Quantitative experimental assessment of macromolecular crowding effects at membrane surfaces

We examined how crowding of the surfaces of lipid vesicles with either grafted polyethyleneglycol (PEG) chains or bilayer-anchored protein molecules affects the binding of soluble proteins to the vesicle surface. Escherichia coli dihydrofolate reductase (DHFR, 18 kDa) or a larger fusion protein, NusA-DHFR (72 kDa), binds reversibly but with high affinity to a methotrexate-modified lipid (MTX-PE) incorporated into large unilamellar vesicles. Incorporation of phosphatidylethanolamine-PEG5000 into the vesicles strongly decreases the affinity of binding of both proteins, to a degree that varies roughly exponentially with the lateral density of the PEG chains. Covalently coupling maltose-binding protein (MBP) to the vesicle surfaces also strongly decreases the affinity of binding of NusDHFR or DHFR, to a degree that likewise varies roughly exponentially with the surface density of anchored MBP. Surface-coupled MBP strongly decreases the rate of binding of NusDHFR to MTX-PE-incorporating vesicles but does not affect the rate of NusDHFR dissociation. The large magnitudes of these effects (easily exceeding an order of magnitude for moderate degrees of surface crowding) support previous theoretical analyses and suggest that surface-crowding effects can markedly influence a variety of important aspects of protein behavior in membranes.     

Posttranscriptional generation of macromolecular complexes

Discrete classes of mRNAs that encode functionally related proteins are associated with sequence-specific RNA-binding proteins in yeast and mammalian cells. recently reported that pre-mRNAs encoding components of inhibitory synapses are bound to neuron-specific Nova RNA-binding proteins.     

Synthesis and biological evaluation of two novel DAT-binding technetium complexes containing a piperidine based analogue of cocaine

Two new technetium complexes containing a piperidine template have been synthesized and evaluated as possible leads for the development of dopamine transporter (DAT) imaging agents. Binding data for the corresponding rhenium complexes containing either a monoaminomonoamide (MAMA') or a diaminodithiol (DADT) chelating unit exhibited significant affinity for the DAT. Initial biodistribution studies in rats revealed only a low brain uptake.     

Synthesis, crystal structures and biological evaluation of water-soluble zinc complexes of zwitterionic carboxylates

Three water-soluble zinc complexes, [Zn(Cbp)₂Br₂] (1) (Cbp = N-(4-carboxybenzyl)pyridinium), {[Zn(BCbpy)₂(H₂O)₄]₃Br₆·2(BCbpy)·2(4,4′-bipy)} (2) (BCbpy = 1-(4-carboxybenzyl)-4,4′-bipyridinium) and {[Zn₄(Bpybc)₆(H₂O)₁₂](OH)₈·9H₂O}_2n (3) (Bpybc = 1,1′-bis(4-carboxybenzyl)-4,4′-bipyridinium), were synthesized and characterized by IR, elemental analysis and single-crystal X-ray crystallography. In complex 1, the central Zn atom adopts a distorted tetrahedral coordination geometry that is formed from two unidentate Cbp ligands and two Br atoms. For complex 2, the Zn atom in [Zn(BCbpy)₂(H₂O)₄]²⁺ is strongly coordinated by four water molecules and two N atoms from two BCbpy ligands, hence forming an octahedral geometry. In complex 3, each Bpybc ligand bridges two [Zn(H₂O)₃]²⁺ units through two terminal carboxylate groups in a monodentate coordination mode, thus forming a flowerlike two-dimensional network. Agarose gel electrophoresis (GE) and ethidium bromide (EB) displacement experiments indicated that complex 3 was capable of converting pBR322 DNA into open circular (OC) and linear forms, and exhibited high binding affinity toward calf-thymus DNA. MTT assay showed that complex 3 displayed inhibitory activities toward the proliferation of lung adenocarcinoma A549 and mouse sarcoma S-180 cells, with the IC₅₀ values being 27.3 and 48.8 μM, respectively.     

Synthesis and crystallographic analysis of two rhizopuspepsin inhibitor complexes.

