A DFT study of the mechanism of Ni superoxide dismutase (NiSOD): role of the active site cysteine-6 residue in the oxidative half-reaction

In the present DFT study, the catalytic mechanism of H2O2 formation in the oxidative half-reaction of NiSOD, E-Ni(II) + O2- + 2H+ --> E-Ni(III) + H2O2, has been investigated. The main objective of this study is to investigate the source of two protons required in this half-reaction. The proposed mechanism consists of two steps: superoxide coordination and H2O2 formation. The effect of protonation of Cys6 and the proton donating roles of side chains (S) and backbones (B) of His1, Asp3, Cys6, and Tyr9 residues in these two steps have been studied in detail. For protonated Cys6, superoxide binding generates a Ni(III)-O2H species in a process that is exothermic by 17.4 kcal/mol (in protein environment using the continuum model). From the Ni(III)-O2H species, H2O2 formation occurs through a proton donation by His1 via Tyr9, which relative to the resting position of the enzyme is exothermic by 4.9 kcal/mol. In this pathway, a proton donating role of His1 residue is proposed. However, for unprotonated Cys6, a Ni(II)-O2- species is generated in a process that is exothermic by 11.3 kcal/mol. From the Ni(II)-O2- species, the only feasible pathway for H2O2 formation is through donation of protons by the Tyr9(S)-Asp3(S) pair. The results discussed in this study elucidate the role of the active site residues in the catalytic cycle and provide intricate details of the complex functioning of this enzyme.     

Multiple layer formation of bovine serum albumin on silver nanoparticles revealed by dynamic light scattering and spectroscopic techniques

It is well known that when nanoparticles (NPs) are exposed to biological fluid, it results into formation of nanoparticle protein corona, which has been the subject of extensive studies for the development of targeted drug delivery. In this work, we demonstrated the dynamic light scattering, fluorescence, and UV-visible spectroscopy as quantitative and qualitative tools to monitor adsorption of BSA protein onto silver nanoparticles (AgNPs). The adsorption resulted in significant gradual increase in average hydrodynamic radius of BSA-AgNP corona from 24 to 35 nm and its attainment of equilibrium point (saturation) that correlated with albumin concentration enables condition for bound and unbound protein adsorption to be interpreted. Using DLS, the dissociation constant (K_D) was obtained for soft corona to be 2.09?±?0.30 μM. The UV-visible and fluorescence spectroscopy results were correlated with DLS. Loss of percent helicity in secondary structure of adsorbed BSA was monitored in both coronas as compared to native protein. Both coronas were found to be biocompatible with RBC membrane. Further, the results of adsorption isotherm model were used to validate the multilayer formation of albumin protein on silver nanoparticles. The obtained results would be relevant in the drug design development for tumor-targeted therapy.

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Characterization of N‐methylated amino acids by GC‐MS after ethyl chloroformate derivatization

Methylation is an essential metabolic process in the biological systems, and it is significant for several biological reactions in living organisms. Methylated compounds are known to be involved in most of the bodily functions, and some of them serve as biomarkers. Theoretically, all α‐amino acids can be methylated, and it is possible to encounter them in most animal/plant samples. But the analytical data, especially the mass spectral data, are available only for a few of the methylated amino acids. Thus, it is essential to generate mass spectral data and to develop mass spectrometry methods for the identification of all possible methylated amino acids for future metabolomic studies. In this study, all N‐methyl and N,N‐dimethyl amino acids were synthesized by the methylation of α‐amino acids and characterized by a GC‐MS method. The methylated amino acids were derivatized with ethyl chloroformate and analyzed by GC‐MS under EI and methane/CI conditions. The EI mass spectra of ethyl chloroformate derivatives of N‐methyl ( 1–18 ) and N,N‐dimethyl amino acids ( 19–35 ) showed abundant [M‐COOC₂H₅]⁺ ions. The fragment ions due to loss of C₂H₄, CO₂, (CO₂ + C₂H₄) from [M‐COOC₂H₅]⁺ were of structure indicative for 1–18 . The EI spectra of 19–35 showed less number of fragment ions when compared with those of 1–18 . The side chain group (R) caused specific fragment ions characteristic to its structure. The methane/CI spectra of the studied compounds showed [M + H]⁺ ions to substantiate their molecular weights. The detected EI fragment ions were characteristic of the structure that made easy identification of the studied compounds, including isomeric/isobaric compounds. Fragmentation patterns of the studied compounds ( 1–35 ) were confirmed by high‐resolution mass spectra data and further substantiated by the data obtained from ¹³C₂‐labeled glycines and N‐ethoxycarbonyl methoxy esters. The method was applied to human plasma samples for the identification of amino acids and methylated amino acids. Copyright © 2016 John Wiley & Sons, Ltd.     

