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PubMedDate not supplied

[The action of cortifen and corticosterone on the thymocyte nucleoid of mice in vivo and in vitro].

The effect of therapeutic doses of a hormonal cytostatic cortifen and corticosterone on supramolecular DNA structures of mice thymocyte nucleoid was studied. Capillary elastoviscometry showed that in vivo damage to supramolecular DNA complex structure there was a difference already two hours after injection of these agents. After 24 hours the damaging effects on nucleoid were markedly higher. The role of the hormone and alkylating group of cortifen in the cytotoxic action of antitumor agents is discussed.

Animals↗
PubMedDate not supplied

[Studies of DNP protein dissociation in the presence of norepinephrine].

Calf thymus DNP dissociation was studied by sepharose 2B gel-chromatography as well as by oxyapatite ion-exchange chromatography. The degree of dissociation was estimated by protein content in the chromatography peaks. Intact DNP and DNP incubated with norepinephrine were filtered simultaneously through two identical columns. In the presence of norepinephrine a partial deproteinization was observed. This effect has some specificity, namely, it was considerably lower in the presence of tyrosine, and was absent when the norepinephrine structure was changed. On the basis of the available data on the norepinephrine ability to form chelatic complexes with polyvalent metals and comparing the deproteinizing effect of norepinephrine and EDTA it was assumed that the norepinephrine dissociating effect was due to its binding with cations incorporated into the DNP complex structure.

Animals↗
PubMed2004

Cobalamin-independent methionine synthase (MetE): a face-to-face double barrel that evolved by gene duplication.

Cobalamin-independent methionine synthase (MetE) catalyzes the transfer of a methyl group from methyltetrahydrofolate to L-homocysteine (Hcy) without using an intermediate methyl carrier. Although MetE displays no detectable sequence homology with cobalamin-dependent methionine synthase (MetH), both enzymes require zinc for activation and binding of Hcy. Crystallographic analyses of MetE from T. maritima reveal an unusual dual-barrel structure in which the active site lies between the tops of the two (betaalpha)(8) barrels. The fold of the N-terminal barrel confirms that it has evolved from the C-terminal polypeptide by gene duplication; comparisons of the barrels provide an intriguing example of homologous domain evolution in which binding sites are obliterated. The C-terminal barrel incorporates the zinc ion that binds and activates Hcy. The zinc-binding site in MetE is distinguished from the (Cys)(3)Zn site in the related enzymes, MetH and betaine-homocysteine methyltransferase, by its position in the barrel and by the metal ligands, which are histidine, cysteine, glutamate, and cysteine in the resting form of MetE. Hcy associates at the face of the metal opposite glutamate, which moves away from the zinc in the binary E.Hcy complex. The folate substrate is not intimately associated with the N-terminal barrel; instead, elements from both barrels contribute binding determinants in a binary complex in which the folate substrate is incorrectly oriented for methyl transfer. Atypical locations of the Hcy and folate sites in the C-terminal barrel presumably permit direct interaction of the substrates in a ternary complex. Structures of the binary substrate complexes imply that rearrangement of folate, perhaps accompanied by domain rearrangement, must occur before formation of a ternary complex that is competent for methyl transfer.

Amino Acid Sequence↗
PubMed1994

Crystal structure of a complex of alpha-cyclodextrin with 2-fluoro-4-nitrophenol.3H2O.

The crystal structure of a complex of alpha-cyclodextrin (alpha-CD) with 2-fluoro-4-nitrophenol.3H2O has been determined by the X-ray diffraction technique. The complex crystallizes in space group P2(1)2(1)2(1) with cell dimensions: a = 13.431(3), b = 15.299(4), c = 24.780(5) A. The structure was solved by direct methods and refined to R = 6.7% for 4483 reflections. The crystal structure is isomorphous to the alpha-CD-4-nitrophenol.3H2O complex. The phenyl group is inside the cavity, so that the O-4 hexagon of the alpha-CD is distorted in a systematic manner: the longest diagonal [O-4(G2)...O-4(G5)] is in the direction of the benzene ring. The phenolic OH group protrudes from the secondary OH side of the cavity and the NO2 group is situated on the primary OH side. The hydrophobic F atom is statistically disordered over two sites and is located in the hydrophilic space, just beyond the rim of the secondary OH side of the cavity.

Carbohydrate Conformation↗
PubMed2005

Development of a model for microphysiological simulations: small nodes of ranvier from peripheral nerves of mice reconstructed by electron tomography.