The crystal structures of rhizopuspepsin complexed with two oligopeptide inhibitors have been determined. CP-69,799, an azahomostatine dipeptide isostere, had previously been associated with a displacement of the C-terminal subdomain of endothiapepsin [Sali, A., Veerapandian, B., Cooper, J. B., Foundling, S. I., Hoover, D. J., & Blundell, T. L. (1989) EMBO J. 8, 2179-2188]. Here, we report the measurement of two data sets, one from crystals soaked in the inhibitor and the other from protein crystallized in the presence of excess inhibitor. In neither case is there any significant movement of the C-terminal subdomain of the rhizopuspepsin. The data suggest that the energy associated with any conformational change is small and is overcome by the crystal packing forces. The second inhibitor, a hydrated difluorostatone, was examined in a search for transition-state analogs that could cast further light on the mechanism of action [Suguna, K., Padlan, E. A., Smith, C. W., Carlson, W. D., & Davies, D. R. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 7009-7013]. The gem-diol provides a set of contact distances with the enzyme that mimic the interactions with the tetrahedral intermediate of the substrate during catalysis. These data provide support for the suggestion that the polarization of the keto group of the peptide substrate is enhanced by a hydrogen bond from the OD1 of Asp 35 (Suguna et al., 1987).     

Preparation of macromolecular complexes for cryo-electron microscopy

This protocol describes the preparation of frozen-hydrated single-particle specimens of macromolecular complexes. First, it describes how to create a grid surface coated with holey carbon by first inducing holes in a Formvar film to act as a template for the holey carbon that is stable under cryo-electron microscopy (cryo-EM) conditions and is sample-friendly. The protocol then describes the steps required to deposit the homogeneous sample on the grid and to plunge-freeze the grid into liquid ethane at the temperature of liquid nitrogen, so that it is suitable for cryo-EM visualization. It takes 4-5 h to make several hundred holey carbon grids and about 1 h to make the frozen-hydrated grids. The time required for sample purification varies from hours to days, depending on the sample and the specific procedure required. A companion protocol details how to collect cryo-EM data using an FEI Tecnai transmission electron microscope that can subsequently be processed to obtain a three-dimensional reconstruction of the macromolecular complex.     

Reversible and irreversible inhibition of phosphate transport in human erythrocytes by a membrane impermeant carbodiimide

Phosphate entry into chloride-loaded human erythrocytes is inhibited by treatment of cells with the water-soluble carbodiimide 1-ethyl-3-(4-azonia-4,4-dimethylpentyl)carbodiimide (EAC) in the absence of added nucleophile. EAC does not penetrate the erythrocyte membrane or lead to significant intermolecular cross-linking of membrane proteins. At neutral extracellular pH in chloride-free medium, only about 50% of transport is rapidly and irreversibly inhibited, but at alkaline pH, inhibition is more rapid and complete. Inhibition by EAC was reversible in the presence of extracellular NaCl. Modification of membrane sulfhydryl groups does not prevent inhibition of phosphate transport by EAC but almost complete protection is afforded by 4,4-dinitrostilbene-2,2-disulfonic acid, a reversible competitive inhibitor of anion transport. N-(4-Azido-2-nitrophenyl)-2-aminoethylsulfonate, a reversible noncompetitive inhibitor of anion transport did not protect against EAC inhibition of transport but prevented reversal of inhibition in saline medium. Transport inhibition by [3H]EAC did not lead to specific incorporation of radioactivity into Band 3, the anion transport protein. These results suggest that inhibition of anion transport by EAC is due to modification of a carboxylic acid residue in or near the transport site accessible from the external face of the membrane. The subsequent fate of the modified carboxyl residue appears to be sensitive to the orientation of the anion transport site.     

Yeast and vertebrate nuclear-pore complexes: evolutionary conserved, yet divergent macromolecular assemblies

