Structural and functional analysis of the sarcoglycan-sarcospan subcomplex

Sarcospan is a component of the dystrophin-glycoprotein complex that forms a tight subcomplex with the sarcoglycans. The sarcoglycan-sarcospan subcomplex functions to stabilize α-dystroglycan at the plasma membrane and perturbations of this subcomplex are associated with autosomal recessive limb-girdle muscular dystrophy. In order to characterize protein interactions within this subcomplex, we first demonstrate that sarcospan forms homo-oligomers within the membrane. Experiments with a panel of site-directed mutants reveal that proper structure of the large extracellular loop is an important determinant of oligo formation. Furthermore, the intracellular N- and C-termini contribute to stability of sarcospan-mediated webs. Point mutation of each cysteine residue reveals that Cys 162 and Cys 164 within the large extracellular loop form disulfide bridges, which are critical for proper sarcospan structure. The extracellular domain of sarcospan also forms the main binding site for the sarcoglycans. We propose a model whereby sarcospan forms homo-oligomers that cluster the components of the dystrophin-glycoprotein complex within the membrane.     

Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy

We explore structural characterization of protein assemblies by a combination of electron cryo-microscopy (cryoEM) and comparative protein structure modeling. Specifically, our method finds an optimal atomic model of a given assembly subunit and its position within an assembly by fitting alternative comparative models into a cryoEM map. The alternative models are calculated by MODELLER [J. Mol. Biol. 234 (1993) 313] from different sequence alignments between the modeled protein and its template structures. The fitting of these models into a cryoEM density map is performed either by FOLDHUNTER [J. Mol. Biol. 308 (2001) 1033] or by a new density fitting module of MODELLER (Mod-EM). Identification of the most accurate model is based on the correlation between the model accuracy and the quality of fit into the cryoEM density map. To quantify this correlation, we created a benchmark consisting of eight proteins of different structural folds with corresponding density maps simulated at five resolutions from 5 to 15 angstroms, with three noise levels each. Each of the proteins in the set was modeled based on 300 different alignments to their remotely related templates (12-32% sequence identity), spanning the range from entirely inaccurate to essentially accurate alignments. The benchmark revealed that one of the most accurate models can usually be identified by the quality of its fit into the cryoEM density map, even for noisy maps at 15 angstroms resolution. Therefore, a cryoEM density map can be helpful in improving the accuracy of a comparative model. Moreover, a pseudo-atomic model of a component in an assembly may be built better with comparative models of the native subunit sequences than with experimentally determined structures of their homologs.     

Structural characterization (shape and dimensions) and stability of polysaccharide/lipid nanoparticles

The structure of a new supramolecular drug carrier (named Biovectors—BV) was studied using light scattering and scanning electronic microscopy techniques. This system consists of a polysaccharide core of chemically cross-linked maltodextrins to which phospholipids (and, in some cases, cholesterol) are added. Both polysaccharide cores and BV cross-linked with phosphate (negatively charged) and epichlorhydrin (no net charge) are spherical particles. The increase in the ionic strength of the medium increases the density of the charged polysaccharide cores. The lipid strongly interacts with neutral and negatively charged cores, decreasing both intra- and interparticle interactions. The results (mainly, ρ = R_g/R_h < 0.775 in some cases) suggest that BV are gel-like particles of variable density, referred to as microgels or soft spheres. Neutral polysaccharides have a strong tendency to self-aggregate. This self-aggregation of polysaccharide neutral cores is prevented by the addition of lipid or dimethylsulfoxide. © 1997 John Wiley & Sons, Inc. Biopoly 41: 511–520, 1997     

Structural biology of RNA polymerase III: mass spectrometry elucidates subcomplex architecture

