Application of singular value decomposition to the analysis of time-resolved macromolecular x-ray data

Singular value decomposition (SVD) is a technique commonly used in the analysis of spectroscopic data that both acts as a noise filter and reduces the dimensionality of subsequent least-squares fits. To establish the applicability of SVD to crystallographic data, we applied SVD to calculated difference Fourier maps simulating those to be obtained in a time-resolved crystallographic study of photoactive yellow protein. The atomic structures of one dark state and three intermediates were used in qualitatively different kinetic mechanisms to generate time-dependent difference maps at specific time points. Random noise of varying levels in the difference structure factor amplitudes, different extents of reaction initiation, and different numbers of time points were all employed to simulate a range of realistic experimental conditions. Our results show that SVD allows for an unbiased differentiation between signal and noise; a small subset of singular values and vectors represents the signal well, reducing the random noise in the data. Due to this, phase information of the difference structure factors can be obtained. After identifying and fitting a kinetic mechanism, the time-independent structures of the intermediates could be recovered. This demonstrates that SVD will be a powerful tool in the analysis of experimental time-resolved crystallographic data.     

Structure of a BRCA1-BARD1 heterodimeric RING-RING complex

The RING domain of the breast and ovarian cancer tumor suppressor BRCA1 interacts with multiple cognate proteins, including the RING protein BARD1. Proper function of the BRCA1 RING domain is critical, as evidenced by the many cancer-predisposing mutations found within this domain. We present the solution structure of the heterodimer formed between the RING domains of BRCA1 and BARD1. Comparison with the RING homodimer of the V(D)J recombination-activating protein RAG1 reveals the structural diversity of complexes formed by interactions between different RING domains. The BRCA1-BARD1 structure provides a model for its ubiquitin ligase activity, illustrates how the BRCA1 RING domain can be involved in associations with multiple protein partners and provides a framework for understanding cancer-causing mutations at the molecular level.     

Erythrocyte,lipid peroxidation and antioxidant enzymes in hypervitaminotic A rats and their modification by dietary protein

Rats fed excess vitamin A showed decreased body weight gain and protein efficiency ratio. In rats fed low protein vitamin A level increased in liver but with an associated decrease in plasma. These changes were reversed in high protein fed state. The amount of protein in diet had little effect on haemoglobin level in erythrocyte, but excess vitamin A in diet significantly decreased haemoglobin level in erythrocyte. Lipid peroxidation (LP) increased in rats fed low protein and decreased in high protein fed rats. Rats fed high protein and excess vitamin A showed minimum level of LP. Result showed that high protein in diet increased the levels of antioxidant enzymes, catalase and superoxide dismutase (SOD) and that excess vitamin A supplementation functions synergistically with high protein in diet to increase antioxidant enzymes level.     

Novel indolo[2,1-b]quinazoline analogues as cytostatic agents: synthesis,biological evaluation and structure-activity relationship

In our endeavor to design and synthesize novel anticancer agents, a new series of indoloquinazoline compounds were prepared and tested initially for anticancer activity in vitro against a panel of human cancer cell lines. Most of these compounds exhibited cytotoxic activity in in vitro screens. Compounds were selected and further evaluated using a modified Hollow Fiber Assay for their preliminary in vivo activity against 12 cell lines implanted in the subcutaneous and intraperitoneal compartments in mice. The results indicate that these compounds may constitute a new class of anticancer agents.     

Characterization of P700 as a photochemical quencher in isolated Photosystem I particles using simultaneous measurements of absorbance changes at 830 nm and photoacoustic signal