The node of Ranvier is a complex structure found along myelinated nerves of vertebrate animals. Specific membrane, cytoskeletal, junctional, extracellular matrix proteins and organelles interact to maintain and regulate associated ion movements between spaces in the nodal complex, potentially influencing response variation during repetitive activations or metabolic stress. Understanding and building high resolution three dimensional (3D) structures of the node of Ranvier, including localization of specific macromolecules, is crucial to a better understanding of the relationship between its structure and function and the macromolecular basis for impaired conduction in disease. Using serial section electron tomographic methods, we have constructed accurate 3D models of the nodal complex from mouse spinal roots with resolution better than 7.5 nm. These reconstructed volumes contain 75-80% of the thickness of the nodal region. We also directly imaged the glial axonal junctions that serve to anchor the terminal loops of the myelin lamellae to the axolemma. We created a model of an intact node of Ranvier by truncating the volume at its midpoint in Z, duplicating the remaining volume and then merging the new half volume with mirror symmetry about the Z-axis. We added to this model the distribution and number of Na+ channels on this reconstruction using tools associated with the MCell simulation program environment. The model created provides accurate structural descriptions of the membrane compartments, external spaces, and formed structures enabling more realistic simulations of the role of the node in modulation of impulse propagation than have been conducted on myelinated nerve previously.

Animals↗
PubMed1991

An iterative algorithm for scanning tomographic acoustic microscopy.

Acoustic microscopy is capable of providing high-resolution images of small objects. When such a microscope operates in the transmission mode, it produces simply a shadow-graph of all the structures encountered by the acoustic wave passing through the object. The resultant images are difficult to comprehend because of diffraction and overlapping of complex structures. Scanning tomographic acoustic microscopy (STAM) overcomes these difficulties and produces unambiguous micrographs of objects of substantial thickness and complexity. STAM uses the back-and-forth propagation algorithm to reconstruct tomograms of various layers to be imaged. When these layers are physically close to one another, ambiguities appear in the reconstructed images. Using an iterative algorithm eliminates these ambiguities and resolves layers that are only two wavelengths apart.

Algorithms↗
PubMed2006

Regulation of hepatocyte cell cycle progression and differentiation by type I collagen structure.

Cell behavior is strongly influenced by the extracellular matrix (ECM) to which cells adhere. Both chemical determinants within ECM molecules and mechanical properties of the ECM network regulate cellular response, including proliferation, differentiation, and apoptosis. Type I collagen is the most abundant ECM protein in the body with a complex structure that can be altered in vivo by proteolysis, cross-linking, and other processes. Because of collagen's complex and dynamic nature, it is important to define the changes in cell response to different collagen structures and its underlying mechanisms. This chapter reviews current knowledge of potential mechanisms by which type I collagen affects cell behavior, and it presents data that elucidate specific intracellular signaling pathways by which changes in type I collagen structure differentially regulate hepatocyte cell cycle progression and differentiation. A network of polymerized fibrillar type I collagen (collagen gel) induces a highly differentiated but growth-arrested phenotype in primary hepatocytes, whereas a film of monomeric collagen adsorbed to a rigid dish promotes cell cycle progression and dedifferentiation. Studies presented here demonstrate that protein kinase A (PKA) activity is significantly elevated in hepatocytes on type I collagen gel relative to collagen film, and inhibition of this elevated PKA activity can promote hepatocyte cell cycle progression on collagen gel. Additional studies are presented that examine changes in hepatocyte cell cycle progression and differentiation in response to increased rigidity of polymerized collagen gel by fiber cross-linking. Potential mechanisms underlying these cellular responses and their implications are discussed.

Animals↗
PubMed1984

Ultrastructure of a complex epithelial system: the pharyngeal lining of the larval lamprey Petromyzon marinus.

Electron microscopy shows that the pharyngeal lining of the larval lamprey Petromyzon marinus is a structurally complex epithelial system that can be separated into eight epithelial types: gill lamellar, gill interlamellar, goblet cell, protective, terminal (taste) bud, preciliated, ciliated in tracts, and ciliated in grooves. Furthermore, these epithelial types encompass at least sixteen different cell types based on ultrastructure and, in some cases, correlative histochemistry (PAS, Alcian blue). Common to nearly all the epithelial types are basal cells and intermediate cells. These two cell types are seen as undifferentiated. Among mature cells, structural specialization as proceeded in three directions: 1) elaboration of mitochondria, probably related to molecular transport (ion-uptake cells, chloride cells); 2) ciliogenesis (preciliated and ciliated cell types); and 3) production of mucous secretory granules (mucous-platelet cells, goblet cells, superficial protective cells, columnar mucous cells, "cobblestone" cells, and marginal and dark cells in the terminal buds). Many of the functions of the cell types relate to the process of suspension feeding in this animal.

Animals↗
PubMed1999

Structure of a transcribing T7 RNA polymerase initiation complex.

