Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer: influence of the crystal environment

Molecular dynamics (MD) simulations of the DNA duplex d(CCAACGTTGG)(2) were used to study the relationship between DNA sequence and structure. Two crystal simulations were carried out; one consisted of one unit cell containing two duplexes, and the other of two unit cells containing four duplexes. Two solution simulations were also carried out, one starting from canonical B-DNA and the other starting from the crystal structure. For many helicoidal parameters, the results from the crystal and solution simulations were essentially identical. However, for other parameters, in particular, alpha, gamma, delta, (epsilon - zeta), phase, and helical twist, differences between crystal and solution simulations were apparent. Notably, during crystal simulations, values of helical twist remained comparable to those in the crystal structure, to include the sequence-dependent differences among base steps, in which values ranged from 20 degrees to 50 degrees per base step. However, in the solution simulations, not only did the average values of helical twist decrease to approximately 30 degrees per base step, but every base step was approximately 30 degrees, suggesting that the sequence-dependent information may be lost. This study reveals that MD simulations of the crystal environment complement solution simulations in validating the applicability of MD to the analysis of DNA structure.     

Penicillin-binding protein-related factor A is required for proper chromosome segregation in Bacillus subtilis

Previous work has shown that the ponA gene, encoding penicillin-binding protein 1 (PBP1), is in a two-gene operon with prfA (PBP-related factor A) (also called recU), which encodes a putative 206-residue basic protein (pI = 10.1) with no significant sequence homology to proteins with known functions. Inactivation of prfA results in cells that grow slower and vary significantly in length relative to wild-type cells. We now show that prfA mutant cells have a defect in chromosome segregation resulting in the production of approximately 0.9 to 3% anucleate cells in prfA cultures grown at 30 or 37 degrees C in rich medium and that the lack of PrfA exacerbates the chromosome segregation defect in smc and spoOJ mutant cells. In addition, overexpression of prfA was found to be toxic for and cause nucleoid condensation in Escherichia coli.     

Heparan/chondroitin sulfate biosynthesis. Structure and mechanism of human glucuronyltransferase I

Human beta1,3-glucuronyltransferase I (GlcAT-I) is a central enzyme in the initial steps of proteoglycan synthesis. GlcAT-I transfers a glucuronic acid moiety from the uridine diphosphate-glucuronic acid (UDP-GlcUA) to the common linkage region trisaccharide Gal beta 1-3Gal beta 1-4Xyl covalently bound to a Ser residue at the glycosaminylglycan attachment site of proteoglycans. We have now determined the crystal structure of GlcAT-1 at 2.3 A in the presence of the donor substrate product UDP, the catalytic Mn(2+) ion, and the acceptor substrate analog Gal beta 1-3Gal beta 1-4Xyl. The enzyme is a alpha/beta protein with two subdomains that constitute the donor and acceptor substrate binding site. The active site residues lie in a cleft extending across both subdomains in which the trisaccharide molecule is oriented perpendicular to the UDP. Residues Glu(227), Asp(252), and Glu(281) dictate the binding orientation of the terminal Gal-2 moiety. Residue Glu(281) is in position to function as a catalytic base by deprotonating the incoming 3-hydroxyl group of the acceptor. The conserved DXD motif (Asp(194), Asp(195), Asp(196)) has direct interaction with the ribose of the UDP molecule as well as with the Mn(2+) ion. The key residues involved in substrate binding and catalysis are conserved in the glucuronyltransferase family as well as other glycosyltransferases.     

Natural coprevalence of Strongwellsea castrans, Cystosporogenes deliaradicae, and Bacillus thuringiensis in the host, Delia radicum

Adult cabbage root flies (Delia radicum) from three Danish localities were diagnosed microscopically for the natural prevalence of Strongwellsea castrans, Cystosporogenes deliaradicae, and Bacillus thuringiensis. C. deliaradicae was significantly coprevalent with S. castrans. B. thuringiensis sporangia were diagnosed in the hemolymph in two D. radicum which were also infected with S. castrans and proved to belong to serovar aizawai and serovar balearica. The biological characterization of S. castrans proved that at 17.5 degrees C flies developed an abdominal hole 7.9 days (mean) after infection and that 5.7 days (mean) passed from the emergence of the hole to the death of the infected host. No mortality effect among D. radicum subjected to B. thuringiensis serovar aizawai, balearica, and kurstaki isolates was detected. RAPD with DNA proved that six B. thuringiensis serovar balearica isolates (all from the same fly) were indistinguisable. This indicates that proliferation of B. thuringiensis in the abdomen of an S. castrans-infected D. radicum may be due to just one genotype. The profiles of one isolated aizawai strain did not correspond to the profiles of other serovar aizawai strains used for comparison. The biological significance of the interaction between the involved pathogens is discussed.     

