Vihra M. Yomtova

Selective silencing of DNA-specific B lymphocytes delays lupus activity in MRL/lpr mice

The pathological DNA‐specific B lymphocytes in lupus are logical targets for a selected therapeutic intervention. We have hypothesized that it should be possible to suppress selectively the activity of these B cells in lupus mice by administering to them an artificial molecule that cross‐links their surface immunoglobulins with the inhibitory FcγIIb surface receptors. A hybrid molecule was constructed by coupling the DNA‐mimicking DWEYSVWLSN peptide to a monoclonal anti‐mouse FcγRIIb antibody. This chimeric antibody was added to cultured spleen cells from sick MRL/lpr mice, immunized with diphtheria toxoid, resulting in reduction of the numbers of anti‐DNA but not of anti‐diphtheria IgG antibody‐producing cells. Intravenous infusions with the DNA‐peptide antibody chimera to 7‐wk‐old animals prevented the appearance of IgG anti‐DNA antibodies and of albuminuria in the next 2 months. The administration of the DNA‐peptide chimeric antibody to 18 wk‐old mice with full‐blown disease resulted in the maintenance of a flat level of IgG anti‐DNA antibodies and in delay of the aggravation of the lupus glomerulonephritis. The use of chimeric antibodies targeting inhibitory B lymphocyte receptors represents a novel approach for the selective suppression of autoreactive disease‐associated B cells in autoimmune diseases.

Catalytic role of vicinal OH in ester aminolysis: proton shuttle versus hydrogen bond stabilization.

This computational study provoked by the process of peptide bond formation in the ribosome investigates the influence of the vicinal OH group in monoacylated diols on the elementary acts of ester aminolysis. Two alternative approaches for this influence on ester ammonolysis were considered: stabilization of the transition states by hydrogen bonds and participation of the vicinal hydroxyl in proton transfer (proton shuttle). The activation due to hydrogen bonds of the vicinal hydroxyl via tetragonal transition states was rather modest; the free energy of activation was reduced by only 5.2 kcal/mol compared to the noncatalyzed reaction. The catalytic activation via the proton shuttle mechanism with participation of the vicinal OH in the proton transfer via hexagonal transition states resulted in considerable reduction of the free energy of activation to 33.5 kcal/mol, i.e., 16.0 kcal/mol lower than in the referent process. Accounting for the influence of the environment on the reaction center by a continuum model (for ε from 5 to 80) resulted in further stabilization of the rate-determining transition state by 4-5 kcal/mol. The overall reduction of the reaction barrier by about 16 kcal/mol as compared to the noncatalyzed process corresponds to about 10(9)-fold acceleration of the reaction, in agreement with the experimental estimate for acceleration of this process in the ribosome.

Advantages of orange-labelled collagen and gelatine as substrates for rapid collagenase activity measurement

A simple method for the determination of collagenase activity utilising dye-labelled substrates is proposed. It consists in labelling gelatine and bovine Achilles tendon collagen under nondenaturing conditions with the dye active orange GT. As verified with two different enzyme preparations, labelling did not dramatically change the susceptibility to collagenases. The kinetic parameters obtained for dye-labelled collagen and gelatine were compared to those obtained for the hydrolysis of native insoluble collagen (Mandls method). The method offers the following advantages: it is rapid, reproducible, does not require special equipment and is more specific for collagenases than the widely used azocoll and Mandl methods.

Hierarchical approach to conformational search and selection of computational method in modeling the mechanism of ester ammonolysis

We describe automated procedures for the first stages of a systematic computational investigation of reaction mechanisms. They include (i) selection of computational method and basis set based on statistical analysis of structural and energy data relating to experimental values, (ii) determination of all distinct conformations of transition states with large conformational freedom, and (iii) generation of unknown geometry of the transition states, based on pre-defined connectivity of the atoms involved in the reaction. For the conformational search we employed an efficient procedure for exploration of various possible conformations of the transition states and elimination of the equivalent structures in several steps using molecular-mechanical and quantum-mechanical methods. The procedure was applied to the determination of the structures of transition states and intermediates in the ammonolysis of monoformylated 1,2-ethanediol, which were subsequently used for identification of the lowest energy reaction paths. For the same reaction system we also used the approach for generation of the initial structures of transition states with unknown geometry. The reported procedures are implemented in the MolRan program suite.

Determination of the optimal position of adjacent proton-donor centers for the activation or inhibition of peptide bond formation – A computational model study

The study reports a computational analysis of the influence of proton donor group adjacent to the reaction center during ester ammonolysis of an acylated diol as a model reaction for peptide bond formation. This analysis was performed using catalytic maps constructed after a detailed scanning of the available space around the reaction centers in different transition states, a water molecule acting as a typical proton donor. The calculations suggest that an adjacent proton donor center can reduce the activation barrier of the rate determining transition states by up to 7.2 kcal/mol, while no inhibition of the reaction can be achieved by such a group.

Semispecific Ester Substrates of Trypsin as Acyl Donors in Kinetically Controlled Peptide Synthesis

Esters of benzoyl-Phe with different size and structure of the leaving group have been synthesized and their acyl-donor properties studied in tryptic kinetically controlled peptide synthesis of model peptides. The results obtained show that: (1) part of the leaving group of these substrates is involved in S12–P12interactions in the extended active site of the enzyme; (2) both hydrophobic and H-bond interactions contribute to the S12–P12-interactions; (3) the lack of secondary hydrolysis provides higher synthetic yields as compared to those when using specific trypsin substrates in kinetically controlled peptide synthesis.