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B P Atanasov

Publications and source records attributed to B P Atanasov.

At least 19 recordsLinked to original sources
PubMed2000

Protonation of the beta-lactam nitrogen is the trigger event in the catalytic action of class A beta-lactamases.

The pH dependence of the pK(a) values of all ionizable groups and of the electrostatic potential at grid points corresponding to catalytically important atoms in the active site of TEM-1 beta-lactamase has been calculated by a mean-field approach for reaction intermediates modeled on the basis of energy minimized x-ray crystallographic coordinates. By estimating electrostatic contributions to the free energy changes accompanying the conversion of the free enzyme into the acylenzyme reaction intermediate, we found that acid-catalyzed protonation of the beta-lactam nitrogen is energetically favored as the initiating event, followed by base-catalyzed nucleophilic attack on the carbonyl carbon of the beta-lactam group. N-protonation is catalyzed through a hydrogen-bonded cluster involving the 2-carboxylate group of the substrate, the side chains of S130 and K234, and a solvent molecule. Nucleophilic attack on the carbonyl carbon is carried out by the side chain of S70 with proton abstraction catalyzed by a water molecule hydrogen-bonded to the side chain of E166. Stabilization of ion pairs in the active site through interactions with distant clusters of charged residues in the enzyme was concluded to be an important driving force of the catalytic mechanism.

Catalysis↗
PubMed1997

Local electrostatic potentials in pyridoxal phosphate labelled horse heart cytochrome c.

The present work shows the application of an optical label pyridoxal phosphate (PLP) for the experimental determination of local electrostatic potentials in singly substituted cytochromes c modified by pyridoxal phosphate at Lys 79 (PLP-Lys-79-cyt.c) or at Lys 86 (PLP-Lys-86-cyt.c). PLP has also been used to calculate the pKa values of all ionizable groups and the electrostatic potentials in the modified proteins and to analyse their properties. The experimental pKa values for the pyridine nitrogen and phenolic hydroxyl of the bound label were obtained from pH-dependent absorbance and fluorescence measurements, as follows: in PLP-Lys-79-cyt.c for pyridine nitrogen 4.5 (absorbance) and 5.1 (fluorescence), for phenolic hydroxyl 8.6 (absorbance) and 8.3 (fluorescence); in PLP-Lys-86-cyt.c for pyridine nitrogen 4.7 (absorbance) and 5.8 (fluorescence), for phenolic hydroxyl 8.3 (absorbance) and 8.5 (fluorescence). The differences between absorbance and fluorescence data are related to differences in the behaviour of the bound label in the ground and excited electronic states and to intermolecular charge-charge interactions. Molecular modelling was used to generate the atomic co-ordinates of the PLP-modified horse heart cytochrome c necessary for the theoretical calculations of the pKa values and electrostatic potentials.

Animals↗
PubMed1994

Spatial optimization of electrostatic interactions between the ionized groups in globular proteins.

A model approach is suggested to estimate the degree of spatial optimization of the electrostatic interactions in protein molecules. The method is tested on a set of 44 globular proteins, representative of the available crystallographic data. The theoretical model is based on macroscopic computation of the contribution of charge-charge interactions to the electrostatic term of the free energy for the native proteins and for a big number of virtual structures with randomly distributed on protein surface charge constellations (generated by a Monte-Carlo technique). The statistical probability of occurrence of random structures with electrostatic energies lower than the energy of the native protein is suggested as a criterion for spatial optimization of the electrostatic interactions. The results support the hypothesis that the folding process optimizes the stabilizing effect of electrostatic interactions, but to very different degree for different proteins. A parallel analysis of ion pairs shows that the optimization of the electrostatic term in globular proteins has increasingly gone in the direction of rejecting the repulsive short contacts between charges of equal sign than of creating of more salt bridges (in comparison with the statistically expected number of short-range ion pairs in the simulated random structures). It is observed that the decrease in the spatial optimization of the electrostatic interactions is usually compensated for by an appearance of disulfide bridges in the covalent structure of the examined proteins.