RNA polymerases (Pol) II and III synthesize eukaryotic mRNAs and tRNAs, respectively. The crystal structure of the 12 subunit Pol II is known, but only limited structural information is available for the 17 subunit Pol III. Using mass spectrometry (MS), we correlated masses of Pol II complexes with the Pol II structure. Analysis of Pol III showed that the complete enzyme contains a single copy of each subunit and revealed a 15 subunit form lacking the Pol III-specific subcomplex C53/37. DMSO treatment dissociated the C17/25 heterodimer of Pol III, confirming a peripheral location as its counterpart in Pol II. Tandem MS revealed the Pol III-specific subunits C82 and C34 dissociating as a heterodimer. C11 was retained, arguing against a stable trimeric subcomplex, C53/37/11. These data suggest that Pol III consists of a 10 subunit Pol II-like core; the peripheral heterodimers C17/25, C53/37, and C82/34; and subunit C31, which bridges between C82/34, C17/25, and the core.     

Genetical analysis of components of overall plant shape

Summary The genetical control of six characters, which were taken as jointly reflecting the overall shape of the plant, was analysed using four true-breeding lines of Nicotiana rustica. F₁ F₂ and first backcross generations were raised from all of the possible pairwise combinations between the lines. The particular relationships between the lines provided a basis for the analysis which was an extension of the normal model fitting procedures described by Mather and Jinks (1971).The first step in the analysis was to test whether the allelic differences present between the inbred lines p₁ and P₅ had been maintained in the two lines B₂ and B₃₅, derived from an earlier cross between the former. If the allelic differences between p₁ and P₅ were present between B₂ and B₃₅, it was possible to proceed straight-forwardly by fitting a model consisting of m, two symmetrical [d]'s and the relevant non-additive parameters. If B₂ and B₃₅ were homozygous for the same alleles at loci by which p₁ and P₅ differed, in other words if significant asymmetry in the gene distributions was present, the model had to be extended to cover the effects of such genes.All six characters investigated were shown to be subject to genetical variation. From the composition of the genetical models that were necessary to account for the observations from each of the characters, it was inferred that they should be amenable to at least partially independent adjustment by selection.     

Structural insights shed light onto septin assemblies and function

While the original septin mutants were identified more than 30 years ago for their role in cytokinesis [Hartwell, LH: Genetic control of the cell division cycle in yeast. IV. Genes controlling bud emergence and cytokinesis. Exp Cell Res 1971, 69: 265-276], the architecture of septin complexes and higher order structures has remained a mystery up until very recently. Over the last few months a number of converging approaches have suddenly provided a wealth of structural information about the different levels of septin organization. Here, we review these advancements and highlight their functional consequences.     

Structural basis of the nic96 subcomplex organization in the nuclear pore channel

Nic96 is a conserved nucleoporin that recruits the Nsp1-Nup49-Nup57 complex, a module with Phe-Gly (FG) repeats, to the central transport channel of the nuclear pore complex (NPC). Nic96 binds the Nsp1 complex via its N domain and assembles into the NPC framework via its central and C domain. Here, we report the crystal structure of a large structural nucleoporin, Nic96 without its N domain (Nic96DeltaN). Nic96DeltaN is composed of three domains and is a straight molecule that--although almost entirely helical--exhibits strong deviations from the predicted alpha-solenoid fold. The missing N domain projects midway from the Nic96 molecule, indicating how the Nsp1 complex might be located with respect to the rod-like Nic96. Notably, Nic96DeltaN binds in vitro to FG repeats of the Nsp1 complex. These data suggest a model of how Nic96 could organize a transport module with coiled-coil domains and FG repeats in the central pore channel.     