The structure of a T7 RNA polymerase (T7 RNAP) initiation complex captured transcribing a trinucleotide of RNA from a 17-base pair promoter DNA containing a 5-nucleotide single-strand template extension was determined at a resolution of 2.4 angstroms. Binding of the upstream duplex portion of the promoter occurs in the same manner as that in the open promoter complex, but the single-stranded template is repositioned to place the +4 base at the catalytic active site. Thus, synthesis of RNA in the initiation phase leads to accumulation or "scrunching" of the template in the enclosed active site pocket of T7 RNAP. Only three base pairs of heteroduplex are formed before the RNA peels off the template.

Amino Acid Motifs↗
PubMed1994

Anatomy of the anterior cruciate ligament: a blueprint for repair and reconstruction.

The anterior cruciate ligament of the knee joint is a complex structure whose orientation, construct, and biology are directly related to its function as a constraint of knee joint motion. While the complexity of its design allows the ligament to function through the normal range of motion as a static stabilizer of the knee, it also makes the exact duplication of this structure very difficult. A fundamental knowledge of the functional anatomy of the anterior cruciate ligament provides the orthopaedic surgeon with an essential blueprint on which to base techniques of repair and reconstruction.

Anterior Cruciate Ligament↗
PubMed2001

Mechanism of hydrolysis of phosphate esters by the dimetal center of 5'-nucleotidase based on crystal structures.

5'-Nucleotidase belongs to a large superfamily of distantly related dinuclear metallophosphatases including the Ser/Thr protein phosphatases and purple acid phosphatases. The protein undergoes a 96 degrees domain rotation between an open (inactive) and a closed (active) enzyme form. Complex structures of the closed form with the products adenosine and phosphate, and with the substrate analogue inhibitor alpha,beta-methylene ADP, have been determined at 2.1 A and 1.85 A resolution, respectively. In addition, a complex of the open form of 5'-nucleotidase with ATP was analyzed at a resolution of 1.7 A. These structures show that the adenosine group binds to a specific binding pocket of the C-terminal domain. The adenine ring is stacked between Phe429 and Phe498. The N-terminal domain provides the ligands to the dimetal cluster and the conserved His117, which together form the catalytic core structure. However, the three C-terminal arginine residues 375, 379 and 410, which are involved in substrate binding, may also play a role in transition-state stabilization. The beta-phosphate group of the inhibitor is terminally coordinated to the site 2 metal ion. The site 1 metal ion coordinates a water molecule which is in an ideal position for a nucleophilic attack on the phosphorus atom, assuming an in-line mechanism of phosphoryl transfer. Another water molecule bridges the two metal ions.

5'-Nucleotidase↗
PubMed2003

Enzymes involved in the biogenesis of the nematode cuticle.

Nematodes include species that are significant parasites of man, his domestic animals and crops, and cause chronic debilitating diseases in the developing world; such as lymphatic filariasis and river blindness caused by filarial species. Around one third of the World's population harbour parasitic nematodes; no vaccines exist for prevention of infection, limited effective drugs are available and drug resistance is an ever-increasing problem. A critical structure of the nematode is the protective cuticle, a collagen-rich extracellular matrix (ECM) that forms the exoskeleton, and is critical for viability. This resilient structure is synthesized sequentially five times during nematode development and offers protection from the environment, including the hosts' immune response. The detailed characterization of this complex structure; it's components, and the means by which they are synthesized, modified, processed and assembled will identify targets that may be exploited in the future control of parasitic nematodes. This review will focus on the nematode cuticle. This structure is predominantly composed of collagens, a class of proteins that are modified by a range of co- and post-translational modifications prior to assembly into higher order complexes or ECMs. The collagens and their associated enzymes have been comprehensively characterized in vertebrate systems and some of these studies will be addressed in this review. Conversely, the biosynthesis of this class of essential structural proteins has not been studied in such detail in the nematodes. As with all morphogenetic, functional and developmental studies in the Nematoda phylum, the free-living species Caenorhabditis elegans has proven to be invaluable in the characterization of the cuticle and the cuticle collagen gene family, and is now proving to be an excellent model in the study of cuticle collagen biosynthetic enzymes. This model system will be the main focus of this review.

Animals↗
PubMed1997

Familial mixed congenital myopathy with rigid spine phenotype.

We describe a father and daughter with a rigid spine syndrome and proximal myopathy. The index patient was a 42-year-old man, who died from respiratory failure after a lifelong, slowly progressive proximal myopathy and a rigid spine phenotype. This was morphologically characterized by cytoplasmic bodies, increased desmin, features of reducing-body myopathy, and sarcoplasmic and intranuclear tubulofilamentous inclusions. These cases are characterized by an early onset and possibly autosomal-dominant inheritance, with associated complex structural hallmarks of both desmin-related and inclusion body myopathies. Together they may be defined as a complex mixed congenital myopathy with a rigid spine phenotype.

Adult↗
PubMed2007

Pillars, layers, pores and networks from nickeltripyrrins: a porphyrin fragment as a versatile building block for the construction of supramolecular assemblies.

