Molecular weight dependence of healing and brittle fracture in amorphous polymers above the entanglement molecular weight

A model based on chain entanglements is developed to predict the molecular weight dependence of the fracture stress for brittle, amorphous polymers. It is then used in conjunction with the reptation model of polymer diffusion to predict the time and molecular weight dependence of the fracture stress in the closely related healing problem. Theoretical predictions are found to be in close agreement with experimental data.     

A designed phenylalanyl-tRNA synthetase variant allows efficient in vivo incorporation of aryl ketone functionality into proteins

Incorporation of non-natural amino acids into proteins in vivo expands the scope of protein synthesis and design. p-Acetylphenylalanine was incorporated into recombinant dihydrofolate reductase (DHFR) in Escherichia coli via a computationally designed mutant form of the phenylalanyl-tRNA synthetase of the host. DHFR outfitted with ketone functionality can be chemoselectively ligated with hydrazide reagents under mild conditions.     

Stress-induced diffusion of macromolecules

A framework for analysis of stress-induced diffusion is presented. Diffusion of macromolecules is considered to be driven by gradients of entropic potential arising from distortion of the molecular conformation by deformation, as well as by gradients of concentration of individual molecular weight species. Resulting concentration profiles in circular capillary flow have been calculated for a system containing a single macromolecular species. Significant variations in concentration with capillary radius are predicted at full development. Estimates of the dynamics of development of these profiles indicate that the length to diameter ratios needed to see a measurable effect are proportional to the Peclet number, which may be quite large for macromolecular fluids depending on the geometry and flow velocity of the system. This effect may have implications in the rheology, chromatography, and technological uses of macromolecular fluids.     

Virtual screening for binding of phenylalanine analogues to phenylalanyl-tRNA synthetase

Although incorporation of nonnatural amino acids provides a powerful means of controlling protein structure and function, experimental investigations of amino acid analogues for utilization by the protein biosynthetic machinery can be costly and time-consuming. In this paper, we describe a computational protocol (HierDock) for predicting the relative energies of binding of phenylalanine analogues to phenylalanyl-tRNA synthetase (PheRS). Starting with the crystal structure of Thermus thermophilus PheRS without bound ligand, HierDock predicts the binding site of phenylalanine (Phe) within 1.1 A of that revealed by the crystal structure of PheRS cocrystallized with Phe. The calculated binding energies of Phe analogues in PheRS, using HierDock, correlate well with the translational activities of the same analogues in Escherichia coli. HierDock identifies p-fluorophenylalanine and 3-thienylalanine as especially good substrates for PheRS, in agreement with experiment. These results suggest that the HierDock protocol may be useful for virtual screening of amino acid analogues prior to experiment.