Fate of cisplatin and its main hydrolysed forms in the presence of thiolates: a comprehensive computational and experimental study

Thiolations and bidentations drive the chemical fate of cisplatin compounds in intracellular medium.

Methionine oxidation by hydrogen peroxide in peptides and proteins: A theoretical and Raman spectroscopy study

The oxidation of proteins results in their deterioration via the oxidation of reactive amino acids. Oxidation of the amino acid, methionine plays an important role during biological conditions of oxidative stress, and equally a role in protein stability. In this study the oxidation of the methionine residue using the tripeptide GlyMetGly with respect to hydrogen peroxide has been studied using both Raman spectroscopy and DFT calculations. Spectral modifications following the formation of methionine sulfoxide are shown with the appearance of the SO vibration whilst there is also the modification of the CS vibrations at approximately 700 cm^-1. The changes in the intensity of the CS stretching band were used to calculate the kinetic rate constant as 7.9 ± 0.6 × 10^-3 dm³ mol^-1 s^-1. The energy barrier for the reaction. is determined both experimentally and using DFT calculations. The reaction of the dairy protein beta-lactoglobulin with hydrogen peroxide is equally studied using the same technique. The solvent accessible surface area of the methionine residues within the protein were also determined and a comparison of the reaction rate constant and the energy barriers of reaction for the oxidation of the tripeptide and for the protein respectively thus, provides information about the role of the protein environment in the oxidation process.

Chemical Forms of Mercury in Human Hair Reveal Sources of Exposure

Humans are contaminated by mercury in different forms from different sources. In practice, contamination by methylmercury from fish consumption is assessed by measuring hair mercury concentration, whereas exposure to elemental and inorganic mercury from other sources is tested by analysis of blood or urine. Here, we show that diverse sources of hair mercury at concentrations as low as 0.5 ppm can be individually identified by specific coordination to C, N, and S ligands with high energy-resolution X-ray absorption spectroscopy. Methylmercury from seafood, ethylmercury used as a bactericide, inorganic mercury from dental amalgams, and exogenously derived atmospheric mercury bind in distinctive intermolecular configurations to hair proteins, as supported by molecular modeling. A mercury spike located by X-ray nanofluorescence on one hair strand could even be dated to removal of a single dental amalgam. Chemical forms of other known or putative toxic metals in human tissues could be identified by this approach with potential broader applications to forensic, energy, and materials science.

A principal component analysis of the dynamics of subdomains and binding sites in human serum albumin

The conformational dynamics of human serum albumin (HSA) was investigated by principal component analysis (PCA) applied to three molecular dynamics trajectories of 200 ns each. The overlap of the essential subspaces spanned by the first 10 principal components (PC) of different trajectories was about 0.3 showing that the PCA based on a trajectory length of 200 ns is not completely convergent for this protein. The contributions of the relative motion of subdomains and of the subdomains (internal) distortion to the first 10 PCs were found to be comparable. Based on the distribution of the first 3 PC, 10 protein conformers are identified showing relative root mean square deviations (RMSD) between 2.3 and 4.6 Å. The main PCs are found to be delocalized over the whole protein structure indicating that the motions of different protein subdomains are coupled. This coupling is considered as being related to the allosteric effects observed upon ligand binding to HSA. On the other hand, the first PC of one of the three trajectories describes a conformational transition of the protein domain I that is close to that experimentally observed upon myristate binding. This is a theoretical support for the older hypothesis stating that changes of the protein onformation favorable to binding can precede the ligand complexation. A detailed all atoms PCA performed on the primary Sites 1 and 2 confirms the multiconformational character of the HSA binding sites as well as the significant coupling of their motions.

