8 research outputs found

    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

    No full text
    <div><p>The β roll molecules with sequence (GAGAGAGQ)<sub>10</sub> 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)<sub>10</sub>, 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).

    No full text
    <p>Simulation lengths and threshold energies for the three different types of accelerated MD simulations (aMD).</p

    LCST Behavior is Manifested in a Single Molecule: Elastin-Like polypeptide (VPGVG)<sub><i>n</i></sub>

    No full text
    The physical origin of the lower critical solution temperature (LCST) behavior of a variety of fluids, including elastin-like polypeptides (ELPs), has been studied for the past few decades. As is the case for polymer solutions, LCST behavior of ELPs is invariably reported for large systems of molecules and is considered evidence for collective behavior. In contrast, we find evidence for properties changes associated with LCST behavior in a single molecule by performing long atomic-level molecular dynamics simulation on the ELP sequences (Val-Pro-Gly-Val-Gly)<i>n</i> for four different length peptides over a wide range of temperatures. We observe a sharp transition in the number of hydrogen bonds between peptide and water and in the number of water molecules within the first hydration shell as temperature rises; this is used to locate the transition temperature. The dependence of the transition temperatures of ELPs on their lengths agrees well with experiments in that both have the same power law exponents. Our simulations reveal that the tendency for pentamers (VPGVG) in ELPs of all lengths to lose H-bonds with water or to gain H-bonds with themselves as temperature rises is independent of the length of the chain in which they are embedded. Thus, the transition temperature of ELPs in pure water is determined by two factors: the hydrogen bonding tendency of the pentamers and the number of pentamers per ELP. Moreover, the hydrogen bonding tendency of pentamers depends only on their sequences, not on the ELP chain length
    corecore