Patents and literature

Protein engineering and site-directed mutagenesis is becoming immensely important in both fundamental studies and commercial applications involving proteins and enzymes in biocatalysis. Protein engineering has become a powerful tool to help biochemists and molecular enzymologists elucidate structure-function relationships in enzymic active sites, to understand the intricacies of protein folding and denaturation, and to alter the selectivity of enzymatic catalysis. Commercial applications of engineered enzymes are being developed to increase protein stability, widen or narrow substrate specificity, and to develop novel approaches for use of enzymes in organic synthesis, drug design, and clinical applications. In addition to protein engineering, novel expression systems have been designed to prepare large quantities of genetically engineered proteins. Recent US patents and scientific literature on protein engineering, site-directed mutagenesis, and protein expression systems related to protein engineering are surveyed. Patent abstracts are summarized individually and a list of literature references are given.     

Ligand-modulated stereo- and regioselective tandem addition reactions of rhenium-bound naphthalene

A series of complexes of the form TpRe(CO)(L)(eta(2)-naphthalene) (Tp = hydridotris(pyrazolyl)borate) undergoes tandem electrophile/nucleophile addition reactions with a high degree of regiocontrol depending on the auxiliary ligand, L. When L = PMe(3), the reaction of the eta(2)-naphthalene complex with triflic acid followed by a silyl ketene acetal favors the 1,4-addition product, whereas when L = pyridine, N,N-dimethylaminopyridine, N-methylimidazole, or NH(3) the 1,2-addition product is favored. These reactions proceed with excellent stereocontrol: both electrophile (H(+), D(+)) and nucleophile (silyl ketene acetal) add anti to the face of metal coordination, and a single coordination diastereomer can be isolated for each reaction. One-electron oxidation of the Re complex affords the corresponding free dihydronaphthalene in good yield.     

Self-assembled luminescent CdSe-ZnS quantum dot bioconjugates prepared using engineered poly-histidine terminated proteins

We report a simple and versatile approach for the conjugation of luminescent CdSe-ZnS core-shell quantum dots (QDs) to proteins through coordination of engineered C-terminal oligohistidine sequences. Several histidine tail containing proteins were self-assembled onto the QD surface using this method. A recombinant antibody specific for the high explosive 2,4,6-trinitrotoluene (TNT) was conjugated to QDs through a carboxy terminal histidine tail and the bioconjugate used to detect TNT by competitive immunoassay. TNT was detected over the range of 10 μg/ml down to 41 ng/ml using the scFv conjugated to QDs. These results open up the possibility to conjugate luminescent QDs to a whole range of proteins to form QD bioconjugates that can be effectively used in bio-oriented applications, such as sensing, imaging, immunoassay and other diagnostics.     

Some reactions of 1-alkyl-1,2,3,4-tetrahydropyridines with organic azides. Synthesis of 1-alkylpiperidylidene-2-sulfonamides

The 1,3-dipolar cycloaddition reaction of 1-substituted-1,2,3,4-tetrahydropyridines 4a-d with organic azides 5 afforded the respective 1-substituted-piperidylidene-2-sulfonamides 6 . In contrast, the reaction of (E)-1-(1-propenyl)-1,2,3,4-tetrahydropyridine ( 4e ) with 4-chlorobenzenesulfonyl azide yielded 6m as well as 1-(4-chlorophenyl)sulfonimine-1,2,3,4-tetrahydropyridine ( 7 ) arising from addition of the azide to the (E)-1-(1-propenyl) substituent of 4e .     

Nonaqueous capillary electrophoretic separation of basic enantiomers using octakis(2,3-O-dimethyl-6-O-sulfo)-gamma-cyclodextrin, a new, single-isomer chiral resolving agent

The enantiomers of 34 pharmaceutical weak-base analytes were separated by nonaqueous capillary electrophoresis in acidic methanol background electrolytes using the sodium salt of the new, single-isomer chiral resolving agent, octakis(2,3-O-dimethyl-6-O-sulfo)-gamma-cyclodextrin (ODMS). The effective mobilities, separation selectivities and peak resolution values of the weak-base analytes were determined as a function of the ODMS concentration in the 0-40 mM range and were found to follow the theoretical predictions of the charged resolving agent migration model (CHARM model) modified for ionic strength effects. Fast, efficient separations were achieved for both comparatively small and large enantiomers.     

Steric interactions mediated by multiblock polymers and biopolymers: role of block size and addition of hydrophilic side chains

To a first approximation, the primary structure of many food proteins maybe thought of as a sequence of short hydrophobic and hydrophilic blocks. The influence of this type of structure on the steric-stabilising properties of such proteins has been considered here. In line with previous studies, using Self-Consistent-Field calculations, it has been shown that the presence of such protein molecules can lead to attraction and consequently bridging flocculation of colloidal particles. In the low adsorption energy limit for the hydrophobic groups (−1k_BT), it is found that the steric potential is significantly influenced by the changes in the number of adsorbed segments, as two surfaces are brought together. This is in contrast to the well-known results in the literature for the high adsorption limiting cases, where the number of such segments remains constant. In particular, the changes in the number of adsorbed hydrophobic units are observed not to be a monotonic function of the separation distance, but increase or decrease in reasonable accord with the oscillatory nature of the steric interactions, observed for various block sizes. Effects of the addition of a moderately sized hydrophilic side chain to the above molecules have also been studied. It is found that, in principle, such a modification can lead to a purely repulsive steric potential in solutions of these hybrid biopolymers. At the hydrophilic side chain sizes considered here, the surface affinity of the molecules is observed not to be drastically different compared to those of unmodified proteins.     

Variational electrostatic projection (VEP) methods for efficient modeling of the macromolecular electrostatic and solvation environment in activated dynamics simulations

New methods for the calculation of electrostatic interactions between the active dynamical region and surrounding external solvated macromolecular environment in hybrid quantum mechanical/molecular mechanical (QM/MM) simulations are presented. The variational electrostatic projection (VEP) method, and related variational reverse-mapping procedure (VEP-RVM) utilize an expansion in Gaussian surface elements for representation of electrostatic interactions. The use of a discretized surface that surrounds the active dynamical region greatly reduces the number of interactions with the particles of the external environment. The methods are tested on two catalytic RNA systems: the hammerhead and the hairpin ribozymes. It is shown that with surface elements numbering from 302 to 1202 points the direct VEP and VEP-RVM methods are able to obtain relative force errors in the range of 0.5-0.05% and 0.09-0.0001%, respectively, using a 4.0 A projection buffer. These results are encouraging and provide an essential step in the development of new variational macromolecular solvent-boundary methods for QM/MM calculations of enzyme reactions.     

Changing DNA grooves--a 1,4,5,8-naphthalene tetracarboxylic diimide bis-intercalator with the linker (beta-Ala)(3)-Lys in the minor groove

We have been investigating a modular, threading DNA polyintercalator design based upon the 1,4,5,8-naphthalene tetracarboxylic diimide (NDI) intercalating unit. Previously, we have reported the NMR analysis of a bis-intercalator-DNA complex in which the peptide linker between NDI units was found to occupy the DNA major groove (Guelev, Lee, Sorey, Hoffman, Iverson, Chem. Biol. 2001, 8, 415-425). Here we describe the NMR analysis of a complex between a related bis-intercalator known to display altered DNA sequence specificity. In this case, the linker resides in the DNA minor groove. We have thus shown that within this set of sequence specific bis-intercalators, both DNA grooves can be accessed, setting the stage for longer threading polyintercalators designed to have linkers occupying both grooves in an alternating fashion.