Protein reactivity with singlet oxygen: Influence of the solvent exposure of the reactive amino acid residues

The singlet oxygen quenching rate constants were measured for three model proteins, bovine serum albumin, β-lactoglobulin and lysozyme. The results were analyzed by comparing them with the corresponding singlet oxygen quenching rate constants for a series of tripeptides with the basic formula GlyAAGly where the central amino acid (AA) was the oxidizable amino acid, tryptophan, tyrosine, methionine and histidine. It was found that the reaction rate constant in proteins can be satisfactorily modelled by the sum of the individual contributions of the oxidizable AA residues corrected for the solvent accessible surface area (SASA) effects. The best results were obtained when the SASA of the AA residues were determined by averaging over molecular dynamics simulated trajectories of the proteins. The limits of this geometrical correction of the AA residue reactivity are also discussed.

Empirical force field for cisplatin based on quantum dynamics data: case study of new parameterization scheme for coordination compounds

Parameterization of molecular complexes containing a metallic compound, such as cisplatin, is challenging due to the unconventional coordination nature of the bonds which involve platinum atoms. In this work, we develop a new methodology of parameterization for such compounds based on quantum dynamics (QD) calculations. We show that the coordination bonds and angles are more flexible than in normal covalent compounds. The influence of explicit solvent is also shown to be crucial to determine the flexibility of cisplatin in quantum dynamics simulations. Two empirical topologies of cisplatin were produced by fitting its atomic fluctuations against QD in vacuum and QD with explicit first solvation shell of water molecules respectively. A third topology built in a standard way from the static optimized structure was used for comparison. The later one leads to an excessively rigid molecule and exhibits much smaller fluctuations of the bonds and angles than QD reveals. It is shown that accounting for the high flexibility of cisplatin molecule is needed for adequate description of its first hydration shell. MD simulations with flexible QD-based topology also reveal a significant decrease of the barrier of passive diffusion of cisplatin accross the model lipid bilayer. These results confirm that flexibility of organometallic compounds is an important feature to be considered in classical molecular dynamics topologies. Proposed methodology based on QD simulations provides a systematic way of building such topologies.

Formation of Mercury Sulfide from Hg(II)-Thiolate Complexes in Natural Organic Matter

Methylmercury is the environmental form of neurotoxic mercury that is biomagnified in the food chain. Methylation rates are reduced when the metal is sequestered in crystalline mercury sulfides or bound to thiol groups in macromolecular natural organic matter. Mercury sulfide minerals are known to nucleate in anoxic zones, by reaction of the thiol-bound mercury with biogenic sulfide, but not in oxic environments. We present experimental evidence that mercury sulfide forms from thiol-bound mercury alone in aqueous dark systems in contact with air. The maximum amount of nanoparticulate mercury sulfide relative to thiol-bound mercury obtained by reacting dissolved mercury and soil organic matter matches that detected in the organic horizon of a contaminated soil situated downstream from Oak Ridge, TN, in the United States. The nearly identical ratios of the two forms of mercury in field and experimental systems suggest a common reaction mechanism for nucleating the mineral. We identified a chemical reaction mechanism that is thermodynamically favorable in which thiol-bound mercury polymerizes to mercury-sulfur clusters. The clusters form by elimination of sulfur from the thiol complexes via breaking of mercury-sulfur bonds as in an alkylation reaction. Addition of sulfide is not required. This nucleation mechanism provides one explanation for how mercury may be immobilized, and eventually sequestered, in oxygenated surface environments.

An experimental and theoretical study of the amino acid side chain Raman bands in proteins

The Raman spectra of a series of tripeptides with the basic formula GlyAAGly where the central amino acid (AA) was tryptophan, tyrosine, phenylalanine, glycine, methionine, histidine, lysine and leucine were measured in H2O. The theoretical Raman spectra obtained using density functional theory (DFT) calculations at the B3LYP/6-311+G(2df,2pd) level of theory allows a precise attribution of the vibrational bands. The experimental results show that there is a blue shift in the frequencies of several bands of the amino acid side chains in tripeptides compared to free amino acids, especially in the case of AAs containing aromatic rings. On the other hand, a very good agreement was found between the Raman bands of AA residues in tripeptides and those measured on three model proteins: bovine serum albumin, β-lactoglobulin and lysozyme. The present analysis contributes to an unambiguous interpretation of the protein Raman spectra that is useful in monitoring the biological reactions involving AA side chains alteration.