Protonation states of the catalytic dyad of β-secretase (BACE1) in the presence of chemically diverse inhibitors: a molecular docking study

In this molecular docking study, the protonation states of the catalytic Asp dyad of the beta-secretase (BACE1) enzyme in the presence of eight chemically diverse inhibitors have been predicted. BACE1 catalyzes the rate-determining step in the generation of Alzheimer amyloid beta peptides and is widely considered as a promising therapeutic target. All the inhibitors were redocked into their corresponding X-ray structures using a combination of eight different protonation states of the Asp dyad for each inhibitor. Five inhibitors were primarily found to favor two different monoprotonated states, and the remaining three favor a dideprotonated state. In addition, five of them exhibited secondary preference for a diprotonated state. These results show that the knowledge of a single protonation state of the Asp dyad is not sufficient to search for the novel inhibitors of BACE1 and the most plausible state for each inhibitor must be determined prior to conducting in-silico screening.     

Characterization of amino acid‐derived betaines by electrospray ionization tandem mass spectrometry

Betaines belong to the naturally occurring osmoprotectants or compatible solutes present in a variety of plants, animals and microorganisms. In recent years, metabolomic techniques have been emerging as a fundamental tool for biologists because the constellation of these molecules and their relative proportions provide with information about the actual biochemical condition of a biological system. Therefore, identification and characterization of biologically important betaines are crucial, especially for metabolomic studies. Most of the natural betaines are derived from amino acids and related homologues. Although, theoretically, all the amino acids can be converted to corresponding betaines by simple methylation of the amine group, only a few of the amino acid‐derived betaines were fully characterized in the literature. Here, we report a combined electrospray ionization tandem and high‐resolution mass spectrometry study of all the betaines derived from amino acids, including the isomeric betaines. The decomposition pathway of protonated, sodiated and potassiated molecule ions that enable unambiguous characterization of the betaines including the isomeric betaines and overlapping ionic species of different betaines is distinctive. Copyright © 2012 John Wiley & Sons, Ltd.     

Combined Alkali‐Organoammonium Structure Direction of High‐Charge‐Density Heteroatom‐Containing Aluminophosphate Molecular Sieves

The charge density mismatch concept was applied to the synthesis of high‐charge‐density silicoaluminophosphate SAPO‐69 (OFF) and SAPO‐79 (ERI) and zincoaluminophosphate PST‐16 (CGS), PST‐17 (BPH), PST‐19 (SBS), and ZnAPO‐88 (MER) molecular sieves. Combined alkali‐organoammonium structure direction in these systems is thus enabled. Structure direction is treated from the perspective of stabilizing an ionic framework, the relationships between reaction charge density (OH^?/H₃PO₄), alkali and organoammonium content, and ionicity of tetrahedral framework atoms in successful structure direction are presented.     

Triply-Logarithmic Parallel Upper and Lower Bounds for Minimum and Range Minima over Small Domains

We consider the problem of computing the minimum ofnvalues, and several well-known generalizations [prefix minima, range minima, and all nearest smaller values (ANSV)] for input elements drawn from the integer domain [1···s], wheres ≥ n. In this article we give simple and efficient algorithms for all of the preceding problems. These algorithms all takeO(log log log s) time using an optimal number of processors andO(ns^ε) space (for constant ε < 1) on the COMMON CRCW PRAM. The best known upper bounds for the range minima and ANSV problems were previouslyO(log log n) (using algorithms for unbounded domains). For the prefix minima and for the minimum problems, the improvement is with regard to the model of computation. We also prove a lower bound of Ω(log log n) for domain sizes = 2^{Ω(log n log log n)}. Since, forsat the lower end of this range, log log n = Ω(log log log s), this demonstrates that any algorithm running ino(log log log s) time must restrict the range ofson which it works.     

Exact Solutions of the Bogoyavlensky–Konoplechenko Equation

We give a Darboux transformation for the Bogoyavlensky–Konoplechenko equation, which is a two-dimensional generalisation of the Korteweg–deVries equation. This transformation is used to construct a family of solutions of this equation.     

Electron-phonon interaction in NbB2: a comparison with MgB2

We present a comparison of electron-phonon interaction in NbB₂ and MgB₂, calculated using full-potential, density-functional-based methods in P6/mmm crystal structure. Our results, described in terms of (i) electronic structure, (ii) phonon density of states F(ω), (iii) Eliashberg function α²F(ω), and (iv) the solutions of the isotropic Eliashberg gap equation, clearly show significant differences in the electron-phonon interaction in NbB₂ and MgB₂. We find that the average electron-phonon coupling constant λ is equal to 0.59 for MgB₂ and 0.43 for NbB₂, leading to superconducting transition temperatures T_c at around 22 K for MgB₂ and 3 K for NbB₂.