Recombinant subunits as tools for the structural and functional characterization of Echinococcus granulosus antigen B

Antigen B (AgB) is a major protein component of the Echinococcus granulosus metacestode. It is oligomeric and this raises several questions regarding the subunit structure and composition of AgB. Several genes that encode different AgB subunits have been identified, and some of these have been cloned and expressed to produce recombinant subunits. The study of these recombinant subunits may provide new insights into the structure, physical-chemical properties, and functional aspects of AgB. Like native AgB, the AgB8/1, AgB8/2, and AgB8/3 recombinant subunits produced in our laboratory form 120-160 kDa oligomers that have stable secondary structures, are strongly antigenic and immunogenic, and selectively bind hydrophobic compounds. Here, we review these results and discuss their implications for the elucidation of the structure and function of AgB. This includes a possible role for AgB in host-parasite interactions.     

Synthesis and characterization of an N-coordinated amidate copper(II) complex of deprotonated N-(2,6-diisopropylphenyl)-2-(bis-(2-pyridylmethyl))aminoethanamide

The title ligand, N-(2,6-diisopropylphenyl)-2-(bis-(2-pyridylmethyl))aminoethanamide (DIPMAE-H), was prepared by a nucleophilic substitution reaction between N-(2,6-diisopropyl)phenyl-2-bromoethanamide and bis-(2-pyridylmethyl)amine. An analogous ligand (TBPMAE-H) in which the 2,6-diisopropylphenyl group was substituted for a tert-butyl group was also prepared in this manner. Then, [(DIPMAE-H)CuBr]⁺Br⁻ and [(TBPMAE-H)CuBr]⁺Br⁻ were prepared by heating one equivalent of ligand and CuBr₂ in CH₃CN. In both compounds the geometry about the copper center is square pyramidal with distortions due to the geometrical constraints of the ligand. The amide oxygen occupies the axial position, and the three amine nitrogens and the bromide ligand form the basal plane of the square pyramid. Pairs of complexes in the unit cell are associated via weak donation of a lone pair on the bromide ligand of one complex to the copper center of another (Cu?Br distances in the range of 3.3576-3.4022 Å).The title compound, (DIPMAE)CuBr, was prepared by deprotonation of [(DIPMAE-H)CuBr]⁺Br⁻ using NaH. The key feature of (DIPMAE)CuBr is the amidate group η¹- and N-coordinated to the copper center. The compound also exhibits distorted trigonal bipyramidal coordination geometry with the bromide and tertiary amine donors occupying the axial sites and the amidate and pyridyl donors occupying the equatorial positions. The copper atom is displaced from the trigonal plane towards the bromide donor apex due to the geometrical demands of the ligand.     

Copper(II) promoted imidazolidine ring formation and complexation: A unique reaction course

The reaction of Cu(II) ions with a sodium salt of new Schiff base ligand NaL¹, sodium N-2-methyl pyridine-2-imine benzoate, in alkaline medium produced an imine bond coupled ligand and a novel complex, Na₂[Cu(L³)₂], L³ = 2,5-di(2-benzoic acid)-4-(2-pyridine)-1-(2-methyl-2-pyridine)-imidazolidine. When the reduced form of the sodium salt of the Schiff base ligand, NaL², is employed, a simple hexacoordinated copper(II) complex, [Cu(L²)₂], [L²]⁻ = bis(N-(2-methylpyridine)-2-aminomethylbenzoate), was isolated. The compounds were characterized by spectroscopic methods and the molecular structures of [Cu(L²)₂] and Na₂[Cu(L³)₂] were determined by single-crystal X-ray diffraction methods. Reaction mechanism for the synthesis of, Na₂[Cu(L³)₂], copper(II) promoted imine bond coupling is proposed and discussed. The redox behavior of [Cu(L²)₂] and Na₂[Cu(L³)₂], studied using cyclic voltammetry and electron paramagnetic resonance spectroscopic methods, are also discussed.     