The relationship between the redox state of P700, the primary donor of PS I, monitored using absorbance changes at 830 nm and photochemical energy storage in PS I reaction centers assayed with the photoacoustic method (PA) was studied in isolated PS I submembrane particles aspirated onto nitrocellulose filters. Several donors have been used to support the electron transport through PS I. NADPH and NADH demonstrated low rates of electron donation to PS I, while ascorbate and ascorbate plus 2,6-dichlorophenolindophenol (DCIP) couple have been found more effective in both P700⁺ reduction and stimulation of the variable component of the PA signal. A linear relationship was found in isolated PS I particles between the (A_830,max – A_830,steady)/A_830,max and (PA_max – PA_steady)/PA_max ratios, which characterized the relative amount of P700 in the reduced state and the relative magnitude of the variable PA component, respectively. That linear relationship was obtained independently from the nature of electron donor used for the reduction of P700⁺. Such linear relationship was also obtained at various wavelengths of modulated light in the range of 660 to 720 nm, only the slope of the linear fits varied with wavelength. It is concluded that reduced P700 act as a photochemical quencher of absorbed energy. Variable thermal dissipation in PS I reaction centers of isolated submembrane particles linearly depends on the amount of reduced P700 and thus constitutes an appropriate indicator of the redox pressure applied to PS I. This revised version was published online in June 2006 with corrections to the Cover Date.     

Harlequin (hlq) and short blue root (sbr), two Arabidopsis mutants that ectopically express an abscisic acid- and auxin-inducible transgenic carrot promoter and have pleiotropic effects on morphogenesis

Plant growth and development is regulated by complex interactions among different hormonal, developmental and environmental signalling pathways. Isolation of mutants in these processes is a powerful approach to dissect unknown mechanisms in regulatory networks. The plant hormones abscisic acid (ABA) and auxin are involved in vegetative, developmental and environmental growth responses, including cell division and elongation, vascular tissue differentiation and stress adaptation. The uidA (-glucuronidase; GUS) reporter gene driven by the carrot (Daucus carota) late embryogenesis-abundant Dc3 promoter in transgenic Arabidopsis thaliana seedlings is ABA-inducible in the root zone of elongation and vasculature. We show here that the ABA-insensitive2-1 mutation (abi2) reduces ABA-inducible Dc3-GUS expression in these root tissues. Dc3-GUS expression is also induced in root cortex cells by indole-3-acetic acid. We mutagenized, with ethyl methane sulfonate, 5100 M₁ abi2/abi2 homozygous plants of a line that carries two independent Dc3-GUS reporter genes and screened M₂ clonal lines for ABA-inducible Dc3-GUS expression in roots. We isolated two novel single-gene nuclear mutants, harlequin (hlq) and short blue root (sbr), that ectopically express Dc3-GUS in roots and have pleiotropic effects on morphogenesis. The hlq mutant expresses Dc3-GUS in a checkered pattern in epidermis of roots and hypocotyls, accumulates callose and has deformed and collapsed epidermal cells and abnormal and reduced root hairs and leaf trichomes. It (hlq) is also dwarfed, skotomorphogenic and sterile. The sbr mutant is a seedling-lethal dwarf that over-expresses Dc3-GUS in the root and has radially swollen epidermal cells in the root and hypocotyl, supernumerary cell number in the root cortex and epidermis, abnormal vasculature, and abnormal epidermal cell patterning in cotyledons and leaves. It (sbr) also exhibits a semidominant root phenotype of reduced growth and lateral root initiation. The hlq and sbr mutants are not rescued by exogenous application of plant growth regulators. The hlqand sbr mutants do not require the abi2-1 mutant gene for their phenotypes and map to chromosome III and I, respectively. Further characterization of the hlq and sbr phenotypes and genes may provide insights into the relationship of hormone- and stress-regulated gene expression to morphogenesis and plant growth.     

Identification of Arabidopsis rat mutants

Limited knowledge currently exists regarding the roles of plant genes and proteins in the Agrobacterium tumefaciens-mediated transformation process. To understand the host contribution to transformation, we carried out root-based transformation assays to identify Arabidopsis mutants that are resistant to Agrobacterium transformation (rat mutants). To date, we have identified 126 rat mutants by screening libraries of T-DNA insertion mutants and by using various “reverse genetic” approaches. These mutants disrupt expression of genes of numerous categories, including chromatin structural and remodeling genes, and genes encoding proteins implicated in nuclear targeting, cell wall structure and metabolism, cytoskeleton structure and function, and signal transduction. Here, we present an update on the identification and characterization of these rat mutants.     