About the structural role of disulfide bridges in serum albumins: evidence from protein simulated unfolding

The role of the 17 disulfide (S-S) bridges in preserving the native conformation of human serum albumin (HSA) is investigated by performing classical molecular dynamics (MD) simulations on protein structures with intact and, respectively, reduced S-S bridges. The thermal unfolding simulations predict a clear destabilization of the protein secondary structure upon reduction of the S-S bridges as well as a significant distortion of the tertiary structure that is revealed by the changes in the protein native contacts fraction. The effect of the S-S bridges reduction on the protein compactness was tested by calculating Gibbs free energy profiles with respect to the protein gyration radius. The theoretical results obtained using the OPLS-AA and the AMBER ff03 force fields are in agreement with the available experimental data. Beyond the validation of the simulation method, the results here reported provide new insights into the mechanism of the protein reductive/oxidative unfolding/folding processes. It is predicted that in the native conformation of the protein, the thiol (-SH) groups belonging to the same reduced S-S bridge are located in potential wells that maintain them in contact. The -SH pairs can be dispatched by specific conformational transitions of the peptide chain located in the neighborhood of the cysteine residues.

Reductive unfolding of serum albumins uncovered by Raman spectroscopy

The reductive unfolding of bovine serum albumin (BSA) and human serum albumin (HSA) induced by dithiothreitol (DTT) is investigated using Raman spectroscopy. The resolution of the S-S Raman band into both protein and oxidized DTT contributions provides a reliable basis for directly monitoring the S-S bridge exchange reaction. The related changes in the protein secondary structure are identified by analyzing the protein amide I Raman band. For the reduction of one S-S bridge of BSA, a mean Gibbs free energy of -7 kJ mol(-1) is derived by studying the reaction equilibrium. The corresponding value for the HSA S-S bridge reduction is -2 kJ mol(-1). The reaction kinetics observed via the S-S or amide I Raman bands are identical giving a reaction rate constant of (1.02 +/- 0.11) M(-1) s(-1) for BSA. The contribution of the conformational Gibbs free energy to the overall Gibbs free energy of reaction is further estimated by combining experimental data with ab initio calculations.

An outbreak of gastroenteritis in a campsite in Romania, July 2007

Between 8 and 13 July 2007, an outbreak of acute gastroenteritis involving 117 holiday-makers (children and adults) at a campsite in Romania was investigated by the Constanta District Public Health Authority (CDPHA). The camp complex has a capacity for 4,200 people and includes four canteens.

Selenocysteine versus cysteine reactivity: a theoretical study of their oxidation by hydrogen peroxide

The cysteine and selenocysteine oxidation by H2O2 in vacuo and in aqueous solution was studied using the integrated molecular orbital + molecular orbital (IMOMO) method combining the quadratic configuration method QCISD(T) and the spin projection of second-order perturbation theory PMP2. It is shown that including in the model system of cysteine (selenocysteine) residue up to 20 atoms has significant consequences upon the calculated reaction energy barrier. On the other hand, it is demonstrated that free cysteine and selenocysteine have very similar reaction energy barriers, 77-79 kJ mol(-1) in aqueous solution. It is thus concluded that the high experimental reaction rate constant reported for the oxidation of the selenocysteine residue in the glutathione peroxidase (GPx) active center is due to an important interaction between selenocysteine and its molecular environment. The sensitivity of the calculated energy barrier to the dielectric constant of the molecular environment observed for both cysteine and selenocysteine as well as the catalytic effect of the NH group emphasized in the case of cysteine supports this hypothesis.

