NMR structures of salt-refolded forms of the 434-repressor DNA-binding domain in 6 M urea

The N-terminal 63-residue fragment of the phage 434-repressor, 434(1-63), has a well-defined globular fold in H(2)O solution, and is unfolded in 6 M urea at pH 7.5. In this study, 434(1-63) has been refolded by adding either 1.7 M NaCl or 0.47 M NaTFA to the solution in 6 M urea, and the NMR structures of both refolded forms have been determined. The two refolded forms have similar free energies of unfolding and are approximately 16 kJ/mol less stable than the protein in H(2)O solution. 434(1-63) refolded with NaCl exhibits NMR chemical shifts very similar to and a three-dimensional structure nearly identical to those of 434(1-63) in H(2)O solution. The protein refolded with NaTFA also has a similar global fold, but it shows local differences near Phe44, of which two different orientations of the aromatic ring are compatible with the experimental data. This local conformational polymorphism attracted our interest because hydrophobic contacts between two subdomains of residues 1-36 and 45-63 are mediated by the Phe44 side chain. Anion binding experiments suggest that this polymorphism is caused by binding of TFA(-) anions to a cluster of positively charged Arg and Lys residues located in the loop connecting the two subdomains, with apparent binding constants for TFA(-) (K(app)) on the order of 30 mM(-1).     

Isolation and characterization of naturally occurring hairpin structures in single-stranded DNA of coliphage M13

With precise conditions of digestion with single-strand-specific nucleases, namely, endonuclease S1 of $\text{Aspergillus oryzae}$ and exonuclease I of $\text{Escherichia coli}$, nuclease-resistant DNA cores can be obtained reproducibly from single-stranded M13 DNA. The DNA cores are composed almost exclusively of two sizes (60 and 44 nucleotides long). These have high (G + C)-contents relative to that of intact M13 DNA, and arise from restricted regions of the M13 genome. The resistance of these fragments to single-strand-specific nucleases and their nondenaturability strongly suggest the presence of double-stranded segments in these core pieces. That the core pieces are only partially double-stranded is shown by their lack of complete base complementarity and their pattern of elution from hydroxyapatite.     

Cardiac desmosomal (dys)function and myocyte viability

Cardiac desmosomes form intercellular junctions at the boundaries or intercalated discs between neighboring cardiomyocytes and are essential for proper cell-to-cell coupling between cardiomyocytes and normal mechanical and electrical function of myocardial tissue. Genetic mutations in desmosomal proteins have been associated with arrhythmogenic right ventricular cardiomyopathy (ARVC), a clinically and genetically heterogeneous cardiac inherited disorder. The disease is characterized by progressive replacement of cardiomyocytes by fibrofatty tissue, ultimately resulting in ventricular dilation, cardiac dysfunction, and the occurrence of life-threatening arrhythmias. Despite increasing knowledge on the genetic basis of ARVC, the etiopathogenesis of the disease remains less understood. The recent development of a number of transgenic mouse models with either heterozygous knock-out of desmosomal proteins or over-expression of aberrant desmosomal components has provided novel insight into the potential mechanisms and final common pathways involved in ARVC. The various disease mechanisms are likely not mutually exclusive and may each contribute to the pathogenesis of ARVC. However, their applicability in the diverse genetic forms of the disease remains uncertain, and may only be ascertained by careful investigation of sequential histopathological and (sub)cellular changes occurring over time during the disease process. Insight into the etiopathogenesis of ARVC will be crucial for the future development of new therapies aimed at delaying onset or progression of this disease.     

Isolation of desmosomes from the epidermis of Xenopus laevis and immunochemical characterization of the Xenopus desmosomal cadherins

Here we report a new method of isolating epidermal desmosomes from Xenopus laevis, and a major constituent of desmosomes designated as Xenopus desmogleins (XDsg). Isolation of desmosomes from Xenopus laevis epidermis was carried out by a two step-incubation with different concentrations of NP-40. After discontinuous sucrose gradient centrifugation at 30,000 g for 60 min, a pure desmosomal fraction was obtained at 30%/40% interface. In the SDS-PAGE of isolated desmosomes, at least 12 bands (XDB1 to XDB12) were observed over a 75 kD region. Among them, three bands (XDB3, XDB7, XDB8; estimated MW 175, 124, and 112 kD respectively) were recognized as glycoproteins based on ConA binding. Monospecific polyclonal antibody against XDB3 cross-reacted with bovine Dsgs and vis-a-vis anti-bovine Dsgs with XDB3. By contrast, monospecific antibody against bovine Dsc a/b did not cross-react with either XDB7 or XDB8. Heterogeneous molecular constituents of desmosomal adhesion molecule, which have been observed among different bovine tissues, were confirmed in a phylogenetically different animal, Xenopus laevis. Combined results with other evidence could suggest an alternative system for desmosome-mediated cell adhesion.     