Mitochondrial F(0)F(1) ATP synthase. Subunit regions on the F1 motor shielded by F(0), Functional significance, and evidence for an involvement of the unique F(0) subunit F(6)

Studies reported here were undertaken to gain greater molecular insight into the complex structure of mitochondrial ATP synthase (F(0)F(1)) and its relationship to the enzyme's function and motor-related properties. Significantly, these studies, which employed N-terminal sequence, mass spectral, proteolytic, immunological, and functional analyses, led to the following novel findings. First, at the top of F(1) within F(0)F(1), all six N-terminal regions derived from alpha + beta subunits are shielded, indicating that one or more F(0) subunits forms a "cap." Second, at the bottom of F(1) within F(0)F(1), the N-terminal region of the single delta subunit and the C-terminal regions of all three alpha subunits are shielded also by F(0). Third, and in contrast, part of the gamma subunit located at the bottom of F(1) is already shielded in F(1), indicating that there is a preferential propensity for interaction with other F(1) subunits, most likely delta and epsilon. Fourth, and consistent with the first two conclusions above that specific regions at the top and bottom of F(1) are shielded by F(0), further proteolytic shaving of alpha and beta subunits at these locations eliminates the capacity of F(1) to couple a proton gradient to ATP synthesis. Finally, evidence was obtained that the F(0) subunit called "F(6)," unique to animal ATP synthases, is involved in shielding F(1). The significance of the studies reported here, in relation to current views about ATP synthase structure and function in animal mitochondria, is discussed.     

A mechanism for the neuroprotective effect of apolipoprotein E: isoform-specific modification by the lipid peroxidation product 4-hydroxynonenal

Inheritance of the apolipoprotein E (apoE) epsilon4 allele increases the risk for Alzheimer's disease and may also influence the pathogenesis of other neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). The influence of apoE genotype on disease susceptibility must ultimately be explained by the fact that apoE proteins differ in only two amino acids: apoE2 has two cysteine residues, apoE3 has one cysteine residue, and apoE4 has none. We previously reported increased protein modification by the lipid peroxidation product 4-hydroxynonenal (HNE), which covalently binds to proteins on cysteine residues, in human ALS lumbar spinal cord. We now report increased levels of HNE-modified apoE in lumbar spinal cord samples from mice expressing an ALS-linked mutation in Cu/Zn-superoxide dismutase relative to controls. Studies of interactions of pure apoE proteins with HNE showed that the isoforms differ in the amount of HNE they can bind, with the order E2 > E3 > E4. This correlated with the differential ability of apoE isoforms to protect against apoptosis induced by HNE in cultures of mouse spinal cord motor neurons and by the amyloid beta-peptide in cultures of rat hippocampal neurons. These data suggest that apoE plays a major role in detoxifying HNE, and the differential neuroprotective effect of its isoforms may help explain the relationship between apoE genotype and the susceptibility to neurodegenerative diseases.     

Interaction of pig kidney and lentil seedling copper-containing amine oxidases with guanidinium compounds

The effect of guanidinium compounds on the catalytic mechanism of pig kidney and lentil seedling amine oxidases has been investigated by polarographic techniques and spectroscopy. Guanidine does not inhibit the lentil enzyme and is a weak inhibitor for pig kidney amine oxidase (Ki=1 mM), whereas aminoguanidine is an irreversible inhibitor of both enzymes, with a Ki value of 10(-6) M. 1,4-Diguanidino butane (arcaine) is a competitive inhibitor for both pig and lentil amine oxidases. Amiloride is a competitive inhibitor for pig enzyme, but upon prolonged incubation with this drug the enzyme gradually loses its activity in an irreversible manner.     

Control of follicular development and luteal function in the mare: effects of a GnRH antagonist

Control of the equine estrous cycle was studied by suppressing gonadotropin secretion by administration of a GnRH antagonist to cyclic pony mares. Four mares received vehicle (control cycle) or a GnRH antagonist, Antarelix (100 microg/kg) on Day 8 of diestrus, and blood samples were collected at 15-min intervals from 0 to 16 h, 24 to 36 h, and daily until the next ovulation. Ovarian activity was monitored by transrectal ultrasonography, and measurement of plasma concentrations of progesterone and estradiol. Antagonist treatment eliminated large diestrous pulses of LH. Progesterone concentrations had fallen significantly in all mares by the day after treatment and, in three of the four mares, remained low until luteolysis. However timing of luteolysis (ie., progesterone concentrations <1 ng/mL) was not affected by antagonist treatment. The preovulatory surges of estradiol and LH were significantly delayed in the treatment cycle, as was the appearance of a preovulatory follicle >30 mm. Cycle length was significantly longer during the treatment than the control cycle. These results show that treatment of diestrous mares with a GnRH antagonist attenuated progesterone secretion, indicating a role for LH in control of CL function in the mare, and delayed ovulation presumably because of lack of gonadotropic support.     

Notes on the Mechanism of ATP Synthesis

The most commonly quoted mechanism of the coupling between the electrochemical proton gradient and the formation of ATP from ADP and P_i assumes that all states of the F₁ portion of the ATP synthase have subunits in tight, loose, and open conformations. Models based on this assumption are inconsistent with some of the available experimental evidence. A mechanism that includes an additional subunit conformation, closed, observed in the rat liver structure overcomes these difficulties.     

No effect of variation in handling on behaviour in a porcine elevated plus-maze - a brief report

The elevated plus-maze is a widely used model of anxiety in rodents and has recently been suggested as a putative model of anxiety or fear in swine. The aim of the present experiment was to examine the effects of a pretest blood sampling procedure on the behaviour of weaned pigs in an elevated plus-maze. Animals in the control group were lifted one-by-one into a transport trolley and moved to the test apparatus, where they were observed for a 5-min period. The treatment group differed from the control group in that these animals were immobilized with a nose snare and a blood sample was extracted from the jugular vein prior to transport to the test room. Behaviour in the porcine elevated plus-maze did not differ significantly between the two handling procedures.