Summary The nuclear-pore complex (NPC), which consists of ca. 50 proteins called nucleoporins, is a huge macromolecular structure that spans the nuclear envelope and is an obligatory passage for molecules in transit between the cytoplasm and the nucleus. In the last years, major progress has allowed the characterization of the so-called soluble phase of nucleocytoplasmic transport, that involves transport substrates, import and export receptors of which some belong to the karyopherin- family, and the small GTPase Ran and its modulators. In addition, the knowledge of the NPC architecture, the identification of its constituents, and the determination of the hierarchy of interactions within the pore should help to understand how nucleoporins are assembled, and how they give rise to a functional NPC through interactions with specific transport factors. In this review, we will focus on recent insights into the stationary phase of nucleocytoplasmic transport (i.e., the NPCs) that have been gained from exploiting the benefits of several organisms, such asXenopus laevis oocytes, mammalian cell lines, and the yeastSaccharomyces cerevisiae.Abbreviations FXFG phenylalanine X phenylalanine glycine - GLFG glycine leucine phenylalanine glycine - NPC nuclear-pore complex - RLNE rat liver nuclear envelope - WGA wheat germ agglutinin     

Evaluating the stoichiometry of macromolecular complexes using multisignal sedimentation velocity

Gleaning information regarding the molecular physiology of macromolecular complexes requires knowledge of their component stoichiometries. In this work, a relatively new means of analyzing sedimentation velocity (SV) data from the analytical ultracentrifuge is examined in detail. The method depends on collecting concentration profile data simultaneously using multiple signals, like Rayleigh interferometry and UV spectrophotometry. If the cosedimenting components of a complex are spectrally distinguishable, continuous sedimentation-coefficient distributions specific for each component can be calculated to reveal the molar ratio of the complex's components. When combined with the hydrodynamic information available from the SV data, a stoichiometry can be derived. Herein, the spectral properties of sedimenting species are systematically explored to arrive at a predictive test for whether a set of macromolecules can be spectrally resolved in a multisignal SV (MSSV) experiment. Also, a graphical means of experimental design and criteria to judge the success of the spectral discrimination in MSSV are introduced. A detailed example of the analysis of MSSV experiments is offered, and the possibility of deriving equilibrium association constants from MSSV analyses is explored. Finally, successful implementations of MSSV are reviewed.     

Synthesis, characterization and preliminary cytotoxicity evaluation of five lanthanide(III)-plumbagin complexes

Plumbagin (5-hydroxy-2-methyl-1,4-naphthoquinone, H-PLN) was isolated from Plumbago zeylanica, the anticancer traditional Chinese medicine (TCM). Five new lanthanide(III) complexes of deprotonated plumbagin: [Y(PLN)₃(H₂O)₂] (1), [La(PLN)₃(H₂O)₂] (2), [Sm(PLN)₃(H₂O)₂]⋅H₂O (3), [Gd(PLN)₃(H₂O)₂] (4), and [Dy(PLN)₃(H₂O)₂] (5) were synthesized by the reaction of plumbagin with the corresponding lanthanide salts, in amounts equal to ligand/metal molar ratio of 3:1. The PLN-lanthanide(III) complexes were characterized by different physicochemical methods: elemental analyses, UV-visible, IR and ¹H NMR and ESI-MS (electrospray ionization mass spectrum) as well as TGA (thermogravimetric analysis). The plumbagin and its lanthanide(III) complexes 1-5, were tested for their in vitro cytotoxicity against BEL7404 (liver cancer) cell lines by MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay. The five PLN-lanthanide (III) complexes 1-5 effectively inhibited BEL7404 cell lines growth with IC₅₀ values of 11.0 ± 3.5, 5.1 ± 1.3, 6.1 ± 1.1, 6.4 ± 1.3, and 9.8 ± 1.5 μM, respectively, and exhibited a significantly enhanced cytotoxicity compared to plumbagin and the corresponding lanthanide salts, suggesting a synergistic effect upon plumbagin coordination to the Ln(III) ion. The lanthanide complexes under investigation also exerted dose- and time-dependent cytotoxic activity. [La(PLN)₃(H₂O)₂] (2) and plumbagin interact with calf thymus DNA (ct-DNA) mainly via intercalation mode, but for [La(PLN)₃(H₂O)₂] (2), the electrostatic interaction should not be excluded; the binding affinity of [La(PLN)₃(H₂O)₂] (2) to DNA is stronger than that of free plumbagin, which may correlate with the enhanced cytotoxicity of the PLN-lanthanide(III) complexes.     

