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.

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.

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.

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 FcgammaIIb surface receptors. A hybrid molecule was constructed by coupling the DNA-mimicking DWEYSVWLSN peptide to a monoclonal anti-mouse FcgammaRIIb antibody.

The syn-oriented 2-OH provides a favorable proton transfer geometry in 1,2-diol monoester aminolysis: implications for the ribosome mechanism.

A computational study of 1-formyl 1,2-ethanediol aminolysis predicts a stepwise mechanism involving syn-2-OH-assisted proton transfer. The syn-oriented 2-OH takes over the catalytic role of the external water or amine molecule previously observed in 2-deoxy ester aminolysis. It provides more favorable, that is, more linear, proton transfer geometry for the rate-limiting transition state resulting in an almost billion-fold rate acceleration of the overall reaction.

Theoretical study of the o-OH participation in catechol ester ammonolysis.

The possible catalytic effect of the vicinal hydroxyl group during the ammonolysis of acetylcatechol has been studied by first principle calculations. A very efficient intramolecular catalysis was found to occur when the catechol ester o-OH group is deprotonated: the activation energy of the ammonolysis decreases by 24 kcal mol(-1) as compared to that of acetylphenol ammonolysis. Using this value, the o-oxyanion-catalysed intramolecular ammonolysis was estimated to be orders of magnitude faster than the ammonolysis of acetylphenol or nonionised acetylcatechol.

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.

N-anthraniloyl-Ala-Ala-Phe-4-nitroanilide, a highly sensitive substrate for subtilisins.

A new substrate for subtilisins, anthraniloyl-Ala-Ala-Phe-4-nitroanilide, has been synthesized and characterized. The peptide is a fluorogenic substrate that is intramolecularly quenched without loss of its chromogenic properties and offers a possibility for double-assay kinetic analysis. The kinetic parameters determined for subtilisin Carlsberg are Km = 0.

An express immunological method for detection of human seminal plasma.

Monoclonal antibodies (Mabs) against human seminal plasma (HSP) were produced and during screening procedures dissociation constants of the antigen/antibody complexes were determined. Mab 1E5 was selected for further studies because of its high reactivity in an enzyme-linked immunoassay (ELISA) and high affinity for its corresponding antigen. The specificity of Mab 1E5 was checked in absorption ELISA with human organ extracts and some biological secretions.

Action of urokinase and trypsin on angiotensin, ACTH and the oxidized B chain of insulin.

N-terminal analysis of the products of hydrolysis of angiotensin, ACTH and the oxidized B chain of insulin after 4 h incubation with trypsin and urokinase reveals a great qualitative similarity in the action of the two enzymes. As expected, the rates of hydrolysis differ significantly and are much higher in the case of trypsin catalysis than in the case of urokinase catalysis. Unexpectedly, however, a decrease in the difference between the catalytic activity of the two enzymes, by increasing the number of Arg and Lys residues present in the substrate, has been observed.

Kinetic study of the effect of heparin on the amidase activity of trypsin, plasmin and urokinase.

It was found that the effect of heparin on the amidase activity of urokinase (E C 3.4.21.

Hydrophobic interactions in the urokinase active centre. Inhibitory action of alkyl ammonium and amidinium ions: comparison with trypsin.

In order to obtain information concerning the binding site of urokinase (EC 3.4.99.