Characterization of the mammalian beta-2 receptor in 8 M urea

Treatment of canine pulmonary membranes with detergent-free 8 M urea yielded a single class of large MW high-affinity binding sites exhibiting the stereospecificity and order of potency for beta-ligands characteristic of the beta receptor. This urea-solubilized receptor, demonstrating a 3–4 fold decreased affinity for beta-ligands as compared to membrane-bound and digitonin-solubilized receptor, exhibited a marked loss of activity when concomitantly exposed to solubilizing concentrations of detergent.     

Solution structures of purine base analogues 9-deazaguanine and 9-deazahypoxanthine

Deaza analogues of nucleobases are potential drugs against infectious diseases caused by parasites. A caveat is that apart from binding their target parasite enzymes, they also bind and inhibit enzymes of the host. In order to design derivatives of deaza analogues which specifically bind target enzymes, knowledge of their molecular structure, protonation state, and predominant tautomers at physiological conditions is essential. We have employed resonance Raman spectroscopy at an excitation wavelength of 260 nm, to decipher solution structure of 9-deazaguanine (9DAG) and 9-deazahypoxanthine (9DAH). These are analogues of guanine and hypoxanthine, respectively, and have been exploited to study static complexes of nucleobase binding enzymes. Such enzymes are known to perturb pK_a of their ligands, and thus, we also determined solution structures of these analogues at two, acidic and alkaline, pH. Structure of each possible protonation state and tautomer was computed using density functional theoretical calculations. Species at various pHs were identified based on isotopic shifts in experimental wavenumbers and by comparing these shifts with corresponding computed isotopic shifts. Our results show that at physiological pH, N1 of pyrimidine ring in 9DAG and 9DAH bears a proton. At lower pH, N3 is place of protonation, and at higher pH, deprotonation occurs at N1 position. The proton at N7 of purine ring remains intact even at pH 12.5. We have further compared these results with naturally occurring nucleotides. Our results identify key vibrational modes which can report on hydrogen bonding interactions, protonation and deprotonation in purine rings upon binding to the active site of enzymes.     

Impaired formation of desmosomal junctions in ADPKD epithelia

Mutations in polycystin-1 (PC-1) are responsible for autosomal dominant polycystic kidney disease (ADPKD), characterized by formation of fluid-filled tubular cysts. The PC-1 is a multifunctional protein essential for tubular differentiation and maturation found in desmosomal junctions of epithelial cells where its primary function is to mediate cell–cell adhesion. To address the impact of mutated PC-1 on intercellular adhesion, we have analyzed the structure/function of desmosomal junctions in primary cells derived from ADPKD cysts. Primary epithelial cells from normal kidney showed co-localization of PC-1 and desmosomal proteins at cell–cell contacts. A striking difference was seen in ADPKD cells, where PC-1 and desmosomal proteins were lost from the intercellular junction membrane, despite unchanged protein expression levels. Instead, punctate intracellular expression for PC-1 and desmosomal proteins was detected. The N-cadherin, but not E-cadherin was expressed in adherens junctions of ADPKD cells. These data together with co-sedimentation analysis demonstrate that, in the absence of functional PC-1, desmosomal junctions cannot be properly assembled and remain sequestered in cytoplasmic compartments. Taken together, our results demonstrate that PC-1 is crucial for formation of intercellular contacts. We propose that abnormal expression of PC-1 causes disregulation of cellular adhesion complexes leading to increased proliferation, loss of polarity and, ultimately, cystogenesis.     

Isolation and primary structures of elephant adrenocorticotropin and beta-lipotropin

Adrenocorticotropin and beta-lipotropin have been isolated and purified from elephant pituitary glands. The primary structures of these two hormones were determined by amino acid and sequence analyses of enzymatically cleaved peptides from the hormones. Peptide purification involved the use of gel filtration, reverse phase high performance liquid chromatography, and paper electrophoresis.     

