Comparison of Relative Activation Energies Obtained by Density Functional Theory and the Random Phase Approximation for Several Claisen Rearrangements.

We investigate several representative density functional theory approaches for the calculation of relative activation energies and free energies of a set of model pericyclic reactions, some of which have been studied experimentally. In particular, we use a standard hybrid functional (B3LYP), the same hybrid functional augmented with a basis set superposition error and dispersion correction, a meta-hybrid functional developed to treat transition states and weak interactions (M06-2X), and the recently implemented random phase approximation (RPA) based on Kohn-Sham orbitals from conventional density functional theory by Furche and co-workers. We apply these methods to calculate relative activation energies and estimated free energies for the amide acetal Claisen rearrangement.

Computational design and selections for an engineered, thermostable terpene synthase.

Terpenoids include structurally diverse antibiotics, flavorings, and fragrances. Engineering terpene synthases for control over the synthesis of such compounds represents a long sought goal. We report computational design, selections, and assays of a thermostable mutant of tobacco 5-epi-aristolochene synthase (TEAS) for the catalysis of carbocation cyclization reactions at elevated temperatures.

Chemical and genetic wrappers for improved phage and RNA display.

An Achilles heel inherent to all molecular display formats, background binding between target and display system introduces false positives into screens and selections. For example, the negatively charged surfaces of phage, mRNA, and ribosome display systems bind with unacceptably high nonspecificity to positively charged target molecules, which represent an estimated 35% of proteins in the human proteome. Here we report the first systematic attempt to understand why a broad class of molecular display selections fail, and then solve the underlying problem for both phage and RNA display.

Dissecting the streptavidin-biotin interaction by phage-displayed shotgun scanning.

Shotgun scanning the streptavidin-biotin interaction identifies long-range hydrophobic interactions that contribute to one of the strongest naturally occurring noncovalent protein-ligand interactions. The femtomolar dissociation constant for this interaction makes it a useful model system to dissect the forces that govern high-affinity molecular recognition between proteins and small molecules. Shotgun scanning combines the diversity and in vitro binding selection of phage-displayed libraries with a binomial mutagenesis strategy.