Heterogeneity in the sn-1 carbon chain of platelet-activating factor glycerophospholipids determines pro- or anti-apoptotic signaling in primary neurons

The platelet-activating factor (PAF) family of glycerophospholipids accumulates in damaged brain tissue following injury. Little is known about the role of individual isoforms in regulating neuronal survival. Here, we compared the neurotoxic and neuroprotective activities of 1-O-hexadecyl-2-acetyl-sn-glycero-3-phosphocholine (C(16)-PAF) and 1-O-octadecyl-2-acetyl-sn-glycero-3-phosphocholine (C(18)-PAF) in cerebellar granule neurons. We find that both C(16)-PAF and C(18)-PAF cause PAF receptor-independent death but signal through different pathways. C(16)-PAF activates caspase-7, whereas C(18)-PAF triggers caspase-independent death in PAF receptor-deficient neurons. We further show that PAF receptor signaling is either pro- or anti-apoptotic, depending upon the identity of the sn-1 fatty acid of the PAF ligand. Activation of the PAF G-protein-coupled receptor (PAFR) by C(16)-PAF stimulation is anti-apoptotic and inhibits caspase-dependent death. Activation of PAFR by C(18)-PAF is pro-apoptotic. These results demonstrate the importance of the long-chain sn-1 fatty acid in regulating PAF-induced caspase-dependent apoptosis, caspase-independent neurodegeneration, and neuroprotection in the presence or absence of the PAF receptor.     

Interactions in native binding sites cause a large change in protein dynamics

Cellular functions are regulated by molecules that interact with proteins and alter their activities. To enable such control, protein activity, and therefore protein conformational distributions, must be susceptible to alteration by molecular interactions at functional sites. Here we investigate whether interactions at functional sites cause a large change in the protein conformational distribution. We apply a computational method, called dynamics perturbation analysis (DPA), to identify sites at which interactions have a large allosteric potential D(x), which is the Kullback-Leibler divergence between protein conformational distributions with and without an interaction. In DPA, a protein is decorated with surface points that interact with neighboring protein atoms, and D(x) is calculated for each of the points in a coarse-grained model of protein vibrations. We use DPA to examine hundreds of protein structures from a standard small-molecule docking test set, and find that ligand-binding sites have elevated values of D(x): for 95% of proteins, the probability of randomly obtaining values as high as those in the binding site is 10(-3) or smaller. We then use DPA to develop a computational method to predict functional sites in proteins, and find that the method accurately predicts ligand-binding-site residues for proteins in the test set. The performance of this method compares favorably with that of a cleft analysis method. The results confirm that interactions at small-molecule binding sites cause a large change in the protein conformational distribution, and motivate using DPA for large-scale prediction of functional sites in proteins. They also suggest that natural selection favors proteins whose activities are capable of being regulated by molecular interactions.     

Characterization of low density lipoprotein receptor ligand interactions by fluorescence resonance energy transfer

The low density lipoprotein receptor (LDLR) is the prototype of a family of cell surface receptors involved in a wide range of biological processes. A soluble low density lipoprotein receptor (sLDLR) and a tryptophan (Trp)-deficient variant human apolipoprotein E3 (apoE3) N-terminal domain (NT) were used in binding studies. The sole cysteine in apoE3-NT was covalently modified with an extrinsic fluorescence probe, N-(iodoacetyl)-N'-(5-sulfo-1-napthyl)ethylenediamine (AEDANS), and the protein was complexed with lipid. Incubation of sLDLR with AEDANS-Trp-null apoE3-NT dimyristoylphosphatidylcholine (DMPC) disks, but not lipid-free AEDANS-apoE, induced an enhancement in AEDANS fluorescence emission intensity (excitation, 280 nm) consistent with intermolecular energy transfer from excited Trp in sLDLR to receptor-bound apoE. Ligand binding to sLDLR required calcium and was saturable. In competition binding assays, unlabeled apoE3-NT DMPC inhibited AEDANS-apoE DMPC binding to sLDLR more effectively than low density lipoprotein. Fluorescence changes in this system reflected pH-dependent ligand binding and release from sLDLR consistent with models derived from the X-ray crystal structure of the receptor at endosomal pH. Intermolecular energy transfer from excited Trp in LDLR family members to fluorescently tagged ligands represents a sensitive and convenient assay for the characterization of the myriad molecular interactions ascribed to this family of receptor.     

