The interaction of dansyl amino acids with bovine serum albumin

The interaction of 5-dimethylaminonaphthalene-1-sulfonyl (DNS or dansyl) amino acids with bovine serum albumin (BSA) was investigated by means of fluorescence measurements. Fluorometric titrations revealed that BSA has one high affinity site (binding constant,K _a=10⁵10⁶ M^–1), and other sites of lower affinity (K _a=10³10⁴ M^–1) for the probes. Static excitation and emission spectra, lifetimes, time resolved emission spectra, and anisotropy data indicated that the binding is stabilized mainly through fixation by the high affinity binding site. The binding constant significantly decreased with the increase of the spacer distance between the dansyl and anionic groups of the probe molecule. This observation was explained by considering the change of the electrostatic interaction between the anionic group of the probe and a cationic residue in the vicinity of the site.     

Thermodynamic aspects of hydrophobicity and biological QSAR

A protein contains a large amount of water molecules, and the nature of the interactions of the water molecules with a protein play an important role in the thermodynamics of the ligand binding process. In this paper, thermodynamic aspects of drug-receptor interactions, enthalpy-entropy compensation or reinforcement, hydrophobicity, and biological 2D- and 3D-QSAR are discussed. Comparisons of the thermodynamic QSAR of phenyl esters of N-benzoyl L-alanine in phosphate buffer and pentanol provide useful insight for the ligand-enzyme interactions.     

A prediction of the three-dimensional structure of maize NADP+-dependent malate dehydrogenase which explains aspects of light-dependent regulation unique to plant enzymes

Summary A model has been built for the plant NADP-malate dehydrogenase from Zea mays, a key enzyme in photosynthesis, which undergoes light-dependent regulation. The model was based on sequence and presumed structural homology to the known three-dimensional structure of mammalian porcine cytosolic NAD-malate dehydrogenase. A cystine-loop present in an extended C-terminal region of plant NADP-malate dehydrogenases was modelled using molecular mechanics and computer graphical methods, based on the assumption that a disulphide bridge exists in the inactive form of the enzyme between Cys³⁵¹ and Cys³⁶³. The predicted conformation of the intact C-terminal cystine-loop suggests that the extended polypeptide will bind in the active centre and inhibit enzyme activity. Another ionizable cysteine residue in the active site is predicted to control the charge of the catalytic His²¹⁵ and might be responsible for the uniquely tight binding of the positively charged nicotinamide ring of NADP⁺ in this and other C4 and C3 plant NADP-malate dehydrogenases.     

Catalytic behavior of a polynuclear Mg-Mo complex and nitrogenase active site (FeMoco) isolated from the enzyme in reactions with C2H2, N2, and CO: A comparative study

In order to identify common and distinctive features in the catalytic behavior of natural and artificial nitrogen-fixation clusters, the kinetics of the catalytic reduction of C₂H₂ in the presence of Mg-Mo-cluster (1) was investigated and compared with the kinetics of acetylene reduction catalyzed by the cluster FeMoco (2) isolated from the enzyme nitrogenase we studied previously. The reactions were conducted in the presence of Zn/Hg and Eu/Hg as reducing agents and PhSH and C₆F₅SH as proton donors, i.e., under the same conditions as had been used in the case of 2. Both polynuclear Mg-Mo-complex and the europium amalgam-reduced FeMoco have multiple interdependent binding sites for substrates and/or inhibitors. Carbon monoxide inhibits the acetylene reduction much less efficiently in systems with cluster 1 than in systems with cluster 2, although the type of inhibition is mixed in both systems: CO binds to multiple sites of the cluster and affects both C₂H₂ complexation to the reduced cluster and decomposition of the catalyst-substrate complex to give the products. Unlike isolated FeMoco, the Mg-Mo-cluster efficiently catalyzes the reduction of molecular nitrogen. The reaction is greatly inhibited by acetylene, while no inhibiting effect of N₂ is observed in acetylene reduction, as was found earlier for a system with the natural cluster as the catalyst. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 766–774, May, 2006.     