Mechanism of Cysteine Oxidation by a Hydroxyl Radical: A Theoretical Study

Cysteine oxidation by HO(.) was studied at a high level of ab initio theory in both gas phase and aqueous solution. Potential energy surface scans in the gas phase performed for the model system methanethiol+HO(.) indicate that the reactants can form two intermediate states: a sulfur-oxygen adduct and a hydrogen bound reactant complex. However these states appear to play a minor role in the reaction mechanism as long as they are fast dissociating states. Thus the main reaction channel predicted at the QCISD(T)/6-311+G(2df,2pd) level of theory is the direct hydrogen atom abstraction. The reaction mechanism is not perturbed by solvation which was found to induce only small variations in the Gibbs free energy of different reactant configurations. The larger size reactant system cysteine+HO* was treated by the integrated molecular orbital+molecular orbital (IMOMO) hybrid method mixing the QCISD(T)/6-311+G(2df,2pd) and the UMP2/6-311+G(d,p) levels of theory. The calculated potential energy, enthalpy, and Gibbs free energy barriers are slightly different from those of methanethiol. The method gave a rate constant for cysteine oxidation in aqueous solution, k=2.4 x 10(9) mol(-1) dm(3) s(-1), which is in good agreement with the experimental rate constant. Further analysis showed that the reaction is not very sensitive to hydrogen bonding and electrical polarity of the molecular environment.

A Computational Study of Thiolate and Selenolate Oxidation by Hydrogen Peroxide

Ab initio molecular orbital calculations have been used to study the effects of the molecular environment on the oxidation of thiolate and selenolate by hydrogen peroxide. The reaction was first examined in vacuo at the QCISD(T)/6-311+G(2df,2pd)//MP2/6-311+G(d,p) level of theory. It was found for both thiolate and selenolate that a reactant aggregate is formed, which has a dissociation rate constant comparable to the activation rate constant (about 10(-3) s(-1) for thiolate and 10(-1) s(-1) for selenolate). Using the polarizable continuum model (PCM) it was then found that the dissociation barrier energy decreases dramatically in water giving a dissociation rate constant of the order of 10(9) s(-1). In this case, the predicted overall rate constant of the thiolate reaction was about 10.2 mol(-1) dm3 s(-1), which is in good agreement with the experimental rate constant of cysteine oxidation in aqueous solution. The calculated rate constant for the selenolate reaction was somewhat higher (about 35.4 mol(-1) dm3 s(-1)). However, this value is several orders of magnitude smaller than the experimental value reported for the oxidation of selenocysteine in glutathione peroxidase. By considering the effect of the PCM dielectric constant on the reaction rate constant it was concluded that the high reactivity of the selenocysteine in glutathione peroxidase, as compared with cysteine, could be mainly due to the molecular environment of the selenocysteine residue.

Adaptive algorithm for blind separation from noisy time-varying mixtures

This article addresses the problem of blind source separation from time-varying noisy mixtures using a state variable model and recursive estimation. An estimate of each source signal is produced real time at the arrival of new observed mixture vector. The goal is to perform the separation and attenuate noise simultaneously, as well as to adapt to changes that occur in the mixing system. The observed data are projected along the eigenvectors in signal subspace. The subspace is tracked real time. Source signals are modeled using low-order AR (autoregressive) models, and noise is attenuated by trading off between the model and the information provided by measurements. The type of zero-memory nonlinearity needed in separation is determined on-line. Predictor-corrector filter structures are proposed, and their performance is investigated in simulation using biomedical and communications signals at different noise levels and a time-varying mixing system. In quantitative comparison to other widely used methods, significant improvement in output signal-to-noise ratio is achieved.