Structural characterization of hellethionins from Helleborus purpurascens

Thionins are relatively small-sized multiple-cystine peptides that are probably involved in the plant defense against pathogens. As such, these peptides constitute promising candidates for engineered plant resistance in the agricultural industry. More recently, thionins have been proposed as potential immunotoxins in tumor therapy. In the search for pharmacologically active natural products, a new family of thionins was recently discovered in the roots of Helleborus purpurascens that accordingly were termed hellethionins. The structural characterization by NMR of one representative member of this family, i.e., of hellethionin D, clearly reveals that thionins from different sources share a highly conserved overall fold. In fact, the well-defined 3D structure of hellethionin D is very similar to those reported so far for viscotoxins, purothionins, or crambin, although distinct differences could be detected in the C-terminal portion, especially for loop 36-39. These differences may derive from the unusual distribution of charged residues in the C-terminal half of the peptide sequence compared to other thionins and from the uncommon occurrence of four contiguous threonine residues in loop 36-39. As expected, reduction of the disulfide bonds in hellethionin D leads to complete unfolding, but upon oxidative refolding by air oxygen in the presence of glutathione the correct isomer is recovered in high yields, confirming the very robust fold of this class of bioactive cystine peptides.     

Structural characterization of myosin from bovine brain

Myosins isolated from bovine brain, rabbit skeletal muscle, and chicken gizzard smooth muscle and their heavy meromyosin and light meromyosin fractions were studied in the electron microscope by negative staining with uranyl acetate. Under similar conditions of preparation and polymerization, the three myosins formed paracrystals of different structures. The light meromyosin portion of the skeletal muscle myosin also assembled in a different fashion than the brain or smooth muscle light meromyosins; the latter two assembled similarly. The heavy meromyosin portion from each of the three myosins was shown to interact with the actins isolated from each of the three tissue sources by the formation of the characteristic arrowhead patterns with similar periodicities. The brain heavy meromyosin attachment to both skeletal and brain actins was dissociated by ATP. It is suggested that differences in the light meromyosin portions of the three myosins may account in part for their differences in assembly in vivo.     

Preparation and characterization of nano-cellulose with new shape from different precursor

Three different precursor materials – 1. China cotton, 2. South African cotton, 3. Waste tissue papers were used to produce nano-cellulose by acid hydrolysis route. No chemical pretreatment has been done for the production of nano-cellulose from these precursors. Prepared nano-cellulose and their corresponding precursor materials were characterized by transmission electron microscopy (TEM), particle size analysis, X-ray diffraction (XRD) study, thermo gravimetric analysis (TGA), differential scanning calorimetric (DSC) analysis and Fourier transformed infra red (FTIR) spectroscopy. A comparative study of the characteristics was done with the properties of raw materials and with that of nano-cellulose. Shape and size of the nano cellulose generally depends on nature of the precursor and hydrolysis condition. Morphology study of nano-cellulose from different sources revealed range of length from 50 to 200 nm and diameter from 10 to 90 nm. Higher thermal stability and crystallinity of nano-cellulose were observed compared to that of precursor from TGA/DSC study.     

Structural proteomics of macromolecular assemblies using oxidative footprinting and mass spectrometry

Understanding the composition, structure and dynamics of macromolecules and their assemblies is at the forefront of biological science today. Hydroxyl-radical-mediated protein footprinting using mass spectrometry can define macromolecular structure, macromolecular assembly and conformational changes of macromolecules in solution based on measurements of reactivity of amino acid side-chain groups with covalent-modification reagents. Subsequent to oxidation by reactive oxygen species, proteins are digested by specific proteases to generate peptides for analysis by mass spectrometry. Accurate measurements of side-chain reactivity are achieved using quantitative liquid-chromatography-coupled mass spectrometry, whereas the side-chain sites within the macromolecular probes are identified using tandem mass spectrometry. In addition, the use of footprinting data in conjunction with computational modeling approaches is a powerful new method for testing and refining structural models of macromolecules and their complexes.     

