Display Selection of a Hybrid Foldamer-Peptide Macrocycle.

Expanding the chemical diversity of peptide macrocycle libraries for display selection is desirable to improve their potential to bind biomolecular targets. We now have implemented a considerable expansion through a large aromatic helical foldamer inclusion. A foldamer was first identified that undergoes flexizyme-mediated tRNA acylation and that is capable of initiating ribosomal translation with yields sufficiently high to perform an mRNA display selection of macrocyclic foldamer-peptide hybrids. A hybrid macrocyclic nanomolar binder to the C-lobe of the E6AP HECT domain was selected that showed a highly converged peptide sequence. A crystal structure and molecular dynamics simulations revealed that both the peptide and foldamer are helical in an intriguing reciprocal stapling fashion. The strong residue convergence could be rationalized based on their involvement in specific interactions with the target protein. The foldamer stabilizes the peptide helix through stapling and through contacts with key residues. These results altogether represent a significant extension of the chemical space amenable to display selection and highlight possible benefits of inserting an aromatic foldamer into a peptide macrocycle for the purpose of protein recognition.

Single Parameter for Predicting the Morphology of Atmospheric Black Carbon.

Black carbon (BC) from fuel combustion is an effective light absorber that contributes significantly to direct climate forcing. The forcing is altered when BC combines with other substances, which modify its mixing state and morphology, making the evaluation of its atmospheric lifetime and climate impact a challenge. To elucidate the associated mechanisms, we exposed BC aerosol to supersaturated vapors of different chemicals to form thin coatings and measured the coating mass required to induce the restructuring of BC aggregates. We found that studied chemicals fall into two distinct groups based on a single dimensionless parameter, χ, which depends on the diameter of BC monomer spheres and the coating material properties, including vapor supersaturation, molar volume, and surface tension. We show that when χ is small (low-volatility chemicals), the highly supersaturated vapor condenses uniformly over aggregates, including convex monomers and concave junctions in between monomers, but when χ is large (intermediate-volatility chemicals), junctions become preferred. The aggregates undergo prompt restructuring when condensation in the junctions dominates over condensation on monomer spheres. For a given monomer diameter, the coating distribution is mostly controlled by vapor supersaturation. The χ factor can be incorporated straightforwardly into atmospheric models to improve simulations of BC aging.

Effect of pore geometry on the compressibility of a confined simple fluid.

Fluids confined in nanopores exhibit properties different from the properties of the same fluids in bulk; among these properties is the isothermal compressibility or elastic modulus. The modulus of a fluid in nanopores can be extracted from ultrasonic experiments or calculated from molecular simulations. Using Monte Carlo simulations in the grand canonical ensemble, we calculated the modulus for liquid argon at its normal boiling point (87.3 K) adsorbed in model silica pores of two different morphologies and various sizes. For spherical pores, for all the pore sizes (diameters) exceeding 2 nm, we obtained a logarithmic dependence of fluid modulus on the vapor pressure. Calculation of the modulus at saturation showed that the modulus of the fluid in spherical pores is a linear function of the reciprocal pore size. The calculation of the modulus of the fluid in cylindrical pores appeared too scattered to make quantitative conclusions. We performed additional simulations at higher temperature (119.6 K), at which Monte Carlo insertions and removals become more efficient. The results of the simulations at higher temperature confirmed both regularities for cylindrical pores and showed quantitative difference between the fluid moduli in pores of different geometries. Both of the observed regularities for the modulus stem from the Tait-Murnaghan equation applied to the confined fluid. Our results, along with the development of the effective medium theories for nanoporous media, set the groundwork for analysis of the experimentally measured elastic properties of fluid-saturated nanoporous materials.