Molecular modelling studies on the ORL1-receptor and ORL1-agonists

The ORLI (opioid receptor like 1)- receptor is a member of the family of rhodopsin-like G protein-coupled receptors (GPCR) and represents an interesting new therapeutical target since it is involved in a variety of biomedical important processes, such as anxiety, nociception, feeding, and memory. In order to shed light on the molecular basis of the interactions of the GPCR with its ligands, the receptor protein and a dataset of specific agonists were examined using molecular modelling methods. For that purpose, the conformational space of a very potent non-peptide ORL1-receptor agonist (Ro 64-6198) with a small number of rotatable bonds was analysed in order to derive a pharmacophoric arrangement. The conformational analyses yielded a conformation that served as template for the superposition of a set of related analogues. Structural superposition was achieved by employing the program FlexS. Using the experimental binding data and the superposition of the ligands, a 3D-QSAR analysis applying the GRID/GOLPE method was carried out. After the ligand-based modelling approach, a 3D model of the ORL1-receptor has been constructed using homology modelling methods based on the crystal structure of bovine rhodopsin. A representative structure of the model taken from molecular dynamics simulations was used for a manual docking procedure. Asp-130 and Thr-305 within the ORL1-receptor model served as important hydrophilic interaction partners. Furthermore, a hydrophobic cavity was identified stabilizing the agonists within their binding site. The manual docking results were supported using FlexX, which identified the same protein-ligand interaction points.     

Elucidation of hydrodesulfurization mechanism on molybdenum‐based catalysts using 35S radioisotope pulse tracer methods

Elucidation of the hydrodesulfurization (HDS) mechanism on molybdenumbased catalysts using radioisotope tracer methods and reaction kinetics is reviewed. Firstly, to investigate the sulfidation state in Mo/Al₂O₃ and Co–Mo/Al₂O₃ catalysts, presulfiding of these catalysts has been performed using a ³⁵S pulse tracer method. Secondly, HDS of radioactive ³⁵Slabeled dibenzothiophene was carried out over a series of sulfided molybdena–alumina catalysts and cobaltpromoted molybdena–alumina catalysts in a pressurized flow reactor to estimate the behavior of sulfur on the working catalysts. Finally, sulfur exchange of a ³⁵Slabeled catalyst with hydrogen sulfide was performed to estimate the relationship between the amount of labile sulfur and catalytically active sites.     

Novel Copper(II)‐Selective Membrane Electrode Based on a New Synthesized Schiff Base

A PVC membrane electrode for copper(II) ion based on a recently synthesized Schiff base as a suitable ion carrier was constructed. The electrode exhibits a Nernstian slope of 28.3 ± 0.6 mV per decade of Cu²⁺ over a wide concentration range of 7.0 × 10^?6‐2.6 × 10^?2 M with a detection limit of 5.0 × 10^?6M in the pH range of 4.2–5.8. The response time is about 10s and it can be used for at least 1 month without any considerable divergence in potential. It was successfully applied as an indicator electrode in the potentiometric titration of copper ions.     

Fluorescence detection of cytosine/guanine transversion based on a hydrogen bond forming ligand

In combination with abasic site (AP site)-containing oligodeoxynucleotides (ODNs), we demonstrate potential use of a hydrogen bond forming ligand, 2-amino-7-methyl-1,8-naphthyridine (AMND), for the fluorescence detection of the cytosine (C)/guanine (G) mutation sequence of the cancer repression gene p53. Our method is based on construction of the AP site in ODN duplexes, which allows small synthetic ligands to bind to target nucleobases accompanied by fluorescence signaling: an AP site-containing ODN is hybridized with a target ODN so as to place the AP site toward a target nucleobase, by which hydrophobic microenvironments are provided for ligands to recognize target nucleobases through hydrogen-bonding. In 10 mM sodium cacodylate buffer solutions (pH, 7.0) containing 100 mM NaCl and 1.0 mM EDTA, AMND is found to strongly bind to C (K_d=1.5×10⁻⁶ M) in the target ODN while the binding affinity for G is relatively moderate (K_d=50×10⁻⁶ M). Significant fluorescence quenching of AMND is observed only when binding to C, making it possible to judge the C/G transversion with the naked eye.     