Hydrodynamic characterization of the size and shape of atropinesterase from Pseudomonas putida

Atropinesterase from Pseudomonas putida has been investigated by means of different ultracentrifugation methods under native and denaturing conditions. The following quantities were determined: sedimentation coefficient, translational diffusion and friction coefficient, partial specific volume and molecular weight. From these data the size, shape and hydration of the enzyme molecule in solution were estimated. The results suggest that atropinesterase is a globular protein which consists of a single polypeptide chain with a molecular weight of about 30,000. In solution under non-denaturing conditions, it occurs mainly as a dimer which hydrodynamically behaves as a rigid impenetrable particle. Calculations based on the spheroid model indicate that this particle resembles a hydrated sphere with a diameter of 6.1 +/- 0.2 nm and a hydration of 0.4 +/- 0.1 g of H2O/g of protein rather than a significantly less hydrated ellipsoid of revolution. Under denaturing conditions dissociation into monomers takes place. The effects of sodium dodecyl sulphate (SDS) on size and shape suggest that dimerization results from side-by-side association of two elongated monomers rather than from end-to-end association. Approximately 57 molecules of SDS are bound per dimer before dissociation occurs concomitant with the additional binding of about 19 molecules of detergent.     

Structural characterization of glutamine synthetase from Azospirillum brasilense

CD spectroscopic study of the secondary structure of partly adenylylated glutamine synthetase (GS) of the bacterium Azospirillum brasilense showed both the native and cation-free (EDTA-treated) enzyme to be highly structured (58 and 49% as alpha-helices, 10 and 20% as beta-structure, respectively). Mg(2+), Mn(2+), or Co(2+), when added to the native GS, had little effect on its CD spectrum, whereas their effects on the cation-free GS were more pronounced. Emission ((57)Co) M?ssbauer spectroscopic (EMS) study of (57)Co(2+)-doped cation-free GS in frozen solution and in the dried state gave similar spectra and M?ssbauer parameters for the corresponding spectral components, reflecting the ability of the Co(2+)-enzyme complex to retain its properties upon drying. The EMS data show that (a) A. brasilense GS has 2 cation-binding sites per active center and (b) one site has a higher affinity to Co(2+) than the other, in line with the data on other bacterial GSs.     

Structural characterization of chondroitin sulfate from sturgeon bone

Chondroitin sulfate (CS) was purified for the first time from the bones of sturgeon and analyzed to evaluate its structure and properties. A single polysaccharide was extracted from sturgeon bone in a concentration of 0.28-0.34% for dry tissue and characterized as CS. By means of specific chondroitinases and HPLC separation of generated unsaturated repeating disaccharides, this polymer was found to be composed of ∼55% of disaccharide monosulfated in position 6 of the GalNAc, ∼38% of disaccharide monosulfated in position 4 of the GalNAc, and ∼7% of nonsulfated disaccharide. The charge density was 0.93 and the ratio of 4:6 sulfated residues was equal to 0.69, a value confirmed by ¹³C NMR experiments. Chondroitinase B confirmed that the purified sturgeon CS contained mainly GlcA (>99.5%) as uronic acid. PAGE analysis showed a CS having a high molecular mass with an average value of 39,880 according to HPSEC values producing a weight average molecular weight (Mw) of 37,500. On the basis of the data collected, it is reasonable to assume that CS isolated from sturgeon bone might be potentially useful for scientific and pharmacological applications, making this bony fish, which is generally discarded after ovary collection, a useful source of this polymer. Finally, this newly identified source of CS would enable the production of this macromolecule having a particular repeating disaccharide composition, structure, and biological properties.     

Structural characterization of phytotoxic terpenoids from Cestrum parqui

Isolation, chemical characterization and phytotoxicity of nine polyhydroxylated terpenes (five C13nor-isoprenoids, two sesquiterpenes, a spirostane and a pseudosapogenin) from Cestrum parqui L'Herr are reported. In this work we completed the phytochemical investigation of the terpenic fraction of the plant and described the structural elucidation of polar isoprenoids using NMR methods. All the configurations of the compounds have been assigned by NOESY experiments. Four new structures have been identified as (3S,5R,6R,7E,9R)-5,6,9-trihydroxy-3-isopropyloxy-7-megastigmene, 5alpha-spirostan-3beta,12beta,15alpha-triol, and 26-O-(3'-isopentanoyl)-beta-d-glucopyranosyl-5alpha-furost-20(22)-ene-3beta,26-diol, and as an unusual tricyclic sesquiterpene. The compounds have been assayed for their phytotoxicity on lettuce at the concentrations ranging between 10(-4) and 10(-7)M. The activities of some compounds were similar to that of the herbicide pendimethalin.     

