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Understanding the impacts of the internal cohesion and surface chemistry of supramolecular systems on the collective behaviors in the contacts between the systems and biomolecules can greatly expand the functional diversity and adaptivity of supramolecular nanostructures. Here we show how the tuned molecular interactions modulate the morphologies and internal cohesion of peptide amphiphile (PA) self-assemblies and their resultant functions. Circular dichroism spectroscopy, fluorescence probing, atomic force and electron microscopy, along with molecular dynamics simulations, revealed that the PA self-assembly formed compact long fibers when surface charge repulsion was screened, but formed loose short fibers or micelle-like assemblies when hydrogen bonding was disrupted or hydrophobic core was enhanced. More importantly, depending on the strength of the phospholipid affinity for the cationic segment of the PA, the same internal cohesion of PA nanostructures can lead to either cell death or cell survival, providing unique insights into the design of supramolecular materials., (© 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The features of transition states and intermediates are important in the study on protein folding. However, transition states and intermediates could not be obviously identified from trajectories obtained by dynamic simulations. In this work, a different method to identify and characterize the transition states and intermediates by combining the root mean square deviation of C(alpha) atoms and the similarity factor Q to the native state is proposed. The unfolding processes based on all-atomic simulations for proteins chymotrypsin inhibitor 2 and barnase are studied, and the related transition states and intermediates are identified by observing an unfolding factor U = 1-F. Comparisons between the conformational cluster analysis and experimental results are also made. The various analyses on the unfolding behaviors indicate that our method can well define the transition states and intermediates, and the factor U (or F) can be used as a reaction coordinate of the folding and unfolding process. It is also found that three-state folding proteins might experience more complicated pathways and have more rugged energy landscapes than two-state folding proteins.