Alcohol Dehydrogenase↗
PubMed1994

Structural modeling and electrostatic properties of aspartate transcarbamylase from Saccharomyces cerevisiae.

In Saccharomyces cerevisiae the first two reactions of the pyrimidine pathway are catalyzed by a multifunctional protein which possesses carbamylphosphate synthetase and aspartate transcarbamylase activities. Genetic and proteolysis studies suggested that the ATCase activity is carried out by an independently folded domain. In order to provide structural information for ongoing mutagenesis studies, a model of the three-dimensional structure of this domain was generated on the basis of the known X-ray structure of the related catalytic subunit from E. coli ATCase. First, a model of the catalytic monomer was built and refined by energy minimization. In this structure, the conserved residues between the two proteins were found to constitute the hydrophobic core whereas almost all the mutated residues are located at the surface. Then, a trimeric structure was generated in order to build the active site as it lies at the interface between adjacent chains in the E. coli catalytic trimer. After docking a bisubstrate analog into the active site, the whole structure was energy minimized to regularize the interactions at the contact areas between subunits. The resulting model is very similar to that obtained for the E. coli catalytic trimer by X-ray crystallography, with a remarkable conservation of the structure of the active site and its vicinity. Most of the interdomain and intersubunit interactions that are essential for the stability of the E. coli catalytic trimer are maintained in the yeast enzyme even though there is only 42% identity between the two sequences. Free energy calculations indicate that the trimeric assembly is more stable than the monomeric form. Moreover an insertion of four amino acids is localized in a loop which, in E. coli ATCase, is at the surface of the protein. This insertion exposes hydrophobic residues to the solvent. Interestingly, such an insertion is present in all the eukaryotic ATCase genes sequences so far, suggesting that this region is interacting with another domain of the multifunctional protein.

Amino Acid Sequence↗
PubMed1993

Urea unfolding and stability of gamma-II crystallin.

The conformational stability of gamma-II crystallin at pH 7.0 was estimated by studying its urea denaturation at isothermal conditions. The conformational states were monitored by far UV-CD and fluorescence measurements. Gamma-II crystallin shows sigmoidal order-disorder transition curves by both methods. The presence of more than one intermediate was confirmed but at neutral pH. The experiment results were critically analyzed in terms of both linear extrapolation and Tanford's models. The Gibbs free energy of unfolding delta G u,H2O = -36 kcal mol-1 was obtained. This value corresponds to the high conformational stability of the protein predicted qualitatively by its crystal structure.

Animals↗
PubMed1988

pH-dependence of photo-induced electron transfer in zinc-substituted sperm whale myoglobin.

The electron transfer between the excited triplet state of zinc-substituted sperm whale myoglobin and Cu2+ has been studied by following the decay rate of delayed fluorescence. The Cu2+ bound on the surface of the myoglobin molecule are efficient quenchers of the excited electron state of Zn-myoglobin. Two bimolecular rate constants of quenching (KQ) for every pH investigated have been calculated. The pH-dependence of KQ1 indicates that the protonation of one amino acid residue (His-GH1 (119] is important for the process. Our results support the idea of the common nature of the mechanism of quenching by Cu2+ and oxidation of oxymyoglobin by Cu2+.

Animals↗
PubMed1984

Pyridoxal phosphate modified cytochromes c. Identification and electron transfer properties.

