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Donald Hilvert

Publications and source records attributed to Donald Hilvert.

42 records · Page 3Linked to original sources
PubMed2002

Probing ligand recognition in the decarboxylase antibody 21D8: implications for the catalytic mechanism.

Antibody 21D8, which was elicited with a naphthalene-1,5-disulfonate hapten, catalyzes the medium-sensitive decarboxylation of 5-nitro-3-carboxybenzisoxazole. Structural studies on the hapten-antibody complex show that the active site contains two anion binding pockets separated by a hydrophobic region. To gain further insight into the ligand binding and catalytic mechanism of 21D8, six site-directed mutants were prepared, four for investigating the role of each of the two hapten sulfonate binding sites and two for examining packing interactions between bound ligands and the binding pocket. With the exception of an Arg(L46)Met substitution in the more deeply buried sulfonate binding pocket, modification of the active site resulted in reductions in catalytic efficiency (k(cat)/k(uncat)), ranging between 3- and 23-fold. Importantly, and contrary to predictions based on computational docking experiments, the differential effects of the individual mutations on the K(m), K(TS), and K(product) parameters suggest that only substrate binding modes which place the carboxylate group in the more solvent-exposed sulfonate binding site are catalytically relevant. Such an orientation would permit a potentially significant interaction between the developing oxyanion in the transition state and the side chain of Arg(L96). Incomplete desolvation of the carboxylate in this orientation may also help explain the modest efficiency of 21D8 compared to the most accelerating aprotic dipolar organic solvents.

Amino Acid Substitution↗
PubMed2002

Direct NMR observation and DFT calculations of a hydrogen bond at the active site of a 44 kDa enzyme.

A hydrogen bond between the amide backbone of Arg7 and the remote imidazole side chain of HisIO6 has been directly observed by improved TROSY-NMR techniques in the 44 kDa trimeric enzyme chorismate mutase from Bacillus subtilis. The presence of this hydrogen bond in the free enzyme and its complexes with a transition state analog and the reaction product was demonstrated by measurement of 15N-15N and 1H-15N trans-hydrogen bond scalar couplings, (2h)J(NN) and (lh)J(HN), and by transfer of nuclear polarization across the hydrogen bond. The conformational dependences of these coupling constants were analyzed using sum-over-states density functional perturbation theory (SOS-DFPT). The observed hydrogen bond might stabilize the scaffold at the active site of BsCM. Because the Arg7-His 106 hydrogen bond has not been observed in any of the high resolution crystal structures of BsCM, the measured coupling constants provide unique information about the enzyme and its complexes that should prove useful for structural refinement of atomic models.

Arginine↗
PubMed2001

Investigating and Engineering Enzymes by Genetic Selection.

Natural enzymes have arisen over millions of years by the gradual process of Darwinian evolution. The fundamental steps of evolution-mutation, selection, and amplification-can also be exploited in the laboratory to create and characterize protein catalysts on a human timescale. In vivo genetic selection strategies enable the exhaustive analysis of protein libraries with 10(10) different members, and even larger ensembles can be studied with in vitro methods. Evolutionary approaches can consequently yield statistically meaningful insight into the complex and often subtle interactions that influence protein folding, structure, and catalytic mechanism. Such methods are also being used increasingly as an adjunct to design, thus providing access to novel proteins with tailored catalytic activities and selectivities.

Journal Article↗
PubMed1999

An Antibody-Catalyzed Allylic Sulfoxide-Sulfenate Rearrangement.

Antibodies SZ-cis-39C11 and SZ-trans-28F8, which were elicited in response to N-aryl-3-methoxyphenyl proline derivatives, catalyze the [2,3]-sigmatropic rearrangement of allylic sulfoxides to sulfenates. Reduction of the sulfenates with dithiothreitol in situ yields allylic alcohols as the final product. The antibodies achieve rate accelerations in the range 10(2)-10(3) over background and exhibit distinctive hapten-dependent substrate specificity and enantio- and diastereoselectivity. Of particular note is the effective chirality transfer from the sulfoxide center to the product alcohol in the SZ-cis-39C11-catalyzed conversion of (Z)-2-(4-methoxyphenyl)-but-2-en-1-yl 4-nitrophenyl sulfoxide. These properties can be contrasted with those of bovine serum albumin (BSA) which accelerates the same reactions to a comparable extent but does not discriminate between substrate isomers. Partitioning of substrate from aqueous solution into the less polar environment of the protein pocket can account for much of the observed rate enhancement, whereas specific conformational constraints programmed by the haptens must orient the flexible substrate within the induced antibody-combining sites so as to favor certain reaction pathways over others. These studies thus expand the scope of antibody catalysis to an important new class of pericyclic reactions and illustrate how medium effects can be exploited together with conformational constraint to control reactivity and selectivity.

Journal Article↗