The C2 domain of PKCalpha is a Ca2+ -dependent PtdIns(4,5)P2 sensing domain: a new insight into an old pathway

The C2 domain is a targeting domain that responds to intracellular Ca²⁺ signals in classical protein kinases (PKCs) and mediates the translocation of its host protein to membranes. Recent studies have revealed a new motif in the C2 domain, named the lysine-rich cluster, that interacts with acidic phospholipids. The purpose of this work was to characterize the molecular mechanism by which PtdIns(4,5)P₂ specifically interacts with this motif. Using a combination of isothermal titration calorimetry, fluorescence resonance energy transfer and time-lapse confocal microscopy, we show here that Ca²⁺ specifically binds to the Ca²⁺-binding region, facilitating PtdIns(4,5)P₂ access to the lysine-rich cluster. The magnitude of PtdIns(4,5)P₂ binding is greater than in the case of other polyphosphate phosphatidylinositols. Very importantly, the residues involved in PtdIns(4,5)P₂ binding are essential for the plasma membrane localization of PKCα when RBL-2H3 cells are stimulated through their IgE receptors. Additionally, CFP-PH and CFP-C1 domains were used as bioprobes to demonstrate the co-existence of PtdIns(4,5)P₂ and diacylglycerol in the plasma membrane, and it was shown that although a fraction of PtdIns(4,5)P₂ is hydrolyzed to generate diacylglycerol and IP₃, an important amount still remains in the membrane where it is available to activate PKCα. These findings entail revision of the currently accepted model of PKCα recruitment to the membrane and its activation.     

Synthesis and characterization of pseudo-affinity ligand for penicillin acylase purification

The aim of this work was to test a chromatographic affinity support containing methacryloyl antipyrine (MAAP) for penicillin acylase (PA) purification by using pure penicillin acylase and crude extract. First, MAAP as a pseudo-specific ligand was synthesized by using methacryloyl chloride and 4-aminoantipyrine. Polymer beads (average size diameter: 40–120 μm) were prepared by suspension polymerization of ethylene glycol dimethacrylate (EGDMA) and MAAP. This approach for the preparation of adsorbent has several advantages over conventional preparation protocols. An expensive and time consuming step in the preparation of adsorbent is immobilization of a ligand to the adsorption matrix. In this procedure, affinity ligand MAAP acts as comonomer without further modification steps. Poly(EGDMA-MAAP) beads were characterized by FTIR, NMR and screen analysis. Elemental analysis of MAAP for nitrogen was estimated as 89.3 μmol/g. The prepared adsorbent was then used for the capture of penicillin acylase in batch system. The maximum penicillin acylase adsorption capacity of the poly(EGDMA-MAAP) beads was found to be 82.2 mg/g at pH 5.0. Chromatography with crude feedstock resulted in 23.2-fold purification and 93% recovery with 1.0 M NaOH.     

Induced‐fit or preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure‐based drug design

Crystal structures of acetylcholinesterase complexed with ligands are compared with side-chain conformations accessed by native acetylcholinesterase in molecular dynamics (MD) simulations. Several crystallographic conformations of a key residue in a specific binding site are accessed in a simulation of native acetylcholinesterase, although not seen in rotomer plots. Conformational changes upon ligand binding thus involve preexisting equilibrium dynamics. Consequently, rational drug design could benefit significantly from conformations monitored by MD simulations of native targets.