The preparation, purification and characterization of the three singly, three doubly and one triply substituted derivatives of cytochrome c modified by pyridoxal phosphate (PLP) at lysine residues are reported. The PLP positions in PLP derivatives were determined by the amino acid analysis and sequence of PLP peptides. The results identified the lysine at position 86 in one of the singly substituted, lysine 79 in the other singly substituted and lysines 86 and 79 in the third doubly substituted cytochrome c derivatives. The area surrounding phenylalanine 82 forms the predominant PLP binding site on the cytochrome c molecule. The visible, CD and proton NMR spectra, the full intensity of the conformation-sensitive 695 nm band and the oxidation-reduction properties provide evidence to confirm the conclusion that singly and doubly substituted PLP cytochromes c retain the native conformation. The ability to restore both succinate and ascorbate/TMPD oxidation in cytochrome c-depleted mitochondria decreases in the order: native cytochrome c greater than PLP-Lys-79-cytochrome c greater than PLP-Lys-86-cytochrome c greater than PLP-Lys-79,86-cytochrome c greater than triply substituted derivative.

Amino Acids↗
PubMed1984

Charge interactions of cytochrome c with cytochrome c oxidase.

The pyridoxal phosphate (PLP) modification of the lysine amino groups in cytochrome c causes decrease in the reaction rate with cytochrome c oxidase. The rate constants for (PLP)2-cyt. c, PLP(Lys 86)-cyt. c, PLP(Lys 79)-cyt. c and native cytochrome c (at pH 7.4, I = 0.02) are 3.6 X 10(-3) sec-1, 5.5 X 10(-3) sec-1, 5.2 X 10(-3) sec-1 and 9.8 X 10(-3) sec-1, respectively. In spite of the same positive charge of singly PLP-cytochromes c the reaction between PLP(Lys 86)-cyt. c and cyt. c oxidase exhibits the ionic strength dependence that differs from those of the PLP(Lys 79)-cyt. c. The rate constants at zero and infinite ionic strength for PLP(Lys 86)-cyt. c is 2-fold less than that for PLP(Lys 79)-cyt. c. The positively charged cytochrome c lysines 86 and 79 form two from four or five predicted complementary charge interactions with carboxyl groups on cytochrome c oxidase.

Animals↗
PubMed1980

[Electron transfer in hemoproteins. III. Physico-chemical characteristics of autoxidation of sperm whale oxymyoglobin].

The influence of pH, temperature and ionic strength on the autoxidation of sperm whale oxy-Mb is described and the data obtained are discussed. The process depends on the ionization of two groups with pKeff approximately or equal to 6. They are not accessible histidines of Mb. There are two parallel processes of autoxidation and each of them have a different temperature dependence. Two regions of ionic strength of opposite influence on the rats of autoxidation both at "low" (10 degrees C) and "high" (30 degrees C) temperatures were found.

Animals↗
PubMed1976

Dependence of magneto-optical rotatory dispersion and magnetic circular dichroism of deoxy- and methemoglobin on their quaternary structure.

Methods of magnetic optical activity, magneto-optical rotatory dispersion (MORD) and magnetic circular dichroism (MCD), were shown to be sensitivie to the quaternary structure of deoxyhemoglobin. The isolated alpha and beta chains, the monomeric hemoglobins (leghemoglobin, fraction III of Chironomus thummi thummi hemoglobin) and hemoglobin in the R state (hemoglobin digested with carboxypeptidases A and B) exhibit in the visible region two MORD minima of equal intensities. In native tetrameric hemoglobins studied (human, horse, porcine, feline, carp, tortoise, frog) the ratio of the intensities of these MORD minima is about 2. The MORD data for deoxy-des Arg-N-ethylsuccinimide-hemoglobin indicate that in solution there is a mixture of the T and R states, the equilibrium between the states being shifted toward the R structure. The identity of the MORD curves for deoxy-bis(N-maleimidoethyl)-ester-hemoglobin and for native deoxyhemoglobin indicates that deoxy-bis(N-maleimidoethyl)ester-hemoglobin has the T structure in solution. Comparison of the MORD curves exhibited by a native methemoglobin, a native metmyoglobin and the modified hemoglobins in the met form in the absence and presence of organic and inorganic phosphates reveals no direct correlation between the MORD changes and methemoglobin quaternary structure.

Binding Sites↗