat (clusters of) ionic bonds as sticky points and find that there is a remarkable resemblance between the relaxation spectra of these complex coacervates and the classical sticky Rouse model for single polymer systems. Salt affects all relaxation processes in the same way, giving rise to a widely applicable time–salt superposition principle. The viscoelastic properties of the complexes are very different from those of the individual components. In the complexes with a chain length mismatch, the effect of the mismatch on the viscoelastic properties is not trivial: changing the length of the polycation affects the relaxation behavior differently from changing the length of the polyanion

HPLC-UV chromatograms (monitored at 254 nm) of the reaction mixture of 4MC, PA, and NaIO₄ with time.

<p>The ratio of 4MC, PA and NaIO₄ is 1:3:0.5.</p

An overview of the proposed structures of the products.

<p>The number under each structure corresponds to the number in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0166490#pone.0166490.s007" target="_blank">S1 Table</a>.</p