Mironel Enescu

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.

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.

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.

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.

Oxidation of Zinc–Thiolate Complexes of Biological Interest by Hydrogen Peroxide: A Theoretical Study

Zinc-thiolate complexes play a major structural and functional role in the living cell. Their stability is directly related to the thiolate reactivity toward reactive oxygen species naturally present in the cell. Oxidation of some zinc-thiolate complexes has a functional role, as is the case of zinc finger redox switches. Herein, we report a theoretical investigation on the oxidation of thiolate by hydrogen peroxide in zinc finger cores of CCCC, CCHC, and CCHH kinds containing either cysteine or histidine residues. In the case of the CCCC core, the calculated energy barrier for the oxidation to sulfenate of the complexed thiolate was found to be 16.0 kcal mol(-1), which is 2 kcal mol(-1) higher than that for the free thiolate. The energy barrier increases to 19.3 and 22.2 kcal mol(-1) for the monoprotonated and diprotonated CCCC cores, respectively. Substitution of cysteine by histidine also induces an increase in the magnitude of the reaction energy barrier: It becomes 20.0 and 20.9 kcal mol(-1) for the CCCH and CCHH cores, respectively. It is concluded that the energy barrier for the oxidation of zinc fingers is strictly dependent on the type of ligands coordinated to zinc and on the protonation state of the complex. These changes in the thiolate reactivity can be explained by the lowering of the nucleophilicity of complexed sulfur and by the internal reorganization of the complex (changes in the metal-ligand distances) upon oxidation. The next reaction steps subsequent to sulfenate formation are also considered. The oxidized thiolate (sulfenate) is predicted to dissociate very fast: For all complexes, the calculated dissociation energy barrier is lower than 3 kcal mol(-1). It is also shown that the dissociated sulfenic acid can interact with a free thiolate to form a sulfur-sulfur (SS) bridge in a reaction that is predicted to be quasi-diffusion limited. The interesting biological consequences of the modulation of thiolate reactivity by the chemical composition of the zinc finger cores are discussed.

Cysteine Oxidation by the Superoxide Radical: A Theoretical Study

The cysteine residue oxidation by the superoxide radical in the gas phase and in aqueous solution is studied using the integrated molecular orbital+molecular orbital (IMOMO) method combining the quadratic configuration interaction [QCISD(T)] and density functional (DFT) methods. The molecular environment effects are systematically investigated by considering two alternative directions of attack of the superoxide radical on the thiol and two different cysteine residue conformations. It is found that hydrogen bonding and the electrostatic interactions between the superoxide radical and cysteine side chain significantly affect the reaction energy barrier, as compared to that derived for the simple thiol model methanethiol. Among the two possible reaction channels, the one involving the sulfinyl radical formation is predicted to be the dominant channel in aqueous solution. In a highly hydrophobic environment the thiyl radical formation channel becomes the main cysteine oxidation channel.

Structure, Bonding, and Stability of Mercury Complexes with Thiolate and Thioether Ligands from High-Resolution XANES Spectroscopy and First-Principles Calculations

We present results obtained from high energy-resolution L3-edge XANES spectroscopy and first-principles calculations for the structure, bonding, and stability of mercury(II) complexes with thiolate and thioether ligands in crystalline compounds, aqueous solution, and macromolecular natural organic matter (NOM). Core-to-valence XANES features that vary in intensity differentiate with unprecedented sensitivity the number and identity of Hg ligands and the geometry of the ligand environment. Post-Hartree-Fock XANES calculations, coupled with natural population analysis, performed on MP2-optimized Hg[(SR)2···(RSR)n] complexes show that the shape, position, and number of electronic transitions observed at high energy-resolution are directly correlated to the Hg and S (l,m)-projected empty densities of states and occupations of the hybridized Hg 6s and 5d valence orbitals. Linear two-coordination, the most common coordination geometry in mercury chemistry, yields a sharp 2p to 6s + 5d electronic transition. This transition varies in intensity for Hg bonded to thiol groups in macromolecular NOM. The intensity variation is explained by contributions from next-nearest, low-charge, thioether-type RSR ligands at 3.0-3.3 Å from Hg. Thus, Hg in NOM has two strong bonds to thiol S and k additional weak Hg···S contacts, or 2 + k coordination. The calculated stabilization energy is -5 kcal/mol per RSR ligand. Detection of distant ligands beyond the first coordination shell requires precise measurement of, and comparison to, spectra of reference compounds as well as accurate calculation of spectra for representative molecular models. The combined experimental and theoretical approaches described here for Hg can be applied to other closed-shell atoms, such as Ag(I) and Au(I). To facilitate further calculation of XANES spectra, experimental data, a new crystallographic structure of a key mercury thioether complex, Cartesian coordinates of the computed models, and examples of input files are provided as Supporting Information .

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.

Free energy calculations on disulfide bridges reduction in proteins by combining ab initio and molecular mechanics methods.

Free energy profiles were calculated for the reduction of the four disulfide bridges in lysozyme by tris(2-carboxyethyl)phosphine (TCEP). The computational method combines high-precision density functional theory (DFT) calculations performed on the core of the reactant system with classical mechanical free energy evaluations based on the sampling of the configuration space of reaction environment. The predicted reaction energy barriers are in satisfactory agreement with experimental data, proving that the present method provides a reliable description of the mechanism of reaction. The role of the protein environment in this mechanism is further emphasized by analyzing the different contributions to the free energy profiles. It is shown that the protein environment affects the reaction by three factors: polarizability, steric hindrance of the reactant site, and S-S bridge distortion due to structural constraints. The corresponding effects are quantitatively evaluated, and the results are discussed in connection with the current two-step reaction model for the reduction of S-S bridges in proteins.

Optical properties of cytostatic drugs used in cancer treatment

A spectroscopical characterization of methotrexate, cytostatic drug used frequently in cancer therapy, was performed. The absorption, emission and excitation spectra were measured for methotrexate solutions in natural saline and sodium hydroxide at concentration in the range 10-5 M -10-6 M and pH 8.4. The absorption bands are noticed in the spectral range 250 nm - 450 nm. The fluorescence excitation was made at 340 nm and 370 nm; the fluorescence emission was detected in the spectral range 400 nm - 500 nm with a maximum at 450 nm. The behavior of absorption and fluorescence spectra of methotrexate solution exposed to uv-visible light was investigated. The irradiation was made using an Xe lamp (emission between 325 nm and 420 nm and power density of 11 mW/cm2). The exposure time was between 15 min. and 3 h. Major modifications on absorption bands for irradiation times longer than 1 hour were observed. Furthermore, the methotrexate solutions become strongly fluorescent after irradiation. The observed changes are not linear with the exposure time indicating complex photochemical processes which implies, at least, one intermediate product.