The fate of desmosomal proteins in apoptotic cells

Activation of caspases results in the disruption of structural and signaling networks in apoptotic cells. Recent biochemical and cell biological studies have shown that components of the cadherin-catenin adhesion complex in epithelial adherens junctions are targeted by caspases during apoptosis. In epithelial cells, desmosomes represent a second type of anchoring junctions mediating strong cell-cell contacts. Using antibodies directed against a set of desmosomal proteins, we show that desmosomes are proteolytically targeted during apoptosis. Desmogleins and desmocollins, representing desmosome-specific members of the cadherin superfamily of cell adhesion molecules, are specifically cleaved after onset of apoptosis. Similar to E-cadherin, the desmoglein-3 cytoplasmic tail is cleaved by caspases. In addition the extracellular domains of desmoglein-3 and desmocollin-3 are released from the cell surface by a metalloproteinase activity. In the presence of caspase and/or metalloproteinase inhibitors, both cleavage reactions are almost completely inhibited. As reported previously, the desmosomal plaque protein plakoglobin is cleaved by caspase-3 during apoptosis. Our studies now show that plakophilin-1 and two other major plaque proteins, desmoplakin-1 and -2, are also cleaved by caspases. Immunofluorescence analysis confirmed that this cleavage results in the disruption of the desmosome structure and thus contributes to cell rounding and disintegration of the intermediate filament system.     

Structure and interactions of desmosomal and other cadherins.

The cadherin superfamily of cell-cell adhesion molecules is now known to include proteins of the desmosome as well as of the adherens type of junction. The desmosomal cadherins consist of two families of proteins, the desmocollins and the desmogleins, both of which are represented by different isoforms which are differentially expressed in epidermis. The desmocollins are quite similar to the classic cadherins in overall structure, but with alternatively spliced variants; the desmogleins have extra cytoplasmic sequences added onto the basic cadherin structure. The cytoplasmic domains are specialized for binding to 'mediator' proteins, such as plakoglobin, which interconnect to the intermediate filament system rather than the actin filaments as do the classic cadherins.     

Effects of level,time, and splitting of urea on the yield of irrigated direct seeded rice

Summary To determine effects of level and time of application of urea on grain yields, components of grain yield, and nitrogen use efficiency by irrigated direct seeded rice (Oryza sativa L. var. IR 298-12-1-1-1), three field experiments were conducted at the Gezira Agricultural Research Station during the period 1976–78. The treatments included the factorial combination of three levels of nitrogen as urea (0,75 and 150 kg N/ha) two or three splits, and three times of topdressing of urea (early season application, 10 days after rice emergence, DRE; maximum tillering stage, 40 DRE; and panicle initiation stage, 75 DRE).Without application of nitrogen, grain yields averaged 1.5 t/ha. The yields averaged for rate and time of split significantly increased with increase in nitrogen applied to 3.9 and 5.0 t/ha, but nitrogen use efficiency (kg rice/kg N) decreased from 31 to 23 with the application of 75 and 150 kg N/ha respectively.As compared to other treatments of time of urea application, topdressing of urea at maximum tillering and panicle initiation stages significantly improved nitrogen use efficiency by promoting production of more panicles per unit land area, and increasing grain weight. Three splits were no better than the two splits given at maximum tillering and panicle initiation stages.     

Theoretical study on the structures and properties of mixtures of urea and choline chloride

In this work, we investigated in detail the structural characteristics of mixtures of choline chloride and urea with different urea contents by performing molecular dynamic (MD) simulations, and offer possible explanations for the low melting point of the eutectic mixture of choline chloride and urea with a ratio of 1:2. The insertion of urea molecules was found to change the density distribution of cations and anions around the given cations significantly, disrupting the long-range ordered structure of choline chloride. Moreover, with increasing urea concentration, the hydrogen bond interactions between choline cations and Cl^? anions decreased, while those among urea molecules obviously increased. From the hydrogen bond lifetimes, it was found that a ratio of 1:2 between choline chloride and urea is necessary for a reasonable strength of hydrogen bond interaction to maintain the low melting point of the mixture of choline chloride with urea. In addition, it was also deduced from the interaction energies that a urea content of 67.7 % may make the interactions of cation–anion, cation–urea and anion–urea modest, and thus results in the lower melting point of the eutectic mixture of choline chloride and urea. The present results may offer assistance to some extent for understanding the physicochemical properties of the eutectic mixture of choline chloride and urea, and give valuable information for the further development and application of deep eutectic solvents.     

Transport properties of rigid, symmetrical oligomeric structures composed of prolate, ellipsoidal subunits

We have calculated translational and rotational diffusion coefficients and intrinsic viscosities of oligomeric structures composed of n identical subunits having a prolate ellipsoidal shape with axial ratio p. Results are presented for p = 1-6 for a variety of structures with n = 1-6. We compare our results with those obtained by a different modeling procedure, proposed by other workers, in which the monomeric subunit is represented as a string of touching, colinear spheres. If n and an estimate of p are known, the structure of the oligomer can be. in most cases, unambiguously determined by comparison of the experimental oligomer-to-monomer ratios of a given property with the numerical results of this work. As examples of the applicability of our results, we examine the relationship between structure and properties for neurophysin. bovine serum albumin, hemoglobin and phycocyanin.