Biomedical subjects

J Ciarkowski

Publications and source records attributed to J Ciarkowski.

33 records · Page 2Linked to original sources

PubMed1996

Mechanism of action of aspartic proteinases: application of transition-state analogue theory.

Applying the semiempirical MO methods AM1 and PM3 as well as the density functional theory to the model of the catalytic site composed of ca. 160-190 atoms, we have carried out studies aimed at the explanation of three aspects of the mechanism of action of aspartic proteinases: the site of dissociation within the catalytic diad COOH/COO- (i) in the free enzyme and (ii) in the Michaelis complex, and (iii) the energy changes associated with the catalytic paths. We have found that the state of dissociation within the catalytic diad is ligand-sensitive. In the free enzyme and in the intermediate complexes, Asp33 prefers to be dissociated with the outer oxygen of Asp213 protonated, while in the Michaelis and product complexes the opposite holds true. This is in agreement with recent mechanistic hypotheses and with some experimental results by FTIR and NMR. The energy diagram for the catalysis indicates that electronic effects are responsible most of all for the relative reduction of energy of the intermediates and possibly transition states on the catalytic reaction path. The shape of the diagram qualitatively agrees with the transition-state analogue theory for the enzymatic reactions.

Aspartic Acid↗

PubMed1994

Prediction of conformation of rat galanin in the presence and absence of water with the use of Monte Carlo methods and the ECEPP/3 force field.

The conformation of the 29-residue rat galanin neuropeptide was studied using the Monte Carlo with energy minimization (MCM) and electrostatically driven Monte Carlo (EDMC) methods. According to a previously elaborated procedure, the polypeptide chain was first treated in a united-residue approximation, in order to enable extensive exploration of the conformational space to be carried out (with the use of MCM). Then the low-energy united-residue conformations were converted to the all-atom representations, and EDMC simulations were carried out for the all-atom polypeptide chains, using the ECEPP/3 force field with hydration included. In order to estimate the effect of environment on galanin conformation, the low-energy conformations obtained as a result of these simulations were taken as starting structures for further EDMC runs that did not include hydration. The lowest-energy conformation obtained in aqueous solution calculations had a nonhelical N-terminal part packed against the nonpolar face of a residual helix that extended from Pro13 toward the C-terminus. One next lowest-energy structure was a nearly-all-helical conformation, but with a markedly higher energy. In contrast, all of the low-energy conformations in the absence of water were all-helical differing only by the extent to which the helix was kinked around Pro13. These results are in qualitative agreement with the available NMR and CD data of galanin in aqueous and nonaqueous solvents.

Amino Acid Sequence↗

PubMed1991

Reaction mechanisms in peptide synthesis. Part 1. Semiquantitative characteristics of the reactivity of 2-methyl-5(4H)-oxazolone with water and ammonia in the gas phase and weakly polar media.

2,4-Dialkyl-5(4H)-oxazolones are well-recognized intermediates in some aminolysis reactions in peptide synthesis. Using the MOPAC molecular orbital programs, detailed geometric and energetic characteristics of the elementary reaction pathways for the additions of water and ammonia to 2-methyl-5(4H)-oxazolone have been determined at the AM1 level. The results demonstrate that the additions must be parsed into a two-step mechanism involving formation of the alpha-hydroxyimine followed by tautomerization to the parent N-acetylamino acid or amide.

Ammonia↗

PubMed1991

Reaction mechanisms in peptide synthesis. Part 2. Tautomerism of the peptide bond.

We had concluded in previous work that ring opening of a 2-alkyl-5(4H)-oxazolone by water or ammonia leads to transient high-energy imidol intermediates which instantly tautomerize to the native amides. Using the MOPAC molecular orbital program, detailed geometric and energetic characteristics of the tautomerism of a peptide bond have been determined on the AM1 level. The results demonstrate that tautomerism of a peptide bond comprises a three-stage process involving three successive transition states and a bimolecular mechanism: (i) E----Z peptide bond isomerization followed by dimerization, (ii) concerted double-hydrogen exchange leading to an alpha-hydroxyimine (imidic acid) followed by splitting of the dimer, and (iii) Z----E N-methylimine inversion. While pathway (iii----ii----i) is predicted as a feasible route terminating in the formation of a peptide bond, the inverse route (iii----ii----i) is excluded as a possible initial step in the generation of a 5(4H)-oxazolone intermediate.

Ammonia↗

PubMed1990

Conformation of cyclo-(D-phenylalanyl-trans-4-fluoro-D-prolyl).

cyclo(D-Phenylalanyl-trans-4-fluoro-D-prolyl), c(D-Phe-D-FPro), was synthesized and its conformation determined both in solution and in the solid state by 1H NMR and X-ray analysis, respectively. In the crystals the 2.5-diketopiperazine (DKP) ring assumes the uncommon conformation, for cyclodipeptides containing Pro residue, of a flattened chair, which seemingly results from a compromise between, on the one hand, the DKP-aromatic intramolecular ring-ring attraction (folding), requiring the C alpha--C beta bond of the Phe to be axial, and, on the other hand, the intrinsic tendency of the Pro residue to have its C alpha--C beta bond equatorial. Unlike the solid state, the 1H NMR data in CDCl3 and C6D6 demonstrate that in both solutions the DKP ring assumes a boat-like shape, typical for the Pro-containing cyclodipeptides, with the equatorial C alpha--C beta bonds in both amino acid residues, which preclude ring-ring folding. A similar conformation was encountered in the closest analog of c(D-Phe-D-FPro), viz, in c(Phe-Pro), both in solution (21, 22, 26) and in the solid state (12). A subtle interplay of intramolecular interactions introduced into a cyclodipeptide by a Pro-type and a Phe-type residue is emphasized.

Magnetic Resonance Spectroscopy↗

PubMed1984

Wound infection caused by Kanagawa-negative Vibrio parahaemolyticus.

Kanagawa-positive Vibrio parahaemolyticus strains are considered to be human pathogens and are most commonly associated with summer diarrhea. Kanagawa-negative strains are most frequently isolated from the environment and are generally considered to be nonpathogens. We report a wound infection caused by a Kanagawa-negative V. parahaemolyticus strain. The infection occurred in October, an unusual time of the year for a V. parahaemolyticus infection to occur in the mid-Atlantic region of the United States.

Adult↗

PubMed1974