Oxidation reactivity of zinc–cysteine clusters in metallothionein

Evaluating the reactivity of the metal–thiolate clusters in metallothionein (MT) is a key step in understanding the biological functions of this protein. The effects of the metal clustering and protein environment on the thiolate reactivity with hydrogen peroxide (H₂O₂) were investigated by performing quantum theory calculations with chemical accuracy at two levels of complexity. At the first level, the reactivity with H₂O₂ of a model system ([(Zn)₃(MeS)₉]^3?, MeS is methanethiolate) of the β domain cluster of MT was evaluated using density functional theory (DFT) with the mPW1PW91 functional. At the second level of complexity, the protein environment was included in the reactant system and the calculations were performed with the hybrid ONIOM method combining the DFT–mPW1PW91 and the semiempirical PM6 levels of theory. In these conditions, the energy barrier for the oxidation of the most reactive terminal thiolate was 21.5 kcal mol^?1. This is 3 kcal mol^?1 higher than that calculated for the terminal thiolate in the model system [(Zn)₃(MeS)₉]^3? and about 7 kcal mol^?1 higher than that obtained for the free thiolate. In spite of this rise of the energy barrier induced by the protein environment, the thiolate oxidation by H₂O₂ is confirmed as a possible way for metal release from MT. On the other hand, the results suggest that the antioxidant role of MT in the living cell cannot be as important as that of glutathione (which bears a free thiol).     

Biochemische Differenzierungen bei Mais unter Mineralstoff mangel

Biochemical Differences in Maize as Related to Mineral Deficiencies. I. Changes in the Activity of some Enzymes. — The enzymatic systems in the different organs of corn seedlings are variously affected in the first growing stages by deficiency in nitrogen, phosphorus or potassium, according to the specific physiological functions of the organs. Deficiency in nitrogen causes an increase in peroxidase and catalase activity and inhibition of pyruvic and glutamic decarboxylase. Deficiency in phosphorus causes an activation of peroxidase and catalase in leaves and an inhibition of acid phosphatasc, invertase, pyruvic and glutatnic decarboxylase in roots. Deficiency in potassium, as compared to deficiency in nitrogen and phosphorus, leads to the severest disturbances of the different enzymatic systems. This deficiency causes a strong increase in leaf invertase, catalase and peroxidase activity, a stimulus in respiration intensity in the roots, and an inhibition in pyruvic and glutaniic decarboxylase in leaves and roots. The activation and inhibition changes in the enzymatic processes, appearing as a consequence of nitrogen, phosphorus and potassium deficiency have different significance and intensity.     

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. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 561–572, 2014.