Sterically hindered nickel- tripyrrins [Ni(trpy)X] with different di-, tri- and tetradentate anions X have been prepared with the aim of finding coordination polymers formed by self-association. The syntheses were performed by simple ligand-exchange reactions and proceeded successfully with the pseudohalides CN(-), OCN(-), SCN(-), SeCN(-), N(CN)(2) (-) (dicyanoamido, dca) and C(CN)(3) (-) (tricyanomethanido, tcm), the cyanidometallates [Ag(CN)(2)](-) and [Ni(CN)(4)](2-) and the salicylate anion (sal(-)). X-ray crystallographic analyses revealed that the complexes with cyanido and isocyanato ligands, as well as the compound with a salicylato ligand, are prototypes for structurally distinct monomeric species in the solid state, whereas one-dimensional coordination polymers or supramolecular three-dimensional networks are formed from all other combinations. The polymeric compounds display a variety of individual pillar and network architectures with functionalised pores and clefts and with the Ni(trpy) fragments in different relative orientations. Hydrogen bonding and pi stacking were found to be additional structure-directing effects, which increased the structural complexity of the system. The Ni(trpy) subunit has thus been proven to be a versatile building block for the construction of supramolecular assemblies and metal organic frameworks (MOFs) from pentacoordinate Ni(II) ions.

Journal Article↗
PubMed2006

Permanent surface modification of polymeric capillary electrophoresis microchips for protein and peptide analysis.

Because of their surface heterogeneity, proteins readily adsorb on polymeric substrates via various interactions, which adversely affects the performance of polymeric microfluidic devices in electrophoresis-based protein/peptide analysis. Therefore, it is necessary to use surface modification techniques such as dynamic coating or more complicated permanent surface modification, which has broader application and better performance, to render the polymeric microchannels protein-resistant. This manuscript is a review of the surface chemistry of microfluidic devices used for electrophoretic separations of proteins and peptides. The structural complexity of proteins as it relates to adsorption is described, followed by a review of the mechanisms and structural characteristics of protein-resistant surfaces. Permanent surface modification techniques used in grafting protein-resistant materials onto the surfaces of electrophoresis microchannels fabricated from polymer substrates are summarized and successful examples are presented.

Electrophoresis, Capillary↗
PubMed1979

The intra-nucleolar localization of amplified rDNA in Xenopus laevis oocytes.

A fluorescent Feulgen-stain was adapted in order to demonstrate DNA-containing structures inside the amplified nucleoli of Xenopus laevis. At all stages of oogenesis this method reveals granules or complex structures of DNA in each nucleolus. The micronucleoli which do not stain with this method and which do not reveal an internal structure in low molarity saline, unlike real nucleoli are considered as nucleolus-like bodies. The DNA-containing structures in the nucleoli can be composed of one or several granules, or they can be arranged in a linear, reticulated or circular form, independant of any correlation with the stage of oogenesis.

Animals↗
PubMed1983

Polymorphic phase preferences of phosphatidic acid: A 31P and 2H NMR study.

31P NMR, 2H NMR and freeze fracture techniques have been employed to investigate the structural preferences of dioleoyl phosphatidic acid (DOPA) under various conditions of pH and divalent cation content. It is shown that DOPA increasingly prefers the HII organization below pH 5, and that low levels of Ca2+ and Mg2+ (Me2+/DOPA = 0.5) induce HII phase structure for pH less than 6.0. Higher Mg2+ and Ca2+ levels (Me2+/DOPA greater than 1.0) induce more complex structures at pH greater than 5.0 which may correspond to intermediates between lamellar and HII organization. This work illustrates the utility of 2H NMR techniques in conjunction with suitable 2H labelled lipids to provide structural information on lipid-water systems, and suggests that 31P NMR techniques for determinations of lipid organization can be applied to advantage in PA containing membranes.

Calcium↗
PubMed2005

Crystallography for protein kinase drug design: PKA and SRC case studies.

Protein crystallography can be used throughout the drug discovery process to obtain diverse information critical for structure based drug design. At a minimum, a single target structure may be available. Optimally, and especially for protein kinases, a broad range of crystal structures should be obtained to characterize target flexibility, structure modulation via co-factor binding or posttranslational modification, ligand induced conformational changes, and off-target complex structures for selectivity optimization. The flexibility of the protein kinases is in contrast to the need for "crystallizable" constructs, that is, proteins that crystallize under varying conditions and in varying crystal packing arrangements. Strategies to produce crystallizable protein kinase constructs include truncation to the catalytic domain, co-crystallization with rigidifying ligands, crystallization of known rigid forms, and point mutation to improve homogeneity or mimic less crystallizable proteins. PKA, the prototypical serine/threonine protein kinase, and SRC, a tyrosine kinase and the first identified oncoprotein, provide multiple examples of these various approaches to protein kinase crystallography for drug design.

Animals↗