Recombinant toxins that bind to the urokinase receptor are cytotoxic without requiring binding to the alpha(2)-macroglobulin receptor

The alpha(2-)macroglobulin receptor (alpha(2)MR) has been reported to mediate the internalization of the urokinase plasminogen activator receptor (uPAR) via ligand binding to both receptors. To target malignant uPAR-expressing cells and to determine whether uPAR can internalize without ligand binding to alpha(2)MR, we engineered two recombinant toxins, ATF-PE38 and ATF-PE38KDEL. Each consists of the amino-terminal fragment (ATF) of human urokinase and a truncated form of Pseudomonas exotoxin (PE) devoid of domain Ia, which binds alpha(2)MR. ATF-PE38 and ATF-PE38KDEL were cytotoxic toward malignant uPAR-bearing cells, with IC(50) values as low as 0.02 ng/ml (0.3 pM). Cytotoxicity could be blocked using either recombinant urokinase or free ATF, indicating that the cytotoxicity of the recombinant toxins was specific. Radiolabeled ATF-PE38 had high affinity for uPAR (K(d) = 0.4-8 nM) on a variety of different malignant cell types and internalized at a rate similar to that of ATF. The cytotoxicity was not diminished by receptor-associated protein, which binds and shields the alpha(2)MR from other proteins, or by incubation with phorbol myristate acetate, which is known to decrease the number of alpha(2)MRs in U937 cells or by antibodies to alpha(2)MR. Therefore, these recombinant toxins appear to internalize via uPAR without association with the alpha(2)MR.     

Use of Inducible Feedback-Resistant N-Acetylglutamate Synthetase (argA) Genes for Enhanced Arginine Biosynthesis by Genetically Engineered Escherichia coli K-12 Strains

The goal of this work was to construct Escherichia coli strains capable of enhanced arginine production. The arginine biosynthetic capacity of previously engineered E. coli strains with a derepressed arginine regulon was limited by the availability of endogenous ornithine (M. Tuchman, B. S. Rajagopal, M. T. McCann, and M. H. Malamy, Appl. Environ. Microbiol. 63:33–38, 1997). Ornithine biosynthesis is limited due to feedback inhibition by arginine of N-acetylglutamate synthetase (NAGS), the product of the argA gene and the first enzyme in the pathway of arginine biosynthesis in E. coli. To circumvent this inhibition, the argA genes from E. coli mutants with feedback-resistant (fbr) NAGS were cloned into plasmids that contain “arg boxes,” which titrate the ArgR repressor protein, with or without the E. coli carAB genes encoding carbamyl phosphate synthetase and the argI gene for ornithine transcarbamylase. The free arginine production rates of “arg-derepressed” E. coli cells overexpressing plasmid-encoded carAB, argI, and fbr argA genes were 3- to 15-fold higher than that of an equivalent system overexpressing feedback-sensitive wild-type (wt) argA. The expression system with fbr argA produced 7- to 35-fold more arginine than a system overexpressing carAB and argI genes on a plasmid in a strain with a wt argA gene on the chromosome. The arginine biosynthetic capacity of arg-derepressed DH5α strains with plasmids containing only the fbr argA gene was similar to that of cells with plasmids also containing the carAB and argI genes. Plasmids containing wt or fbr argA were stably maintained under normal growth conditions for at least 18 generations. DNA sequencing identified different point mutations in each of the fbr argA mutants, specifically H15Y, Y19C, S54N, R58H, G287S, and Q432R.     

Solvent Exchange Rates of Side-chain Amide Protons in Proteins

Solvent exchange rates and temperature coefficients for Asn/Gln side-chain amide protons have been measured in Escherichia coli HPr. The protons of the eight side-chain amide groups (two Asn and six Gln) exhibit varying exchange rates which are slower than some of the fast exchanging backbone amide protons. Differences in exchange rates of the E and Z protons of the same side-chain amide group are obtained by measuring exchange rates at pH values > 8. An NOE between a side-chain amide proton and a bound water molecule was also observed.