Douglas A. Bergman

A novel thioether linker: Chemical synthesis of a HIV-1 protease analogue by thioether ligation

Using the novel thioether linker 4-[N-Boc-2-aminoethylmercapto] methyl phenoxyacetic acid, peptides bearing a C-terminal thiol functionality were synthesieed. Reaction of the thiol functionalised peptide with an N-terminal bromoacetylated peptide led to ligation of the two peptides via a thioether bond. The strategy was used to synthesise an enzymatically active analogue of HIV-1 Protease.

Quantitative affinity chromatography: increased versatility of the technique for studies of ligand binding

The potential of affinity chromatography for the characterization of strong solute-ligand interactions is explored by studying the NADH-dependent elution of rabbit muscle lactate dehydrogenase from a column of trinitrophenyl-Sepharose in 0.067 M phosphate, pH 7.2. An interesting development is the simplification of the general affinity chromatography theory that emanates from the use of affinity matrices with a high concentration of immobilized reactant groups. The resultant expression allows evaluation of the intrinsic association constant for solute-ligand interactions from a single series of either zonal or frontal affinity chromatographic experiments conducted in the presence of a range of free ligand concentrations. Thus, contrary to previous belief, an affinity matrix designed for solute purification work should prove to be an asset for, rather than an impediment to, the study of solute-ligand interactions by quantitative affinity chromatography.

Effects of thermodynamic nonideality on the kinetics of ester hydrolysis by α-chymotrypsin: A model system with preexistence of the isomerization equilibrium

The effects of a small inert solute, sucrose, on the kinetics of hydrolysis of N-acetyl-tryptophan ethyl ester by bovine alpha-chymotrypsin have been investigated. In studies at pH 7 and 20 degrees C the presence of 0.5 M sucrose in assay mixtures caused no discernible change in kinetic parameters, a result consistent with existence of the enzyme in a single conformational state under those conditions. However, at pH 3.5 and 50 degrees C, conditions under which the enzyme comprises an equilibrium mixture of compact and expanded isomeric states, inclusion of the inert solute led to a considerable decrease in Michaelis constant (0.84 to 0.61 mM) but no significant change in maximal velocity. These results were shown to be amenable to quantitative interpretation in terms of thermodynamic nonideality effects on catalysis by an enzyme undergoing reversible isomerization in the absence of substrate. For that analysis, which required experimental estimates of the equilibrium constant for preexisting isomerization of enzyme and the activity coefficient of substrate, the magnitude of the former (0.3) was obtained by difference spectroscopy: liquid-liquid partition studies with bromobenzene as organic phase were used to determine the effect of sucrose on the activity coefficient of N-acetyltryptophan ethyl ester. Such agreement between experimental kinetic findings and theoretical predictions based on considerations of excluded volume points to the possible use of the space-filling effects of small solutes for delineating the gross extent of conformational changes associated with reversible isomerization of proteins, and hence to the potential of thermodynamic nonideality as a probe for studying protein denaturation mechanisms as well as substrate-mediated changes associated with enzyme reaction mechanisms.

Structure-activity relationships for macrocyclic peptidomimetic inhibitors of HIV-1 protease

Abstract A series of appended macrocycles were synthesized and tested as inhibitors of HIV-1 protease (HIV PR). The macrocycle structurally mimics an N-terminal tripeptide component of peptide substrates. Structure-activity relationships explore steric limitations to the size and shape of the substituents and provide evidence for functional mimicry of substrate components.

Space-filling effects of inert solutes as probes for the detection and study of substrate-mediated conformational changes by enzyme kinetics: Theoretical considerations

From expressions derived for the space-filling effects of small inert solutes on kinetic parameters for univalent enzymes undergoing isomerizations that are substrate-induced and pre-existing, it is concluded that experimental observation of an enhanced maximal velocity in the presence of inert solute can only reflect the existence of the former type of conformational change; and that the isomerization must be governed by a relatively small equilibrium constant. Similar conclusions apply to multivalent enzymes exhibiting Michaelis-Menten kinetics. Extension of the theory to provide quantitative expressions for multivalent enzymes has made possible the numerical simulation of thermodynamic non-ideality effects on systems conforming with the Monod and Koshland models of allostery. In that regard the simulated Scatchard plots for the two models differ sufficiently in form to suggest that detailed examination of the space-filling effects of small solutes on the kinetics of an allosteric enzyme may, under favourable circumstances, allow identification of the appropriate allosteric mechanism. Finally, these considerations of thermodynamic non-ideality in relation to the kinetics of allosteric enzymes have revealed formal similarities between the consequences of space-filling by inert solutes and the specific effects of allosteric activators or inhibitors. Attention is drawn to the possible implications of this observation in relation to the functioning of allosteric enzymes in vivo, where catalytic performance may be modified by factors no more specific than the ability of unrelated solutes to occupy space in the highly concentrated cellular environment.

Kinetic properties of HIV-1 protease produced by total chemical synthesis with cysteine residues replaced by isosteric L-α-amino-n-butyric acid

Human immunodeficiency virus-1 protease, produced by total chemical synthesis with the cysteine residues replaced by L-α-amino-n-butyric acid ([Aba67,95] HIV-1 PR), has been used extensively for the X-ray crystallographic structural analysis of the enzyme and its complexes utilized in drug design. Here we report kinetic studies on the synthetic enzyme. The pH optimum is 5.5 at ionic strengths of 0.1 and 1.0. The acid pH optimum is due to a decrease in binding affinity at higher pH values rather than to a reduction in catalytic efficiency. Activity is markedly increased by high ionic strength, although the major effect is on Km and not Kcat. The effect of pH and ionic strength on the kinetic constants determined for substrates and inhibitors is demonstrated and attention is drawn to the need for assay conditions to be explicitly reported in studies on inhibitor activity. The effect of a number of inhibitors has been measured against the synthetic enzyme and a recombinant HIV-1 PR. This work shows that [Aba67,95] HIV-1 PR has full enzymatic activity and normal kinetic properties.

Simple cis-epoxide-based inhibitors of HIV-1 protease

Abstract The 4-nitrophenoxy-based epoxide 6a, conveniently synthesized using Sharpless epoxidation chemistry, has been shown to be an irreversible inhibitor of HIV-1 protease (Kinact 1.8 μM, pH 6.5, I = 0.1 M). Related analogues, differing in the mode of attachment to the epoxide core, have also been prepared and assayed against HIV-1 protease.

Anomalous electrophoretic behavior of creatine kinase: A thiol-dependent isomeric system with migration subject to kinetic control

Abstract Moving boundary electrophoresis of creatine kinase in 0.1 I diethylbarbiturate buffer, pH 8.9, has yielded anomalous migration behavior that indicates intereonversion between two coexisting states of the enzyme at a rate comparable with the rate at which the two enzymic forms tend to separate by differential migration. Whereas a single, symmetrical boundary is observed in the ascending limb, distinct bimodality of the descending pattern is evident in electrophoresis of enzyme isolated from skeletal muscle of either rabbit or fish ( Mugil cephalus ): pronounced changes in the nature of this bimodality with time are observed in the case of fish muscle creatine kinase. The abnormal migration behavior is eliminated by inclusion of dithiothreitol in the electrophoresis medium or by covalent modification of the enzyme with 5,5′-dithiobis(2-nitrobenzoic acid). Velocity and equilibrium sedimentation studies have been used to identify the macromolecular event as an isomerization, and studies of sulfhydryl content to implicate either reversible sulfhydryl oxidation or thiol-disulfide interchange in the isomerization mechanism.