U(IV)/Ln(III) unexpected mixed site in polymetallic oxalato complexes. Part I. Substitution of Ln(III) for U(IV) from the new oxalate (NH4)2U2(C2O4)5·0.7H2O

A new ammonium uranium (IV) oxalate (NH₄)₂U₂(C₂O₄)₅·0.7H₂O (1) and three mixed uranium (IV)-lanthanide (III) oxalates, (N₂H₅)_2.6U_1.4M_0.6(C₂O₄)₅·xH₂O (M=Nd (2) and M=Sm (3)), Na_2.56U_1.44Nd_0.56(C₂O₄)₅·7.6H₂O (4) and Na₃UCe(C₂O₄)₅·10.4H₂O (5), have been prepared. The crystal structures of compounds 1, 4 and 5 have been determined by single-crystal X-ray diffraction. The crystal structures were solved by the direct methods and Fourier difference techniques, and refined by a least square method on the basis of F² for all unique reflections. Compounds 2 and 3 are isotypic with 1. Crystallographic data: 1, hexagonal, space group P6₃/mmc, a=19.177(3), c=12.728(4) Å, Z=6, R₁=0.0575 for 52 parameters with 1360 reflections with I?2σ(I); 2, hexagonal, space group P6₃/mmc, a=19.243(4), c=12.760(5) Å, Z=6; 3, hexagonal, space group P6₃/mmc, a=19.211(3), c=12.274(4) Å, Z=6; 4, orthorhombic, space group Pbcn, a=18.79(3), b=11.46(1), c=12.77(2) Å, Z=4, R₁=0.0511 for 183 parameters with 3026 reflections with I?2σ(I); 5, monoclinic, space group C2/c, a=18.878(6), b=11.684(4), c=12.932(4) Å, β=95.97(1)°, Z=4, R₁=0.0416 for 213 parameters with 4060 reflections with I?2σ(I). The honeycomb-like structure of the five compounds is built from the same three-dimensional arrangement of metallic and oxalate ions. Similar hexagonal rings of alternating metallic and oxalate ions form layers parallel to the (001) plane that are pillared by another oxalate ion. Indeed, some torsions or rotations of the bridging oxalate ligands led to modifications of the network symmetry. The monovalent cations and the water molecules occupy the hexagonal tunnels running down the [001] direction. Starting from the uranium (IV) compound A₂U₂(C₂O₄)₅·0.7H₂O with A=NH₄⁺ (1), the mixed U(IV)/Ln(III) oxalates are obtained by partial substitution of U(IV) by Ln(III) in a ten-coordinated site, the charge deficit being compensated by intercalation of supplementary monovalent ions within the tunnels. The distortion of the arrangement in the [001] direction for the Na-containing compounds allows the accommodation of a greater number of water molecules that insure an octahedral coordination of the Na atoms.     

Catalytic application of K2Ce(PO4)2 in Knoevenagel condensation -A green protocol

A framework connected phosphate material K₂Ce(PO₄)₂, explored for the first time for the Knoevenagel condensation of aldehydes with malononitrile in water. The catalyst was prepared by newly developed solid-state method and characterized using XRD, RAMAN, FTIR, BET surface area, TPD, XPS, SEM and HRTEM. The developed protocol showed the substrate compatibility along with the catalyst reusability. Moreover, the catalyst was scaled up to 30 g and also showed reusability. The role of predominant Ce(IV) species was also discussed apart from phosphate basic sites.