Hydrodynamic shielding of spherical subunits in macromolecular complexes

The Garcia de la Torre-Bloomfield hydrodynamic interaction tensor was used to calculate the shielding coefficient matrices for each spherical friction bead in the rigid arrays of a rod and helix. Negative values for the average shielding coefficient result for small beads adjacent to large beads, suggesting premature truncation in the series expansions employed in the hydrodynamic interaction tensor. Numerical analysis also suggests that the magnitude of geometric asymmetry is not a good measure of the extent of friction asymmetry of the molecule due to extensive hydrodynamic shielding by other subunit beads.     

Hydrodynamics of macromolecular complexes. II. Rotation

We have used the modified Oseen hydrodynamic interaction tensor along with iterative numerical solution of the coupled hydrodynamic interaction equations to calculate the rotational diffusion coefficients of macromolecular complexes composed of nonidentical spherical subunits. For the one structure, a prolate ellipsoid of revolution, for which exact solutions are available, a subunit model with the same length and volume gives asymptotic agreement with the Perrin equations. Other structures considered include plane polygonal rings, lollipops, and dumbbells.     

Synthesis, X-ray structures, electrochemical properties and cytotoxic effects of Co(II) complexes

1-Benzothiazol-2-yl-3,5-dimethyl-1H-pyrazole (1a) and 1-benzothiazol-2-yl-5-(2-hydroxyphenyl)-3-methyl-1H-pyrazole-4-carboxylic acid methyl ester (1b) were reacted with the hexahydrates of cobalt(II) chloride, cobalt(II) nitrate and cobalt(II) perchlorate to give the corresponding complexes 2a-4a and 2b-5b, respectively. Obtained compounds differ in coordination spheres of central atoms. The complex 2a includes a fivefold coordinated cobalt(II) ion, whereas 3a shows a distorted octahedral configuration around the cobalt(II) ion. All complexes were characterised by FTIR spectroscopy, MS and elemental analysis. The X-ray structures of 2a, 3a and 5b complexes were also solved. The cytotoxic properties of the ligand 1a and both series of Co(II) complexes were examined on human leukemia NALM-6 and HL-60 cells and melanoma WM-115 cells. The ligands, were found to have very low cytotoxicity. Complex 3b exhibited the highest cytotoxic activity with IC₅₀ values in the range of 6.9-17.1 μM for three examined cell lines.     

A simple method for freeze-drying of macromolecules and macromolecular complexes

We present a simple approach for effective freeze-drying and rotary shadowing of large molecules, molecular assemblies, and cell organelles. Simply, a suspension of specimen is adsorped to a glass coverslip, stabilized, and rinsed with 30% methanol. A second coverslip is "sandwiched" on top, and excess methanol is withdrawn from the edges then frozen by plunging into liquid nitrogen and split. Following either rotary or unidirectional shadowing and replication, the coverslip is dissolved in hydrofluoric acid. In addition to avoiding the problems encountered with air-drying specimens for rotary shadowing, the technique also reproducibly provides the thin layer of solution necessary for proper freeze-drying, regardless of how hydrophobic the sample is. The "glass sandwich" technique allows modification of the glass substrate (making it hydrophobic with carbon or hydrophilic by soaking it in alcian blue) which clearly alters the shape of macromolecular assemblies such as myosin filaments and decorated thin filaments.     

Synthesis and macromolecular organization of gastrointestinal mucin.