Excited-state dynamics of fully reduced flavins and flavoenzymes studied at subpicosecond time resolution

The photophysics of the fully reduced states of a number of flavins (flavin mononucleotide, flavin adenine dinucleotide and 3-N-methyllumiflavin) and flavoenzymes (glucose oxidase from Aspergillus niger and the flavodehydrogenase component isolated from flavocytochrome b2) was studied using subpicosecond laser excitation at lambda = 312 nm. The prompt transient absorption spectra (measured from 400 to 850 nm) were all closely similar in the case of the free flavins in aqueous solution. The decay of the transient absorbance obeyed biexponential kinetics with a fast component of lifetime ranging from 4 to 130 ps and a slower phase with a lifetime above 1 ns. The spectral structure changed appreciably during the rapid decay phase. In contrast, in the case of the enzymes only a very slight decay was apparent over the probed time interval (1 ns) and the shape of the spectrum remained unchanged. It is proposed that the two transient spectra appearing in the free flavins correspond to two conformations differing by their degree of nonplanarity, whereas in the flavoenzymes only one conformation is possible.

Dynamic and thermodynamic effects of glycerol on bovine serum albumin in aqueous solution: a tryptophan phosphorescence study

The phosphorescence decay of bovine serum albumin in water-glycerol solutions at room temperature is analysed by the maximum entropy method. While in pure water the decay was found to be quasi-monoexponential, in water-glycerol mixtures it is associated with more complex lifetime distributions. This is a direct proof for the existence of multiple protein conformers. It was also found that the increase of the glycerol concentration induces a continuous shift of the lifetime pattern to longer lifetimes. This effect is analysed in connection with the coupling between the solvent viscosity and the internal protein mobility.

Paediatric burns in Bucharest, Romania; 4327 cases over a 5-year period

This is a retrospective study based upon 4327 paediatric burns (0-16 years of age) admitted over a period of 5 years, as from January 1988. Epidemiological data include age, sex, cause of burn, extent of injury, social and economic status, period of time between the accident and the admission to hospital. The overall mortality rate was 5.8 per cent. We tried to correlate the mortality rate with the epidemiological data. The recent use of Flamazine cream in our centre (as from January, 1993) seems to have decreased the mortality rate to 2.6 per cent (12 deaths out of 450 patients admitted during the first 7 months of 1993). No study of childhood burns has previously been reported from Romania.

Quenching of merocyanine 540 triplet state by nitroxyl radicals in liposomal systems: a laser flash photolysis study

Laser flash photolysis experiments were undertaken to investigate the interaction between stearic acid nitroxide spin probes and photoexcited merocyanine 540 (MC540) in dimyristoyl-L-alpha-phosphatidylcholine liposomes (membrane model). The measurements of the paramagnetic signal decay kinetics of four different spin-labelled stearic acids (n-DSA) show that the direct interaction between the dye and the probe is affected by the position of the nitroxyl group along the carbon chain. Laser flash photolysis results reveal a significant decrease in the MC540 triplet lifetime in the presence of n-DSA, the effect depending on the depth at which the nitroxyl moiety is localized in the bilayer. Previous results on the rate of disappearance of the electron spin resonance (ESR) nitroxide signal on continuous photolysis of the same systems do not show the same dependence on the localization of the nitroxyl moiety in the liposome. Although the MC540 triplet state seems to be implicated in the reaction process, the results suggest that ESR and laser flash experiments demonstrate two different kinds of mechanism.

Phosphorescence lifetime studies of interactions between serum albumins and sodium dodecyl sulfate

Binding of sodium dodecyl sulfate (SDS) to bovine serum albumin (BSA) and human serum albumin (HSA) in aqueous solutions at room temperature induces significant changes in the phosphorescence lifetime of tryptophan (Trp) residues. A steep rise of the phosphorescence lifetime from 1.9 ms to 10.0 ms for BSA and from 1.9 ms to 5.5 ms for HSA is observed when the total SDS concentration increases from 0.0 mM to 0.22 mM at 1 mg/mL protein concentration. As the total SDS concentration is further increased to 2.2 mM, a slower increase in the phosphorescence lifetime is observed, from 10.0 ms to 19.5 ms for BSA and from 5.5 ms to 7.2 ms for HSA. It appears that the phosphorescence lifetime modifications are mainly due to an increase of protein matrix rigidity around Trp residues. The observed differences (between HSA and BSA) allow us to distinguish the contribution of the two Trp residues to the BSA phosphorescence.