Structural characterization of gangliosides from murine T lymphocytes

Mouse spleen cells were prepared from CBA/J mice, and T lymphocytes were selectively stimulated with the T cell mitogen concanavalin A and further propagated in the presence of the T cell growth factor interleukin-2. The T cells were metabolically labeled with D-[1-14C]galactose and D[1-14C]glucosamine, and the gangliosides were extracted and purified by DEAE-Sepharose column chromatography. Carbohydrate backbone structures of the asialogangliosides, prepared by mild acid hydrolysis, were determined by high-performance liquid chromatography, treatment with exoglycosidases and immunostaining. Monosialylated gangliosides were isolated by gradient elution from DEAE-Sepharose and further separated by preparative high-performance thin-layer chromatography in two solvent systems. Isolated fractions were characterized by preparation of asialogangliosides by mild acid hydrolysis, the action of Vibrio cholerae neuraminidase, and fast-atombombardment mass spectrometry. The following structures were identified: IVNeuAc-GgOse4Cer; IVNeuGc-GgOse4Cer; IVNeuAc-GgOse5Cer; and IVNeu-Gc-GgOse5Cer. The latter two gangliosides were not detected on B lymphoblasts and may be T-cell-specific structures. All gangliosides were heterogeneous in their ceramide moieties, being substituted with C16:0, C24:0, and C24:1 fatty acids. A preliminary study of several other mouse strains showed no strain-specific genetic variations in the T cell gangliosides. The possible role of these gangliosides is discussed.     

Structural characterization of glucooligosaccharide oxidase from Acremonium strictum

Glucooligosaccharide oxidase from Acremonium strictum was screened for potential applications in oligosaccharide acid production and carbohydrate detection. This protein is a unique covalent flavoenzyme which catalyzes the oxidation of a variety of carbohydrates with high selectivity for cello- and maltooligosaccharides. Kinetic measurements suggested that this enzyme possesses an open carbohydrate-binding groove, which is mainly composed of two glucosyl-binding subsites. The encoding gene was subsequently cloned, and one intron was detected in the genomic DNA. Large amounts of active enzymes were expressed in Pichia pastoris, with a yield of 300 mg per liter medium. The protein was predicted to share structural homology with plant cytokinin dehydrogenase and related flavoproteins that share a conserved flavin adenine dinucleotide (FAD)-binding domain. The closest sequence matches are those of plant berberine bridge enzyme-like proteins, particularly the characteristic flavinylation site. Unexpectedly, mutation of the putative FAD-attaching residue, H70, to alanine, serine, cysteine, and tyrosine did not abolish the covalent FAD linkage and had little effect on the Km. Instead, the variants displayed kcat values that were 50- to 600-fold lower, indicating that H70 is crucial for efficient redox catalysis, perhaps through modulation of the oxidative power of the flavin.     

Separation and partial characterization of isolectins with different subunit compositions from Datura stramonium seeds

The lectin from Datura stramonium seeds was separated into three individual isolectins by hydrophobic-interaction chromatography on phenyl-Sepharose. Two of these isolectins are homodimers made up of two A- or two B-subunits, whereas the third is a heterodimer composed of one A- and one B-subunit. Analysis of the homodimeric AA- and BB-isolectins revealed that the A- and B-subunits have similar but not identical M_r values (32 000 and 28 000, respectively), amino acid and carbohydrate compositions. The A-subunit has a higher affinity for N-acetyl-D-glucosamine oligomers than the B-subunit, whereas the latter is more specific for the carbohydrate determinants of some animal glycoproteins such as fetuin, asialofetuin and ovomucoid.