Mucus glycoproteins (mucins), the principal determinants of mucus protective qualities and mucosal defense, are studied extensively to define pathological aberrations in the relation to gastrointestinal disease and to develop the mucous barrier strengthening agents. Recent work from our laboratory provided evidence as to the initial stages of the gastrointestinal mucin synthesis, molecular size of the apomucin, its macromolecular organization and interaction with other elements of gastrointestinal mucus. Using monoclonal antibodies against apomucin (clone 1H7), O-glycosylated with N-acetylgalactosamine apomucin (clone 2B4), and that against carboxyl terminal of the apomucin (clone 3G12), the mucin synthesizing polysomes were isolated and glycosylated peptides ranging in size from 6-60 kDa identified. The in vitro synthesis in the cell-free system also afforded 60-64 kDa products recognized by 1H7 and 3G12 antimucin MAbs. The obtained results provided evidence that the mucin core consists of 60 kDa peptide which at cotranslational stage is O-glycosylated with N-acetylgalactosamine. Studies on mucin polymer assembly revealed that mucin preparations prepared by equilibrium density gradient centrifugation and Sepharose 2B chromatography (Mantle, M., Mantle, D., and Allen, A. (1981) Biochem. J. 195, 277-285) are not completely purified and contain DNA and extraneous proteins. The evidence was obtained that so called mucin "link protein", 118 kDa glycopeptide, is a N-glycosylated fragment of fibronectin, whereas the supposedly native undegraded mucin isolated by Carlstedt et al. (Biochem. J. (1983) 211, 13-22) was found to contain mucin-fibronectin-DNA complexes. The general picture that emerged from the studies is that the pure mucin consists of 60 kDa glycosylated peptides only. The carboxyl terminal (8-12 kDa fragment) of these peptides is not glycosylated (naked) and is responsible for mucin interaction with fibronectin and other fibronectin-like extracellular matrix proteins. While the formation of the mucosal coat depends on many other factors and extracellular components, our findings on mucin structure and interaction with the extracellular matrix proteins provide explanation as to the possible mechanism of mucin adherence to the epithelial surfaces.     

Synthesis,biological characterization and evaluation of molecular mechanisms of novel copper complexes as anticancer agents

BackgroundTo overcome the hurdles of cisplatin, majorly its toxicity and resistance, there has been extensive search for alternative anti-cancer metal-based compounds. Here, three Cu(II)-complexes, Cu(Sal-Gly)(phen), Cu(Sal-Gly)(pheamine), Cu(Sal-Gly)(phepoxy) are characterized for their interaction with DNA, cytotoxicity and mechanism of action.MethodsThe binding ability of the complexes to Calf-Thymus DNA was evaluated by competition fluorescence studies with thiazole-orange, UV–Vis and circular dichroism spectroscopic titrations. Cytotoxicity was evaluated by MTT analysis. The DNA damage was analyzed through cleavage of supercoiled DNA via agarose gel-electrophoresis, and 8-oxo-guanidine and ɣH2AX staining in cells. Apoptosis was detected via DNA condensation/fragmentation, mitochondrial membrane potential, Annexin V staining and caspase 3/7 activity. Formation of reactive oxygen species was determined by DCFDA- and GSSG/GSH-analysis.ResultsBinding constants to DNA were evaluated as 1.7 × 10⁶ (Cu(Sal-Gly)(phen)), 2.5 × 10⁶ (Cu(Sal-Gly)(pheamine)) and 3.2 × 10⁵ (Cu(Sal-Gly)(phepoxy)). All compounds induced DNA damage. Apoptosis was the main form of cell death. There was an increase in ROS, which is most likely responsible for the observed DNA-damage. Although the compounds were cytotoxic to all tested cancer cell lines, only Cu(Sal-Gly)(pheamine) displayed significantly lower toxicity towards non-cancer cells, its associated phenotypes differing from the other two Cu-complexes. Thus, Cu(Sal-Gly)(pheamine) was further assayed for molecular changes in response to drug treatment using a custom designed RT-qPCR array. Results showed that Harakiri was significantly upregulated. Presence of p53 was not required for apoptosis in response to Cu-complexes.Conclusions and general significanceThese Cu-complexes, namely Cu(Sal-Gly)(pheamine), may be considered promising anticancer agents with activity in cancer cells even with deficient p53 status.     

Time-course effects of two barbiturates on cardiovascular activity and temperature in the squirrel monkey

Heart rate (HR), mean arterial blood pressure (BP) and core temperature (TEMP) were recorded from conscious, chair-restrained squirrel monkeys surgically prepared with chronically indwelling arterial and venous catheters to determine the effects of acute intravenous injections of methohexital and secobarbital. Methohexital (0.3–17.0 mg/kg) and secobarbital (1.0–30.0 mg/kg) decreased HR, BP and TEMP in a dose-dependent manner. Methohexital resulted in a greater decrease in blood pressure than secobarbital, but the latter caused greater decreases in heart rate and temperature. The duration of all effects of methohexital was substantially briefer than the effects of secobarbital at the higher doses studied. The data show that these two barbiturates differ not only in duration of action but also in the magnitude of effect on cardiovascular activity in the squirrel monkey.